Лаборатория биофизики макромолекул

This manuscript describes the chemical synthesis of a compound similar to fluorene and Congo red, including characterization of its spectral properties. It was shown that the dye, during interaction with amyloid-like fibrils of several proteins (lysozyme, insulin, and beta-2-microglobulin), has the ability to change fluorescent spectrum. In contrast, monomeric forms of these proteins did not induce significant spectral changes. © 2019 Elsevier Ltd

This work focuses on the study of multimeric alpha-lactalbumin oleic acid and lactoferrin oleic acid complexes. The purpose of the research is to study possible mechanisms involved in their pro-apoptotic activities, as seen in some tumor cell cultures. Complexes featuring oleic acid (OA) with human alpha-lactalbumin (hAl) or with bovine alpha-lactalbumin (bAl), and human lactoferrin (hLf) were investigated using small-angle neutron scattering (SANS). It was shown that while alpha-lactalbumin protein complexes were formed on the surface of polydisperse OA micelles, the lactoferrin complexes comprised a monodisperse system of nanoscale particles. Both hAl and hLf complexes appeared to interact with the chromatin of isolated nuclei affecting chromatin structural organization. The possible roles of these processes in the specific anti-tumor activity of these complexes are discussed. © 2019 Elsevier Inc.

@ARTICLE{Nag20192270,
author={Nag, S. and Krasikova, R. and Airaksinen, A.J. and Arakawa, R. and Petukhovd, M. and Gulyas, B.},
title={Synthesis and biological evaluation of [18F]fluorovinpocetine, a potential PET radioligand for TSPO imaging},
journal={Bioorganic and Medicinal Chemistry Letters},
year={2019},
volume={29},
number={16},
pages={2270-2274},
doi={10.1016/j.bmcl.2019.06.037},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067891805&doi=10.1016%2fj.bmcl.2019.06.037&partnerID=40&md5=039425a06c8d92bde0fe18f6ade9f6de},
affiliation={Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden; N.P. Bechtereva Institute of Human Brain Russian Academy of Sciences, St.-Petersburg, Russian Federation; Department of Chemistry – Radiochemistry, University of Helsinki, Finland; Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC “Kurchatov Institute”, Gatchina, Russian Federation; Peter the Great St.-Petersburg Polytechnic University, St.-Petersburg, Russian Federation; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore},
abstract={Despite of various PET radioligands targeting the translocator protein TSPO 18-KDa are used for the investigations of neuroinflammatory conditions associated with neurological disorders, development of new TSPO radiotracers is still an active area of the researches with a major focus on the 18F-labelled radiotracers. Here, we report the radiochemical synthesis of [18F]vinpocetine, fluorinated analogue of previously reported TSPO radioligand, [11C]vinpocetine. Radiolabeling was achieved by [18F]fluoroethylation of apovincaminic acid with [18F]fluoroethyl bromide. [18F]vinpocetine was obtained in quantities >2.7 GBq in RCY of 13% (non–decay corrected), and molar activity >60 GBq/µmol within 95 min synthesis time. Preliminary PET studies in a cynomolgus monkey and metabolite studies by HPLC demonstrated similar results by [18F]vinpocetine as for [11C]vinpocetine, including high blood-brain barrier permeability, regional uptake pattern and fast washout from the NHP brain. These results demonstrate that [18F]fluorovinpocetine warrants further evaluation as an easier accessible alternative to [11C]vinpocetine. © 2019 Elsevier Ltd},
author_keywords={Fluorine-18;  Kinetics;  Monkey;  PET;  Radiometabolites;  TSPO radioligands;  Vinpocetine},
correspondence_address1={Nag, S.; Karolinska Institutet, Department of Clinical Neuroscience, Psychiatry Section, Karolinska HospitalSweden; email: sangram.nag@ki.se},
publisher={Elsevier Ltd},
issn={0960894X},
coden={BMCLE},
pubmed_id={31257082},
language={English},
abbrev_source_title={Bioorg. Med. Chem. Lett.},
document_type={Article},
source={Scopus},
}

Despite of various PET radioligands targeting the translocator protein TSPO 18-KDa are used for the investigations of neuroinflammatory conditions associated with neurological disorders, development of new TSPO radiotracers is still an active area of the researches with a major focus on the 18F-labelled radiotracers. Here, we report the radiochemical synthesis of [18F]vinpocetine, fluorinated analogue of previously reported TSPO radioligand, [11C]vinpocetine. Radiolabeling was achieved by [18F]fluoroethylation of apovincaminic acid with [18F]fluoroethyl bromide. [18F]vinpocetine was obtained in quantities >2.7 GBq in RCY of 13% (non–decay corrected), and molar activity >60 GBq/µmol within 95 min synthesis time. Preliminary PET studies in a cynomolgus monkey and metabolite studies by HPLC demonstrated similar results by [18F]vinpocetine as for [11C]vinpocetine, including high blood-brain barrier permeability, regional uptake pattern and fast washout from the NHP brain. These results demonstrate that [18F]fluorovinpocetine warrants further evaluation as an easier accessible alternative to [11C]vinpocetine. © 2019 Elsevier Ltd

@ARTICLE{Zabrodskaya20193041,
author={Zabrodskaya, Y.A. and Shvetsov, A.V. and Tsvetkov, V.B. and Egorov, V.V.},
title={A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation},
journal={Journal of Biomolecular Structure and Dynamics},
year={2019},
volume={37},
number={12},
pages={3041-3047},
doi={10.1080/07391102.2018.1507837},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057526040&doi=10.1080%2f07391102.2018.1507837&partnerID=40&md5=dc9e3dd4be9952bbf1ecf50dce04cf09},
affiliation={Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, St. Petersburg, Russian Federation; Molecular and Radiation Biophysics Department, Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center “Kurchatov Institute”, Gatchina, Russian Federation; Supercomputer Center, Peter the Great Saint-Petersburg State Polytechnic University, St. Petersburg, Russian Federation; Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Moscow, Russian Federation; Polyelectrolytes and Biomedical Polymers Laboratory, A.V. Topchiev Institute of Petrochemical Synthesis, RAS Moscow, Russian Federation; Molecular Genetics Department, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, St. Petersburg, Russian Federation},
abstract={Communicated by Ramaswamy H. Sarma. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.},
}

Communicated by Ramaswamy H. Sarma. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.

@ARTICLE{Ryzhov2019943,
author={Ryzhov, V.A. and Multhoff, G. and Shevtsov, M.A.},
title={Detection of Magnetosome-Like Structures in Eukaryotic Cells Using Nonlinear Longitudinal Response to ac Field},
journal={Applied Magnetic Resonance},
year={2019},
volume={50},
number={8},
pages={943-957},
doi={10.1007/s00723-019-01122-y},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063221793&doi=10.1007%2fs00723-019-01122-y&partnerID=40&md5=98e79df65983481215e5f369e489d8d9},
affiliation={NRC “Kurchatov Institute”, Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; Klinikum rechts der Isar, Radiation Immuno-Oncology Group, Center for Translational Cancer Research Technische Universität München (TranslaTUM), Einsteinstr. 25, Munich, 81675, Germany; Institute of Cytology, Russian Academy of Sciences (RAS), Tikhoretsky Ave., 4, St. Petersburg, 194064, Russian Federation; First Pavlov State Medical University of St. Petersburg, L’va Tolstogo Str. 6/8, St. Petersburg, 197022, Russian Federation; Almazov National Medical Research Centre, Russian Polenov Neurosurgical Institute, Mayakovskogo Str. 12, St. Petersburg, 191104, Russian Federation},
abstract={Although magnetosomes have been discovered in bacteria since several decades, until today the question remains open whether such biomineralized structures do exist in eukaryotic cells. Herein, evidence was provided for the existence of magnetosome-like Fe-based structures in different viable eukaryotic cells by the registration of second harmonic of magnetization M2(H) of longitudinal nonlinear response to weak ac field. The behavior of the field hysteresis of the M2 response from cells in suspension and/or in pellet indicated a multi-domain state of magnetosome-like structures in certain type of cells, and a single-domain state in other cell lines. The amounts of magnetosomes in cells range from ≤ 1÷2 to 5÷8 per cell. The presence of magnetosome-like structures was analyzed in normal tissue samples obtained from Wistar rats and C57/Bl6 mice. Additionally, the tumor tissue (orthotopic rat C6 glioma and mouse GL261 glioma) were assessed for magnetosomes. Detected magnetosomes in certain tissues (i.e., brain, heart, lungs) matched to a single-domain magnetite nanoparticle, whereas in other organs they exhibited characteristics attributable to a multi-domain state, better corresponding to Fe(0) composition of their magnetic cores. Subsequent studies are necessary to elucidate the role of the Fe-based magnetosome-like structures in the biology and physiology of eukaryotic cells. © 2019, The Author(s).},
funding_details={Deutsche ForschungsgemeinschaftSFB824},
funding_details={Russian Foundation for Basic Research19-08-00024},
}

Although magnetosomes have been discovered in bacteria since several decades, until today the question remains open whether such biomineralized structures do exist in eukaryotic cells. Herein, evidence was provided for the existence of magnetosome-like Fe-based structures in different viable eukaryotic cells by the registration of second harmonic of magnetization M2(H) of longitudinal nonlinear response to weak ac field. The behavior of the field hysteresis of the M2 response from cells in suspension and/or in pellet indicated a multi-domain state of magnetosome-like structures in certain type of cells, and a single-domain state in other cell lines. The amounts of magnetosomes in cells range from ≤ 1÷2 to 5÷8 per cell. The presence of magnetosome-like structures was analyzed in normal tissue samples obtained from Wistar rats and C57/Bl6 mice. Additionally, the tumor tissue (orthotopic rat C6 glioma and mouse GL261 glioma) were assessed for magnetosomes. Detected magnetosomes in certain tissues (i.e., brain, heart, lungs) matched to a single-domain magnetite nanoparticle, whereas in other organs they exhibited characteristics attributable to a multi-domain state, better corresponding to Fe(0) composition of their magnetic cores. Subsequent studies are necessary to elucidate the role of the Fe-based magnetosome-like structures in the biology and physiology of eukaryotic cells. © 2019, The Author(s).

@ARTICLE{Ryzhov2019,
author={Ryzhov, V.A. and Kiselev, I.A. and Smirnov, O.P. and Chernenkov, Y.P. and Deriglazov, V.V. and Marchenko, Y.Y. and Yakovleva, L.Y. and Nikolaev, B.P. and Bogachev, Y.V.},
title={Comprehensive characterization of magnetite-based colloid for biomedical applications},
journal={Applied Physics A: Materials Science and Processing},
year={2019},
volume={125},
number={5},
doi={10.1007/s00339-019-2596-7},
art_number={322},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064278760&doi=10.1007%2fs00339-019-2596-7&partnerID=40&md5=40f4ec1a1aafe7c949d6a228dace2ea7},
affiliation={Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center Kurchatov Institute, 1 Orlova roscha mcr, Gatchina, Leningrad Region  188300, Russian Federation; Research Institute of Highly Pure Biopreparations, 7 Pudozhskaya st, St-Petersburg, 197110, Russian Federation; St-Petersburg State Electrotechnical University LETI, 5 Prof. Popov st, St-Petersburg, 197376, Russian Federation},
abstract={An aqueous colloidal solution of dextran-coated magnetite nanoparticles was studied by nonlinear second-harmonic magnetic response (M2), transmission electron microscopy (TEM), dynamic light scattering (DLS) and electron magnetic resonance (EMR). Nanoparticles were found to aggregate. A set of magnetic parameters of the aggregates, such as the mean magnetic moment, the magnetization damping constant, the longitudinal relaxation time, the field and energy of magnetic anisotropy, and others were evaluated from M2 measurements with the data processing formalism based on the Gilbert–Landau–Lifshitz (GLL) equation for the stochastic dynamics of superparamagnetic (SP) particles. Combined with TEM and DLS, the M2 technique additionally enabled the differentiation between magnetic and nonmagnetic components of the colloid. To achieve full numerical consistency between the parameters obtained from the M2 and TEM data, magnetic correlations of nanoparticles inside the aggregates were taken into account and their correlation radius was evaluated. The observed crossover in the magnetic field dependence of the EMR signal occurring due to the break of the dipole–dipole (d–d) coupling between nanoparticles in the aggregates was described using the M2 and TEM data. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.},
correspondence_address1={Deriglazov, V.V.; Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center Kurchatov Institute, 1 Orlova roscha mcr, Russian Federation; email: deriglazov_vv@pnpi.nrcki.ru},
publisher={Springer Verlag},
issn={09478396},
coden={APAMF},
language={English},
abbrev_source_title={Appl Phys A},
document_type={Article},
source={Scopus},
}

An aqueous colloidal solution of dextran-coated magnetite nanoparticles was studied by nonlinear second-harmonic magnetic response (M2), transmission electron microscopy (TEM), dynamic light scattering (DLS) and electron magnetic resonance (EMR). Nanoparticles were found to aggregate. A set of magnetic parameters of the aggregates, such as the mean magnetic moment, the magnetization damping constant, the longitudinal relaxation time, the field and energy of magnetic anisotropy, and others were evaluated from M2 measurements with the data processing formalism based on the Gilbert–Landau–Lifshitz (GLL) equation for the stochastic dynamics of superparamagnetic (SP) particles. Combined with TEM and DLS, the M2 technique additionally enabled the differentiation between magnetic and nonmagnetic components of the colloid. To achieve full numerical consistency between the parameters obtained from the M2 and TEM data, magnetic correlations of nanoparticles inside the aggregates were taken into account and their correlation radius was evaluated. The observed crossover in the magnetic field dependence of the EMR signal occurring due to the break of the dipole–dipole (d–d) coupling between nanoparticles in the aggregates was described using the M2 and TEM data. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

@ARTICLE{Shevtsov2019,
author={Shevtsov, M. and Stangl, S. and Nikolaev, B. and Yakovleva, L. and Marchenko, Y. and Tagaeva, R. and Sievert, W. and Pitkin, E. and Mazur, A. and Tolstoy, P. and Galibin, O. and Ryzhov, V. and Steiger, K. and Smirnov, O. and Khachatryan, W. and Chester, K. and Multhoff, G.},
title={Granzyme B Functionalized Nanoparticles Targeting Membrane Hsp70-Positive Tumors for Multimodal Cancer Theranostics},
journal={Small},
year={2019},
volume={15},
number={13},
doi={10.1002/smll.201900205},
art_number={1900205},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062364915&doi=10.1002%2fsmll.201900205&partnerID=40&md5=94d7b54710320cc39d17d9efcd89854f},
affiliation={Center for Translational Cancer Research Technische Universität München (TranslaTUM), Radiation Immuno-Oncology group, Klinikum rechts der Isar, Einsteinstr. 25, Munich, 81675, Germany; Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky ave., 4, St. Petersburg, 194064, Russian Federation; First Pavlov State Medical University of St. Petersburg, L'va Tolstogo str. 6/8, St. Petersburg, 197022, Russian Federation; Almazov National Medical Research Centre, Russian Polenov Neurosurgical Institute, Mayakovskogo str. 12, St. Petersburg, 191104, Russian Federation; Research Institute of Highly Pure Biopreparations, Pudozhskaya str. 12, St. Petersburg, 191014, Russian Federation; Wharton School, University of Pennsylvania, Walnut Street 3730, Philadelphia, PA  19104, United States; Saint Petersburg State University, Universitetskaya nab. 7-9, St. Petersburg, 199034, Russian Federation; NRC “Kurchatov Institute”, Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; Institute of Pathology, Technische Universität München, Trogerstr. 18, Munich, 81675, Germany; UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6DD, United Kingdom},
abstract={Functionalized superparamagnetic iron oxide nanoparticles (SPIONs) have emerged as potential clinical tools for cancer theranostics. Membrane-bound 70 kDa heat shock protein (mHsp70) is ubiquitously expressed on the cell membrane of various tumor types but not normal cells and therefore provides a tumor-specific target. The serine protease granzyme B (GrB) that is produced as an effector molecule by activated T and NK cells has been shown to specifically target mHsp70 on tumor cells. Following binding to Hsp70, GrB is rapidly internalized into tumor cells. Herein, it is demonstrated that GrB functionalized SPIONs act as a contrast enhancement agent for magnetic resonance imaging and induce specific tumor cell apoptosis. Combinatorial regimens employing stereotactic radiotherapy and/or magnetic targeting are found to further enhance the therapeutic efficacy of GrB-SPIONs in different tumor mouse models. © 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim},
author_keywords={glioblastoma;  granzyme B;  magnetic targeting;  radiotherapy;  superparamagnetic nanoparticles},
funding_details={Deutsche ForschungsgemeinschaftSTA1520/1-1, SFB824/3},
funding_details={Bundesministerium für Bildung und Forschung01GU0823, 02NUK038A0},
funding_details={Allianz Industrie ForschungZF4320102CS7},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)19-08-00024},
}

Functionalized superparamagnetic iron oxide nanoparticles (SPIONs) have emerged as potential clinical tools for cancer theranostics. Membrane-bound 70 kDa heat shock protein (mHsp70) is ubiquitously expressed on the cell membrane of various tumor types but not normal cells and therefore provides a tumor-specific target. The serine protease granzyme B (GrB) that is produced as an effector molecule by activated T and NK cells has been shown to specifically target mHsp70 on tumor cells. Following binding to Hsp70, GrB is rapidly internalized into tumor cells. Herein, it is demonstrated that GrB functionalized SPIONs act as a contrast enhancement agent for magnetic resonance imaging and induce specific tumor cell apoptosis. Combinatorial regimens employing stereotactic radiotherapy and/or magnetic targeting are found to further enhance the therapeutic efficacy of GrB-SPIONs in different tumor mouse models. © 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

In this work, monoclonal antibodies to the adenovirus protein hexon were produced, and their biological and diagnostic properties were characterized. The specific activities of the new monoclonal antibodies, with respect to various adenovirus types, were studied by enzyme-linked immunosorbent assay, indirect immunofluorescence, and western blot analysis. The data demonstrate the potential of the monoclonal antibodies developed, namely 4B7 and 6B12, for use in the development of modern diagnostic assays. © 2019 International Alliance for Biological Standardization

Purpose: The interaction between malignant cells and surrounding healthy tissues is a critical factor in the metastatic progression of breast cancer (BC). Extracellular vesicles, especially exosomes, are known to be involved in inter-cellular communication during cancer progression. In the study presented herein, we aimed to evaluate the role of circulating plasma exosomes in the metastatic dissemination of BC and to investigate the underlying molecular mechanisms of this phenomenon. Methods: Exosomes isolated from plasma of healthy female donors were applied in various concentrations into the medium of MDA-MB-231 and MCF-7 cell lines. Motility and invasive properties of BC cells were examined by random migration and Transwell invasion assays, and the effect of plasma exosomes on the metastatic dissemination of BC cells was demonstrated in an in vivo zebrafish model. To reveal the molecular mechanism of interaction between plasma exosomes and BC cells, a comparison between un-treated and enzymatically modified exosomes was performed, followed by mass spectrometry, gene ontology, and pathway analysis. Results: Plasma exosomes stimulated the adhesive properties, two-dimensional random migration, and transwell invasion of BC cells in vitro as well as their in vivo metastatic dissemination in a dose-dependent manner. This stimulatory effect was mediated by interactions of surface exosome proteins with BC cells and consequent activation of focal adhesion kinase (FAK) signaling in the tumor cells. Conclusions: Plasma exosomes have a potency to stimulate the metastasis-promoting properties of BC cells. This pro-metastatic property of normal plasma exosomes may have impact on the course of the disease and on its prognosis. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.

@ARTICLE{Antimonova201978,
author={Antimonova, O.I. and Lebedev, D.V. and Zabrodskaya, Y.A. and Grudinina, N.A. and Timkovsky, A.L. and Ramsay, E. and Shavlovsky, M.M. and Egorov, V.V.},
title={Changing times: Fluorescence-lifetime analysis of amyloidogenic SF-IAPP fusion protein},
journal={Journal of Structural Biology},
year={2019},
volume={205},
number={1},
pages={78-83},
doi={10.1016/j.jsb.2018.11.006},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057404969&doi=10.1016%2fj.jsb.2018.11.006&partnerID=40&md5=dc975e67546d305821164b0badc9f5e1},
affiliation={Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 Akademika Pavlova St. 12, St. Petersburg, Russian Federation; Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 mkr. Orlova roshcha 1, Gatchina, Russian Federation; Department of Molecular Biology of Viruses, Smorodintsev Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, 197376 Prof. Popov St. 15/17, St. Petersburg, Russian Federation; Peter the Great St. Petersburg Polytechnic University, 195251 Polytechnicheskaya St. 29, St. Petersburg, Russian Federation; North-Western State Medical University named after I.I. Mechnikov, 191015 Kirochnaya St. 41, St. Petersburg, Russian Federation},
abstract={In a number of conformational diseases, intracellular accumulation of proteins bearing non-native conformations occurs. The search for compounds that are capable of hindering the formation and accumulation of toxic protein aggregates and fibrils is an urgent task. Present fluorescent methods of fibrils’ detection prevent simple real-time observations. We suppose to use green fluorescent protein fused with target protein and fluorescence lifetime measurement technique for this purpose. The recombinant proteins analyzed were produced in E. coli. Mass spectrometry was used for the primary structure of the recombinant proteins and post-translational modifications identification. The fluorescence lifetime of the superfolder green fluorescent protein (SF) and the SF protein fused with islet amyloid polypeptide (SF-IAPP) were studied in polyacrylamide gel using Fluorescent-Lifetime Imaging Microscopy (FLIM). It was shown that the SF average fluorescence lifetime in gel slightly differs from that of the SF-IAPP monomer under these conditions. SF-IAPP does not lose the ability to form amyloid-like fibrils. Under the same conditions (in polyacrylamide gel), SF and SF-IAPP monomers have similar fluorescence time characteristics and the average fluorescence lifetime of SF-IAPP in fibrils significantly decreases. We propose the application of FLIM to the measurement of average fluorescence lifetimes of fusion proteins (amyloidogenic protein-SF) in the context of studies using cellular models of conformational diseases. © 2018 Elsevier Inc.},
author_keywords={Amyloid-like fibrils;  Atomic force microscopy;  Conformational diseases;  FLIM;  Green fluorescent protein;  IAPP},
correspondence_address1={Zabrodskaya, Y.A.; Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 mkr. Orlova roshcha 1, Russian Federation; email: zabrodskaya_ya@pnpi.nrcki.ru},
publisher={Academic Press Inc.},
issn={10478477},
coden={JSBIE},
pubmed_id={30458241},
language={English},
abbrev_source_title={J. Struct. Biol.},
document_type={Article},
source={Scopus},
}

In a number of conformational diseases, intracellular accumulation of proteins bearing non-native conformations occurs. The search for compounds that are capable of hindering the formation and accumulation of toxic protein aggregates and fibrils is an urgent task. Present fluorescent methods of fibrils’ detection prevent simple real-time observations. We suppose to use green fluorescent protein fused with target protein and fluorescence lifetime measurement technique for this purpose. The recombinant proteins analyzed were produced in E. coli. Mass spectrometry was used for the primary structure of the recombinant proteins and post-translational modifications identification. The fluorescence lifetime of the superfolder green fluorescent protein (SF) and the SF protein fused with islet amyloid polypeptide (SF-IAPP) were studied in polyacrylamide gel using Fluorescent-Lifetime Imaging Microscopy (FLIM). It was shown that the SF average fluorescence lifetime in gel slightly differs from that of the SF-IAPP monomer under these conditions. SF-IAPP does not lose the ability to form amyloid-like fibrils. Under the same conditions (in polyacrylamide gel), SF and SF-IAPP monomers have similar fluorescence time characteristics and the average fluorescence lifetime of SF-IAPP in fibrils significantly decreases. We propose the application of FLIM to the measurement of average fluorescence lifetimes of fusion proteins (amyloidogenic protein-SF) in the context of studies using cellular models of conformational diseases. © 2018 Elsevier Inc.

@ARTICLE{Timoshicheva201947,
author={Timoshicheva, T.A. and Zabrodskaya, Ya.A. and Amosova, I.V.},
title={Hexon-based scaffold for generation of diagnostic monoclonal antibodies against diverse adenovirus types},
journal={Russian Journal of Infection and Immunity},
year={2019},
volume={9},
number={1},
pages={47-56},
doi={10.15789/2220-7619-2019-1-47-56},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066428134&doi=10.15789%2f2220-7619-2019-1-47-56&partnerID=40&md5=6b5a29e3fe851fb7839289f2f320b4d0},
affiliation={Smorodintsev Research Institute of Influenza of the Ministry of Healthcare, Prof. Popov Str., 15/17, St. Petersburg, 117997, Russian Federation; Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC Kurchatov Institute, St. Petersburg, Russian Federation},
abstract={Infectious diseases hold one of the most crucial places in healthcare. In Russia, annual prevalence of infectious diseases comprises around 50 million cases, wherein acute respiratory viral infections cover up to 90%. In non-influenza (non-peak) season, adenoviruses, respiratory syncytial virus, parainfluenza viruses etc. represent the main infectious cause of acute respiratory viral infections. Adenovirus-induced infections are characterized by heterogeneous manifestations poising them both as an interesting challenge, yet difficult in clinical diagnostics. Use of rapid, sensitive and specific tests is of high priority for routine clinical laboratory practice. In Russia, differential diagnostics of adenoviral infections includes a widely used ELISA and immunofluorescence analysis based on polyclonal specific sera. Importantly, a pattern and range of specific reactions depend on origin of animal-derived antibodies and their composition. Introduction of monoclonal antibodies specific to certain viral antigenic epitopes ensures high sensitivity and specificity allowing to reach an expected standardization level for such diagnostic products. Adenovirus hexon protein bears genus-specific antigens and relatively conserved amino acid sequence among diverse adenoviruses. Moreover, it is produced at high amount in infected cells and may be purified in a native form. Moreover, it is produced at high amount in infected cells and may be purified in a native form, thereby posing it as a promising antigen for producing monoclonal antibodies able to detect various adenoviruses types. A panel of adenovirus hexon-specific monoclonal antibodies was generated, which were further examined for biological and diagnostics properties. Western blotting data allowed to conclude that all of monoclonal antibodies generated by us were able to bind to adenovirus hexon oligomers. Specific activity of the new monoclonal antibodies against various adenovirus types was examined by ELISA and indirect immunofluorescence assay. In particular, monoclonal antibodies 4B7 and 6B12 were shown display top specific activity measured by ELISA (antibody titers comprised as high as 10-6). Moreover, monoclonal antibody 6B12 exhibited peak hexon-specific activity assessed in indirect immunofluorescence assay (against various adenovirus types), which resulted in prominent granular nuclear f luorescence in cells infected with adenovir us types 3, 4, 6, and 19. Thus, the data obtained evidence that monoclonal antibodies developed 4B7 and 6B12 may be potentially used for developing high-quality adenovirus-specific diagnostic assays. © 2019 Saint Petersburg Pasteur Institute. All rights reserved.},
author_keywords={Adenovirus;  Diagnostics;  Enzyme-linked immunosorbent assay;  Hexon;  Immunofluorescence assay;  Monoclonal antibodies},
correspondence_address1={Timoshicheva, T.A.; Smorodintsev Research Institute of Influenza of the Ministry of Healthcare, Prof. Popov Str., 15/17, Russian Federation; email: tatianatim@mail.ru},
publisher={Saint Petersburg Pasteur Institute},
issn={22207619},
language={Russian},
abbrev_source_title={Rus. J. Infect. Immun.},
document_type={Article},
source={Scopus},
}

Infectious diseases hold one of the most crucial places in healthcare. In Russia, annual prevalence of infectious diseases comprises around 50 million cases, wherein acute respiratory viral infections cover up to 90%. In non-influenza (non-peak) season, adenoviruses, respiratory syncytial virus, parainfluenza viruses etc. represent the main infectious cause of acute respiratory viral infections. Adenovirus-induced infections are characterized by heterogeneous manifestations poising them both as an interesting challenge, yet difficult in clinical diagnostics. Use of rapid, sensitive and specific tests is of high priority for routine clinical laboratory practice. In Russia, differential diagnostics of adenoviral infections includes a widely used ELISA and immunofluorescence analysis based on polyclonal specific sera. Importantly, a pattern and range of specific reactions depend on origin of animal-derived antibodies and their composition. Introduction of monoclonal antibodies specific to certain viral antigenic epitopes ensures high sensitivity and specificity allowing to reach an expected standardization level for such diagnostic products. Adenovirus hexon protein bears genus-specific antigens and relatively conserved amino acid sequence among diverse adenoviruses. Moreover, it is produced at high amount in infected cells and may be purified in a native form. Moreover, it is produced at high amount in infected cells and may be purified in a native form, thereby posing it as a promising antigen for producing monoclonal antibodies able to detect various adenoviruses types. A panel of adenovirus hexon-specific monoclonal antibodies was generated, which were further examined for biological and diagnostics properties. Western blotting data allowed to conclude that all of monoclonal antibodies generated by us were able to bind to adenovirus hexon oligomers. Specific activity of the new monoclonal antibodies against various adenovirus types was examined by ELISA and indirect immunofluorescence assay. In particular, monoclonal antibodies 4B7 and 6B12 were shown display top specific activity measured by ELISA (antibody titers comprised as high as 10-6). Moreover, monoclonal antibody 6B12 exhibited peak hexon-specific activity assessed in indirect immunofluorescence assay (against various adenovirus types), which resulted in prominent granular nuclear f luorescence in cells infected with adenovir us types 3, 4, 6, and 19. Thus, the data obtained evidence that monoclonal antibodies developed 4B7 and 6B12 may be potentially used for developing high-quality adenovirus-specific diagnostic assays. © 2019 Saint Petersburg Pasteur Institute. All rights reserved.

@ARTICLE{Rak201913,
author={Rak, A.Y. and Trofimov, A.V. and Protasov, E.A. and Rodin, S.V. and Zhahov, A.V. and Zabrodskaya, Y.A. and Ischenko, A.M.},
title={Spontaneous Proteolytic Processing of Human Recombinant Anti-Mullerian Hormone: Structural and Functional Differences of the Molecular Forms},
journal={Applied Biochemistry and Microbiology},
year={2019},
volume={55},
number={1},
pages={13-20},
doi={10.1134/S0003683819010149},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063724530&doi=10.1134%2fS0003683819010149&partnerID=40&md5=e5de197b812d7a0bc61fbd16ada849b1},
affiliation={State Research Institute of Highly Pure Biopreparations, Federal Medical-Biological Agency (FMBA), St. Petersburg, 197110, Russian Federation; St. Petersburg State University, St. Petersburg, 199034, Russian Federation; Research Institute of Influenza, Ministry of Health of Russia, St. Petersburg, 197376, Russian Federation},
abstract={Abstract: The technology for the production of highly purified human recombinant anti-mullerian hormone (AMH)—a potential antitumor agent for the treatment of certain types of malignant neoplasms—is described. It was found that spontaneous proteolytic processing of the hormone is possible during the storage of AMH preparations under physiological conditions. This leads to the formation of C-terminal homodimer of AMH (activated form) and, later, to an inactive state during the further proteolysis. Sites at which spontaneous processing of the hormone molecule occurred during prolonged storage with the formation of active and inactive fragments were identified. The structural and functional differences in the molecular forms of the C-terminal fragment contained in the preparations are analyzed. © 2019, Pleiades Publishing, Inc.},
author_keywords={AMH;  anti-mullerian hormone;  chromatography;  MALDI mass-spectrometry;  monoclonal antibodies;  proteolysis;  recombinant protein},
correspondence_address1={Rak, A.Y.; State Research Institute of Highly Pure Biopreparations, Federal Medical-Biological Agency (FMBA)Russian Federation; email: rak@hpb-spb.com},
publisher={Pleiades Publishing},
issn={00036838},
language={English},
abbrev_source_title={Appl. Biochem. Microbiol.},
document_type={Article},
source={Scopus},
}

Abstract: The technology for the production of highly purified human recombinant anti-mullerian hormone (AMH)—a potential antitumor agent for the treatment of certain types of malignant neoplasms—is described. It was found that spontaneous proteolytic processing of the hormone is possible during the storage of AMH preparations under physiological conditions. This leads to the formation of C-terminal homodimer of AMH (activated form) and, later, to an inactive state during the further proteolysis. Sites at which spontaneous processing of the hormone molecule occurred during prolonged storage with the formation of active and inactive fragments were identified. The structural and functional differences in the molecular forms of the C-terminal fragment contained in the preparations are analyzed. © 2019, Pleiades Publishing, Inc.

Nicotinamide adenine dinucleotide (NAD) and its phosphorylated form, NADP, are the major coenzymes of redox reactions in central metabolic pathways. Nicotinamide adenine dinucleotide is also used to generate second messengers, such as cyclic ADP-ribose, and serves as substrate for protein modifications including ADP-ribosylation and protein deacetylation by sirtuins. The regulation of these metabolic and signaling processes depends on NAD availability. Generally, human cells accomplish their NAD supply through biosynthesis using different forms of vitamin B3: Nicotinamide (Nam) and nicotinic acid as well as nicotinamide riboside (NR) and nicotinic acid riboside (NAR). These precursors are converted to the corresponding mononucleotides NMN and NAMN, which are adenylylated to the dinucleotides NAD and NAAD, respectively. Here, we have developed an NMR-based experimental approach to detect and quantify NAD(P) and its biosynthetic intermediates in human cell extracts. Using this method, we have determined NAD, NADP, NMN and Nam pools in HEK293 cells cultivated in standard culture medium containing Nam as the only NAD precursor. When cells were grown in the additional presence of both NAR and NR, intracellular pools of deamidated NAD intermediates (NAR, NAMN and NAAD) were also detectable. We have also tested this method to quantify NAD+ in human platelets and erythrocytes. Our results demonstrate that 1 H NMR spectroscopy provides a powerful method for the assessment of the cellular NAD metabolome. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Ebola virus (EBOV) infection causes severe hemorrhagic fever. EBOV transcription is controlled by host protein phosphatase 1 (PP1), which dephosphorylates VP30 protein. We previously developed 1E7-03, a compound targeting a noncatalytic site of PP1 that induced VP30 phosphorylation and inhibited EBOV transcription. Here, we attempted to further improve 1E7-03, which was not stable in murine serum. Results. High-throughput screening with EBOV-green fluorescent protein was conducted on 72 1E7-03 analogs and identified 6 best inhibitory and the least toxic compounds. A parallel in silico screening of compounds from the ZINC database by docking to PP1 identified the best-binding compound C31, which was also present among the top 6 compounds found in the viral screen. C31 showed the best EBOV inhibitory activity among the top 6 compounds and also inhibited EBOV minigenome. C31 bound to the PP1 C-terminal groove in vitro and increased VP30 phosphorylation in cultured cells. C31 demonstrated improved stability in mouse plasma and cell permeability, compared with 1E7-03. It was also detected for 24 hours after injection in mice. Conclusion. C31 represents a novel PP1-targeting EBOV inhibitor with improved pharmacological properties that can be further evaluated for future antifiloviral therapy. © 2018. This article contains public sector information licensed under the Open Government Licence v3.0.

Abstract—: Nicotinamide adenine dinucleotide (NAD) plays a key role in the vital metabolic and regulatory processes in mammals. Disturbance of the NAD level regulation is associated with the development of such serious diseases as pellagra, neurodegenerative and cardiovascular disorders, diabetes, cancer and others. This paper presents an experimental approach that allows to determine the amount of NAD+ in mouse tissues using NMR spectroscopy, as well as the level of NAD+-dependent deacetylation of proteins in the cytosol and mitochondria. © 2018, Pleiades Publishing, Ltd.

@ARTICLE{Brodskaia2018147,
author={Brodskaia, A.V. and Timin, A.S. and Gorshkov, A.N. and Muslimov, A.R. and Bondarenko, A.B. and Tarakanchikova, Y.V. and Zabrodskaya, Y.A. and Baranovskaya, I.L. and Il'inskaja, E.V. and Sakhenberg, E.I. and Sukhorukov, G.B. and Vasin, A.V.},
title={Inhibition of influenza A virus by mixed siRNAs, targeting the PA, NP, and NS genes, delivered by hybrid microcarriers},
journal={Antiviral Research},
year={2018},
volume={158},
pages={147-160},
doi={10.1016/j.antiviral.2018.08.003},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85051969568&doi=10.1016%2fj.antiviral.2018.08.003&partnerID=40&md5=3472df2ecf59849e439848c52616313e},
affiliation={Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, St. Petersburg, 197376, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russian Federation; RASA Center, National Research Tomsk Polytechnic University, Lenin Avenue, 30, Tomsk, 634050, Russian Federation; Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave. 4, St. Petersburg, 194064, Russian Federation; First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, St. Petersburg, 197022, Russian Federation; St. Petersburg State University, Vasilyevsky Island, Liniya 16-ya, 29, St. Petersburg, 199178, Russian Federation; Saratov State University, Astrakhanskaya Street 83, Saratov, 410012, Russian Federation; Petersburg Nuclear Physics Institute in Honor of B. P. Konstantinov, National Research Center “Kurchatov Institute”, Gatchina, 188300, Russian Federation; School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom; St. Petersburg State Chemical Pharmaceutical Academy, Prof. Popova str., 14 A, St. Petersburg, 197376, Russian Federation; RASA Center, Tomsk Polytechnic University, Lenin Avenue, 30, Tomsk, 634050, Russian Federation; Research, Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, St. Petersburg, 197376, Russian Federation},
abstract={In the present study, a highly effective carrier system has been developed for the delivery of antiviral siRNA mixtures. The developed hybrid microcarriers, made of biodegradable polymers and SiO2 nanostructures, more efficiently mediate cellular uptake of siRNA than commercially available liposome-based reagents and polyethyleneimine (PEI); they also demonstrate low in vitro toxicity and protection of siRNA from RNase degradation. A series of siRNA designs (targeting the most conserved regions of three influenza A virus (IAV) genes: NP, NS, and PA) were screened in vitro using RT-qPCR, ELISA analysis, and hemagglutination assay. Based on the results of screening, the three most effective siRNAs (PA-1630, NP-717, and NS-777) were selected for in situ encapsulation into hybrid microcarriers. It was revealed that pre-treatment of cells with a mixture of PA-1630, NP-717, and NS-777 siRNAs, delivered by hybrid microcarriers, provided stronger inhibition of viral M1 mRNA expression and control of NP protein level, after viral infection, than single pre-treatment by any of three encapsulated siRNAs used in the study. Moreover, the effective inhibition of replication in several IAV subtypes (H1N1, H1N1pdm, H5N2, and H7N9) using a cocktail of the three selected siRNAs, delivered by our hybrid capsules to the cells, was achieved. In conclusion, we have developed a proof-of-principle which shows that our hybrid microcarrier technology (utilizing a therapeutic siRNA cocktail) may represent a promising approach in anti-influenza therapy. © 2018 Elsevier B.V.},
author_keywords={Hybrid microcontainers;  Influenza A virus;  RNAi therapy;  siRNA delivery},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)18-015-00100},
funding_details={Russian Science Foundation17-73-10023, 15-15-00170},
funding_details={11.1233.2017/4.6, 11.7293.2017/8.9},
}

In the present study, a highly effective carrier system has been developed for the delivery of antiviral siRNA mixtures. The developed hybrid microcarriers, made of biodegradable polymers and SiO2 nanostructures, more efficiently mediate cellular uptake of siRNA than commercially available liposome-based reagents and polyethyleneimine (PEI); they also demonstrate low in vitro toxicity and protection of siRNA from RNase degradation. A series of siRNA designs (targeting the most conserved regions of three influenza A virus (IAV) genes: NP, NS, and PA) were screened in vitro using RT-qPCR, ELISA analysis, and hemagglutination assay. Based on the results of screening, the three most effective siRNAs (PA-1630, NP-717, and NS-777) were selected for in situ encapsulation into hybrid microcarriers. It was revealed that pre-treatment of cells with a mixture of PA-1630, NP-717, and NS-777 siRNAs, delivered by hybrid microcarriers, provided stronger inhibition of viral M1 mRNA expression and control of NP protein level, after viral infection, than single pre-treatment by any of three encapsulated siRNAs used in the study. Moreover, the effective inhibition of replication in several IAV subtypes (H1N1, H1N1pdm, H5N2, and H7N9) using a cocktail of the three selected siRNAs, delivered by our hybrid capsules to the cells, was achieved. In conclusion, we have developed a proof-of-principle which shows that our hybrid microcarrier technology (utilizing a therapeutic siRNA cocktail) may represent a promising approach in anti-influenza therapy. © 2018 Elsevier B.V.

In this study, we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine’s mechanism of action as it pertains to SI peptide fibril formation. © 2017, © 2017 Informa UK Limited, trading as Taylor & Francis Group.

@ARTICLE{Ivanov2018,
author={Ivanov, A. and Lin, X. and Ammosova, T. and Ilatovskiy, A.V. and Kumari, N. and Lassiter, H. and Afangbedji, N. and Niu, X. and Petukhov, M.G. and Nekhai, S.},
title={HIV-1 Tat phosphorylation on Ser-16 residue modulates HIV-1 transcription},
journal={Retrovirology},
year={2018},
volume={15},
number={1},
doi={10.1186/s12977-018-0422-5},
art_number={39},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047482579&doi=10.1186%2fs12977-018-0422-5&partnerID=40&md5=80ac4eaa0e53385e032d2c6db96a912e},
affiliation={Howard University, Center for Sickle Cell Disease, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC  20001, United States; Howard University, Department of Medicine, Washington, DC, United States; Yakut Science Center for Complex Medical Problems, Yakutsk, Russian Federation; Petersburg Nuclear Physics Institute, Division of Molecular and Radiation Biophysics, Gatchina, Russian Federation; Research Center for Nanobiotechnologies, St. Petersburg, Russian Federation},
abstract={Background: HIV-1 transcription activator protein Tat is phosphorylated in vitro by CDK2 and DNA-PK on Ser-16 residue and by PKR on Tat Ser-46 residue. Here we analyzed Tat phosphorylation in cultured cells and its functionality. Results: Mass spectrometry analysis showed primarily Tat Ser-16 phosphorylation in cultured cells. In vitro, CDK2/cyclin E predominantly phosphorylated Tat Ser-16 and PKR-Tat Ser-46. Alanine mutations of either Ser-16 or Ser-46 decreased overall Tat phosphorylation. Phosphorylation of Tat Ser-16 was reduced in cultured cells treated by a small molecule inhibitor of CDK2 and, to a lesser extent, an inhibitor of DNA-PK. Conditional knock-downs of CDK2 and PKR inhibited and induced one round HIV-1 replication respectively. HIV-1 proviral transcription was inhibited by Tat alanine mutants and partially restored by S16E mutation. Pseudotyped HIV-1 with Tat S16E mutation replicated well, and HIV-1 Tat S46E-poorly, but no live viruses were obtained with Tat S16A or Tat S46A mutations. TAR RNA binding was affected by Tat Ser-16 alanine mutation. Binding to cyclin T1 showed decreased binding of all Ser-16 and Ser-46 Tat mutants with S16D and Tat S46D mutationts showing the strongest effect. Molecular modelling and molecular dynamic analysis revealed significant structural changes in Tat/CDK9/cyclin T1 complex with phosphorylated Ser-16 residue, but not with phosphorylated Ser-46 residue. Conclusion: Phosphorylation of Tat Ser-16 induces HIV-1 transcription, facilitates binding to TAR RNA and rearranges CDK9/cyclin T1/Tat complex. Thus, phosphorylation of Tat Ser-16 regulates HIV-1 transcription and may serve as target for HIV-1 therapeutics. © 2018 The Author(s).},
funding_details={National Heart, Lung, and Blood InstituteNIDA},
funding_details={District of Columbia Developmental Center for AIDS ResearchAI117970},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)12-04-91444-NIZ},
funding_details={NIH Blueprint for Neuroscience Research1R01HL125005, U19AI109664, P30AI117970, 1P50HL118006, 1UM1AI26617, 5G12MD007597},
funding_details={Ministry of Education and Science of the Russian Federation2012-1.5-12-000-1001-030},
}

Background: HIV-1 transcription activator protein Tat is phosphorylated in vitro by CDK2 and DNA-PK on Ser-16 residue and by PKR on Tat Ser-46 residue. Here we analyzed Tat phosphorylation in cultured cells and its functionality. Results: Mass spectrometry analysis showed primarily Tat Ser-16 phosphorylation in cultured cells. In vitro, CDK2/cyclin E predominantly phosphorylated Tat Ser-16 and PKR-Tat Ser-46. Alanine mutations of either Ser-16 or Ser-46 decreased overall Tat phosphorylation. Phosphorylation of Tat Ser-16 was reduced in cultured cells treated by a small molecule inhibitor of CDK2 and, to a lesser extent, an inhibitor of DNA-PK. Conditional knock-downs of CDK2 and PKR inhibited and induced one round HIV-1 replication respectively. HIV-1 proviral transcription was inhibited by Tat alanine mutants and partially restored by S16E mutation. Pseudotyped HIV-1 with Tat S16E mutation replicated well, and HIV-1 Tat S46E-poorly, but no live viruses were obtained with Tat S16A or Tat S46A mutations. TAR RNA binding was affected by Tat Ser-16 alanine mutation. Binding to cyclin T1 showed decreased binding of all Ser-16 and Ser-46 Tat mutants with S16D and Tat S46D mutationts showing the strongest effect. Molecular modelling and molecular dynamic analysis revealed significant structural changes in Tat/CDK9/cyclin T1 complex with phosphorylated Ser-16 residue, but not with phosphorylated Ser-46 residue. Conclusion: Phosphorylation of Tat Ser-16 induces HIV-1 transcription, facilitates binding to TAR RNA and rearranges CDK9/cyclin T1/Tat complex. Thus, phosphorylation of Tat Ser-16 regulates HIV-1 transcription and may serve as target for HIV-1 therapeutics. © 2018 The Author(s).

Background: Glioblastoma is the most devastating primary brain tumor of the central nervous system in adults. Magnetic nanocarriers may help not only for a targeted delivery of chemotherapeutic agents into the tumor site but also provide contrast enhancing properties for diagnostics using magnetic resonance imaging (MRI). Methods: Synthesized hybrid chitosan-dextran superparamagnetic nanoparticles (CS-DX-SPIONs) were characterized using transmission electron microscopy (TEM) and relaxometry studies. Nonlinear magnetic response measurements were employed for confirming the superparamagnetic state of particles. Following in vitro analysis of nanoparticles cellular uptake tumor targeting was assessed in the model of the orthotopic glioma in rodents. Results: CS-DX-SPIONs nanoparticles showed a uniform diameter of 55 nm under TEM and superparamagentic characteristics as determined by T1 (spin-lattice relaxation time) and T2 (spin-spin relaxation time) proton relaxation times. Application of the chitosan increased the charge from +8.9 to +19.3 mV of the dextran-based SPIONs. The nonlinear magnetic response at second harmonic of CS-DX-SPIONs following the slow change of stationary magnetic fields with very low hysteresis evidenced superparamagnetic state of particles at ambient temperatures. Confocal microscopy and flow cytometry studies showed an enhanced internalization of the chitosan-based nanoparticles in U87, C6 glioma and HeLa cells as compared to dextran-coated particles. Cytotoxicity assay demonstrated acceptable toxicity profile of the synthesized nanoparticles up to a concentration of 10 μg/ml. Intravenously administered CS-DX-SPIONs in orthotopic C6 gliomas in rats accumulated in the tumor site as shown by high-resolution MRI (11.0 T). Retention of nanoparticles resulted in a significant contrast enhancement of the tumor image that was accompanied with a dramatic drop in T2 values (P<0.001). Subsequent histological studies proved the accumulation of the nanoparticles inside glioblastoma cells. Conclusion: Hybrid chitosan-dextran magnetic particles demonstrated high MR contrast enhancing properties for the delineation of the brain tumor. Due to a significant retention of the particles in the tumor an application of the CS-DX-SPIONs could not only improve the tumor imaging but also could allow a targeted delivery of chemotherapeutic agents. © 2018 Shevtsov et al.

The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6–13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures. In this paper, it was shown that PB1(6–13) peptide is prone to form the amyloid-like fibrillar aggregates. The peptide homo-oligomerization kinetics were examined, and the affinity and characteristic interaction time of PB1(6–13) peptide monomers and the influenza virus polymerase complex PB1 subunit N-terminal region were evaluated by the SPR and TR-SAXS methods. Based on the data obtained, a hypothesis about the PB1(6–13) peptide mechanism of action was proposed: the peptide in its monomeric form is capable of altering the conformation of the PB1 subunit N-terminal region, causing a change from an alpha helix to a beta structure. This conformational change disrupts PB1 and PA subunit interaction and, by that mechanism, the peptide displays antiviral activity. © 2018 Elsevier B.V.

The aim of this study is to determine the optimal parameters of the electric pulses and shock waves generated by them for the soft destruction of the virus and yeast envelopes with no changes in the structure of antigenic surface albumin and in the cell morphology in order to use them to produce antivirus vaccines and in biotechnology. The pulse electric discharges in water have been studied for different values of amplitude, pulse duration and the rate of the rise in the current. A mathematical model has been developed to estimate the optimal parameters of pulsed electric charges and shock waves for the complete destruction of the yeast cell envelopes and virus particles at a minimum of pulses. © 2018, Pleiades Publishing, Ltd.

@ARTICLE{Tsybalova201868,
author={Tsybalova, L.M. and Stepanova, L.A. and Shuklina, M.A. and Petrov, S.V. and Kovaleva, A.A. and Potapchuk, M.V. and Shaldzhan, A.A. and Zabrodskaya, Y.A. and Egorov, V.V.},
title={Cross-protective properties of an influenza vaccine based on HBc4M2e recombinant protein},
journal={Voprosy Virusologii},
year={2018},
volume={63},
number={2},
pages={68-76},
doi={10.18821/0507-4088-2018-63-2-68-76},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059573577&doi=10.18821%2f0507-4088-2018-63-2-68-76&partnerID=40&md5=cb7ea4163ef5f81a294eadb05ab11185},
affiliation={Department of Vaccinology, Research Institute of Influenza, St. Petersburg, 197376, Russian Federation},
abstract={One of the main problems in the area of influenza prophylaxis and pandemic prevention is the development of cross-reactive vaccines, i.e. vaccines directed against all subtypes of human influenza viruses. Such vaccines are being developed in many countries for more than 10 years. A number of vaccines are presently undergoing clinical trials. We created Uniflu candidate vaccine based on recombinant HBc4M2e protein consisting of 4 tandem-connected copies of the highly conserved ectodomain of M2 protein of the influenza A virus. These 4 copies were genetically fused to the carrier protein, namely hepatitis B core antigen. Commercially available Derinat was used as adjuvant in the candidate vaccine. Preclinical studies on laboratory animals (mice, ferrets) demonstrated that immunization with Uniflu leads to significantly higher level of specific immunoglobulins in the blood and bronchoalveolar lavages. Moreover, it produces immunoglobulins belonging to subtype lgG2a that is the most important mediator of antibody-dependent cytotoxicity. The vaccine under review stimulates the proliferation of T-lymphocytes, as well as the formation of CD4+ and CD8+ T-cells synthesizing γ-IFN. When infected with the lethal doses (5 LD50) of influenza A viruses of the subtypes H1N1, H2N2, H3N2, and H1N1pdm09, immunized animals typically developed mild form of illness. This kept them alive in 90-100% of cases, which demonstrated almost complete protection from death. Replication of the virus in the lungs of immunized mice was reduced by 1.8-4.8 Iog10. High immunogenicity of the vaccine, and reduced clinical symptoms following experimental infection, were demonstrated in ferrets as well. The developed recombinant vaccine Uniflu has high specific activity and cross-protection. Uniflu can be proposed as pre-pandemic vaccine, provided that it passes clinical trials. © 2018 Izdatel'stvo Meditsina.All Rights Reserved.},
author_keywords={Cross-protection;  Immunogenicity;  Influenza A;  Laboratory animals;  Recombinant vaccine},
correspondence_address1={Tsybalova, L.M.; Department of Vaccinology, Research Institute of InfluenzaRussian Federation; email: sovet@influenza.spb.ru},
publisher={Izdatel'stvo Meditsina},
issn={05074088},
coden={VVIRA},
language={Russian},
abbrev_source_title={Vopr. Virusol.},
document_type={Review},
source={Scopus},
}

One of the main problems in the area of influenza prophylaxis and pandemic prevention is the development of cross-reactive vaccines, i.e. vaccines directed against all subtypes of human influenza viruses. Such vaccines are being developed in many countries for more than 10 years. A number of vaccines are presently undergoing clinical trials. We created Uniflu candidate vaccine based on recombinant HBc4M2e protein consisting of 4 tandem-connected copies of the highly conserved ectodomain of M2 protein of the influenza A virus. These 4 copies were genetically fused to the carrier protein, namely hepatitis B core antigen. Commercially available Derinat was used as adjuvant in the candidate vaccine. Preclinical studies on laboratory animals (mice, ferrets) demonstrated that immunization with Uniflu leads to significantly higher level of specific immunoglobulins in the blood and bronchoalveolar lavages. Moreover, it produces immunoglobulins belonging to subtype lgG2a that is the most important mediator of antibody-dependent cytotoxicity. The vaccine under review stimulates the proliferation of T-lymphocytes, as well as the formation of CD4+ and CD8+ T-cells synthesizing γ-IFN. When infected with the lethal doses (5 LD50) of influenza A viruses of the subtypes H1N1, H2N2, H3N2, and H1N1pdm09, immunized animals typically developed mild form of illness. This kept them alive in 90-100% of cases, which demonstrated almost complete protection from death. Replication of the virus in the lungs of immunized mice was reduced by 1.8-4.8 Iog10. High immunogenicity of the vaccine, and reduced clinical symptoms following experimental infection, were demonstrated in ferrets as well. The developed recombinant vaccine Uniflu has high specific activity and cross-protection. Uniflu can be proposed as pre-pandemic vaccine, provided that it passes clinical trials. © 2018 Izdatel'stvo Meditsina.All Rights Reserved.

@ARTICLE{Ryzhov201884,
author={Ryzhov, V.A. and Lashkul, A.V. and Matveev, V.V. and Molkanov, P.L. and Kurbakov, A.I. and Kiselev, I.A. and Lisunov, K.G. and Galimov, D. and Lähderanta, E.},
title={Magnetic phase separation and unusual scenario of its temperature evolution in porous carbon-based nanomaterials doped with Au and Co},
journal={Journal of Magnetism and Magnetic Materials},
year={2018},
volume={445},
pages={84-94},
doi={10.1016/j.jmmm.2017.08.077},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028947889&doi=10.1016%2fj.jmmm.2017.08.077&partnerID=40&md5=43b994d1622fcb87cbbbb213b64d90e0},
affiliation={Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 1, Orlova roscha mcr., Gatchina, Leningrad Region  188300, Russian Federation; Department of Mathematics and Physics, Lappeenranta University of Technology, PO Box 20, Lappeenranta, FIN-53851, Finland; Saint-Petersburg University, Petergof, Ulyanovskaya str., 3, Saint-Petersburg, 198504, Russian Federation; Institute of Applied Physics ASM, Academiei Str., 5, Kishinev, MD  2028, Moldova; South Ural State University, Chelyabinsk, 454080, Russian Federation},
abstract={Two porous glassy carbon-based samples doped with Au and Co were investigated. The magnetization study as well as measurements of the nonlinear longitudinal response to a weak ac field (NLR) and electron magnetic resonance give evidences for a presence of magnetic nanoparticles (MNPs) embedded in paramagnetic/ferromagnetic matrix respectively, both samples being in magnetically phase-separated state at temperatures above 300 K. Matrix, forming by paramagnetic centers located in matrix outside the MNPs, reveals exchange interactions providing its ferromagnetic (FM) ordering below TC ≈ 210 K in Au-doped sample and well above 350 K in Co-doped one. For the former, NLR data suggest a percolation character of the matrix long-range FM order, which is mainly caused by a porous amorphous sample structure. Temperature dependence of the magnetization in the Au-doped sample evidences presence of antiferromagnetic (AF) interactions of MNPs with surrounding matrix centers. At magnetic ordering below TC these interactions promote origination of “domains” involving matrix fragment and surrounding MNPs with near opposite orientation of their moments that decreases the magnetostatic energy. On further cooling, the domains exhibit AF ordering below Tcr ∼ 140 K < TC, resulting in formation of a peculiar “ferrimagnet”. The porous amorphous structure leads to absence of translational and other symmetry features through the samples that allows canted ordering of magnetic moments in domains and in whole sample providing “canted ferrimagnetism”. At low temperatures Ttr ∼ 3 K, “order-oder” transition, evidencing the non-Heisenberg character of this magnetic material, occurs from ordering like “canted ferrimagnet” to FM alignment, which is stimulated by external magnetic field. The data for Co-doped sample imply the similar evolution of magnetic state but at higher temperatures above 350 K. This state exhibits more homogeneous arrangement of the FM nanoparticles and the FM matrix. Order-order transition occurs in it at higher Ttr ∼ 10–15 K as well and followed by formation of long-range FM ordering found earlier by neutron diffraction. Doping of carbon-based nanomaterials by magnetic metals provides advantages for their possible practical applications as Co-doped sample with higher TC (>350 K) and larger remanent magnetization evidences. © 2017 Elsevier B.V.},
author_keywords={Carbon-based materials;  Magnetic ordering;  Magnetic phase separation},
}

Two porous glassy carbon-based samples doped with Au and Co were investigated. The magnetization study as well as measurements of the nonlinear longitudinal response to a weak ac field (NLR) and electron magnetic resonance give evidences for a presence of magnetic nanoparticles (MNPs) embedded in paramagnetic/ferromagnetic matrix respectively, both samples being in magnetically phase-separated state at temperatures above 300 K. Matrix, forming by paramagnetic centers located in matrix outside the MNPs, reveals exchange interactions providing its ferromagnetic (FM) ordering below TC ≈ 210 K in Au-doped sample and well above 350 K in Co-doped one. For the former, NLR data suggest a percolation character of the matrix long-range FM order, which is mainly caused by a porous amorphous sample structure. Temperature dependence of the magnetization in the Au-doped sample evidences presence of antiferromagnetic (AF) interactions of MNPs with surrounding matrix centers. At magnetic ordering below TC these interactions promote origination of “domains” involving matrix fragment and surrounding MNPs with near opposite orientation of their moments that decreases the magnetostatic energy. On further cooling, the domains exhibit AF ordering below Tcr ∼ 140 K < TC, resulting in formation of a peculiar “ferrimagnet”. The porous amorphous structure leads to absence of translational and other symmetry features through the samples that allows canted ordering of magnetic moments in domains and in whole sample providing “canted ferrimagnetism”. At low temperatures Ttr ∼ 3 K, “order-oder” transition, evidencing the non-Heisenberg character of this magnetic material, occurs from ordering like “canted ferrimagnet” to FM alignment, which is stimulated by external magnetic field. The data for Co-doped sample imply the similar evolution of magnetic state but at higher temperatures above 350 K. This state exhibits more homogeneous arrangement of the FM nanoparticles and the FM matrix. Order-order transition occurs in it at higher Ttr ∼ 10–15 K as well and followed by formation of long-range FM ordering found earlier by neutron diffraction. Doping of carbon-based nanomaterials by magnetic metals provides advantages for their possible practical applications as Co-doped sample with higher TC (>350 K) and larger remanent magnetization evidences. © 2017 Elsevier B.V.

Nicotinamide adenine dinucleotide (NAD) plays a key role in vital metabolic and regulatory processes in mammals. Violation of the NAD level regulation is associated with such serious diseases as pellagra, neurode-generative and cardiovascular disorders, diabetes, cancer and others. This paper presents an experimental approach that allows to determine the amount of NAD+ in mouse tissues using NMR spectroscopy, as well as the level of NAD + -dependent protein deacetylation in the cytosol and mitochondria. © 2018 Sankt Peterburg. All rights reserved.

@ARTICLE{Metelev20171129,
author={Metelev, M. and Osterman, I.A. and Ghilarov, D. and Khabibullina, N.F. and Yakimov, A. and Shabalin, K. and Utkina, I. and Travin, D.Y. and Komarova, E.S. and Serebryakova, M. and Artamonova, T. and Khodorkovskii, M. and Konevega, A.L. and Sergiev, P.V. and Severinov, K. and Polikanov, Y.S.},
title={Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel},
journal={Nature Chemical Biology},
year={2017},
volume={13},
number={10},
pages={1129-1136},
doi={10.1038/nchembio.2462},
note={cited By 15},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031012229&doi=10.1038%2fnchembio.2462&partnerID=40&md5=c5d5cfc278f69e76c4a9e942481d352e},
affiliation={Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russian Federation; Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russian Federation; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russian Federation; Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russian Federation; Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States; Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation; Waksman Institute for Microbiology Rutgers, State University of New Jersey, Piscataway, NJ, United States; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States},
abstract={Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-Translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-Terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome-KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.},
publisher={Nature Publishing Group},
issn={15524450},
coden={NCBAB},
pubmed_id={28846667},
language={English},
abbrev_source_title={Nat. Chem. Biol.},
document_type={Article},
source={Scopus},
}

Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-Translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-Terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome-KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.

@ARTICLE{Yakimov20179788,
author={Yakimov, A. and Pobegalov, G. and Bakhlanova, I. and Khodorkovskii, M. and Petukhov, M. and Baitin, D.},
title={Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide},
journal={Nucleic Acids Research},
year={2017},
volume={45},
number={16},
pages={9788-9796},
doi={10.1093/nar/gkx687},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031894382&doi=10.1093%2fnar%2fgkx687&partnerID=40&md5=7c23734641d4dc586d4b273bd6883cd5},
affiliation={Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, B.P.Konstantinov of National Research Centre Kurchatov Institute, Gatchina, 188300, Russian Federation; Peter the Great St Petersburg Polytechnic University, St-Petersburg, 195251, Russian Federation},
abstract={The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance. © The Author(s) 2017.},
correspondence_address1={Baitin, D.; Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, B.P.Konstantinov of National Research Centre Kurchatov InstituteRussian Federation; email: dimabaitin@yahoo.com},
publisher={Oxford University Press},
issn={03051048},
coden={NARHA},
pubmed_id={28934502},
language={English},
abbrev_source_title={Nucleic Acids Res.},
document_type={Article},
source={Scopus},
}

The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance. © The Author(s) 2017.

@CONFERENCE{Egorov2017,
author={Egorov, V.V. and Zabrodskaya, Ya.A. and Lebedev, D.V. and Gorshkov, A.N. and Kuklin, A.I.},
title={Structural features of the ionic self-complementary amyloidogenic peptide},
journal={Journal of Physics: Conference Series},
year={2017},
volume={848},
number={1},
doi={10.1088/1742-6596/848/1/012022},
art_number={012022},
note={cited By 3; Conference of 3rd International Conference on Small Angle Neutron Scattering Dedicated to the 80th Anniversary of Yu.M. Ostanevich, YuMO 2016 ; Conference Date: 6 June 2016 Through 9 June 2016;  Conference Code:128461},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85022023780&doi=10.1088%2f1742-6596%2f848%2f1%2f012022&partnerID=40&md5=084042060f223b6ec55b44af680ae297},
affiliation={DMRB PNPI NRC KI, Gatchina, Russian Federation; Influenza Institute MH of Russia, Saint-Petersburg, Russian Federation; Joint Institute for Nuclear Research, Dubna, Russian Federation; Moscow Institute of Physics and Technology, State University, Dolgoprudny, Russian Federation},
abstract={In this study we investigate the effect of triazavirine on ionic self-complementary (iSCM) containing peptides fibrils with transmission electron microscopy (TEM), small-angle neutron scattering (SANS) and MALDI mass-spectrometry (MS). It was shown that triazavirine is capable to dissociate iSCM amyloid fibrils. The mechanism of such an action is proposed. © Published under licence by IOP Publishing Ltd.},
correspondence_address1={Egorov, V.V.; DMRB PNPI NRC KI, GatchinaRussian Federation; email: vlaegur@omrb.pnpi.spb.ru},
sponsors={},
publisher={Institute of Physics Publishing},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

In this study we investigate the effect of triazavirine on ionic self-complementary (iSCM) containing peptides fibrils with transmission electron microscopy (TEM), small-angle neutron scattering (SANS) and MALDI mass-spectrometry (MS). It was shown that triazavirine is capable to dissociate iSCM amyloid fibrils. The mechanism of such an action is proposed. © Published under licence by IOP Publishing Ltd.

@ARTICLE{Malkov2017431,
author={Malkov, V.M. and Kiselev, I.A. and Shatalov, I.V. and Duk, A.A. and Emelyanova, A.V.},
title={Ejectors for pressure recovery systems of supersonic chemical lasers},
journal={Thermophysics and Aeromechanics},
year={2017},
volume={24},
number={3},
pages={431-447},
doi={10.1134/S0869864317030118},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85026852637&doi=10.1134%2fS0869864317030118&partnerID=40&md5=e74158db0f795f5640ef82585c36ed32},
affiliation={SPE Advent, Saint Petersburg, Russian Federation; Ustinov Voenmekh Baltic State Technical University, Saint Petersburg, Russian Federation},
abstract={Results of a numerical study of performance characteristics of supersonic ejectors with nozzles of different types are reported. The work was carried out with the aim of developing a high-performance ejector for pressure recovery systems of supersonic chemical lasers. A specific feature of the operation of ejectors in pressure recovery systems consists in that, in this case, the ejecting and ejected gases, as they undergo mixing, have different thermodynamic properties, and the ejection coefficient depends on the ratio between the temperatures of the gases and on the ratio of their molecular masses. Since the operation of an ejector is based on the mixing process, the task consisted in intensification of this process using nozzles of special geometries. The performance of ejectors was judged considering an integral parameter, the product of induction by compression ratio. The calculations of the 3D viscous gas flow in the ejector channel were performed using ANSYS software. In verifying the numerical model, a comparison with experimental data obtained earlier on a model ejector facility and during tests of real pressure recovery systems in operation with supersonic chemical lasers was performed. © 2017, Pleiades Publishing, Ltd.},
author_keywords={compression ratio;  ejection coefficient;  experimental data;  multi-nozzle ejectors;  nozzles;  parametric numerical studies;  pressure recovery system;  supersonic chemical lasers;  supersonic ejectors;  verification},
correspondence_address1={Malkov, V.M.; SPE AdventRussian Federation; email: v.m.malkov@gmail.com},
publisher={Maik Nauka-Interperiodica Publishing},
issn={08698643},
language={English},
abbrev_source_title={Thermophys. Aeromech.},
document_type={Article},
source={Scopus},
}

Results of a numerical study of performance characteristics of supersonic ejectors with nozzles of different types are reported. The work was carried out with the aim of developing a high-performance ejector for pressure recovery systems of supersonic chemical lasers. A specific feature of the operation of ejectors in pressure recovery systems consists in that, in this case, the ejecting and ejected gases, as they undergo mixing, have different thermodynamic properties, and the ejection coefficient depends on the ratio between the temperatures of the gases and on the ratio of their molecular masses. Since the operation of an ejector is based on the mixing process, the task consisted in intensification of this process using nozzles of special geometries. The performance of ejectors was judged considering an integral parameter, the product of induction by compression ratio. The calculations of the 3D viscous gas flow in the ejector channel were performed using ANSYS software. In verifying the numerical model, a comparison with experimental data obtained earlier on a model ejector facility and during tests of real pressure recovery systems in operation with supersonic chemical lasers was performed. © 2017, Pleiades Publishing, Ltd.

@ARTICLE{Rychkov2017460,
author={Rychkov, G.N. and Ilatovskiy, A.V. and Nazarov, I.B. and Shvetsov, A.V. and Lebedev, D.V. and Konev, A.Y. and Isaev-Ivanov, V.V. and Onufriev, A.V.},
title={Partially Assembled Nucleosome Structures at Atomic Detail},
journal={Biophysical Journal},
year={2017},
volume={112},
number={3},
pages={460-472},
doi={10.1016/j.bpj.2016.10.041},
note={cited By 15},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009290748&doi=10.1016%2fj.bpj.2016.10.041&partnerID=40&md5=11a123be201359b0889bc6505c1b6dc0},
affiliation={Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute” Orlova Roscha, Gatchina, Russian Federation; Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, United States; Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation; Institute of Applied Mathematics and Mechanics, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Departments of Computer Science and Physics Virginia Tech, Blacksburg, Virginia, United States},
abstract={The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. © 2017 Biophysical Society},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)obr-i 14-24-01103},
funding_details={Ministry of Education and Science of the Russian Federation8482 07.09.2012},
funding_details={Russian Science Foundation14-50-00068},
funding_details={National Institutes of HealthR01 GM099450, GM076121},
}

The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. © 2017 Biophysical Society

@ARTICLE{Petrova-Brodskaya2017259,
author={Petrova-Brodskaya, A.V. and Bondarenko, A.B. and Timin, A.S. and Plotnikova, M.A. and Afanas'Ev, M.V. and Semenova, A.A. and Lebedev, K.I. and Gorshkov, A.N. and Gorshkova, M.Yu. and Egorov, V.V. and Klotchenko, S.A. and Vasin, A.V.},
title={Comparison of influenza A virus inhibition in vitro by siRNA complexes with chitosan derivatives, polyethyleneimine and hybrid polyarginine-inorganic microcapsules},
journal={Voprosy Virusologii},
year={2017},
volume={62},
number={6},
pages={259-265},
doi={10.18821/0507-4088-2017-62-6-259-265},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047249423&doi=10.18821%2f0507-4088-2017-62-6-259-265&partnerID=40&md5=36fb813cdb03809a674193c9b766bc39},
affiliation={Laboratory of Intracellular Signaling and Transport, Research Institute of Influenza, St.-Petersburg, 197376, Russian Federation; Peter the Great St. Petersburg Polytechnic University, St.-Petersburg, 195251, Russian Federation; St. Petersburg State University, St.-Petersburg, 199034, Russian Federation; National Research Tomsk Polytechnic University, Tomsk, 634050, Russian Federation; St. Petersburg State Chemical Pharmaceutical Academy, St.-Petersburg, 197376, Russian Federation; A.V. Topchiev Institute of Petrochemical Synthesis, Moscow, 119991, Russian Federation; Institute of Cytology, St.-Petersburg, 194064, Russian Federation},
abstract={Anti-influenza drugs and vaccines have a limited effect due to the high mutation rate of virus genome. The direct impact on the conservative virus genome regions should significantly improve therapeutic effectiveness. The RNA interference mechanism (RNAi) is one of the modern approaches used to solve this problem. In this work, we have investigated the antiviral activity of small interfering RNA (siRNA) against the influenza A/PR/8/34 (H1N1), targeting conserved regions of NP and PA. Polycations were used for intracellular siRNA delivery: chitosan's derivatives (methylglycol and quaternized chitosan), polyethyleneimine, lipofectamine, and hybrid organic/non-organic microcapsules. A comparative study of these delivery systems with fluorescent labeled siRNA was conducted. The antiviral activity of three small interfering RNAs targeting the NP (NP-717, NP-1496) and PA (PA-1630) influenza A viruses genes was demonstrated, depending on the chosen carrier. The most effective intracellular delivery and antiviral activity were observed for hybrid microcapsules. © 2017 Izdatel'stvo Meditsina. All rights reserved.},
author_keywords={Antiviral activity;  Chitosan;  Delivery systems;  Lipofectamine;  Microcapsules;  NP, PA, small interfering RNA (siRNA);  Polyeth-yleneimine},
correspondence_address1={Petrova-Brodskaya, A.V.; Laboratory of Intracellular Signaling and Transport, Research Institute of InfluenzaRussian Federation; email: alexandra.b_05@mail.ru},
publisher={Izdatel'stvo Meditsina},
issn={05074088},
coden={VVIRA},
language={Russian},
abbrev_source_title={Vopr. Virusol.},
document_type={Article},
source={Scopus},
}

Anti-influenza drugs and vaccines have a limited effect due to the high mutation rate of virus genome. The direct impact on the conservative virus genome regions should significantly improve therapeutic effectiveness. The RNA interference mechanism (RNAi) is one of the modern approaches used to solve this problem. In this work, we have investigated the antiviral activity of small interfering RNA (siRNA) against the influenza A/PR/8/34 (H1N1), targeting conserved regions of NP and PA. Polycations were used for intracellular siRNA delivery: chitosan's derivatives (methylglycol and quaternized chitosan), polyethyleneimine, lipofectamine, and hybrid organic/non-organic microcapsules. A comparative study of these delivery systems with fluorescent labeled siRNA was conducted. The antiviral activity of three small interfering RNAs targeting the NP (NP-717, NP-1496) and PA (PA-1630) influenza A viruses genes was demonstrated, depending on the chosen carrier. The most effective intracellular delivery and antiviral activity were observed for hybrid microcapsules. © 2017 Izdatel'stvo Meditsina. All rights reserved.

@ARTICLE{Antimonova2016468,
author={Antimonova, O.I. and Grudinina, N.A. and Egorov, V.V. and Polyakov, D.S. and Il’in, V.V. and Shavlovskii, M.M.},
title={Interaction of the dye Congo red with fibrils of lysozyme, beta2-microglobulin, and transthyretin},
journal={Cell and Tissue Biology},
year={2016},
volume={10},
number={6},
pages={468-475},
doi={10.1134/S1990519X1606002X},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85004097403&doi=10.1134%2fS1990519X1606002X&partnerID=40&md5=66d2aeadc5edcb106b57c5883748aba4},
affiliation={Institute of Experimental Medicine, St. Petersburg, 197376, Russian Federation; Almazov Northwestern Federal Center of Medical Research, Ministry of Healthcare of the Russian Federation, St. Petersburg, 197341, Russian Federation; Institute of Influenza Research, Ministry of Healthcare of the Russian Federation, St. Petersburg, 197022, Russian Federation; Konstantinov Institute of Nuclear Physics, Russian Research Centre Kurchatov Institute, Gatchina, Leningrad oblast, 188300, Russian Federation; Mechnikov Northwestern State Medical University, Ministry of Healthcare of the Russian Federation, St. Petersburg, 191015, Russian Federation},
abstract={Interaction of the dye Congo red (CR) with fibrils of three model proteins—hen egg lysozyme, recombinant human beta 2-microglobulin (b2M), and recombinant human transthyretin (TTR)—has been investigated using spectrophotometry. Considerable amounts of impurities were detected in the commercial dye formulation. A procedure of dye purification has been developed. The molar extinction coefficient of the dye at 490 nm (ε490) has been measured; the coefficient was 3.3 × 104 M–1 cm–1 at pH > 6.0. The formation of a complex between CR and the fibrils was accompanied by a change in the absorption spectrum of the dye in the visible wavelength range. Titration of fibril solutions with excessive amounts of dye showed that the number of CR molecules bound to a protein monomer within the lysozyme fibrils was close to five, whereas the respective ratio for b2M was close to four, and the ratio for TTR fibrils was close to four molecules per protein subunit. © 2016, Pleiades Publishing, Ltd.},
author_keywords={amyloidogenic proteins;  amyloidosis;  beta2-microglobulin;  Congo red;  lysozyme;  spectrophotometry;  transthyretin},
correspondence_address1={Antimonova, O.I.; Institute of Experimental MedicineRussian Federation; email: oa0584@mail.ru},
publisher={Maik Nauka-Interperiodica Publishing},
issn={1990519X},
language={English},
abbrev_source_title={Cell Tissue Biol.},
document_type={Article},
source={Scopus},
}

Interaction of the dye Congo red (CR) with fibrils of three model proteins—hen egg lysozyme, recombinant human beta 2-microglobulin (b2M), and recombinant human transthyretin (TTR)—has been investigated using spectrophotometry. Considerable amounts of impurities were detected in the commercial dye formulation. A procedure of dye purification has been developed. The molar extinction coefficient of the dye at 490 nm (ε490) has been measured; the coefficient was 3.3 × 104 M–1 cm–1 at pH > 6.0. The formation of a complex between CR and the fibrils was accompanied by a change in the absorption spectrum of the dye in the visible wavelength range. Titration of fibril solutions with excessive amounts of dye showed that the number of CR molecules bound to a protein monomer within the lysozyme fibrils was close to five, whereas the respective ratio for b2M was close to four, and the ratio for TTR fibrils was close to four molecules per protein subunit. © 2016, Pleiades Publishing, Ltd.

@ARTICLE{Shevtsov2016,
author={Shevtsov, M.A. and Parr, M.A. and Ryzhov, V.A. and Zemtsova, E.G. and Arbenin, A.Yu. and Ponomareva, A.N. and Smirnov, V.M. and Multhoff, G.},
title={Zero-valent Fe confined mesoporous silica nanocarriers (Fe(0) @ MCM-41) for targeting experimental orthotopic glioma in rats},
journal={Scientific Reports},
year={2016},
volume={6},
doi={10.1038/srep29247},
art_number={29247},
note={cited By 11},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84977617915&doi=10.1038%2fsrep29247&partnerID=40&md5=40ac41f41c4f4d20ac7541f455917d8f},
affiliation={Klinikum Rechts der Isar, Department Radiation Oncology, Technische Universität München, Ismaniger Str. 22, Munich, 81675, Germany; Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky ave., 4, St-Petersburg, 194064, Russian Federation; Saint Petersburg State University, Universitetskaya nab. 7 - 9, St-Petersburg, 199034, Russian Federation; NRC 'Kurchatov Institute', B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation},
abstract={Mesoporous silica nanoparticles (MSNs) impregnated with zero-valent Fe (Fe(0) @ MCM-41) represent an attractive nanocarrier system for drug delivery into tumor cells. The major goal of this work was to assess whether MSNs can penetrate the blood-brain barrier in a glioblastoma rat model. Synthesized MSNs nanomaterials were characterized by energy dispersive X-ray spectroscopy, measurements of X-ray diffraction, scanning electron microscopy and Mössbauer spectroscopy. For the detection of the MSNs by MR and for biodistribution studies MSNs were labeled with zero-valent Fe. Subsequent magnetometry and nonlinear-longitudinal-response-M2 (NLR-M2) measurements confirmed the MR negative contrast enhancement properties of the nanoparticles. After incubation of different tumor (C6 glioma, U87 glioma, K562 erythroleukemia, HeLa cervix carcinoma) and normal cells such as fibroblasts and peripheral blood mononuclear cells (PBMCs) MSNs rapidly get internalized into the cytosol. Intracellular residing MSNs result in an enhanced cytotoxicity as Fe(0) @ MCM-41 promote the reactive oxygen species production. MRI and histological studies indicated an accumulation of intravenously injected Fe(0) @ MCM-41 MSNs in orthotopic C6 glioma model. Biodistribution studies with measurements of second harmonic of magnetization demonstrated an increased and dose-dependent retention of MSNs in tumor tissues. Taken together, this study demonstrates that MSNs can enter the blood-brain barrier and accumulate in tumorous tissues.},
funding_details={B25.31.0017, 15-08-08148 A},
funding_details={Deutsche ForschungsgemeinschaftSFB824/2},
funding_details={Russian Science Foundation14-50-00068},
funding_details={Ministry of Education and Science of the Russian Federation32},
}

Mesoporous silica nanoparticles (MSNs) impregnated with zero-valent Fe (Fe(0) @ MCM-41) represent an attractive nanocarrier system for drug delivery into tumor cells. The major goal of this work was to assess whether MSNs can penetrate the blood-brain barrier in a glioblastoma rat model. Synthesized MSNs nanomaterials were characterized by energy dispersive X-ray spectroscopy, measurements of X-ray diffraction, scanning electron microscopy and Mössbauer spectroscopy. For the detection of the MSNs by MR and for biodistribution studies MSNs were labeled with zero-valent Fe. Subsequent magnetometry and nonlinear-longitudinal-response-M2 (NLR-M2) measurements confirmed the MR negative contrast enhancement properties of the nanoparticles. After incubation of different tumor (C6 glioma, U87 glioma, K562 erythroleukemia, HeLa cervix carcinoma) and normal cells such as fibroblasts and peripheral blood mononuclear cells (PBMCs) MSNs rapidly get internalized into the cytosol. Intracellular residing MSNs result in an enhanced cytotoxicity as Fe(0) @ MCM-41 promote the reactive oxygen species production. MRI and histological studies indicated an accumulation of intravenously injected Fe(0) @ MCM-41 MSNs in orthotopic C6 glioma model. Biodistribution studies with measurements of second harmonic of magnetization demonstrated an increased and dose-dependent retention of MSNs in tumor tissues. Taken together, this study demonstrates that MSNs can enter the blood-brain barrier and accumulate in tumorous tissues.

@ARTICLE{Vasin2016,
author={Vasin, A.V. and Petrova, A.V. and Egorov, V.V. and Plotnikova, M.A. and Klotchenko, S.A. and Karpenko, M.N. and Kiselev, O.I.},
title={The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure},
journal={BMC Research Notes},
year={2016},
volume={9},
number={1},
doi={10.1186/s13104-016-2083-6},
art_number={279},
note={cited By 6},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84974721006&doi=10.1186%2fs13104-016-2083-6&partnerID=40&md5=f1376d24d3b93b6d9f0ce60f93d9ce9a},
affiliation={Research Institute of Influenza, St-Petersburg, 197376, Russian Federation; Peter the Great St-Petersburg Polytechnic University, St-Petersburg, 195251, Russian Federation},
abstract={Background: Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures. Results: We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages. Conclusions: These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle. © 2016 The Author(s).},
author_keywords={Evolution;  Influenza A virus;  NS gene;  Pathogenicity;  RNA hairpin;  RNA secondary structure},
correspondence_address1={Vasin, A.V.; Research Institute of InfluenzaRussian Federation; email: vasin@influenza.spb.ru},
publisher={BioMed Central Ltd.},
issn={17560500},
pubmed_id={27206548},
language={English},
abbrev_source_title={BMC Res. Notes},
document_type={Article},
source={Scopus},
}

Background: Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures. Results: We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages. Conclusions: These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle. © 2016 The Author(s).

@ARTICLE{Shevtsov2016611,
author={Shevtsov, M.A. and Nikolaev, B.P. and Ryzhov, V.A. and Yakovleva, L.Y. and Dobrodumov, A.V. and Marchenko, Y.Y. and Margulis, B.A. and Pitkin, E. and Mikhrina, A.L. and Guzhova, I.V. and Multhoff, G.},
title={Detection of experimental myocardium infarction in rats by MRI using heat shock protein 70 conjugated superparamagnetic iron oxide nanoparticle},
journal={Nanomedicine: Nanotechnology, Biology, and Medicine},
year={2016},
volume={12},
number={3},
pages={611-621},
doi={10.1016/j.nano.2015.10.017},
note={cited By 9},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959419944&doi=10.1016%2fj.nano.2015.10.017&partnerID=40&md5=6b7b12fd8f36bb60b70a279e6d469cf5},
affiliation={Institute of Cytology of the Russian Academy of Sciences (RAS), St. Petersburg, Russian Federation; A.L. Polenov Russian Research Scientific Institute of Neurosurgery, St. Petersburg, Russian Federation; Technische Universität München, Klinikum rechts der Isar, Radiation Oncology, Munich, Germany; Research Institute of Highly Pure Biopreparations, St. Petersburg, Russian Federation; National Research Centre Kurchatov Inst. B.P. Konstantinov Petersburg Nuclear Phor2 S Inst., Gatchina, Russian Federation; Institute of Macromolecular Compounds of the Russian Academy of Sciences (RAS), St. Petersburg, Russian Federation; The Wharton School, University of Pennsylvania, Philadelphia, PA, United States; I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences (RAS), St. Petersburg, Russian Federation},
abstract={Superparamagnetic iron-oxide based contrast agents can provide important diagnostic information regarding the assessment of cardiac inflammatory diseases. The aim of the study was to analyze whether nanoparticles conjugated to recombinant 70-kDa heat shock protein (Hsp70-SPION) can be applied for the detection of acute myocardium infarct by MRI. Cellular experiments demonstrated increased CD40-mediated uptake of Hsp70-SPIONs in comparison to non-conjugated SPIONs. Following induction of an acute infarct in rats by ligation of the left anterior descending artery SPIONs and Hsp70-SPION conjugates were injected intravenously on day 4. The animals underwent sequential MRI that showed the presence of the particles in the infarcted zone. Subsequent biodistribution analyses with the help of method on non-linear magnetic response indicated the preferential accumulation of the Hsp70-SPIONs in the heart tissue that was further confirmed with histological analyses. The study demonstrated that an acute infarct can be visualized by MRI using Hsp70-functionalized SPION conjugates. © 2015 Elsevier Inc.},
author_keywords={CD40;  Hsp70;  Magnetic resonance imaging;  Myocardial infarction;  Superparamagnetic nanoparticles},
correspondence_address1={Shevtsov, M.A.; Institute of Cytology (RAS)Russian Federation; email: shevtsov-max@mail.ru},
publisher={Elsevier Inc.},
issn={15499634},
pubmed_id={26656626},
language={English},
abbrev_source_title={Nanomed. Nanotechnol. Biol. Med.},
document_type={Article},
source={Scopus},
}

Superparamagnetic iron-oxide based contrast agents can provide important diagnostic information regarding the assessment of cardiac inflammatory diseases. The aim of the study was to analyze whether nanoparticles conjugated to recombinant 70-kDa heat shock protein (Hsp70-SPION) can be applied for the detection of acute myocardium infarct by MRI. Cellular experiments demonstrated increased CD40-mediated uptake of Hsp70-SPIONs in comparison to non-conjugated SPIONs. Following induction of an acute infarct in rats by ligation of the left anterior descending artery SPIONs and Hsp70-SPION conjugates were injected intravenously on day 4. The animals underwent sequential MRI that showed the presence of the particles in the infarcted zone. Subsequent biodistribution analyses with the help of method on non-linear magnetic response indicated the preferential accumulation of the Hsp70-SPIONs in the heart tissue that was further confirmed with histological analyses. The study demonstrated that an acute infarct can be visualized by MRI using Hsp70-functionalized SPION conjugates. © 2015 Elsevier Inc.

@ARTICLE{Egorov2016322,
author={Egorov, V.V. and Shaldzhyan, A.A. and Gorshkov, A.N. and Zabrodskaya, Y.A. and Lebedev, D.V. and Kuklin, A.I. and Ksenofontova, O.I. and Shvetsov, A.V. and Vasin, A.V. and Tsybalova, L.M. and Isaev-Ivanov, V.V.},
title={On the structural features of influenza A nucleoprotein particles from small-angle X-ray scattering data},
journal={Journal of Surface Investigation},
year={2016},
volume={10},
number={2},
pages={322-325},
doi={10.1134/S1027451016020063},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84969631002&doi=10.1134%2fS1027451016020063&partnerID=40&md5=c8e26f670f4f965820146f882137a0ac},
affiliation={Petersburg Nuclear Physics Institute, Scientific Research Center “Kurchatov Institute”, Gatchina, St. Petersburg, 188300, Russian Federation; Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, 197376, Russian Federation; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 141700, Russian Federation; Joint Institute of Nuclear Physics, Dubna, 141980, Russian Federation; Institute of Applied Mathematics and Mechanics, St. Petersburg State Polytechnic University, St. Petersburg, 194064, Russian Federation; Institute of Physics, Nanotechnologies, and Telecommunications, St. Petersburg State Polytechnic University, St. Petersburg, 195251, Russian Federation},
abstract={The structure of ribonucleic particles of influenza A virus of the A/California/07/09pdm strain is investigated by transmission electron microscopy and small-angle X-ray scattering. The small-angle X-ray scattering data obtained at room temperature correspond to previously reported data of ribonucleic particles of this virus. At higher temperatures, noticeable changes in the morphology of ribonucleic complexes are observed. © 2016, Pleiades Publishing, Ltd.},
author_keywords={atomic force microscopy;  electron microscopy;  influenza virus;  ribonucleic particles;  small-angle scattering},
correspondence_address1={Egorov, V.V.; Petersburg Nuclear Physics Institute, Scientific Research Center “Kurchatov Institute”Russian Federation; email: vlaegur@omrb.pnpi.spb.ru},
publisher={Maik Nauka-Interperiodica Publishing},
issn={10274510},
language={English},
abbrev_source_title={J. Surf. Invest.},
document_type={Article},
source={Scopus},
}

The structure of ribonucleic particles of influenza A virus of the A/California/07/09pdm strain is investigated by transmission electron microscopy and small-angle X-ray scattering. The small-angle X-ray scattering data obtained at room temperature correspond to previously reported data of ribonucleic particles of this virus. At higher temperatures, noticeable changes in the morphology of ribonucleic complexes are observed. © 2016, Pleiades Publishing, Ltd.

@ARTICLE{Sivak2016231,
author={Sivak, K.V. and Vasin, A.V. and Egorov, V.V. and Tsevtkov, V.B. and Kuzmich, N.N. and Savina, V.A. and Kiselev, O.I.},
title={Adenosine A2A receptor as a drug target for treatment of sepsis},
journal={Molekuliarnaia biologiia},
year={2016},
volume={50},
number={2},
pages={231-245},
doi={10.7868/S0026898416020233},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976542400&doi=10.7868%2fS0026898416020233&partnerID=40&md5=98a4ae68a1a8369ea1608a901bd70640},
affiliation={Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation},
abstract={Sepsis is a generalized infection accompanied by response of the body that manifests in a clinical and laboratory syndrome, namely, in the systemic inflammatory response syndrome (SIRS) from the organism to the infection. Although sepsis is a widespread and life-threatening disease, the assortment of drugs for its treatment is mostly limited by antibiotics. Therefore, the search for new cellular targets for drug therapy of sepsis is an urgent task of modern medicine and pharmacology. One of the most promising targets is the adenosine A(2A) receptor (A(2A)AR). The activation of this receptor, which is mediated by extracellular adenosine, manifests in almost all types of immune cells (lymphocytes, monocytes, macrophages, and dendritic cells) and results in reducing the severity of inflammation and reperfusion injury in various tissues. The activation of adenosine A(2A) receptor inhibits the proliferation of T cells and production of proinflammatory cytokines, which contributes to the activation of the synthesis of anti-inflammatory cytokines, thereby suppressing the systemic response. For this reason, various selective A(2A)AR agonists and antagonists may be considered to be drug candidates for sepsis pharmacotherapy. Nevertheless, they remain only efficient ligands and objects of pre-clinical and clinical trials. This review examines the molecular mechanisms of inflammatory response in sepsis and the structure and functions of A(2A)AR and its role in the pathogenesis of sepsis, as well as examples of using agonists and antagonists of this receptor for the treatment of SIRS and sepsis.},
author_keywords={adenosine;  adenosine A2A receptors;  agonists and antagonists of adenosine receptors;  Sepsis;  systemic inflammatory response syndrome},
issn={00268984},
pubmed_id={27239843},
language={Russian},
abbrev_source_title={Mol. Biol. (Mosk.)},
document_type={Review},
source={Scopus},
}

Sepsis is a generalized infection accompanied by response of the body that manifests in a clinical and laboratory syndrome, namely, in the systemic inflammatory response syndrome (SIRS) from the organism to the infection. Although sepsis is a widespread and life-threatening disease, the assortment of drugs for its treatment is mostly limited by antibiotics. Therefore, the search for new cellular targets for drug therapy of sepsis is an urgent task of modern medicine and pharmacology. One of the most promising targets is the adenosine A(2A) receptor (A(2A)AR). The activation of this receptor, which is mediated by extracellular adenosine, manifests in almost all types of immune cells (lymphocytes, monocytes, macrophages, and dendritic cells) and results in reducing the severity of inflammation and reperfusion injury in various tissues. The activation of adenosine A(2A) receptor inhibits the proliferation of T cells and production of proinflammatory cytokines, which contributes to the activation of the synthesis of anti-inflammatory cytokines, thereby suppressing the systemic response. For this reason, various selective A(2A)AR agonists and antagonists may be considered to be drug candidates for sepsis pharmacotherapy. Nevertheless, they remain only efficient ligands and objects of pre-clinical and clinical trials. This review examines the molecular mechanisms of inflammatory response in sepsis and the structure and functions of A(2A)AR and its role in the pathogenesis of sepsis, as well as examples of using agonists and antagonists of this receptor for the treatment of SIRS and sepsis.

@ARTICLE{Sivak2016200,
author={Sivak, K.V. and Vasin, A.V. and Egorov, V.V. and Tsevtkov, V.B. and Kuzmich, N.N. and Savina, V.A. and Kiselev, O.I.},
title={Adenosine A2A receptor as a drug target for treatment of sepsis},
journal={Molecular Biology},
year={2016},
volume={50},
number={2},
pages={200-212},
doi={10.1134/S0026893316020230},
note={cited By 6},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84969509097&doi=10.1134%2fS0026893316020230&partnerID=40&md5=df971fd09c73b37ae5af721e3ccac3e7},
affiliation={Research Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; St. Petersburg State Polytechnical University, St. Petersburg, 195251, Russian Federation},
abstract={Sepsis is a generalized infection accompanied by response of the body that manifests in a clinical and laboratory syndrome, namely, in the systemic inflammatory response syndrome (SIRS) from the organism to the infection. Although sepsis is a widespread and life-threatening disease, the assortment of drugs for its treatment is mostly limited by antibiotics. Therefore, the search for new cellular targets for drug therapy of sepsis is an urgent task of modern medicine and pharmacology. One of the most promising targets is the adenosine A2A receptor (A2AAR). The activation of this receptor, which is mediated by extracellular adenosine, manifests in almost all types of immune cells (lymphocytes, monocytes, macrophages, and dendritic cells) and results in reducing the severity of inflammation and reperfusion injury in various tissues. The activation of adenosine A2A receptor inhibits the proliferation of T cells and production of proinflammatory cytokines, which contributes to the activation of the synthesis of anti-inflammatory cytokines, thereby suppressing the systemic response. For this reason, various selective A2AAR agonists and antagonists may be considered to be drug candidates for sepsis pharmacotherapy. Nevertheless, they remain only efficient ligands and objects of pre-clinical and clinical trials. This review examines the molecular mechanisms of inflammatory response in sepsis and the structure and functions of A2AAR and its role in the pathogenesis of sepsis, as well as examples of using agonists and antagonists of this receptor for the treatment of SIRS and sepsis. © 2016, Pleiades Publishing, Inc.},
author_keywords={adenosine;  adenosine A2A receptors;  agonists and antagonists of adenosine receptors;  sepsis;  systemic inflammatory response syndrome},
correspondence_address1={Sivak, K.V.; Research Institute of Influenza, Ministry of Health of the Russian FederationRussian Federation; email: konstantin.sivak@influenza.spb.ru},
publisher={Maik Nauka Publishing / Springer SBM},
issn={00268933},
language={English},
abbrev_source_title={Mol. Biol.},
document_type={Review},
source={Scopus},
}

Sepsis is a generalized infection accompanied by response of the body that manifests in a clinical and laboratory syndrome, namely, in the systemic inflammatory response syndrome (SIRS) from the organism to the infection. Although sepsis is a widespread and life-threatening disease, the assortment of drugs for its treatment is mostly limited by antibiotics. Therefore, the search for new cellular targets for drug therapy of sepsis is an urgent task of modern medicine and pharmacology. One of the most promising targets is the adenosine A2A receptor (A2AAR). The activation of this receptor, which is mediated by extracellular adenosine, manifests in almost all types of immune cells (lymphocytes, monocytes, macrophages, and dendritic cells) and results in reducing the severity of inflammation and reperfusion injury in various tissues. The activation of adenosine A2A receptor inhibits the proliferation of T cells and production of proinflammatory cytokines, which contributes to the activation of the synthesis of anti-inflammatory cytokines, thereby suppressing the systemic response. For this reason, various selective A2AAR agonists and antagonists may be considered to be drug candidates for sepsis pharmacotherapy. Nevertheless, they remain only efficient ligands and objects of pre-clinical and clinical trials. This review examines the molecular mechanisms of inflammatory response in sepsis and the structure and functions of A2AAR and its role in the pathogenesis of sepsis, as well as examples of using agonists and antagonists of this receptor for the treatment of SIRS and sepsis. © 2016, Pleiades Publishing, Inc.

@ARTICLE{Kadochnikov201698,
author={Kadochnikov, V.V. and Egorov, V.V. and Shvetsov, A.V. and Kuklin, A.I. and Isaev-Ivanov, V.V. and Lebedev, D.V.},
title={Modeling of conformational transitions of fibrillogenic peptide, homologous to beta-domain of human alpha-lactalbumin},
journal={Crystallography Reports},
year={2016},
volume={61},
number={1},
pages={98-105},
doi={10.1134/S1063774516010089},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955560824&doi=10.1134%2fS1063774516010089&partnerID=40&md5=60272cd63686444584475f84d5406cce},
affiliation={Institute of Physics, Nanotechnology and Telecommunications, St. Petersburg State Polytechnical University, ul. Politekchnicheskaya 29, St. Petersburg, 195251, Russian Federation; St. Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute,”, Orlova Roshcha, Gatchina, Leningrad oblast, 188300, Russian Federation; Research Institute of Influenza, Ministry of Health of the Russian Federation, ul. Prof. Popova 15/17, St. Petersburg, 197976, Russian Federation; Joint Institute for Nuclear Research, ul. Zholio-Kyuri 6, Dubna, Moscow oblast, 141980, Russian Federation; Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudnyi, Moscow oblast, 141700, Russian Federation; Institute of Applied Mathematics and Mechanics, St. Petersburg State Polytechnical University, ul. Politekchnicheskaya 29, St. Petersburg, 195251, Russian Federation},
abstract={The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT. © 2016, Pleiades Publishing, Inc.},
correspondence_address1={Kadochnikov, V.V.; Institute of Physics, Nanotechnology and Telecommunications, St. Petersburg State Polytechnical University, ul. Politekchnicheskaya 29, Russian Federation; email: toizeg@gmail.com},
publisher={Maik Nauka-Interperiodica Publishing},
issn={10637745},
language={English},
abbrev_source_title={Crystallogr. Rep.},
document_type={Article},
source={Scopus},
}

The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT. © 2016, Pleiades Publishing, Inc.

@ARTICLE{Schmidt2016149,
author={Schmidt, A.E. and Shvetsov, A.V. and Kuklin, A.I. and Lebedev, D.V. and Surzhik, M.A. and Sergeev, V.R. and Isaev-Ivanov, V.V.},
title={Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase},
journal={Crystallography Reports},
year={2016},
volume={61},
number={1},
pages={149-152},
doi={10.1134/S1063774516010223},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955578899&doi=10.1134%2fS1063774516010223&partnerID=40&md5=ec97b1e534a5b01b73f260682af7ee41},
affiliation={Konstantinov Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad oblast, 188300, Russian Federation; Joint Institute for Nuclear Research, ul. Joliot-Curie 6, Dubna, Moscow region, 141980, Russian Federation; Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow region, 141700, Russian Federation; St. Petersburg State Polytechnical University, Politekhnicheskaya ul. 29, St. Petersburg, 195251, Russian Federation},
abstract={Glucoamylase from fungus Aspergillus awamori is glycoside hydrolase that catalyzes the hydrolysis of α-1,4- and α-1,6-glucosidic bonds in glucose polymers and oligomers. This glycoprotein consists of a catalytic domain and a starch-binding domain connected by an O-glycosylated polypeptide chain. The conformation of the linker, the relative arrangement of the domains, and the structure of the full-length enzyme are unknown. The structure of the recombinant glucoamylase GA1 was studied by molecular modelling and small-angle neutron scattering (SANS) methods. The experimental SANS data provide evidence that glucoamylase exists as a monomer in solution and contains a glycoside component, which makes a substantial contribution to the scattering. The model of full-length glucoamylase, which was calculated without taking into account the effect of glycosylation, is consistent with the experimental data and has a radius of gyration of 33.4 ± 0.6 Å. © 2016, Pleiades Publishing, Inc.},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)14-24-01103 ofi-m},
}

Glucoamylase from fungus Aspergillus awamori is glycoside hydrolase that catalyzes the hydrolysis of α-1,4- and α-1,6-glucosidic bonds in glucose polymers and oligomers. This glycoprotein consists of a catalytic domain and a starch-binding domain connected by an O-glycosylated polypeptide chain. The conformation of the linker, the relative arrangement of the domains, and the structure of the full-length enzyme are unknown. The structure of the recombinant glucoamylase GA1 was studied by molecular modelling and small-angle neutron scattering (SANS) methods. The experimental SANS data provide evidence that glucoamylase exists as a monomer in solution and contains a glycoside component, which makes a substantial contribution to the scattering. The model of full-length glucoamylase, which was calculated without taking into account the effect of glycosylation, is consistent with the experimental data and has a radius of gyration of 33.4 ± 0.6 Å. © 2016, Pleiades Publishing, Inc.

Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed. © 2016, Pleiades Publishing, Inc.

@ARTICLE{Yakimov201670,
author={Yakimov, A.P. and Afanaseva, A.S. and Khodorkovskiy, M.A. and Petukhov, M.G.},
title={Design of Stable a-Helical Peptides and Thermostable Proteins in Biotechnology and Biomedicine},
journal={Acta Naturae},
year={2016},
volume={8},
number={4},
pages={70-81},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85013157865&partnerID=40&md5=8887130bc0b486ff8c9978c48ea477c9},
affiliation={Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg, 195251, Russian Federation; Petersburg Nuclear Physics Institute, National Research Center 'Kurchatov Institute', Orlova Roscha, 1, Gatchina, 188300, Russian Federation},
abstract={a-Heli?es are the most frequently occurring elements of the secondary structure in water-soluble globular proteins. Their increased conformational stability is among the main reasons for the high thermal stability of proteins in thermophilic bacteria. In addition, a-helices are often involved in protein interactions with other proteins, nucleic acids, and the lipids of cell membranes. That is why the highly stable a-helical peptides used as highly active and specific inhibitors of protein-protein and other interactions have recently found more applications in medicine. Several different approaches have been developed in recent years to improve the conformational stability of a-helical peptides and thermostable proteins, which will be discussed in this review. We also discuss the methods for improving the permeability of peptides and proteins across cellular membranes and their resistance to intracellular protease activity. Special attention is given to the SEQOPT method (http://mml.spbstu.ru/services/seqopt/), which is used to design conformationally stable short a-helices. © 2016 Park-media, Ltd.},
author_keywords={a-helix;  AGADIR, ALB, HELIX -the statistical mechanical models describing the conformational A-helix-coil transitions in short monomeric peptides;  CD -circular dichroism spectroscopy;  Conformational stability;  Factors of thermal stability;  HC -A-helix content;  MD -molecular dynamics method;  Membrane permeability;  PDB -protein database;  Resistance to intracellular proteolysis;  SEQOPT -method for A-helix amino acid sequence optimization},
correspondence_address1={Yakimov, A.P.; Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, Russian Federation; email: yaleks@nanobio.spbstu.ru},
publisher={Russian Federation Agency for Science and Innovation},
issn={20758251},
language={English},
abbrev_source_title={Acta Naturae},
document_type={Article},
source={Scopus},
}

a-Heli?es are the most frequently occurring elements of the secondary structure in water-soluble globular proteins. Their increased conformational stability is among the main reasons for the high thermal stability of proteins in thermophilic bacteria. In addition, a-helices are often involved in protein interactions with other proteins, nucleic acids, and the lipids of cell membranes. That is why the highly stable a-helical peptides used as highly active and specific inhibitors of protein-protein and other interactions have recently found more applications in medicine. Several different approaches have been developed in recent years to improve the conformational stability of a-helical peptides and thermostable proteins, which will be discussed in this review. We also discuss the methods for improving the permeability of peptides and proteins across cellular membranes and their resistance to intracellular protease activity. Special attention is given to the SEQOPT method (http://mml.spbstu.ru/services/seqopt/), which is used to design conformationally stable short a-helices. © 2016 Park-media, Ltd.

TIP49a and TIP49b, highly conserved proteins belonging to the AAA+ superfamily of DNA-dependent ATPases, participate in numerous cell processes, such as chromatin remodeling, regulation of gene transcription and mitotic cell division, maintenance of genome stability, and snoRNP biogenesis, as well as in the formation of active DNA–telomerase complexes. It has been shown that they are involved in complex networks of protein–protein interactions and, in spite of their structural similarity, sometimes perform opposite functions. Although these proteins exhibit a wide range of activities, the mechanisms of their actions are still poorly understood. In this work, ring-shaped heterohexameric TIP49a/b complexes containing in their central channel short fragments of double-stranded DNA (dsDNA, 20 base pairs of different GC composition) were obtained for the first time using the molecular docking technique, while methods of molecular dynamics in a periodic water box were applied to investigate the conformational dynamics of these proteins and the mechanisms of their helicase activity. It was found that (1) interaction of a DNA helix with positively charged protein loops inside the central channel of the ring-shaped hexameric complex caused unwinding of the helix; (2) the unwinding occurred only inside the hexameric ring, whereas the tails of the helix, which lie outside, retained the initial classical B-form conformation throughout the 50 ns of molecular dynamics; and (3) the presence of ATP in TIP49a/b complexes affected the dynamics and the final structure of dsDNA, causing partial breaking of complementary bonds in GC-poor DNA sequences. © 2016, Pleiades Publishing, Ltd.

@ARTICLE{Antimonova2016156,
author={Antimonova, O.I. and Grudinina, N.A. and Egorov, V.V. and Polyakov, D.S. and Iljin, V.V. and Shavlovsky, M.M.},
title={INTERACTION OF THE DYE CONGO RED WITH FIBRILS OF LYSOZYME, BETA2-MICROGLOBULIN AND TRANSTHYRETIN},
journal={Tsitologiia},
year={2016},
volume={58},
number={2},
pages={156-163},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84974707541&partnerID=40&md5=702444fe93955416eb93042a9ec5d63b},
abstract={By means of spectrophotometric assay we investigated interaction of the dye Congo red (CR) with fibrils of model proteins--hen egg white lysozyme, recombinant human beta2-microglobulin (b2M) and recombinant human transthyretin (TTR). The commercial dye sample was found to contain a significant amount of impurities. Methods for the dye purification are disclosed and CR molar extinction coefficient at 490 nm (ε490) was determined to be 3.3 x 10(4) M(-1) x cm(-1) at pH above 6.0. Formation of the CR-fibril complex results in changes in the dye visible absorption spectrum. According to the data on titration of fibril solutions with excess of the dye, CR binds to lysozyme fibrils at a ratio of about 5 molecules per protein monomer within fibril structure, to b2M fibrils--about 4 molecules per monomer, to TTR fibrils--about 4 molecules per subunit of the protein.},
issn={00413771},
pubmed_id={27228663},
language={Russian},
abbrev_source_title={Tsitologiia},
document_type={Article},
source={Scopus},
}

By means of spectrophotometric assay we investigated interaction of the dye Congo red (CR) with fibrils of model proteins–hen egg white lysozyme, recombinant human beta2-microglobulin (b2M) and recombinant human transthyretin (TTR). The commercial dye sample was found to contain a significant amount of impurities. Methods for the dye purification are disclosed and CR molar extinction coefficient at 490 nm (ε490) was determined to be 3.3 x 10(4) M(-1) x cm(-1) at pH above 6.0. Formation of the CR-fibril complex results in changes in the dye visible absorption spectrum. According to the data on titration of fibril solutions with excess of the dye, CR binds to lysozyme fibrils at a ratio of about 5 molecules per protein monomer within fibril structure, to b2M fibrils–about 4 molecules per monomer, to TTR fibrils–about 4 molecules per subunit of the protein.

@ARTICLE{Shevtsov201520652,
author={Shevtsov, M.A. and Nikolaev, B.P. and Ryzhov, V.A. and Yakovleva, L.Y. and Marchenko, Y.Y. and Parr, M.A. and Rolich, V.I. and Mikhrina, A.L. and Dobrodumov, A.V. and Pitkin, E. and Multhoff, G.},
title={Ionizing radiation improves glioma-specific targeting of superparamagnetic iron oxide nanoparticles conjugated with cmHsp70.1 monoclonal antibodies (SPION-cmHsp70.1)},
journal={Nanoscale},
year={2015},
volume={7},
number={48},
pages={20652-20664},
doi={10.1039/c5nr06521f},
note={cited By 25},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84949033821&doi=10.1039%2fc5nr06521f&partnerID=40&md5=36b3248c53b99ca280620e5276db5afc},
affiliation={Institute of Cytology, Russian Academy of Sciences (RAS), Tikhoretsky ave. 4, St. Petersburg, 194064, Russian Federation; Technische Universität München, Klinikum Rechts der Isar, Ismaniger Str. 22, Munich, 81675, Germany; A.L. Polenov Neurosurgical Institute, Mayakovsky str. 12, St. Petersburg, 191014, Russian Federation; Research Institute of Highly Pure Biopreparations, Pudozhskaya str. 12, St. Petersburg, 191014, Russian Federation; NRC Kurchatov Institute, Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; V.F. Fock Institute of Physics, St. Petersburg State University, St. Petersburg, Russian Federation; I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences (RAS), pr. Torez 44, St. Petersburg, 194223, Russian Federation; Institute of Macromolecular Compounds, Russian Academy of Sciences (RAS), Bolshoi pr. 31, St. Petersburg, 199004, Russian Federation; Wharton School, University of Pennsylvania, Philadelphia, PA, United States},
abstract={The stress-inducible 72 kDa heat shock protein Hsp70 is known to be expressed on the membrane of highly aggressive tumor cells including high-grade gliomas, but not on the corresponding normal cells. Membrane Hsp70 (mHsp70) is rapidly internalized into tumor cells and thus targeting of mHsp70 might provide a promising strategy for theranostics. Superparamagnetic iron oxide nanoparticles (SPIONs) are contrast negative agents that are used for the detection of tumors with MRI. Herein, we conjugated the Hsp70-specific antibody (cmHsp70.1) which is known to recognize mHsp70 to superparamagnetic iron nanoparticles to assess tumor-specific targeting before and after ionizing irradiation. In vitro experiments demonstrated the selectivity of SPION-cmHsp70.1 conjugates to free and mHsp70 in different tumor cell types (C6 glioblastoma, K562 leukemia, HeLa cervix carcinoma) in a dose-dependent manner. High-resolution MRI (11 T) on T2-weighted images showed the retention of the conjugates in the C6 glioma model. Accumulation of SPION-cmHsp70.1 nanoparticles in the glioma resulted in a nearly 2-fold drop of values in comparison to non-conjugated SPIONs. Biodistribution analysis using NLR-M2 measurements showed a 7-fold increase in the tumor-to-background (normal brain) uptake ratio of SPION-cmHsp70.1 conjugates in glioma-bearing rats in comparison to SPIONs. This accumulation within Hsp70-positive glioma was further enhanced after a single dose (10 Gy) of ionizing radiation. Elevated accumulation of the magnetic conjugates in the tumor due to radiosensitization proves the combination of radiotherapy and application of Hsp70-targeted agents in brain tumors. © 2015 The Royal Society of Chemistry.},
funding_details={Russian Foundation for Basic Research15-08-08148A},
correspondence_address1={Shevtsov, M.A.; Institute of Cytology, Russian Academy of Sciences (RAS), Tikhoretsky ave. 4, Russian Federation; email: shevtsov-max@mail.ru},
publisher={Royal Society of Chemistry},
issn={20403364},
pubmed_id={26599206},
language={English},
abbrev_source_title={Nanoscale},
document_type={Article},
source={Scopus},
}

The stress-inducible 72 kDa heat shock protein Hsp70 is known to be expressed on the membrane of highly aggressive tumor cells including high-grade gliomas, but not on the corresponding normal cells. Membrane Hsp70 (mHsp70) is rapidly internalized into tumor cells and thus targeting of mHsp70 might provide a promising strategy for theranostics. Superparamagnetic iron oxide nanoparticles (SPIONs) are contrast negative agents that are used for the detection of tumors with MRI. Herein, we conjugated the Hsp70-specific antibody (cmHsp70.1) which is known to recognize mHsp70 to superparamagnetic iron nanoparticles to assess tumor-specific targeting before and after ionizing irradiation. In vitro experiments demonstrated the selectivity of SPION-cmHsp70.1 conjugates to free and mHsp70 in different tumor cell types (C6 glioblastoma, K562 leukemia, HeLa cervix carcinoma) in a dose-dependent manner. High-resolution MRI (11 T) on T2-weighted images showed the retention of the conjugates in the C6 glioma model. Accumulation of SPION-cmHsp70.1 nanoparticles in the glioma resulted in a nearly 2-fold drop of values in comparison to non-conjugated SPIONs. Biodistribution analysis using NLR-M2 measurements showed a 7-fold increase in the tumor-to-background (normal brain) uptake ratio of SPION-cmHsp70.1 conjugates in glioma-bearing rats in comparison to SPIONs. This accumulation within Hsp70-positive glioma was further enhanced after a single dose (10 Gy) of ionizing radiation. Elevated accumulation of the magnetic conjugates in the tumor due to radiosensitization proves the combination of radiotherapy and application of Hsp70-targeted agents in brain tumors. © 2015 The Royal Society of Chemistry.

@ARTICLE{Kulikova201527124,
author={Kulikova, V. and Shabalin, K. and Nerinovski, K. and Dölle, C. and Niere, M. and Yakimov, A. and Redpath, P. and Khodorkovskiy, M. and Migaud, M.E. and Ziegler, M. and Nikiforov, A.},
title={Generation, release, and uptake of the NAD precursor nicotinic acid riboside by human cells},
journal={Journal of Biological Chemistry},
year={2015},
volume={290},
number={45},
pages={27124-27137},
doi={10.1074/jbc.M115.664458},
note={cited By 30},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84946771272&doi=10.1074%2fjbc.M115.664458&partnerID=40&md5=dd8c3ee31be043ff4bcc5144ca8e8f96},
affiliation={Peter Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russian Federation; National Research Centre Kurchatov Institute, Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; St. Petersburg State University, St. Petersburg, 199034, Russian Federation; Dept. of Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway; School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, BT97BL, United Kingdom; Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation; Dept. of Neurology, Haukeland University Hospital, Bergen, 5021, Norway; Dept. of Clinical Medicine, University of Bergen, Bergen, 5020, Norway},
abstract={Background: Nicotinamide riboside (NR) and nicotinic acid riboside (NAR) can serve as precursors ofNADin human cells. Results: Human cells generate and release NR and NAR. Conclusion: NR and NAR are authentic intermediates of human NAD metabolism. Significance: Different cell populations might support each other's NAD pools by providing ribosides as NAD precursors. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.},
funding_details={Russian Foundation for Basic Research14-04-01765},
funding_details={Russian Foundation for Basic Research14-04-32117},
correspondence_address1={Ziegler, M.; Dept. of Molecular Biology, University of Bergen, Thormøhlensgate 55, Norway; email: mathias.ziegler@mbi.uib.no},
publisher={American Society for Biochemistry and Molecular Biology Inc.},
issn={00219258},
coden={JBCHA},
pubmed_id={26385918},
language={English},
abbrev_source_title={J. Biol. Chem.},
document_type={Article},
source={Scopus},
}

Background: Nicotinamide riboside (NR) and nicotinic acid riboside (NAR) can serve as precursors ofNADin human cells. Results: Human cells generate and release NR and NAR. Conclusion: NR and NAR are authentic intermediates of human NAD metabolism. Significance: Different cell populations might support each other's NAD pools by providing ribosides as NAD precursors. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

@ARTICLE{Afanasyeva20151973,
author={Afanasyeva, A. and Izmailov, S. and Grigoriev, M. and Petukhov, M.},
title={AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites},
journal={Journal of Computational Chemistry},
year={2015},
volume={36},
number={26},
pages={1973-1977},
doi={10.1002/jcc.24022},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941055115&doi=10.1002%2fjcc.24022&partnerID=40&md5=9671042d23952f7578ea3a68548318eb},
affiliation={Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, Leningrad district, 188300, Russian Federation; Department of Computational Physics, Saint-Petersburg State University, Peterhof, Botanikaya 64/2198504, Russian Federation; Laboratory of Molecular Biology of Eucaryotes (LBME) UMR 5099 CNRS, Toulouse, France; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO, United States},
abstract={We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small-molecule ligands. We tested its efficiency on a representative set of human ATP-binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein-ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design. AquaBridge is a tool for seeking structural water molecules within protein binding pockets, developed as a module for the ICM-Pro software package for molecular modeling. This utility is based on Monte Carlo energy minimization algorithms and selects the water molecule conformations that can form "water bridges" by calculating the values of the total energy of a modeled water molecule and of the number of hydrogen bonds that it can form between the target protein and the ligand. © 2015 Wiley Periodicals, Inc.},
author_keywords={ATPase;  molecular docking;  structural water},
correspondence_address1={Afanasyeva, A.; Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Russian Federation},
publisher={John Wiley and Sons Inc.},
issn={01928651},
coden={JCCHD},
pubmed_id={26339759},
language={English},
abbrev_source_title={J. Comput. Chem.},
document_type={Article},
source={Scopus},
}

We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small-molecule ligands. We tested its efficiency on a representative set of human ATP-binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein-ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design. AquaBridge is a tool for seeking structural water molecules within protein binding pockets, developed as a module for the ICM-Pro software package for molecular modeling. This utility is based on Monte Carlo energy minimization algorithms and selects the water molecule conformations that can form "water bridges" by calculating the values of the total energy of a modeled water molecule and of the number of hydrogen bonds that it can form between the target protein and the ligand. © 2015 Wiley Periodicals, Inc.

@ARTICLE{Kharitonskii2015221,
author={Kharitonskii, P.V. and Gareev, K.G. and Ionin, S.A. and Ryzhov, V.A. and Bogachev, Y.V. and Klimenkov, B.D. and Kononova, I.E. and Moshnikov, V.A.},
title={Microstructure and magnetic state of Fe3O4-SiO2 colloidal particles},
journal={Journal of Magnetics},
year={2015},
volume={20},
number={3},
pages={221-228},
doi={10.4283/JMAG.2015.20.3.221},
note={cited By 13},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84942247713&doi=10.4283%2fJMAG.2015.20.3.221&partnerID=40&md5=60abc5a6091650117edcdc6230c871e2},
affiliation={Saint Petersburg Electrotechnical University ‘LETI’, 5th Prof. Popova Str, Saint-Petersburg, 197376, Russian Federation; Petersburg Nuclear Physics Institute Named by B.P. Konstantinov, National Research Centre ‘Kurchatov Institute’, Leningrad District, Orlova Roscha, Gatchina, 188300, Russian Federation; Saint Petersburg Polytechnic University, 29th Polytechnicheskaya Str, Saint-Petersburg, 195251, Russian Federation},
abstract={Colloidal particles consisted of individual nanosized magnetite grains on the surface of the silica cores were obtained by two-stage sol-gel technique. Size distribution and microstructure of the particles were analyzed using atomic force microscopy, X-ray diffraction and Nitrogen thermal desorption. Magnetic properties of the particles were studied by the method of the longitudinal nonlinear response. It has been shown that nanoparticles of magnetite have a size corresponding to a superparamagnetic state but exhibit hysteresis properties. The phenomenon was explained using the magnetostatic interaction model based on the hypothesis of iron oxide particles cluster aggregation on the silica surface. © The Korean Magnetics Society. All rights reserved.},
author_keywords={Colloidal particles;  Longitudinal nonlinear response;  Magnetite;  Magnetostatic interaction;  Silica;  Superparamagnetism},
funding_details={Russian Foundation for Basic Research14-03-31534},
correspondence_address1={Gareev, K.G.; Saint Petersburg Electrotechnical University ‘LETI’, 5th Prof. Popova Str, Russian Federation; email: kggareev@yandex.ru},
publisher={Seoul National University 501-321},
issn={12261750},
language={English},
abbrev_source_title={J. Magn.},
document_type={Article},
source={Scopus},
}

Colloidal particles consisted of individual nanosized magnetite grains on the surface of the silica cores were obtained by two-stage sol-gel technique. Size distribution and microstructure of the particles were analyzed using atomic force microscopy, X-ray diffraction and Nitrogen thermal desorption. Magnetic properties of the particles were studied by the method of the longitudinal nonlinear response. It has been shown that nanoparticles of magnetite have a size corresponding to a superparamagnetic state but exhibit hysteresis properties. The phenomenon was explained using the magnetostatic interaction model based on the hypothesis of iron oxide particles cluster aggregation on the silica surface. © The Korean Magnetics Society. All rights reserved.

Brain tumor targeting efficiency and biodistribution of the superparamagnetic nanoparticles conjugated with heat shock protein Hsp70 (SPION-Hsp70) were evaluated in experimental glioma model. Synthesized conjugates were characterized using the method of longitudinal nonlinear response of magnetic nanoparticles to a weak ac magnetic field with measurements of second harmonic of magnetization (NLR-M2). Cellular interaction of magnetic conjugates was analyzed in 9L glioma cell culture. The biodistribution of the nanoparticles and their accumulation in tumors was assessed by the latter approach as well. The efficacy of Hsp70-conjugates for contrast enhancement in the orthotopic model of 9L glioma was assessed by MR imaging (11 T). Magnetic nanoparticles conjugated with Hsp70 had the relaxivity properties of the MR-negative contrast agents. Morphological observation and cell viability test demonstrated good biocompatibility of Hsp70-conjugates. Analysis of the T2-weighted MR scans in tumor-bearing rats demonstrated the high efficacy of Hsp70-conjugates in contrast enhancement of the glioma in comparison to non-conjugated nanoparticles. High contrast enhancement of the glioma was provided by the accumulation of the SPION-Hsp70 particles in the glioma tissue (as shown by the histological assay). Biodistribution analysis by NLR-M2 measurements evidenced the many-fold increase ( 40) in the tumor-to-normal brain uptake ratio in the Hsp70-conjugates treated animals. Biodistribution pattern of Hsp70-decorated nanoparticles differed from that of non-conjugated SPIONs. Coating of the magnetic nanoparticles with Hsp70 protein enhances the tumor-targeting ability of the conjugates that could be applied in the MR imaging of the malignant brain tumors. © 2015 Elsevier B.V.

@ARTICLE{Kiselev2015480,
author={Kiselev, O.I. and Vasin, A.V. and Shevyryova, M.P. and Deeva, E.G. and Sivak, K.V. and Egorov, V.V. and Tsvetkov, V.B. and Egorov, A.Y. and Romanovskaya-Romanko, E.A. and Stepanova, L.A. and Komissarov, A.B. and Tsybalova, L.M. and Ignatjev, G.M.},
title={Ebola hemorrhagic fever: Properties of the pathogen and development of vaccines and chemotherapeutic agents},
journal={Molecular Biology},
year={2015},
volume={49},
number={4},
pages={480-493},
doi={10.1134/S002689331504007X},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939146460&doi=10.1134%2fS002689331504007X&partnerID=40&md5=834035e73c6aa0e53773fa87a0e7b7bb},
affiliation={Institute of Influenza, Ministry of Health of the Russian Federation, St. Petersburg, 197376, Russian Federation; St. Petersburg State Polytechnic University, St. Petersburg, 195251, Russian Federation; Ministry of Health of the Russian Federation, Moscow, 127994, Russian Federation; Topchiev Institute of Petrochemical Synthesis, Moscow, 119991, Russian Federation},
abstract={Ebola hemorrhagic fever (EHF) epidemic currently ongoing in West Africa is not the first among numerous epidemics in the continent. Yet it seems to be the worst EHF epidemic outbreak caused by Ebola virus Zaire since 1976 as regards its extremely large scale and rapid spread in the population. Experiments to study the agent have continued for more than 20 years. The EHF virus has a relatively simple genome with seven genes and additional reading frame resulting from RNA editing. While being of a relatively low genetic capacity, the virus can be ranked as a standard for pathogenicity with the ability to evade the host immune response in uttermost perfection. The EHF virus has similarities with retroviruses, but belongs to (–)RNA viruses of a nonretroviral origin. Genetic elements of the virus, NIRV, were detected in animal and human genomes. EHF virus glycoprotein (GP) is a class I fusion protein and shows more similarities than distinctions in tertiary structure with SIV and HIV gp41 proteins and even influenza virus hemagglutinin. EHF is an unusual infectious disease, and studying the molecular basis of its pathogenesis may contribute to new findings in therapy of severe conditions leading to a fatal outcome. © 2015, Pleiades Publishing, Inc.},
author_keywords={antiviral drugs;  Ebola virus;  genome;  hemorrhagic fever;  interferon antagonists;  vaccines},
correspondence_address1={Vasin, A.V.; Institute of Influenza, Ministry of Health of the Russian FederationRussian Federation},
publisher={Maik Nauka Publishing / Springer SBM},
issn={00268933},
language={English},
abbrev_source_title={Mol. Biol.},
document_type={Review},
source={Scopus},
}

Ebola hemorrhagic fever (EHF) epidemic currently ongoing in West Africa is not the first among numerous epidemics in the continent. Yet it seems to be the worst EHF epidemic outbreak caused by Ebola virus Zaire since 1976 as regards its extremely large scale and rapid spread in the population. Experiments to study the agent have continued for more than 20 years. The EHF virus has a relatively simple genome with seven genes and additional reading frame resulting from RNA editing. While being of a relatively low genetic capacity, the virus can be ranked as a standard for pathogenicity with the ability to evade the host immune response in uttermost perfection. The EHF virus has similarities with retroviruses, but belongs to (–)RNA viruses of a nonretroviral origin. Genetic elements of the virus, NIRV, were detected in animal and human genomes. EHF virus glycoprotein (GP) is a class I fusion protein and shows more similarities than distinctions in tertiary structure with SIV and HIV gp41 proteins and even influenza virus hemagglutinin. EHF is an unusual infectious disease, and studying the molecular basis of its pathogenesis may contribute to new findings in therapy of severe conditions leading to a fatal outcome. © 2015, Pleiades Publishing, Inc.

@ARTICLE{Lazuta2015,
author={Lazuta, A.V. and Ryzhov, V.A. and Runov, V.V. and Khavronin, V.P. and Deriglazov, V.V.},
title={Temperature evolution of superparamagnetic clusters in single-crystal La0.85Sr0.15CoO3 characterized by nonlinear magnetic ac response and neutron depolarization},
journal={Physical Review B - Condensed Matter and Materials Physics},
year={2015},
volume={92},
number={1},
doi={10.1103/PhysRevB.92.014404},
art_number={014404},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84937883010&doi=10.1103%2fPhysRevB.92.014404&partnerID=40&md5=aa92824aeacd5e1bf80c32634a0f699b},
affiliation={NRC Kurchatov Institute PNPI, Gatchina, 188300, Russian Federation},
abstract={The representative measurements of the second harmonic in ac magnetization complemented by neutron depolarization have been performed for single-crystal La0.85Sr0.15CoO3 in the temperature range 97K<T<230K, where occurrence of a small fraction (≲10-3) of nanoscale ferromagnetic clusters (FMC) has been found. Magnetic, geometrical, and dynamical parameters of the FMC system have been evaluated in the temperature range T<140 K, where superparamagnetic regime installs, by means of the formalism involving the Fokker-Planck equation. With lowering the temperature, the amount of clusters fraction, the cluster size, and magnetic moment along with its diffusion relaxation time strongly increase, each in its own temperature interval. Below 130 K, FMC contribute essentially to the total linear magnetic susceptibility. The damping factor of the order 10-1 proves the importance of precession in thermal relaxation of the cluster magnetic moment. The FMC are a precursor of long-range ferromagnetic correlations seen below 100 K with neutron-scattering techniques. ©2015 American Physical Society.},
publisher={American Physical Society},
issn={10980121},
coden={PRBMD},
language={English},
abbrev_source_title={Phys. Rev. B Condens. Matter Mater. Phys.},
document_type={Article},
source={Scopus},
}

The representative measurements of the second harmonic in ac magnetization complemented by neutron depolarization have been performed for single-crystal La0.85Sr0.15CoO3 in the temperature range 97K<T<230K, where occurrence of a small fraction (≲10-3) of nanoscale ferromagnetic clusters (FMC) has been found. Magnetic, geometrical, and dynamical parameters of the FMC system have been evaluated in the temperature range T<140 K, where superparamagnetic regime installs, by means of the formalism involving the Fokker-Planck equation. With lowering the temperature, the amount of clusters fraction, the cluster size, and magnetic moment along with its diffusion relaxation time strongly increase, each in its own temperature interval. Below 130 K, FMC contribute essentially to the total linear magnetic susceptibility. The damping factor of the order 10-1 proves the importance of precession in thermal relaxation of the cluster magnetic moment. The FMC are a precursor of long-range ferromagnetic correlations seen below 100 K with neutron-scattering techniques. ©2015 American Physical Society.

@ARTICLE{Rusinov2015275,
author={Rusinov, V.L. and Sapozhnikova, I.M. and Ulomskii, E.N. and Medvedeva, N.R. and Egorov, V.V. and Kiselev, O.I. and Deeva, E.G. and Vasin, A.V. and Chupakhin, O.N.},
title={Nucleophilic substitution of nitro group in nitrotriazolotriazines as a model of potential interaction with cysteine-containing proteins},
journal={Chemistry of Heterocyclic Compounds},
year={2015},
volume={51},
number={3},
pages={275-280},
doi={10.1007/s10593-015-1695-4},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84953354086&doi=10.1007%2fs10593-015-1695-4&partnerID=40&md5=d3ba1311a60e70bf3af9efa09f7884c4},
affiliation={Ural Federal University Named after the First President of Russia Boris Yeltsin, 19 Mira St., Yekaterinburg, 620002, Russian Federation; Institute of Organic Synthesis, Ural Branch, Russian Academy of Sciences, 22 S. Kovalevskoi St. / 20 Akademicheskaya St., Yekaterinburg, 620990, Russian Federation; Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, 15/17 Prof. Popov St., Saint-Petersburg, 197376, Russian Federation},
abstract={[Figure not available: see fulltext.] The nucleophilic susbstitution of nitro group in [1,2,4]triazolo[5,1-c][1,2,4]triazinones upon treatment with cysteine and glutathione was studied as a model for the interaction with thiol groups of virus proteins, which mimics the metabolic transformations of antiviral drug Triazavirin® and its derivatives. © 2015 Springer Science+Business Media New York.},
author_keywords={azolo[5,1-c]triazines;  cysteine;  glutathione;  metabolic transformations;  nitro compounds;  nucleophilic substitution;  Triazavirin},
correspondence_address1={Sapozhnikova, I.M.; Ural Federal University Named after the First President of Russia Boris Yeltsin, 19 Mira St., Russian Federation; email: i.m.sapozhnikova@urfu.ru},
publisher={Springer New York LLC},
issn={00093122},
coden={CHCCA},
language={English},
abbrev_source_title={Chem. Heterocycl. Compd.},
document_type={Article},
source={Scopus},
}

[Figure not available: see fulltext.] The nucleophilic susbstitution of nitro group in [1,2,4]triazolo[5,1-c][1,2,4]triazinones upon treatment with cysteine and glutathione was studied as a model for the interaction with thiol groups of virus proteins, which mimics the metabolic transformations of antiviral drug Triazavirin® and its derivatives. © 2015 Springer Science+Business Media New York.

@BOOK{Shvetsov201511,
author={Shvetsov, A. and Lebedev, D. and Isaev-Ivanov, V.},
title={Using the molecular dynamics simulation and neutron scattering methods to study structural and functional properties of biological macromolecules},
journal={Computational Materials and Biological Sciences},
year={2015},
pages={11-23},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84960307812&partnerID=40&md5=d2c8565fcaa12dcde34f3de979499b68},
affiliation={FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Institute of Applied Mathematics and Mechanics, St. Petersburg State Polytechnical University, Saint-Petersburg, Russian Federation},
abstract={Molecular Dynamics (MD) simulations were used together with existing X-ray structures to build the structures of RecA proteins[10, 2]. We built missing loops L1 and L2 of RecA from D. radiodurans using ICM[11, 12] homology and loop modeling modules. The structure verification via SANS experiments was performed to build realistic all-atom models of quite large macromolecular multicomponent complexes like it was done for RecA::RecX::ssDNA and RecX::ssDNA complexes (this structure was predicted via MM and MD and then verified by SANS). © 2015 by Nova Science Publishers, Inc. All rights reserved.},
author_keywords={Dynamics;  Full-Atom Structure;  MD Modeling;  RecA and RecX Complexes;  Veryfication},
correspondence_address1={Shvetsov, A.; FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov InstituteRussian Federation; email: alexxy@omrb.pnpi.spb.ru},
publisher={Nova Science Publishers, Inc.},
isbn={9781634825719; 9781634825412},
language={English},
abbrev_source_title={Comput. Mater. and Biol. Sci.},
document_type={Book Chapter},
source={Scopus},
}

Molecular Dynamics (MD) simulations were used together with existing X-ray structures to build the structures of RecA proteins[10, 2]. We built missing loops L1 and L2 of RecA from D. radiodurans using ICM[11, 12] homology and loop modeling modules. The structure verification via SANS experiments was performed to build realistic all-atom models of quite large macromolecular multicomponent complexes like it was done for RecA::RecX::ssDNA and RecX::ssDNA complexes (this structure was predicted via MM and MD and then verified by SANS). © 2015 by Nova Science Publishers, Inc. All rights reserved.

@ARTICLE{Afanasyeva2015671,
author={Afanasyeva, A.S. and Yakimov, A.P. and Grigoriev, M.Y. and Petukhov, M.G.},
title={DYNAMICS AND MECHANISMS OF INTERACTION OF HETERO-HEXAMERIC TIP49a/b COMPLEXES WITH DS-DNA},
journal={Tsitologiia},
year={2015},
volume={57},
number={10},
pages={671-678},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964694492&partnerID=40&md5=c64d2e18ccf2d38ebab30d59af323785},
abstract={Evolutionary conserved TIP49a and TIP49b ATPases belong to the AAA+ superfamily of DNA-dependent ATPases that are involved in many cellular processes such as chromatin remodeling, regulation of transcription and cell division during mitosis, the maintenance of genome stability, snoRNP biogenesis, and participate in the formation of active form of telomerase. These proteins are involved in the complex networks of protein-protein interactions and, in spite of high structural similarity, in some cases, can perform opposite functions. Despite of the variety of their different activities, the exact mechanisms of action of TIP49a and TIP49b are still poorly understood. In this paper, by means of molecular docking approaches we first modeled the structures of hetero-hexameric TIP49 complexes with short ds-DNA fragments (20 base pairs with different GC content) within the central channel of hexameric ring. Using molecular dynamics simulations in the periodic water box (MD) we investigated conformational dynamics and mechanisms of DNA unwinding activity of these proteins. We shown that: a) the interaction between the positively charged protein loops and DNA within the central channel of protein ring leads to the partial unwinding of the DNA helix; b) DNA unwinding occurs only in the region within the protein ring, while the terminal parts of DNA outside the protein complex remain in its initial b-form conformation; c) the presence of ATP in the active sites of protein complex affects both the dynamics and the structure of DNA, leading to the breakage of some complementary bonds in AT-rich DNA sequences.},
issn={00413771},
pubmed_id={26863765},
language={Russian},
abbrev_source_title={Tsitologiia},
document_type={Article},
source={Scopus},
}

Evolutionary conserved TIP49a and TIP49b ATPases belong to the AAA+ superfamily of DNA-dependent ATPases that are involved in many cellular processes such as chromatin remodeling, regulation of transcription and cell division during mitosis, the maintenance of genome stability, snoRNP biogenesis, and participate in the formation of active form of telomerase. These proteins are involved in the complex networks of protein-protein interactions and, in spite of high structural similarity, in some cases, can perform opposite functions. Despite of the variety of their different activities, the exact mechanisms of action of TIP49a and TIP49b are still poorly understood. In this paper, by means of molecular docking approaches we first modeled the structures of hetero-hexameric TIP49 complexes with short ds-DNA fragments (20 base pairs with different GC content) within the central channel of hexameric ring. Using molecular dynamics simulations in the periodic water box (MD) we investigated conformational dynamics and mechanisms of DNA unwinding activity of these proteins. We shown that: a) the interaction between the positively charged protein loops and DNA within the central channel of protein ring leads to the partial unwinding of the DNA helix; b) DNA unwinding occurs only in the region within the protein ring, while the terminal parts of DNA outside the protein complex remain in its initial b-form conformation; c) the presence of ATP in the active sites of protein complex affects both the dynamics and the structure of DNA, leading to the breakage of some complementary bonds in AT-rich DNA sequences.

@ARTICLE{Egorov2015,
author={Egorov, V. and Grudinina, N. and Vasin, A. and Lebedev, D.},
title={Peptide-Induced Amyloid-Like Conformational Transitions in Proteins},
journal={International Journal of Peptides},
year={2015},
volume={2015},
doi={10.1155/2015/723186},
art_number={723186},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84942278959&doi=10.1155%2f2015%2f723186&partnerID=40&md5=b0360c5e5bd8f63ab660aac0906d6e07},
affiliation={FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, 15/17 Professor Popova Street, Saint-Petersburg, 197376, Russian Federation; FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Orlova Roscha, Gatchina, 188300, Russian Federation; FSBSI Institute of Experimental Medicine, 12 Akademika Pavlova, Saint-Petersburg, 197376, Russian Federation; FSBI Federal Almazov Medical Research Centre, 2 Akkuratova Street, St. Saint-Petersburg, 197341, Russian Federation; Saint-Petersburg State Polytechnical University, 29 Polytechnicheskaya Street, Saint-Petersburg, 195251, Russian Federation},
abstract={Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function. © 2015 Vladimir Egorov et al.},
funding_details={Russian Foundation for Basic Research14-04-01912},
funding_details={Russian Foundation for Basic Research14-24-01103},
correspondence_address1={Egorov, V.; FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, 15/17 Professor Popova Street, Russian Federation},
publisher={Hindawi Publishing Corporation},
issn={16879767},
language={English},
abbrev_source_title={Int. J. Pepl.},
document_type={Article},
source={Scopus},
}

Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function. © 2015 Vladimir Egorov et al.

@ARTICLE{Ryzhov2015117,
author={Ryzhov, V.A. and Khavronin, V.P. and Deriglazov, V.V. and Mukovskii, Y.M. and Chichkov, V.I.},
title={Magneto-electronic phase separation in la0.7sr0.3mno3 with metallic behavior in paramagnetic region},
journal={Solid State Phenomena},
year={2015},
volume={233-234},
pages={117-120},
doi={10.4028/www.scientific.net/SSP.233-234.117},
note={cited By 1; Conference of 6th Moscow International Symposium on Magnetism, MISM 2014 ; Conference Date: 29 June 2014 Through 3 July 2014;  Conference Code:122919},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84945198970&doi=10.4028%2fwww.scientific.net%2fSSP.233-234.117&partnerID=40&md5=47477a0e2d5594f1fe5803c3f77614e7},
affiliation={Petersburg Nuclear Physics Institute, NRC ‘Kurchatov Institute’, Gatchina, 188300, Russian Federation; National Research and Technology University, MISiS, Moscow, 119049, Russian Federation},
abstract={The data on transport and magnetic properties (ac linear and nonlinear (second and third orders) susceptibilities) are presented for La0.7Sr0.3MnO3 single crystal with metallic behavior in paramagnetic (PM) region and ferromagnetic (FM) metallic ground state. The FM clusters originate in the PM matrix of the compound below some temperature T* > 425 K, their nonlinear response being weakly T-dependent down to 367 K. This was attributed to clusters arising in the preferable sites formed by chemical inhomogeneities introduced by doping. On cooling below T# ≈ 366 K > TC ≈ 363.3 K, a fast growth of cluster response without the change of its parameters is observed that was attributed to the development of homogeneous nucleation of the FM clusters. The latter stage continues below TC and is accompanied by a crossover to the steeper decreasing of resistivity with cooling that suggests metallic properties of the clusters. The cluster nonlinear response masks completely that of matrix at T = 360.3 K < TC, where it is well described by the model of ensemble of magnetic single-domain nanoparticles in superparamagnetic regime based on the formalism involving Gilbert-Landau-Lifshits equation. Below TD = 359.6 K at the stage of domain formation, a weak interaction of matrix and cluster subsystems leads to their mutual ordering, which is accompanied by a sharp decrease of the nonlinear response to a weak ac field in small steady field H. The latter suggests an “antiferromagnetic” type of arrangement of these subsystems that provides decreasing the magnetostatic energy of the sample. © (2015) Trans Tech Publications, Switzerland.},
author_keywords={Ac susceptibility;  Doped manganites;  Magnetic phase transitions;  Magneto-electronic phase separation;  Nonlinear response to a weak ac field},
correspondence_address1={Ryzhov, V.A.; Petersburg Nuclear Physics Institute, NRC ‘Kurchatov Institute’Russian Federation},
editor={Perov N., Semisalova A.},
sponsors={Electromagnetics of Russian Academy of Sciences; et al; Institute for Theoretical and Applied; Japan Society for the Promotion of Science; Lomonosov Moscow State University; Russian Foundation for Basic Research},
publisher={Trans Tech Publications Ltd},
issn={16629779},
isbn={9783038354826},
language={English},
abbrev_source_title={Solid State Phenomena},
document_type={Conference Paper},
source={Scopus},
}

The data on transport and magnetic properties (ac linear and nonlinear (second and third orders) susceptibilities) are presented for La0.7Sr0.3MnO3 single crystal with metallic behavior in paramagnetic (PM) region and ferromagnetic (FM) metallic ground state. The FM clusters originate in the PM matrix of the compound below some temperature T* > 425 K, their nonlinear response being weakly T-dependent down to 367 K. This was attributed to clusters arising in the preferable sites formed by chemical inhomogeneities introduced by doping. On cooling below T# ≈ 366 K > TC ≈ 363.3 K, a fast growth of cluster response without the change of its parameters is observed that was attributed to the development of homogeneous nucleation of the FM clusters. The latter stage continues below TC and is accompanied by a crossover to the steeper decreasing of resistivity with cooling that suggests metallic properties of the clusters. The cluster nonlinear response masks completely that of matrix at T = 360.3 K < TC, where it is well described by the model of ensemble of magnetic single-domain nanoparticles in superparamagnetic regime based on the formalism involving Gilbert-Landau-Lifshits equation. Below TD = 359.6 K at the stage of domain formation, a weak interaction of matrix and cluster subsystems leads to their mutual ordering, which is accompanied by a sharp decrease of the nonlinear response to a weak ac field in small steady field H. The latter suggests an “antiferromagnetic” type of arrangement of these subsystems that provides decreasing the magnetostatic energy of the sample. © (2015) Trans Tech Publications, Switzerland.

@ARTICLE{Matusevich20154,
author={Matusevich, O.V. and Egorov, V.V. and Gluzdikov, I.A. and Titov, M.I. and Zarubaev, V.V. and Shtro, A.A. and Slita, A.V. and Dukov, M.I. and Shurygina, A.-P.S. and Smirnova, T.D. and Kudryavtsev, I.V. and Vasin, A.V. and Kiselev, O.I.},
title={Synthesis and antiviral activity of PB1 component of the influenza A RNA polymerase peptide fragments},
journal={Antiviral Research},
year={2015},
volume={113},
pages={4-10},
doi={10.1016/j.antiviral.2014.10.015},
note={cited By 6},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84911884647&doi=10.1016%2fj.antiviral.2014.10.015&partnerID=40&md5=ee11406f9aea9680cc6c4c4cec4df9af},
affiliation={Saint Petersburg State University, Faculty of Chemistry, 26, Universitetskii pr., Petrodvorets, St.-Petersburg, 198504, Russian Federation; Research Institute of Influenza, Molecular Virology Department, 15/17, Prof. Popova str., St.-Petersburg, 197376, Russian Federation; Inst. of Experimental Medicine of the North-West Branch of the Russian Academy of Medical Sciences, 12, Akad. Pavlova str., St.-Petersburg, 197376, Russian Federation; Petersburg Nuclear Physics Institute, NRC KI, Orlova roscha, Gatchina, 188300, Russian Federation; Far East Federal University, 8, Suhanova str., Vladivostok, 690950, Russian Federation; State Polytechnical University, 29, Polytecnicheskaya str., St.-Petersburg, 195251, Russian Federation},
abstract={This study is devoted to the antiviral activity of peptide fragments from the PB1 protein - a component of the influenza A RNA polymerase. The antiviral activity of the peptides synthesized was studied in MDCK cell cultures against the pandemic influenza strain A/California/07/2009 (H1N1) pdm09. We found that peptide fragments 6-13, 6-14, 26-30, 395-400, and 531-540 of the PB1 protein were capable of suppressing viral replication in cell culture. Terminal modifications i.e. N-acetylation and C-amidation increased the antiviral properties of the peptides significantly. Peptide PB1 (6-14) with both termini modified showed maximum antiviral activity, its inhibitory activity manifesting itself during the early stages of viral replication. It was also shown that the fluorescent-labeled analog of this peptide was able to penetrate into the cell. The broad range of virus-inhibiting activity of PB1 (6-14) peptide was confirmed using a panel of influenza A viruses of H1, H3 and H5 subtypes including those resistant to oseltamivir, the leading drug in anti-influenza therapy. Thus, short peptide fragments of the PB1 protein could serve as leads for future development of influenza prevention and/or treatment agents. © 2014 Elsevier B.V. All rights reserved.},
author_keywords={Antiviral peptides;  Influenza A;  Influenza A polymerase;  PB1},
correspondence_address1={Egorov, V.V.; Research Institute of Influenza, Molecular Virology Department, 15/17, Prof. Popova str., Russian Federation},
publisher={Elsevier B.V.},
issn={01663542},
coden={ARSRD},
pubmed_id={25446335},
language={English},
abbrev_source_title={Antiviral Res.},
document_type={Article},
source={Scopus},
}

This study is devoted to the antiviral activity of peptide fragments from the PB1 protein - a component of the influenza A RNA polymerase. The antiviral activity of the peptides synthesized was studied in MDCK cell cultures against the pandemic influenza strain A/California/07/2009 (H1N1) pdm09. We found that peptide fragments 6-13, 6-14, 26-30, 395-400, and 531-540 of the PB1 protein were capable of suppressing viral replication in cell culture. Terminal modifications i.e. N-acetylation and C-amidation increased the antiviral properties of the peptides significantly. Peptide PB1 (6-14) with both termini modified showed maximum antiviral activity, its inhibitory activity manifesting itself during the early stages of viral replication. It was also shown that the fluorescent-labeled analog of this peptide was able to penetrate into the cell. The broad range of virus-inhibiting activity of PB1 (6-14) peptide was confirmed using a panel of influenza A viruses of H1, H3 and H5 subtypes including those resistant to oseltamivir, the leading drug in anti-influenza therapy. Thus, short peptide fragments of the PB1 protein could serve as leads for future development of influenza prevention and/or treatment agents. © 2014 Elsevier B.V. All rights reserved.

@ARTICLE{Tyagi20151,
author={Tyagi, M. and Iordanskiy, S. and Ammosova, T. and Kumari, N. and Smith, K. and Breuer, D. and Ilatovskiy, A.V. and Kont, Y.S. and Ivanov, A. and Üren, A. and Kovalskyy, D. and Petukhov, M. and Kashanchi, F. and Nekhai, S.},
title={Reactivation of latent HIV-1 provirus via targeting protein phosphatase-1},
journal={Retrovirology},
year={2015},
volume={12},
number={1},
pages={1-17},
doi={10.1186/s12977-015-0190-4},
note={cited By 13},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84942468554&doi=10.1186%2fs12977-015-0190-4&partnerID=40&md5=8ee259f33c5246c123a47a2b5d90e288},
affiliation={Department of Medicine, The George Washington University, Washington, DC  2003, United States; National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA  20110, United States; Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC  20059, United States; Department of Medicine, Howard University, Washington, DC  20059, United States; Yakut Science Center for Complex Medical Problems, Yakutsk, 677019, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Instiute of Nanobiotechnologies, St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC  20057, United States; Department of Biochemistry, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX  78229, United States},
abstract={Background: HIV-1 escapes antiretroviral drugs by integrating into the host DNA and forming a latent transcriptionally silent HIV-1 provirus. This provirus presents the major hurdle in HIV-1 eradication and cure. Transcriptional activation, which is prerequisite for reactivation and the eradication of latent proviruses, is impaired in latently infected T cells due to the lack of host transcription factors, primarily NF-κB and P-TEFb (CDK9/cyclin T1). We and others previously showed that protein phosphatase-1 (PP1) regulates HIV-1 transcription by modulating CDK9 phosphorylation. Recently we have developed a panel of small molecular compounds targeting a non-catalytic site of PP1. Results: Here we generated a new class of sulfonamide-containing compounds that activated HIV-1 in acute and latently infected cells. Among the tested molecules, a small molecule activator of PP1 (SMAPP1) induced both HIV-1 replication and reactivation of latent HIV-1 in chronically infected cultured and primary cells. In vitro, SMAPP1 interacted with PP1 and increased PP1 activity toward a recombinant substrate. Treatment with SMAPP1 increased phosphorylation of CDK9's Ser90 and Thr186 residues, but not Ser175. Proteomic analysis showed upregulation of P-TEFb and PP1 related proteins, including PP1 regulatory subunit Sds22 in SMAPP1-treated T cells. Docking analysis identified a PP1 binding site for SMAPP1 located within the C-terminal binding pocket of PP1. Conclusion: We identified a novel class of PP1-targeting compounds that reactivate latent HIV-1 provirus by targeting PP1, increasing CDK9 phosphorylation and enhancing HIV transcription. This compound represents a novel candidate for anti-HIV-1 therapeutics aiming at eradication of latent HIV-1 reservoirs. © 2015 Tyagi et al.},
funding_details={Russian Science Foundation14-34-00023},
funding_details={National Institutes of Health1P50HL118006},
funding_details={National Institutes of Health1R01HL125005},
funding_details={National Institutes of Health5G12MD007597},
funding_details={National Institutes of Health5R03DA033900-02},
funding_details={National Institute on Drug Abuse5R21DA033924-02},
funding_details={National Institutes of HealthF31NS086453},
funding_details={National Institutes of HealthR01AI043894},
funding_details={National Institutes of HealthR21 AI114490},
funding_details={National Institutes of HealthR21AI13140},
funding_details={National Institutes of HealthU19AI109664},
correspondence_address1={Nekhai, S.; Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, United States; email: snekhai@howard.edu},
publisher={BioMed Central Ltd.},
issn={17424690},
pubmed_id={26178009},
language={English},
abbrev_source_title={Retrovirology},
document_type={Article},
source={Scopus},
}

Background: HIV-1 escapes antiretroviral drugs by integrating into the host DNA and forming a latent transcriptionally silent HIV-1 provirus. This provirus presents the major hurdle in HIV-1 eradication and cure. Transcriptional activation, which is prerequisite for reactivation and the eradication of latent proviruses, is impaired in latently infected T cells due to the lack of host transcription factors, primarily NF-κB and P-TEFb (CDK9/cyclin T1). We and others previously showed that protein phosphatase-1 (PP1) regulates HIV-1 transcription by modulating CDK9 phosphorylation. Recently we have developed a panel of small molecular compounds targeting a non-catalytic site of PP1. Results: Here we generated a new class of sulfonamide-containing compounds that activated HIV-1 in acute and latently infected cells. Among the tested molecules, a small molecule activator of PP1 (SMAPP1) induced both HIV-1 replication and reactivation of latent HIV-1 in chronically infected cultured and primary cells. In vitro, SMAPP1 interacted with PP1 and increased PP1 activity toward a recombinant substrate. Treatment with SMAPP1 increased phosphorylation of CDK9's Ser90 and Thr186 residues, but not Ser175. Proteomic analysis showed upregulation of P-TEFb and PP1 related proteins, including PP1 regulatory subunit Sds22 in SMAPP1-treated T cells. Docking analysis identified a PP1 binding site for SMAPP1 located within the C-terminal binding pocket of PP1. Conclusion: We identified a novel class of PP1-targeting compounds that reactivate latent HIV-1 provirus by targeting PP1, increasing CDK9 phosphorylation and enhancing HIV transcription. This compound represents a novel candidate for anti-HIV-1 therapeutics aiming at eradication of latent HIV-1 reservoirs. © 2015 Tyagi et al.

The fibrillogenesis of a peptide corresponding to residues 35-51 of human α-lactalbumin (1GYDTQAIVENNESTEYG17) can be dramatically enhanced by the addition of a tetrapeptide TDYG homologous to its C-terminus (TEYG). Generation of spontaneous hydrolytic products similar to this peptide was demonstrated by mass-spectrometry analysis of GYDTQAIVE NNESTEYG peptide solution components during fibrillogenesis. Possible mechanisms and roles of short peptides in protein metabolism are discussed. © 2014 Taylor & Francis Group, LLC.

@ARTICLE{Vasin201453,
author={Vasin, A.V. and Temkina, O.A. and Egorov, V.V. and Klotchenko, S.A. and Plotnikova, M.A. and Kiselev, O.I.},
title={Molecular mechanisms enhancing the proteome of influenza A viruses: An overview of recently discovered proteins},
journal={Virus Research},
year={2014},
volume={185},
pages={53-63},
doi={10.1016/j.virusres.2014.03.015},
note={cited By 76},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84898638820&doi=10.1016%2fj.virusres.2014.03.015&partnerID=40&md5=233e781cb478e6c644144343962c0d9d},
affiliation={Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russian Federation},
abstract={Influenza A virus is one of the major human pathogens. Despite numerous efforts to produce absolutely effective anti-influenza drugs or vaccines, no such agent has been developed yet. One of the main reasons for this complication is the high mutation rate and the specific structure of influenza A viruses genome. For more than 25 years since the first mapping of the viral genome, it was believed that its 8 genome segments encode 10 proteins. However, the proteome of influenza A viruses has turned out to be much more complex than previously thought. In 2001, the first accessory protein, PB1-F2, translated from the alternative open reading frame, was discovered. Subsequently, six more proteins, PB1-N40, PA-X, PA-N155, PA-N182, M42, and NS3, have been found. It is important to pay close attention to these novel proteins in order to evaluate their role in the pathogenesis of influenza, especially in the case of outbreaks of human infections with new avian viruses, such as H5N1 or H7N9. In this review we summarize the data on the molecular mechanisms used by influenza A viruses to expand their proteome and on the possible functions of the recently discovered viral proteins. © 2014 Elsevier B.V.},
author_keywords={Influenza A virus;  Influenza virus proteome;  M42;  NEG8;  PA-X;  PB1-N40},
correspondence_address1={Vasin, A.V.; Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russian Federation; email: vasin@influenza.spb.ru},
publisher={Elsevier},
issn={01681702},
coden={VIRED},
pubmed_id={24675275},
language={English},
abbrev_source_title={Virus Res.},
document_type={Review},
source={Scopus},
}

Influenza A virus is one of the major human pathogens. Despite numerous efforts to produce absolutely effective anti-influenza drugs or vaccines, no such agent has been developed yet. One of the main reasons for this complication is the high mutation rate and the specific structure of influenza A viruses genome. For more than 25 years since the first mapping of the viral genome, it was believed that its 8 genome segments encode 10 proteins. However, the proteome of influenza A viruses has turned out to be much more complex than previously thought. In 2001, the first accessory protein, PB1-F2, translated from the alternative open reading frame, was discovered. Subsequently, six more proteins, PB1-N40, PA-X, PA-N155, PA-N182, M42, and NS3, have been found. It is important to pay close attention to these novel proteins in order to evaluate their role in the pathogenesis of influenza, especially in the case of outbreaks of human infections with new avian viruses, such as H5N1 or H7N9. In this review we summarize the data on the molecular mechanisms used by influenza A viruses to expand their proteome and on the possible functions of the recently discovered viral proteins. © 2014 Elsevier B.V.

@ARTICLE{Afanasyeva2014549,
author={Afanasyeva, A. and Hirtreiter, A. and Schreiber, A. and Grohmann, D. and Pobegalov, G. and McKay, A.R. and Tsaneva, I. and Petukhov, M. and Käs, E. and Grigoriev, M. and Werner, F.},
title={Lytic water dynamics reveal evolutionarily conserved mechanisms of ATP hydrolysis by TIP49 AAA+ ATPases},
journal={Structure},
year={2014},
volume={22},
number={4},
pages={549-559},
doi={10.1016/j.str.2014.02.002},
note={cited By 12},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84898431978&doi=10.1016%2fj.str.2014.02.002&partnerID=40&md5=d0de41cbac2f5d2f3463f48082ae0b53},
affiliation={Department of Biophysics, Saint Petersburg State Polytechnical University, Saint-Petersburg 195251, Russian Federation; Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom; Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Braunschweig 38106, Germany; Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; UMR 5099, CNRS, Toulouse F-31000, France; Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse F-31000, France; Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, United Kingdom},
abstract={Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. © 2014 The Authors.},
funding_details={Wellcome Trust079351/Z/06/Z},
funding_details={Biotechnology and Biological Sciences Research CouncilBB/E008232/1},
funding_details={Ministry of Education and Science of the Russian Federation11.519.11.2002},
}

Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. © 2014 The Authors.

@ARTICLE{Shvetsov2014948,
author={Shvetsov, A.V. and Lebedev, D.V. and Chervyakova, D.B. and Bakhlanova, I.V. and Yung, I.A. and Radulescu, A. and Kuklin, A.I. and Baitin, D.M. and Isaev-Ivanov, V.V.},
title={Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering},
journal={FEBS Letters},
year={2014},
volume={588},
number={6},
pages={948-955},
doi={10.1016/j.febslet.2014.01.053},
note={cited By 9},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896097512&doi=10.1016%2fj.febslet.2014.01.053&partnerID=40&md5=487e046cfe30940a5f92c492c0bbc21f},
affiliation={Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Saint-Petersburg State University, Saint-Petersburg, Russian Federation; St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; Joint Centre for Nuclear Research, Dubna, Russian Federation; Jülich Centre for Neutron Science Outstation at FRM II, Garching, Germany},
abstract={Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA. Formation of RecX::RecA::ssDNA filaments in solution was confirmed by SANS measurements which were in agreement with the spectra computed from the molecular dynamics simulations. © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.},
author_keywords={GROMACS;  Molecular dynamics;  RecA;  RecX;  Small angle neutron scattering},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)12-02-12053-ofi-m, 11-04-01229-a, 14-04-00817a},
}

Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA. Formation of RecX::RecA::ssDNA filaments in solution was confirmed by SANS measurements which were in agreement with the spectra computed from the molecular dynamics simulations. © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

@ARTICLE{Surzhik2014118,
author={Surzhik, M.A. and Schmidt, A.E. and Glazunov, E.A. and Firsov, D.L. and Petukhov, M.G.},
title={Introduction of additional thiol groups into glucoamylase in Aspergillus Awamori and their effect on the thermal stability and catalytic activity of the enzyme},
journal={Applied Biochemistry and Microbiology},
year={2014},
volume={50},
number={2},
pages={118-124},
doi={10.1134/S0003683814020185},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897790640&doi=10.1134%2fS0003683814020185&partnerID=40&md5=71e70330501a996dfb4ab4ef6c53ceda},
affiliation={Konstantinov Institute of Nuclear Physics, National Research Centre Kurchatov Institute, Gatchina, Leningrad oblast, 188300, Russian Federation; Department of Biophysics, Institute of Physics, Nanotechnology, and Telecommunications, St. Petersburg State Polytechnical University, St. Petersburg, 195251, Russian Federation},
abstract={Five mutant forms of glucoamylase (GA) from the filamentous fungus Aspergillus awamori with artificial disulfide bonds (4D-G137A\A14C, 6D-A14C\Y419C\G137A, 10D-V13C\G396C, 11D-V13C\G396C\A14C\Y419C\G137A, and 20D-G137A\A246C\A14C) were constructed using molecular modeling simulations and experimentally tested for thermostability. The introduction of two additional disulfide bonds between its first and thirteenth α-helices and that of the loop located close to a catalytic residue-E400-made it possible to assess the effects of disulfide bridges on protein thermostability. The mutant proteins with combined amino acid substitutions G137A\A14C, V13C\G396C\A14C\Y419C\G137A, and G137A\A246C\A14C showed higher thermal stability as compared to the wild-type protein. At the same time, new disulfide bridges in the mutant A14C\Y419C\G137A and V13C\G396C proteins led to the destabilization of their structure and the loss of thermal stability. © 2014 Pleiades Publishing, Inc.},
correspondence_address1={Surzhik, M. A.; Konstantinov Institute of Nuclear Physics, National Research Centre Kurchatov Institute, Gatchina, Leningrad oblast, 188300, Russian Federation; email: pmg@omrb.pnpi.spb.ru},
issn={00036838},
language={English},
abbrev_source_title={Appl. Biochem. Microbiol.},
document_type={Article},
source={Scopus},
}

Five mutant forms of glucoamylase (GA) from the filamentous fungus Aspergillus awamori with artificial disulfide bonds (4D-G137A\A14C, 6D-A14C\Y419C\G137A, 10D-V13C\G396C, 11D-V13C\G396C\A14C\Y419C\G137A, and 20D-G137A\A246C\A14C) were constructed using molecular modeling simulations and experimentally tested for thermostability. The introduction of two additional disulfide bonds between its first and thirteenth α-helices and that of the loop located close to a catalytic residue-E400-made it possible to assess the effects of disulfide bridges on protein thermostability. The mutant proteins with combined amino acid substitutions G137A\A14C, V13C\G396C\A14C\Y419C\G137A, and G137A\A246C\A14C showed higher thermal stability as compared to the wild-type protein. At the same time, new disulfide bridges in the mutant A14C\Y419C\G137A and V13C\G396C proteins led to the destabilization of their structure and the loss of thermal stability. © 2014 Pleiades Publishing, Inc.

@ARTICLE{Ryzhov2014,
author={Ryzhov, V.A. and Lazuta, A.V. and Khavronin, V.P. and Molkanov, P.L. and Mukovskii, Ya.M.},
title={Magnetic phase transition and clustered state in Ca-doped lanthanum cobaltite and manganite with insulator ground states.},
journal={Journal of Physics Condensed Matter},
year={2014},
volume={26},
number={7},
doi={10.1088/0953-8984/26/7/076001},
art_number={076001},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893389071&doi=10.1088%2f0953-8984%2f26%2f7%2f076001&partnerID=40&md5=78fe74df45d6a2704f73e0fb4dd1babf},
affiliation={Petersburg Nuclear Physics Institute, NRC 'Kurchatov Institute', Orlova Coppice, Gatchina 188300, Russian Federation; National Research and Technology University 'Misis', Leninskii Prospekt 4, Moscow 119049, Russian Federation},
abstract={The transport and magnetic properties (ac linear and nonlinear (second and third orders) susceptibilities) are presented for La0.8Ca 0.2MnO3 and La0.8Ca0.2CoO 3 single crystals with insulator ground states. The ferromagnetic (FM) clusters with similar magnetic characteristics originate in the paramagnetic phases of both compounds below some temperature T*. At high temperatures the FM clusters arise at the preferable sites that can be attributed to the chemical inhomogeneities, their density being weakly T-dependent. On cooling a homogeneous nucleation of the FM clusters develops below a definite temperature T# that is characterized by a fast growth of their density. These two stages are observed in both compounds. At the third stage a coalescence of the FM clusters starts in the doped cobaltite, whereas in the manganite the development of matrix FM ordering occurs which changes a cluster's behavior. The indicated features support the common nature of the cluster state in the doped cobaltite and manganite. The difference in their evolution is a consequence of the different magnetic properties of the matrices in the manganite and cobaltite. © 2014 IOP Publishing Ltd.},
author_keywords={magnetic phase separation;  magnetic phase transitions;  response to ac field-linear and nonlinear susceptibilities;  transition metal oxides},
correspondence_address1={Petersburg Nuclear Physics Institute, NRC 'Kurchatov Institute', Orlova Coppice, Gatchina 188300, Russian Federation},
issn={09538984},
coden={JCOME},
language={English},
abbrev_source_title={J Phys Condens Matter},
document_type={Article},
source={Scopus},
}

The transport and magnetic properties (ac linear and nonlinear (second and third orders) susceptibilities) are presented for La0.8Ca 0.2MnO3 and La0.8Ca0.2CoO 3 single crystals with insulator ground states. The ferromagnetic (FM) clusters with similar magnetic characteristics originate in the paramagnetic phases of both compounds below some temperature T*. At high temperatures the FM clusters arise at the preferable sites that can be attributed to the chemical inhomogeneities, their density being weakly T-dependent. On cooling a homogeneous nucleation of the FM clusters develops below a definite temperature T# that is characterized by a fast growth of their density. These two stages are observed in both compounds. At the third stage a coalescence of the FM clusters starts in the doped cobaltite, whereas in the manganite the development of matrix FM ordering occurs which changes a cluster's behavior. The indicated features support the common nature of the cluster state in the doped cobaltite and manganite. The difference in their evolution is a consequence of the different magnetic properties of the matrices in the manganite and cobaltite. © 2014 IOP Publishing Ltd.

@ARTICLE{Nekhai2014,
author={Nekhai, S. and Petukhov, M. and Breuer, D.},
title={Regulation of CDK9 activity by phosphorylation and dephosphorylation},
journal={BioMed Research International},
year={2014},
volume={2014},
doi={10.1155/2014/964964},
art_number={964964},
note={cited By 14},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893776798&doi=10.1155%2f2014%2f964964&partnerID=40&md5=43597b129d4bdb05cf26f67f09aeefbe},
affiliation={Center for Sickle Cell Disease, Department of Medicine, Howard University, 520 W Street, N.W., Washington, DC 20059, United States; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188350, Russian Federation; Department of Biophysics, St. Petersburg State Polytechnical University, Polytechnicheskaya Street 29, St. Petersburg 195251, Russian Federation},
abstract={HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication and potential for being targeted for drug development. We propose a novel pathway of HIV-1 transcription regulation via CDK9 Ser-90 phosphorylation by CDK2 and CDK9 Ser-175 dephosphorylation by protein phosphatase-1. © 2014 Sergei Nekhai et al.},
correspondence_address1={Nekhai, S.; Center for Sickle Cell Disease, Department of Medicine, Howard University, 520 W Street, N.W., Washington, DC 20059, United States; email: snekhai@howard.edu},
issn={23146133},
pubmed_id={24524087},
language={English},
abbrev_source_title={BioMed Res. Int.},
document_type={Review},
source={Scopus},
}

HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication and potential for being targeted for drug development. We propose a novel pathway of HIV-1 transcription regulation via CDK9 Ser-90 phosphorylation by CDK2 and CDK9 Ser-175 dephosphorylation by protein phosphatase-1. © 2014 Sergei Nekhai et al.

@ARTICLE{Ryzhov201468,
author={Ryzhov, V.A. and Lazuta, A.V. and Khavronin, V.P. and Molkanov, P.L. and Mukovskii, Y.M. and Pestun, A.E.},
title={Temperature evolution of the cluster state in La0.8Ca0.2MnO3 and La0.8Ca0.2CoO3},
journal={Physics of the Solid State},
year={2014},
volume={56},
number={1},
pages={68-76},
doi={10.1134/S1063783414010326},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893620256&doi=10.1134%2fS1063783414010326&partnerID=40&md5=03c0fc2a2af93fd59c588a2d9c4cdc01},
affiliation={Konstantinov Petersburg Nuclear Physics Institute, National Research Centre Kurchatov Institute, Orlova Roshcha, Gatchina, Leningrad oblast, 188300, Russian Federation; National University of Science and Technology MISiS, Leninskii pr. 4, Moscow, 119049, Russian Federation},
abstract={The results of investigations of the transport and magnetic properties (ac linear and nonlinear (second- and third-order) susceptibilities) of La0.8Ca0.2MnO3 and La0.8Ca0.2CoO3 single crystals have been presented. It has been found that both compounds in the paramagnetic phase contain ferromagnetic clusters with close magnetic characteristics. At high temperatures, ferromagnetic clusters nucleate in preferred sites associated with chemical inhomogeneities. Cooling below a specific temperature is accompanied by homogeneous nucleation of clusters. These two stages are observed in both compounds. In the doped cobaltite, the coalescence of clusters begins to develop at the third stage, whereas in the manganite, their behavior changes due to the development of ferromagnetic ordering of the matrix. These features indicate that the cluster state in doped manganites and cobaltites has a common nature. The difference in the behavior of ferromagnetic clusters is a consequence of the magnetically active character of the matrix in the case of manganites and the neutral character of the matrix in the case of cobaltites. © 2014 Pleiades Publishing, Ltd.},
correspondence_address1={Ryzhov, V. A.; Konstantinov Petersburg Nuclear Physics Institute, National Research Centre Kurchatov Institute, Orlova Roshcha, Gatchina, Leningrad oblast, 188300, Russian Federation; email: ryzhov@omrb.pnpi.spb.ru},
issn={10637834},
language={English},
abbrev_source_title={Phys. Solid State},
document_type={Article},
source={Scopus},
}

The results of investigations of the transport and magnetic properties (ac linear and nonlinear (second- and third-order) susceptibilities) of La0.8Ca0.2MnO3 and La0.8Ca0.2CoO3 single crystals have been presented. It has been found that both compounds in the paramagnetic phase contain ferromagnetic clusters with close magnetic characteristics. At high temperatures, ferromagnetic clusters nucleate in preferred sites associated with chemical inhomogeneities. Cooling below a specific temperature is accompanied by homogeneous nucleation of clusters. These two stages are observed in both compounds. In the doped cobaltite, the coalescence of clusters begins to develop at the third stage, whereas in the manganite, their behavior changes due to the development of ferromagnetic ordering of the matrix. These features indicate that the cluster state in doped manganites and cobaltites has a common nature. The difference in the behavior of ferromagnetic clusters is a consequence of the magnetically active character of the matrix in the case of manganites and the neutral character of the matrix in the case of cobaltites. © 2014 Pleiades Publishing, Ltd.

@ARTICLE{Yakimov20141,
author={Yakimov, A. and Rychkov, G. and Petukhov, M.},
title={De novo design of stable α-helices},
journal={Methods in Molecular Biology},
year={2014},
volume={1216},
pages={1-14},
doi={10.1007/978-1-4939-1486-9_1},
note={cited By 6},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84921740210&doi=10.1007%2f978-1-4939-1486-9_1&partnerID=40&md5=65710a7e9cfa8e5cfd033b24d7eca07b},
affiliation={Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Saint Petersburg State Polytechnical University, Saint Petersburg, Russian Federation},
abstract={Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization. © Springer Science+Business Media New York 2014.},
author_keywords={Sequence optimization;  Solubility;  Stability;  α-Helix},
funding_details={Russian Foundation for Basic Research12-04-91444-NIH_a},
publisher={Humana Press Inc.},
issn={10643745},
pubmed_id={25213408},
language={English},
abbrev_source_title={Methods Mol. Biol.},
document_type={Article},
source={Scopus},
}

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization. © Springer Science+Business Media New York 2014.

@ARTICLE{Ryzhov2014339,
author={Ryzhov, V.A. and Pleshakov, I.V. and Nechitailov, A.A. and Glebova, N.V. and Pyatyshev, E.N. and Malkova, A.V. and Kiselev, I.A. and Matveev, V.V.},
title={Magnetic Study of Nanostructural Composite Material Based on Cobalt Compounds and Porous Silicon},
journal={Applied Magnetic Resonance},
year={2014},
volume={45},
number={4},
pages={339-352},
doi={10.1007/s00723-014-0527-5},
note={cited By 15},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897958371&doi=10.1007%2fs00723-014-0527-5&partnerID=40&md5=664f83070848f9fedb3d4ccb72fdee29},
affiliation={Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russian Federation; Ioffe Physical-Technical Institute of the Russian Academy of Sciences, Saint Petersburg, 194021, Russian Federation; Saint Petersburg State Polytechnical University, Saint Petersburg, 195251, Russian Federation; St. Petersburg State University, Saint Petersburg, 198504, Russian Federation},
abstract={In present work, an investigation of a magnetically ordered material, which is a composite structure obtained by embedding of cobalt-containing substance into pores of silicon matrix, was performed. The samples were characterized by steady-state magnetometry and electron microscopy. The methods of longitudinal nonlinear response to a weak ac magnetic field and registration of electron magnetic resonance were used for detail study of their properties. It was established that the material forms a structure of ferromagnetic particles at the inner surface of pores. It was agued that they are mainly nonmetallic magnetic particles like Co2B and/or Co3B. The possibility to apply the concept of blocking temperature to specify the magnetic behavior of the compound on temperature confirmed the single-domain state of these particles. © 2014 Springer-Verlag Wien.},
}

In present work, an investigation of a magnetically ordered material, which is a composite structure obtained by embedding of cobalt-containing substance into pores of silicon matrix, was performed. The samples were characterized by steady-state magnetometry and electron microscopy. The methods of longitudinal nonlinear response to a weak ac magnetic field and registration of electron magnetic resonance were used for detail study of their properties. It was established that the material forms a structure of ferromagnetic particles at the inner surface of pores. It was agued that they are mainly nonmetallic magnetic particles like Co2B and/or Co3B. The possibility to apply the concept of blocking temperature to specify the magnetic behavior of the compound on temperature confirmed the single-domain state of these particles. © 2014 Springer-Verlag Wien.

@ARTICLE{Surzhik2014139,
author={Surzhik, M.A. and Shmidt, A.E. and Glazunov, E.A. and Firsov, D.L. and Petukhov, M.G.},
title={[Introduction of additional thiol groups into glucoamylase in Aspergillus awamori and their effect on the thermal stability and catalytic activity of the enzyme].},
journal={Prikladnaia biokhimiia i mikrobiologiia},
year={2014},
volume={50},
number={2},
pages={139-146},
doi={10.7868/S0555109914020184},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907611887&doi=10.7868%2fS0555109914020184&partnerID=40&md5=803c85902077bd96a64585bd0d293a98},
abstract={Five mutant forms of glucoamylase (GA) from the filamentous fungus Aspergillus awamori with artificial disulfide bonds (4D-G137A\A14C, 6D-A14C\Y419C\G137A, 10D-V13C\G396C, 11D-V13C\G396C\A14C\Y419C\G137A, and 20D-G137A\A246C\A14C) were constructed using computer simulation and experimentally tested for thermostability. The introduction of two additional disulfide bonds between its first and thirteenth alpha-helices and that of the loop located close to a catalytic residue--E400--made it possible to assess the effects of disulfide bridges on protein thermostability. The mutant proteins with combined amino acid substitutions G137A\A14C, V13C\G396C\A14C\Y419C\G137A, and G137A\A246C\A14C showed higher thermal stability as compared to the wild-type protein. At the same time, new disulfide bridges in the mutant A14C\Y419C\G137A and V13C\G396C proteins led to the destabilization of their structure and the loss of thermal stability.},
correspondence_address1={Surzhik, M.A.},
issn={05551099},
pubmed_id={25272730},
language={Russian},
abbrev_source_title={Prikl. Biokhim. Mikrobiol.},
document_type={Article},
source={Scopus},
}

Five mutant forms of glucoamylase (GA) from the filamentous fungus Aspergillus awamori with artificial disulfide bonds (4D-G137A\A14C, 6D-A14C\Y419C\G137A, 10D-V13C\G396C, 11D-V13C\G396C\A14C\Y419C\G137A, and 20D-G137A\A246C\A14C) were constructed using computer simulation and experimentally tested for thermostability. The introduction of two additional disulfide bonds between its first and thirteenth alpha-helices and that of the loop located close to a catalytic residue–E400–made it possible to assess the effects of disulfide bridges on protein thermostability. The mutant proteins with combined amino acid substitutions G137A\A14C, V13C\G396C\A14C\Y419C\G137A, and G137A\A246C\A14C showed higher thermal stability as compared to the wild-type protein. At the same time, new disulfide bridges in the mutant A14C\Y419C\G137A and V13C\G396C proteins led to the destabilization of their structure and the loss of thermal stability.

@CONFERENCE{Vashchenkov2014,
author={Vashchenkov, V.E. and Fedoseev, A.I. and Petukhov, M.G. and Khavinson, V.K. and Savvateeva-Popova, E.V. and Lushnikov, S.G.},
title={Study of low-frequency dynamics of short peptides by Brillouin light scattering and Monte-Carlo global energy minimization},
journal={Journal of Physics: Conference Series},
year={2014},
volume={572},
number={1},
doi={10.1088/1742-6596/572/1/012015},
art_number={012015},
note={cited By 1; Conference of 16th Russian Youth Conference on Physics and Astronomy, PhysicA.SPb 2013 ; Conference Date: 23 October 2013 Through 24 October 2013;  Conference Code:109566},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84919459116&doi=10.1088%2f1742-6596%2f572%2f1%2f012015&partnerID=40&md5=d54ee3ccdf36516aef783201ce70239a},
affiliation={Ioffe Physical Technical Institute, St.Petersburg, Russian Federation; St.Petersburg State University, St.Petersburg, Russian Federation; St.Petersburg State Polytechnical University, St.Petersburg, Russian Federation; Petersburg Institute of Nuclear Physics, Gatchina, Leningrad district, Russian Federation; Pavlov Institute of Physiology, St.Petersburg, Russian Federation},
abstract={Brillouin light scattering studies of the behavior of hypersound velocity in solutions of short peptides Asp-Ser, Glu-Asp-Arg, Ala-Glu-Asp-Leu with widely varying concentrations at temperatures ranging from 295 to 360K are presented. As shown by analysis of experimental data and molecular simulation, the dipeptide Asp-Ser is characterized by formation of dimers which decompose at high temperatures. High-concentration solutions of tri- and tetrapeptides form aggregates at high temperatures which are preserved on cooling. © Published under licence by IOP Publishing Ltd.},
funding_details={Russian Foundation for Basic Research12-04-01737-?},
editor={Averkiev N.S., Sokolovskii G.S., Poniaev S.A.},
sponsors={},
publisher={Institute of Physics Publishing},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

Brillouin light scattering studies of the behavior of hypersound velocity in solutions of short peptides Asp-Ser, Glu-Asp-Arg, Ala-Glu-Asp-Leu with widely varying concentrations at temperatures ranging from 295 to 360K are presented. As shown by analysis of experimental data and molecular simulation, the dipeptide Asp-Ser is characterized by formation of dimers which decompose at high temperatures. High-concentration solutions of tri- and tetrapeptides form aggregates at high temperatures which are preserved on cooling. © Published under licence by IOP Publishing Ltd.

@ARTICLE{Yakimov2014106,
author={Yakimov, A.P. and Seregina, T.A. and Kholodnyak, A.A. and Kreneva, R.A. and Mironov, A.S. and Perumov, D.A. and Timkovskii, A.L.},
title={Possible function of the ribT gene of Bacillus subtilis: Theoretical prediction, cloning, and expression},
journal={Acta Naturae},
year={2014},
volume={6},
number={22},
pages={106-109},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84908394416&partnerID=40&md5=e9574ffa58abf486552d26a2043ec902},
affiliation={B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Orlova Roshcha, Gatchina, Leningrad Region, 188300, Russian Federation; St. Petersburg State Polytechnical University, Polytechnicheskaya Str., 29, St. Petersburg, 195251, Russian Federation; State Research Institute of Genetics and Selection of Industrial Microorganisms, 1st Dorozhnyi Proezd, 1, Moscow, 117545, Russian Federation},
abstract={The complete decipherment of the functions and interactions of the elements of the riboflavin biosynthesis operon (rib operon) of Bacillus subtilis are necessary for the development of superproducers of this important vitamin. The function of its terminal ribT gene has not been established to date. In this work, a search for homologs of the hypothetical amino acid sequence of the gene product through databases, as well as an analysis of the homolgs, was performed; the distribution of secondary structure elements was theoretically predicted; and the tertiary structure of the RibT protein was proposed. The ribT gene nucleotide sequence was amplified and cloned into the standard high-copy expression vector pET15b and then expressed after induction with IPTG in E. coli BL21 (DE3) strain cells containing the inducible phage T7 RNA polymerase gene. The ribT gene expression was confirmed by SDS-PAGE. The protein product of the expression was purified by affinity chromatography. Therefore, the real possibility of RibT protein production in quantities sufficient for further investigation of its structure and functional activity was demonstrated. © 2014 Park-media, Ltd.},
author_keywords={Bioinformatics;  Gene cloning;  Homology search;  Inducible expression;  Proteomics;  Theoretical protein structure},
correspondence_address1={Timkovskii, A.L.; B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Orlova RoshchaRussian Federation},
publisher={Russian Federation Agency for Science and Innovation},
issn={20758251},
language={English},
abbrev_source_title={Acta Naturae},
document_type={Article},
source={Scopus},
}

The complete decipherment of the functions and interactions of the elements of the riboflavin biosynthesis operon (rib operon) of Bacillus subtilis are necessary for the development of superproducers of this important vitamin. The function of its terminal ribT gene has not been established to date. In this work, a search for homologs of the hypothetical amino acid sequence of the gene product through databases, as well as an analysis of the homolgs, was performed; the distribution of secondary structure elements was theoretically predicted; and the tertiary structure of the RibT protein was proposed. The ribT gene nucleotide sequence was amplified and cloned into the standard high-copy expression vector pET15b and then expressed after induction with IPTG in E. coli BL21 (DE3) strain cells containing the inducible phage T7 RNA polymerase gene. The ribT gene expression was confirmed by SDS-PAGE. The protein product of the expression was purified by affinity chromatography. Therefore, the real possibility of RibT protein production in quantities sufficient for further investigation of its structure and functional activity was demonstrated. © 2014 Park-media, Ltd.

@CONFERENCE{Matveev2014,
author={Matveev, V. and Ryzhov, V. and Lashkul, A. and Mazur, A. and Semenov, V. and Lähderanta, E.},
title={Study of magnetic nanocomposites by NMR and bulk magnetization techniques},
journal={EPJ Web of Conferences},
year={2014},
volume={75},
doi={10.1051/epjconf/20147505015},
art_number={05015},
note={cited By 0; Conference of 7th Joint European Magnetic Symposia, JEMS 2013 ; Conference Date: 24 August 2013 Through 30 August 2013},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904706748&doi=10.1051%2fepjconf%2f20147505015&partnerID=40&md5=e22c7f881ed91bdbc5f3bdeb8bed02b1},
affiliation={Lappeenranta University of Technology, 53851, Lappeenranta, Finland; Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation; Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Russian Federation; Physico-Technical Institute, NAN of Ukraine, Donetsk, Ukraine},
abstract={Magnetic nanocomposites possess complex and nonuniform magnetic structure. As a result it is necessary to use different physical methods to describe their properties. In this work we have applied a combination of micro and macro approaches to understand more deeply magnetic properties of some cobaltcontaining nanocomposites. Testing of magnetic structure of the samples at molecular level was done with NMR and Mössbauer techniques whereas static (SQUID) and dynamic magnetic (M2, see below) measurements - at macro level. © Owned by the authors, published by EDP Sciences, 2014.},
correspondence_address1={Matveev, V.; Lappeenranta University of Technology, 53851, Lappeenranta, Finland; email: vmatveev@nmr.phys.spbu.ru},
sponsors={European Physical Society (EPS)},
publisher={EDP Sciences},
address={Rhodes},
issn={21016275},
language={English},
abbrev_source_title={EPJ Web Conf.},
document_type={Conference Paper},
source={Scopus},
}

Magnetic nanocomposites possess complex and nonuniform magnetic structure. As a result it is necessary to use different physical methods to describe their properties. In this work we have applied a combination of micro and macro approaches to understand more deeply magnetic properties of some cobaltcontaining nanocomposites. Testing of magnetic structure of the samples at molecular level was done with NMR and Mössbauer techniques whereas static (SQUID) and dynamic magnetic (M2, see below) measurements - at macro level. © Owned by the authors, published by EDP Sciences, 2014.

@ARTICLE{Ksenofontova201466,
author={Ksenofontova, O.I. and Vasin, A.V. and Egorov, V.V. and Bobyl', A.V. and Soldatenkov, F.Y. and Terukov, E.I. and Ulin, V.P. and Ulin, N.V. and Kiselev, O.I.},
title={Porous silicon and its applications in biology and medicine},
journal={Technical Physics},
year={2014},
volume={59},
number={1},
pages={66-77},
doi={10.1134/S1063784214010083},
note={cited By 25},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893302229&doi=10.1134%2fS1063784214010083&partnerID=40&md5=4842ed7deb9a26fc89795cb38e7cb973},
affiliation={Ministry of Healthcare of the Russian Federation Research Institute of Influenza, ul. Prof. Popova 15/17, St. Petersburg, 197376, Russian Federation; Ioffe Physical Technical Institute, Russian Academy of Sciences, Politekhnicheskaya ul. 26, St. Petersburg, 194021, Russian Federation; St. Petersburg State Electrotechnical University, ul. Prof. Popova 5, St. Petersburg, 197376, Russian Federation},
abstract={Development of safe container materials for targeted and controlled drug delivery to the right site in the body is one of the most important aspects of modern biotechnologies. In the last decade, a significant progress has been achieved in the study of nanostructured drug carriers, but the use of many nanomaterials is fraught with the enormous risk because of their high toxicity. The real breakthrough became the use of porous silicon, which has such important properties as biocompatibility, bioavailability, and biodegradability, which makes it possible to use it for solving a wide range of biological and medical problems in the field of diagnosis and treatment of diseases, implantology, and biomolecular screening. © 2014 Pleiades Publishing, Ltd.},
correspondence_address1={Vasin, A. V.; Ministry of Healthcare of the Russian Federation Research Institute of Influenza, ul. Prof. Popova 15/17, St. Petersburg, 197376, Russian Federation; email: vasin@influenza.spb.ru},
issn={10637842},
language={English},
abbrev_source_title={Tech. Phys.},
document_type={Article},
source={Scopus},
}

Development of safe container materials for targeted and controlled drug delivery to the right site in the body is one of the most important aspects of modern biotechnologies. In the last decade, a significant progress has been achieved in the study of nanostructured drug carriers, but the use of many nanomaterials is fraught with the enormous risk because of their high toxicity. The real breakthrough became the use of porous silicon, which has such important properties as biocompatibility, bioavailability, and biodegradability, which makes it possible to use it for solving a wide range of biological and medical problems in the field of diagnosis and treatment of diseases, implantology, and biomolecular screening. © 2014 Pleiades Publishing, Ltd.

@ARTICLE{Vasin201332,
author={Vasin, A.V. and Sandybaev, N.T. and Plotnikova, M.A. and Klotchenko, S.A. and Chervyakova, O.V. and Strochkov, V.M. and Taylakova, E.T. and Temkina, O.A. and Brodskaya, A.V. and Zabrodskaya, Y.A. and Nikulenkov, K.P. and Egorov, V.V. and Koshemetov, J.K. and Sansyzbay, A.R. and Kisslev, O.I.},
title={Universal diagnostic oligonucleotide microarray for subtyping of human and animal influenza A viruses},
journal={Voprosy Virusologii},
year={2013},
volume={58},
number={5},
pages={32-37},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84889039150&partnerID=40&md5=f0115b9ea45b298ea935ec618887841d},
affiliation={Federal State Research Institute of Influenza, Ministry of Health of the Russian Federation, St.-Petersburg, Russian Federation; Research Institute for Biological Safety Problems, Gvardeiskiy, Kazakhstan},
abstract={The diagnostic oligonucleotide microarray for subtyping of human and animal influenza A viruses (IAVs) was developed. We proposed a simple method of the fluorescent labeling of genomic segments of all known IAVs subtypes, the composition of the hybridization buffer, as well as the software of the data processing. 48 IAVs strains of different subtypes were analyzed using our microarray. All of them were identified, while 45 of 48 strains were unambiguously subtyped.},
author_keywords={Hemagglutinin;  Influenza A virus;  Microarray;  Molecular diagnosis;  Neuraminidase},
correspondence_address1={Federal State Research Institute of Influenza, Ministry of Health of the Russian Federation, St.-Petersburg, Russian Federation},
issn={05074088},
coden={VVIRA},
pubmed_id={24640169},
language={Russian},
abbrev_source_title={Vopr. Virusol.},
document_type={Review},
source={Scopus},
}

The diagnostic oligonucleotide microarray for subtyping of human and animal influenza A viruses (IAVs) was developed. We proposed a simple method of the fluorescent labeling of genomic segments of all known IAVs subtypes, the composition of the hybridization buffer, as well as the software of the data processing. 48 IAVs strains of different subtypes were analyzed using our microarray. All of them were identified, while 45 of 48 strains were unambiguously subtyped.

@ARTICLE{Shvetsov20131124,
author={Shvetsov, A.V. and Schmidt, A.E. and Lebedev, D.V. and Isaev-Ivanov, V.V.},
title={Method for calculating small-angle neutron scattering spectra using all-atom molecular dynamics trajectories},
journal={Journal of Surface Investigation},
year={2013},
volume={7},
number={6},
pages={1124-1127},
doi={10.1134/S1027451013060372},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84894624021&doi=10.1134%2fS1027451013060372&partnerID=40&md5=9c21ae53478b9b2390b81ac4210dddc2},
affiliation={Petersburg Institute for Nuclear Physics, National Research Center Kurchatov Institute, Gatchina, Leningrad oblast, Russian Federation},
abstract={A method for calculating small-angle neutron scattering (SANS) spectra based on data obtained using the method of the all-atom molecular dynamics of biomacromolecular structures is considered. When interpreting the SANS data, this approach makes it possible to take into account the fact that the structure of biomacromolecules in a solution is not a static object. This method is implemented in the form of a module for the GROMACS software package and will be available in version 4.6 of this popular program package for simulating biomacromolecular-structure dynamics. © 2013 Pleiades Publishing, Ltd.},
correspondence_address1={Shvetsov, A. V.; Petersburg Institute for Nuclear Physics, National Research Center Kurchatov Institute, Gatchina, Leningrad oblast, Russian Federation; email: alexxy@omrb.pnpi.spb.ru},
issn={10274510},
language={English},
abbrev_source_title={J. Surf. Invest.},
document_type={Article},
source={Scopus},
}

A method for calculating small-angle neutron scattering (SANS) spectra based on data obtained using the method of the all-atom molecular dynamics of biomacromolecular structures is considered. When interpreting the SANS data, this approach makes it possible to take into account the fact that the structure of biomacromolecules in a solution is not a static object. This method is implemented in the form of a module for the GROMACS software package and will be available in version 4.6 of this popular program package for simulating biomacromolecular-structure dynamics. © 2013 Pleiades Publishing, Ltd.

@ARTICLE{Yung20131137,
author={Yung, I.A. and Pantina, R.A. and Lebedev, D.V. and Filatov, M.V. and Isaev-Ivanov, V.V.},
title={Distance distribution functions of replication origins in HeLa and glioma human cells according to the data of confocal microscopy},
journal={Journal of Surface Investigation},
year={2013},
volume={7},
number={6},
pages={1137-1142},
doi={10.1134/S1027451013060414},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84894613123&doi=10.1134%2fS1027451013060414&partnerID=40&md5=90679420c913620df35e1385632cd253},
affiliation={National Research Center Kurchatov Institute, Petersburg Nuclear Physics Institute, Gatchina, Leningrad oblast, 188300, Russian Federation},
abstract={The distribution of replication origins in the nuclei of different cells is studied by confocal microscopy. Based on the obtained images, three-dimensional maps of the positions of the origin centers is constructed and the distribution functions of the pair distances between them are calculated. It is established that the distance distribution function for HeLa and glioma human cells is linear at sizes up to 2 μm, which indicates that the size of the origin system is close to 2. The amplitude of the distance distribution function at small sizes has a power dependence on the nucleus size and is inversely proportional to the nucleus volume to the power of 0.9. Thus, the replication-origin distribution in a nucleus cannot be described by a model with a single Hausdorff dimension in the whole range of sizes. © 2013 Pleiades Publishing, Ltd.},
correspondence_address1={Yung, I. A.; National Research Center Kurchatov Institute, Petersburg Nuclear Physics Institute, Gatchina, Leningrad oblast, 188300, Russian Federation; email: Igor.Yung@rambler.ru},
issn={10274510},
language={English},
abbrev_source_title={J. Surf. Invest.},
document_type={Article},
source={Scopus},
}

The distribution of replication origins in the nuclei of different cells is studied by confocal microscopy. Based on the obtained images, three-dimensional maps of the positions of the origin centers is constructed and the distribution functions of the pair distances between them are calculated. It is established that the distance distribution function for HeLa and glioma human cells is linear at sizes up to 2 μm, which indicates that the size of the origin system is close to 2. The amplitude of the distance distribution function at small sizes has a power dependence on the nucleus size and is inversely proportional to the nucleus volume to the power of 0.9. Thus, the replication-origin distribution in a nucleus cannot be described by a model with a single Hausdorff dimension in the whole range of sizes. © 2013 Pleiades Publishing, Ltd.

Myocilin is a protein with a molecular weight near 50 kDa. It is expressed in almost all organs and tissues.1 We showed that the peptide DQLETQTR ELETA YSNLLRD corresponding to N-terminal leucine zipper motif (LZM) of the protein is able to form amyloid-like fibrils. The possible role of this motif in myocilin aggregation is discussed. © 2013 Landes Bioscience.

@ARTICLE{Babkina2013131,
author={Babkina, L.A. and Garmai, Y.P. and Lebedev, D.V. and Pantina, R.A. and Filatov, M.V. and Isaev-Ivanov, V.V.},
title={Using Zernike moments for analysis of images},
journal={Numerical Analysis and Applications},
year={2013},
volume={6},
number={2},
pages={131-144},
doi={10.1134/S1995423913020055},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878847142&doi=10.1134%2fS1995423913020055&partnerID=40&md5=ae022d86a3cfca1a839a87e852e65b87},
affiliation={Konstantinov Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; Biophysics Scientific-Educational Structure at the St. Petersburg State Polytechnic University, Konstantinov Petersburg Nuclear Physics Institute, St. Petersburg, Russian Federation},
abstract={A method for analyzing AFM images of the cell nuclei of higher organisms by expanding these images by Zernike moments is proposed. This method allows for expanding the pilot image by Zernike moments whose spatial harmonics are Zernike polynomials. It is shown that the reverse procedure of image reconstruction using Zernike polynomials converges to the experimental image and the expansion amplitude is a quantitative spectral characteristic in comparing the morphological features of different images. It is shown that expansion amplitudes can be used as input vectors for cluster analysis of images by PCA. © 2013 Pleiades Publishing, Ltd.},
author_keywords={atomic force microscopy;  cell nuclei of higher organisms;  image analysis;  PCA;  Zernike moments},
funding_details={Ministry of Education and Science of the Russian Federation2.2.1.1/1166},
}

A method for analyzing AFM images of the cell nuclei of higher organisms by expanding these images by Zernike moments is proposed. This method allows for expanding the pilot image by Zernike moments whose spatial harmonics are Zernike polynomials. It is shown that the reverse procedure of image reconstruction using Zernike polynomials converges to the experimental image and the expansion amplitude is a quantitative spectral characteristic in comparing the morphological features of different images. It is shown that expansion amplitudes can be used as input vectors for cluster analysis of images by PCA. © 2013 Pleiades Publishing, Ltd.

@ARTICLE{Egorov2013,
author={Egorov, V.V. and Matusevich, O.V. and Shaldzhyan, A.A. and Skvortsov, A.N. and Zabrodskaya, Y.A. and Garmay, Y.P. and Landa, S.B. and Lebedev, D.V. and Zarubayev, V.V. and Sirotkin, A.K. and Vasin, A.V. and Kiselev, O.I.},
title={Structural features of the peptide homologous to 6-25 fragment of influenza A PB1 protein},
journal={International Journal of Peptides},
year={2013},
volume={2013},
doi={10.1155/2013/370832},
art_number={370832},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896133325&doi=10.1155%2f2013%2f370832&partnerID=40&md5=b584320d34c7ff94d17c5f5f28d7a700},
affiliation={Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, 15/17, Professor Popova Street, Saint-Petersburg 197376, Russian Federation; Department of Molecular and Radiation Biophysics, Kurchatov Institute, FSBI St. Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; Faculty of Chemistry, Saint Petersburg State University, Saint-Petersburg 198504, Russian Federation},
abstract={A mirror-symmetry motif was discovered in the N-terminus of the influenza virus PB1 protein. Structure of peptide comprised of the corresponding part of PB1 (amino acid residues 6-25) was investigated by circular dichroism and in silico modeling. We found that peptide PB1 (6-25) in solution assumes beta-hairpin conformation. A truncated peptide PB1 (6-13), containing only half of the mirror-symmetry motif, appeared to stabilize the beta-structure of the original peptide and, at high concentrations, was capable of reacting with peptide to form insoluble aggregates in vitro. Ability of PB1 (6-13) peptide to interact with the N-terminal domain of PB1 protein makes it a potential antiviral agent that inhibits PA-PB1 complex formation by affecting PB1 N-terminus structure. © 2013 Vladimir V. Egorov et al.},
correspondence_address1={Egorov, V.V.; Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, 15/17, Professor Popova Street, Saint-Petersburg 197376, Russian Federation; email: sondyn@yandex.ru},
publisher={Hindawi Publishing Corporation},
issn={16879767},
language={English},
abbrev_source_title={Int. J. Pepl.},
document_type={Article},
source={Scopus},
}

A mirror-symmetry motif was discovered in the N-terminus of the influenza virus PB1 protein. Structure of peptide comprised of the corresponding part of PB1 (amino acid residues 6-25) was investigated by circular dichroism and in silico modeling. We found that peptide PB1 (6-25) in solution assumes beta-hairpin conformation. A truncated peptide PB1 (6-13), containing only half of the mirror-symmetry motif, appeared to stabilize the beta-structure of the original peptide and, at high concentrations, was capable of reacting with peptide to form insoluble aggregates in vitro. Ability of PB1 (6-13) peptide to interact with the N-terminal domain of PB1 protein makes it a potential antiviral agent that inhibits PA-PB1 complex formation by affecting PB1 N-terminus structure. © 2013 Vladimir V. Egorov et al.

@ARTICLE{Ilatovskiy2012298,
author={Ilatovskiy, A.V. and Lebedev, D.V. and Filatov, M.V. and Petukhov, M.G. and Isaev-Ivanov, V.V.},
title={Current insights into chromatin structure organization},
journal={Tsitologiya},
year={2012},
volume={54},
number={4},
pages={298-306},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864496725&partnerID=40&md5=fe62933099f2553f60478e65194b7c41},
affiliation={Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; St. Petersburg State Polytechnic University, Russian Federation},
abstract={This review summarizes current insights into organization of chromatin structure at different levels of DNA compaction. Analysis of available experimental data allowed concluding that only nucleosomal level of structural organization was sufficiently investigated, whereas structure of a 30-nm chromatin fiber remains an open issue. The data on the chromatin structure obtained at the level of the nucleus speak in favor of a biphasic fractal organization of chromatin.},
author_keywords={30-nm fiber;  Chromatin;  DNA;  Fractal;  Nucleosome},
correspondence_address1={Ilatovskiy, A.V.; Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; email: andrcyi@omrb.pnpi.spb.ru},
issn={00413771},
coden={TSITA},
pubmed_id={22724366},
language={Russian},
abbrev_source_title={Tsitologiya},
document_type={Review},
source={Scopus},
}

This review summarizes current insights into organization of chromatin structure at different levels of DNA compaction. Analysis of available experimental data allowed concluding that only nucleosomal level of structural organization was sufficiently investigated, whereas structure of a 30-nm chromatin fiber remains an open issue. The data on the chromatin structure obtained at the level of the nucleus speak in favor of a biphasic fractal organization of chromatin.

@ARTICLE{Breuer2012,
author={Breuer, D. and Kotelkin, A. and Ammosova, T. and Kumari, N. and Ivanov, A. and Ilatovskiy, A.V. and Beullens, M. and Roane, P.R. and Bollen, M. and Petukhov, M.G. and Kashanchi, F. and Nekhai, S.},
title={CDK2 Regulates HIV-1 Transcription by Phosphorylation of CDK9 on Serine 90},
journal={Retrovirology},
year={2012},
volume={9},
doi={10.1186/1742-4690-9-94},
art_number={94},
note={cited By 30},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868544558&doi=10.1186%2f1742-4690-9-94&partnerID=40&md5=6fe1ac3061f0269990ff350ce0c0e8b5},
affiliation={Center for Sickle Cell Disease, Department of Medicine, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20001, United States; Department of Microbiology, Howard University, Washington, DC, 20059, United States; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Research and Education Center Biophysics, PNPI RAS and St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium; National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, United States},
abstract={Background: HIV-1 transcription is activated by the viral Tat protein that recruits host positive transcription elongation factor-b (P-TEFb) containing CDK9/cyclin T1 to the HIV-1 promoter. P-TEFb in the cells exists as a lower molecular weight CDK9/cyclin T1 dimer and a high molecular weight complex of 7SK RNA, CDK9/cyclin T1, HEXIM1 dimer and several additional proteins. Our previous studies implicated CDK2 in HIV-1 transcription regulation. We also found that inhibition of CDK2 by iron chelators leads to the inhibition of CDK9 activity, suggesting a functional link between CDK2 and CDK9. Here, we investigate whether CDK2 phosphorylates CDK9 and regulates its activity.Results: The siRNA-mediated knockdown of CDK2 inhibited CDK9 kinase activity and reduced CDK9 phosphorylation. Stable shRNA-mediated CDK2 knockdown inhibited HIV-1 transcription, but also increased the overall level of 7SK RNA. CDK9 contains a motif (90SPYNR94) that is consensus CDK2 phosphorylation site. CDK9 was phosphorylated on Ser90 by CDK2 in vitro. In cultured cells, CDK9 phosphorylation was reduced when Ser90 was mutated to an Ala. Phosphorylation of CDK9 on Ser90 was also detected with phospho-specific antibodies and it was reduced after the knockdown of CDK2. CDK9 expression decreased in the large complex for the CDK9-S90A mutant and was correlated with a reduced activity and an inhibition of HIV-1 transcription. In contrast, the CDK9-S90D mutant showed a slight decrease in CDK9 expression in both the large and small complexes but induced Tat-dependent HIV-1 transcription. Molecular modeling showed that Ser 90 of CDK9 is located on a flexible loop exposed to solvent, suggesting its availability for phosphorylation.Conclusion: Our data indicate that CDK2 phosphorylates CDK9 on Ser 90 and thereby contributes to HIV-1 transcription. The phosphorylation of Ser90 by CDK2 represents a novel mechanism of HIV-1 regulated transcription and provides a new strategy for activation of latent HIV-1 provirus. © 2012 Breuer et al.; licensee BioMed Central Ltd.},
correspondence_address1={Nekhai, S.; Center for Sickle Cell Disease, Department of Medicine, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20001, United States; email: snekhai@howard.edu},
issn={17424690},
pubmed_id={23140174},
language={English},
abbrev_source_title={Retrovirology},
document_type={Article},
source={Scopus},
}

Background: HIV-1 transcription is activated by the viral Tat protein that recruits host positive transcription elongation factor-b (P-TEFb) containing CDK9/cyclin T1 to the HIV-1 promoter. P-TEFb in the cells exists as a lower molecular weight CDK9/cyclin T1 dimer and a high molecular weight complex of 7SK RNA, CDK9/cyclin T1, HEXIM1 dimer and several additional proteins. Our previous studies implicated CDK2 in HIV-1 transcription regulation. We also found that inhibition of CDK2 by iron chelators leads to the inhibition of CDK9 activity, suggesting a functional link between CDK2 and CDK9. Here, we investigate whether CDK2 phosphorylates CDK9 and regulates its activity.Results: The siRNA-mediated knockdown of CDK2 inhibited CDK9 kinase activity and reduced CDK9 phosphorylation. Stable shRNA-mediated CDK2 knockdown inhibited HIV-1 transcription, but also increased the overall level of 7SK RNA. CDK9 contains a motif (90SPYNR94) that is consensus CDK2 phosphorylation site. CDK9 was phosphorylated on Ser90 by CDK2 in vitro. In cultured cells, CDK9 phosphorylation was reduced when Ser90 was mutated to an Ala. Phosphorylation of CDK9 on Ser90 was also detected with phospho-specific antibodies and it was reduced after the knockdown of CDK2. CDK9 expression decreased in the large complex for the CDK9-S90A mutant and was correlated with a reduced activity and an inhibition of HIV-1 transcription. In contrast, the CDK9-S90D mutant showed a slight decrease in CDK9 expression in both the large and small complexes but induced Tat-dependent HIV-1 transcription. Molecular modeling showed that Ser 90 of CDK9 is located on a flexible loop exposed to solvent, suggesting its availability for phosphorylation.Conclusion: Our data indicate that CDK2 phosphorylates CDK9 on Ser 90 and thereby contributes to HIV-1 transcription. The phosphorylation of Ser90 by CDK2 represents a novel mechanism of HIV-1 regulated transcription and provides a new strategy for activation of latent HIV-1 provirus. © 2012 Breuer et al.; licensee BioMed Central Ltd.

The magnetic, transport and structural properties are studied for La 0.83Sr 0.17MnO 3 and La 0.82Sr 0.18CoO 3 single crystals with nearly the same doping and the metallic ground state. Their comparisons have shown that ferromagnetic clusters originate in the paramagnetic matrix below >T C in both samples and exhibit similar properties. This suggests the possible universality of such phenomena in doped mixed-valence oxides of transition metals with the perovskite-type structure. The cluster density increases on cooling and plays an important role on the physical properties of these systems. The differences in cluster evolutions and scenarios of their insulator-metal transitions are related to different magnetic behaviors of the matrixes in these crystals that is mainly due to distinct spin states of the Mn 3 and Co 3 ions. © 2012 Elsevier B.V.

@ARTICLE{Petukhov20121321,
author={Petukhov, M. and Dagkessamanskaja, A. and Bommer, M. and Barrett, T. and Tsaneva, I. and Yakimov, A. and Quéval, R. and Shvetsov, A. and Khodorkovskiy, M. and Käs, E. and Grigoriev, M.},
title={Large-scale conformational flexibility determines the properties of AAA+ TIP49 ATPases},
journal={Structure},
year={2012},
volume={20},
number={8},
pages={1321-1331},
doi={10.1016/j.str.2012.05.012},
note={cited By 22},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864860915&doi=10.1016%2fj.str.2012.05.012&partnerID=40&md5=8472c6907266a0469ae6fe0f520d7095},
affiliation={Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 197376, Russian Federation; Institute for Nanobiotechnologies, Saint Petersburg State Polytechnical University, Saint Petersburg 197376, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, National Research Centre Kurchatov Institute, Gatchina 188300, Russian Federation; Unité Mixte de Recherche 5099, Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, 31000 Toulouse, France; Université Paul Sabatier, Université de Toulouse, Laboratoire de Biologie Moléculaire Eucaryote, 31000 Toulouse, France; Department of Biological Sciences, Institute of Structural Molecular Biology, Crystallography, Birkbeck College, London E11 4HL, United Kingdom; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom},
abstract={The TIP49a and TIP49b proteins belong to the family of AAA+ ATPases and play essential roles in vital processes such as transcription, DNA repair, snoRNP biogenesis, and chromatin remodeling. We report the crystal structure of a TIP49b hexamer and the comparative analysis of large-scale conformational flexibility of TIP49a, TIP49b, and TIP49a/TIP49b complexes using molecular modeling and molecular dynamics simulations in a water environment. Our results establish key principles of domain mobility that affect protein conformation and biochemical properties, including a mechanistic basis for the downregulation of ATPase activity upon protein hexamerization. These approaches, applied to the lik-TIP49b mutant reported to possess enhanced DNA-independent ATPase activity, help explain how a three-amino acid insertion remotely affects the structure and conformational dynamics of the ATP binding and hydrolysis pocket while uncoupling ATP hydrolysis from DNA binding. This might be similar to the effects of conformations adopted by TIP49 heterohexamers. © 2012 Elsevier Ltd.},
funding_details={Ministry of Education and Science of the Russian Federation02.740.11.5223},
funding_details={Ministry of Education and Science of the Russian Federation11.519.11.2002, 16.552.11.7037, 2.2.1.1.4663},
}

The TIP49a and TIP49b proteins belong to the family of AAA+ ATPases and play essential roles in vital processes such as transcription, DNA repair, snoRNP biogenesis, and chromatin remodeling. We report the crystal structure of a TIP49b hexamer and the comparative analysis of large-scale conformational flexibility of TIP49a, TIP49b, and TIP49a/TIP49b complexes using molecular modeling and molecular dynamics simulations in a water environment. Our results establish key principles of domain mobility that affect protein conformation and biochemical properties, including a mechanistic basis for the downregulation of ATPase activity upon protein hexamerization. These approaches, applied to the lik-TIP49b mutant reported to possess enhanced DNA-independent ATPase activity, help explain how a three-amino acid insertion remotely affects the structure and conformational dynamics of the ATP binding and hydrolysis pocket while uncoupling ATP hydrolysis from DNA binding. This might be similar to the effects of conformations adopted by TIP49 heterohexamers. © 2012 Elsevier Ltd.

@ARTICLE{Dobrovolska2012,
author={Dobrovolska, O. and Rychkov, G. and Shumilina, E. and Nerinovski, K. and Schmidt, A. and Shabalin, K. and Yakimov, A. and Dikiy, A.},
title={Structural insights into interaction between mammalian methionine sulfoxide reductase B1 and thioredoxin},
journal={Journal of Biomedicine and Biotechnology},
year={2012},
volume={2012},
doi={10.1155/2012/586539},
art_number={586539},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859726670&doi=10.1155%2f2012%2f586539&partnerID=40&md5=d880f44788e267595adc09bd0e60cd97},
affiliation={Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Biophysics Department, St. Petersburg State Polytechnical University, St. Petersburg 195251, Russian Federation; Center of Nanobiotechnology, St. Petersburg State Polytechnical University, St. Petersburg 195251, Russian Federation; Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, RAS, Gatchina 188300, Russian Federation; Department of Quantum Magnetic Phenomena, St. Petersburg State University, St. Petersburg 198504, Russian Federation},
abstract={Maintenance of the cellular redox balance has vital importance for correcting organism functioning. Methionine sulfoxide reductases (Msrs) are among the key members of the cellular antioxidant defence system. To work properly, methionine sulfoxide reductases need to be reduced by their biological partner, thioredoxin (Trx). This process, according to the available kinetic data, represents the slowest step in the Msrs catalytic cycle. In the present paper, we investigated structural aspects of the intermolecular complex formation between mammalian MsrB1 and Trx. NMR spectroscopy and biocomputing were the two mostly used through the research approaches. The formation of NMR detectable MsrB1/Trx complex was monitored and studied in attempt to understand MsrB1 reduction mechanism. Using NMR data, molecular mechanics, protein docking, and molecular dynamics simulations, it was found that intermediate MsrB1/Trx complex is stabilized by interprotein -layer. The complex formation accompanied by distortion of disulfide bond within MsrB1 facilitates the reduction of oxidized MsrB1 as it is evidenced by the obtained data. Copyright © 2012 Olena Dobrovolska et al.},
correspondence_address1={Dikiy, A.; Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway; email: alex.dikiy@biotech.ntnu.no},
issn={11107243},
coden={JBBOA},
pubmed_id={22505815},
language={English},
abbrev_source_title={J. Biomed. Biotechnol.},
document_type={Article},
source={Scopus},
}

Maintenance of the cellular redox balance has vital importance for correcting organism functioning. Methionine sulfoxide reductases (Msrs) are among the key members of the cellular antioxidant defence system. To work properly, methionine sulfoxide reductases need to be reduced by their biological partner, thioredoxin (Trx). This process, according to the available kinetic data, represents the slowest step in the Msrs catalytic cycle. In the present paper, we investigated structural aspects of the intermolecular complex formation between mammalian MsrB1 and Trx. NMR spectroscopy and biocomputing were the two mostly used through the research approaches. The formation of NMR detectable MsrB1/Trx complex was monitored and studied in attempt to understand MsrB1 reduction mechanism. Using NMR data, molecular mechanics, protein docking, and molecular dynamics simulations, it was found that intermediate MsrB1/Trx complex is stabilized by interprotein -layer. The complex formation accompanied by distortion of disulfide bond within MsrB1 facilitates the reduction of oxidized MsrB1 as it is evidenced by the obtained data. Copyright © 2012 Olena Dobrovolska et al.

@CONFERENCE{Garmay2012,
author={Garmay, Yu. and Shvetsov, A. and Karelov, D. and Lebedev, D. and Radulescu, A. and Petukhov, M. and Isaev-Ivanov, V.},
title={Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament},
journal={Journal of Physics: Conference Series},
year={2012},
volume={340},
doi={10.1088/1742-6596/340/1/012094},
art_number={012094},
note={cited By 5; Conference of 5th European Conference on Neutron Scattering, ECNS 2011 ; Conference Date: 17 July 2011 Through 21 July 2011;  Conference Code:88897},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858591060&doi=10.1088%2f1742-6596%2f340%2f1%2f012094&partnerID=40&md5=2cb59944a3da46d332057e808a6cdb78},
affiliation={Petersburg Nuclear Physics Institute, Russian Federation; Jülich Center for Neutron Science, Germany; Research and Education Centre Biophysics, St. Petersburg State Polytecnic University, St. Petersburg, Russian Federation},
abstract={Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.},
correspondence_address1={Garmay, Yu.; Petersburg Nuclear Physics InstituteRussian Federation},
sponsors={},
publisher={Institute of Physics Publishing},
address={Prague},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

@CONFERENCE{Ilatovskiy2012,
author={Ilatovskiy, A.V. and Lebedev, D.V. and Filatov, M.V. and Petukhov, M.G. and Isaev-Ivanov, V.V.},
title={SANS spectra of the fractal supernucleosomal chromatin structure models},
journal={Journal of Physics: Conference Series},
year={2012},
volume={351},
number={1},
doi={10.1088/1742-6596/351/1/012007},
art_number={012007},
note={cited By 7; Conference of 2nd International Workshop on SANS-YuMO User Meeting at the Start-up of Scientific Experiments on the IBR-2M Reactor: Devoted to the 75th Anniversary of Yu M Ostanevich's Birth ; Conference Date: 27 May 2011 Through 30 May 2011;  Conference Code:89603},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860655272&doi=10.1088%2f1742-6596%2f351%2f1%2f012007&partnerID=40&md5=4cb28476bafca2cc34da1a137dfb05ea},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; Research and Education Center Biophysics, PNPI RAS, St. Petersburg State Polytechnic University, St. Petersburg, Russian Federation},
abstract={The eukaryotic genome consists of chromatin - a nucleoprotein complex with hierarchical architecture based on nucleosomes, the organization of higher-order chromatin structures still remains unknown. Available experimental data, including SANS spectra we had obtained for whole nuclei, suggested fractal nature of chromatin. Previously we had built random-walk supernucleosomal models (up to 106 nucleosomes) to interpret our SANS spectra. Here we report a new method to build fractal supernucleosomal structure of a given fractal dimension or two different dimensions. Agreement between calculated and experimental SANS spectra was significantly improved, especially for model with two fractal dimensions - 3 and 2. © Published under licence by IOP Publishing Ltd.},
correspondence_address1={Ilatovskiy, A.V.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; email: andreyi@omrb.pnpi.spb.ru},
sponsors={Comenius University in Bratislava; Horia Hulubei Natl. Inst. Phys. Nucl. Eng. (IFIN HH); Institute of Macromolecular Chemistry AS CR; Jt. Inst. Nucl. Res., Frank Lab. Neutron Phys.},
publisher={Institute of Physics Publishing},
address={Dubna},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

The eukaryotic genome consists of chromatin - a nucleoprotein complex with hierarchical architecture based on nucleosomes, the organization of higher-order chromatin structures still remains unknown. Available experimental data, including SANS spectra we had obtained for whole nuclei, suggested fractal nature of chromatin. Previously we had built random-walk supernucleosomal models (up to 106 nucleosomes) to interpret our SANS spectra. Here we report a new method to build fractal supernucleosomal structure of a given fractal dimension or two different dimensions. Agreement between calculated and experimental SANS spectra was significantly improved, especially for model with two fractal dimensions - 3 and 2. © Published under licence by IOP Publishing Ltd.

@ARTICLE{Lazuta2012679,
author={Lazuta, A.V. and Ryzhov, V.A. and Kurbakov, A.I. and Khavronin, V.P. and Molkanov, P.L. and Mukovskii, Ya.M. and Pestun, A.E. and Privezentsev, R.V.},
title={Nucleation and development of clustered state in La1-xSr xCoO3 and La1-xCaxCoO3 single crystals at x = 0.15},
journal={Solid State Phenomena},
year={2012},
volume={190},
pages={679-682},
doi={10.4028/www.scientific.net/SSP.190.679},
note={cited By 2; Conference of 5th Moscow International Symposium on Magnetism, MISM 2011 ; Conference Date: 21 August 2011 Through 25 August 2011;  Conference Code:91339},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864183368&doi=10.4028%2fwww.scientific.net%2fSSP.190.679&partnerID=40&md5=ab04450c02005ef215e39f2ae601e48a},
affiliation={Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; Moscow Steel and Alloys Institute, Leninskii prosp. 4, Moscow 117936, Russian Federation},
abstract={Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the La1-xSrxCoO 3 and La1-xCaxCoO3 at x = 0.15 single crystals. It is founf that these compounds are insulators and exhibit the rhombohedral R3-c space group. According to the magnetic measurements, the development of the ferromagnetic (F) clustered state proceeds into three stages. On cooling, during the first stage, the F clusters nucleate at the preferential sites that are likely produced by variation in oxygen and doping stoichiometry. The second stage is characterized by sharp increasing the concetraion of the isolated F clusters on cooling. This is the process of the homogeneous nucleation. A coalescence of the isolated F clusters into some large-scale complexes containig some ammount of the domains is associated with the third stage. Note that it is the typical behavior observed at a first order phase transition. The data allow one to determined reliably the temperature boundaries of the stages. © (2012) Trans Tech Publications.},
author_keywords={Clustered state;  Cobaltites;  Phase separation;  Phase transitions},
correspondence_address1={Lazuta, A.V.; Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; email: alexandr@VL9467.spb.edu},
sponsors={147th Committee of Japanese Society for Promotion of Science; Dynasty Foundation; Moscow State University; NT-MDT Nanotechnology; Russ. Acad. Sci. Kapitza Inst. Phys. Probl.; Russian Foundation for Basic Research},
publisher={Trans Tech Publications Ltd},
address={Moscow},
issn={10120394},
isbn={9783037854365},
coden={DDBPE},
language={English},
abbrev_source_title={Diffus Def Data Pt B},
document_type={Conference Paper},
source={Scopus},
}

Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the La1-xSrxCoO 3 and La1-xCaxCoO3 at x = 0.15 single crystals. It is founf that these compounds are insulators and exhibit the rhombohedral R3-c space group. According to the magnetic measurements, the development of the ferromagnetic (F) clustered state proceeds into three stages. On cooling, during the first stage, the F clusters nucleate at the preferential sites that are likely produced by variation in oxygen and doping stoichiometry. The second stage is characterized by sharp increasing the concetraion of the isolated F clusters on cooling. This is the process of the homogeneous nucleation. A coalescence of the isolated F clusters into some large-scale complexes containig some ammount of the domains is associated with the third stage. Note that it is the typical behavior observed at a first order phase transition. The data allow one to determined reliably the temperature boundaries of the stages. © (2012) Trans Tech Publications.

@CONFERENCE{Klotchenko2012,
author={Klotchenko, S.A. and Vasin, A.V. and Sandybaev, N.T. and Plotnikova, M.A. and Chervyakova, O.V. and Smirnova, E.A. and Kushnareva, E.V. and Strochkov, V.M. and Taylakova, E.T. and Egorov, V.V. and Koshemetov, J.K. and Kiselev, O.I. and Sansyzbay, A.R.},
title={Oligonucleotide microarray for subtyping of influenza A viruses},
journal={Journal of Physics: Conference Series},
year={2012},
volume={345},
number={1},
doi={10.1088/1742-6596/345/1/012041},
art_number={012041},
note={cited By 1; Conference of 4th Nanotechnology International Forum, RUSNANOTECH 2011 ; Conference Date: 26 October 2011 Through 28 October 2011;  Conference Code:88965},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858210160&doi=10.1088%2f1742-6596%2f345%2f1%2f012041&partnerID=40&md5=1538ff405c4201f6907d703d3c16df94},
affiliation={Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg, Russian Federation; Research Research Institute for Biological Safety Problems, RK NBC/SC ME and S RK, Gvardeiskiy, Kazakhstan},
abstract={Influenza is one of the most widespread respiratory viral diseases, infecting humans, horses, pigs, poultry and some other animal populations. Influenza A viruses (IAV) are classified into subtypes on the basis of the surface hemagglutinin (H1 to H16) and neuraminidase (N1 to N9) glycoproteins. The correct determination of IAV subtype is necessary for clinical and epidemiological studies. In this article we propose an oligonucleotide microarray for subtyping of IAV using universal one-step multisegment RT-PCR fluorescent labeling of viral gene segments. It showed to be an advanced approach for fast detection and identification of IAV.},
correspondence_address1={Klotchenko, S.A.; Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg, Russian Federation},
sponsors={},
publisher={Institute of Physics Publishing},
address={Moscow},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

Influenza is one of the most widespread respiratory viral diseases, infecting humans, horses, pigs, poultry and some other animal populations. Influenza A viruses (IAV) are classified into subtypes on the basis of the surface hemagglutinin (H1 to H16) and neuraminidase (N1 to N9) glycoproteins. The correct determination of IAV subtype is necessary for clinical and epidemiological studies. In this article we propose an oligonucleotide microarray for subtyping of IAV using universal one-step multisegment RT-PCR fluorescent labeling of viral gene segments. It showed to be an advanced approach for fast detection and identification of IAV.

@ARTICLE{Ilatovskiy2011,
author={Ilatovskiy, A.V. and Lebedev, D.V. and Filatov, M.V. and Grigoriev, M. and Petukhov, M.G. and Isaev-Ivanov, V.V.},
title={Modeling and small-angle neutron scattering spectra of chromatin supernucleosomal structures at genome scale},
journal={Journal of Applied Physics},
year={2011},
volume={110},
number={10},
doi={10.1063/1.3661987},
art_number={102217},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-82555167434&doi=10.1063%2f1.3661987&partnerID=40&md5=8a4868aeeffdd6637dac55d1e4fa84a9},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; Research and Education Center Biophysics, PNPI RAS, St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; Laboratoire Biologie Moléculaire Eukaryote, CNRS-Université Paul-Sabathier, Toulouse, France},
abstract={Eukaryotic genome is a highly compacted nucleoprotein complex organized in a hierarchical structure based on nucleosomes. Detailed organization of this structure remains unknown. In the present work we developed algorithms for geometry modeling of the supernucleosomal chromatin structure and for computing distance distribution functions and small-angle neutron scattering (SANS) spectra of the genome-scale (∼106 nucleosomes) chromatin structure at residue resolution. Our physical nucleosome model was based on the mononucleosome crystal structure. A nucleosome was assumed to be rigid within a local coordinate system. Interface parameters between nucleosomes can be set for each nucleosome independently. Pair distance distributions were computed with Monte Carlo simulation. SANS spectra were calculated with Fourier transformation of weighted distance distribution; the concentration of heavy water in solvent and probability of H/D exchange were taken into account. Two main modes of supernucleosomal structure generation were used. In a free generation mode all interface parameters were chosen randomly, whereas nucleosome self-intersections were not allowed. The second generation mode (generation in volume) enabled spherical or cubical wall restrictions. It was shown that calculated SANS spectra for a number of our models were in general agreement with available experimental data. © 2011 American Institute of Physics.},
correspondence_address1={Ilatovskiy, A.V.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russian Federation; email: andreyi@omrb.pnpi.spb.ru},
issn={00218979},
coden={JAPIA},
language={English},
abbrev_source_title={J Appl Phys},
document_type={Conference Paper},
source={Scopus},
}

Eukaryotic genome is a highly compacted nucleoprotein complex organized in a hierarchical structure based on nucleosomes. Detailed organization of this structure remains unknown. In the present work we developed algorithms for geometry modeling of the supernucleosomal chromatin structure and for computing distance distribution functions and small-angle neutron scattering (SANS) spectra of the genome-scale (∼106 nucleosomes) chromatin structure at residue resolution. Our physical nucleosome model was based on the mononucleosome crystal structure. A nucleosome was assumed to be rigid within a local coordinate system. Interface parameters between nucleosomes can be set for each nucleosome independently. Pair distance distributions were computed with Monte Carlo simulation. SANS spectra were calculated with Fourier transformation of weighted distance distribution; the concentration of heavy water in solvent and probability of H/D exchange were taken into account. Two main modes of supernucleosomal structure generation were used. In a free generation mode all interface parameters were chosen randomly, whereas nucleosome self-intersections were not allowed. The second generation mode (generation in volume) enabled spherical or cubical wall restrictions. It was shown that calculated SANS spectra for a number of our models were in general agreement with available experimental data. © 2011 American Institute of Physics.

The possibility of obtaining recombinant fibrillogenic fusion proteins such as transthyretin (TTR) and β2-microglobulin (β2M) with a superfolder green fluorescent protein (sfGFP) was studied. According to the literature data, sfGFP is resistant to denaturating influences, does not aggregate during renaturation, possesses improved kinetic characteristics of folding, and folds well when fused to different polypeptides. The corresponding DNA constructs for expression in Escherichia coli were created. It could be shown that during expression of these constructs in E. coli, soluble forms of the fusion proteins are synthesized. Efficient isolation of the fusion proteins was performed with the help of nickel-affinity chromatography. For this purpose a polyhistidine sequence (6-His-tag) was incorporated into the C-terminus of the sfGFP. We could show that the purified fusion proteins contained full-size sequences of the most amyloidogenic TTR variant, TTR(L55P) and β2M, and also sfGFP possessing fluorescent properties. In the course of fibrillogenesis both fusion proteins demonstrated their ability to form fibrils that were clearly detectable by atomic force microscopy. Furthermore, with the help of confocal microscopy we were able to reveal structures (exhibiting fluorescence) that are formed during fibrillogenesis.Thus, the use of sfGFP has made it possible to avoid formation of inclusion bodies (IB) during the synthesis of recombinant fusion proteins and to obtain soluble forms of TTR(L55P) and β2M that are suitable for further studies. Copyright © Taylor & Francis Group, LLC.

@ARTICLE{Malkov2011381,
author={Malkov, V.M. and Kiselev, I.A. and Orlov, A.E. and Shatalov, I.V.},
title={A pressure recovery system for chemical oxygen-iodine laser based on an active diffuser},
journal={Thermophysics and Aeromechanics},
year={2011},
volume={18},
number={3},
pages={381-395},
doi={10.1134/S0869864311030048},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856715277&doi=10.1134%2fS0869864311030048&partnerID=40&md5=6ccbc92f565397e8c604656e933c7356},
affiliation={Advent Scientific Production Association, St. Petersburg, Russian Federation; Laser Systems Ltd., St. Petersburg, Russian Federation},
abstract={An open-type pressure recovery system (PRS) for chemical oxygen-iodine laser was designed and fabricated. As a first stage, an active diffuser was used in which the ejecting gas supply was organized through nozzles disposed around the channel periphery. The second stage was a supersonic ejector. Numerical simulation data for the viscous turbulent flow with heat release through the diffuser gas-dynamic channel, and also data obtained by testing the active diffuser in operation on a model facility equipped with a vacuum chamber, are reported. The obtained data were used to develop a full-scale setup with exhaust of laser gas into the atmosphere; this has allowed us to optimize the performance characteristics of the setup and substantially improve its mass-dimensional characteristics. Special attention was paid to parameter matching and synchronization of laser start with the operation of PRS components. © 2011 Pleiades Publishing, Ltd.},
author_keywords={diffuser;  ejector;  experiment;  numerical simulation;  pressure recovery system;  supersonic chemical laser},
correspondence_address1={Orlov, A. E.; Laser Systems Ltd., St. Petersburg, Russian Federation; email: orlov@lsystems.ru},
issn={08698643},
language={English},
abbrev_source_title={Thermophys. Aeromech.},
document_type={Article},
source={Scopus},
}

An open-type pressure recovery system (PRS) for chemical oxygen-iodine laser was designed and fabricated. As a first stage, an active diffuser was used in which the ejecting gas supply was organized through nozzles disposed around the channel periphery. The second stage was a supersonic ejector. Numerical simulation data for the viscous turbulent flow with heat release through the diffuser gas-dynamic channel, and also data obtained by testing the active diffuser in operation on a model facility equipped with a vacuum chamber, are reported. The obtained data were used to develop a full-scale setup with exhaust of laser gas into the atmosphere; this has allowed us to optimize the performance characteristics of the setup and substantially improve its mass-dimensional characteristics. Special attention was paid to parameter matching and synchronization of laser start with the operation of PRS components. © 2011 Pleiades Publishing, Ltd.

The transport properties, ac susceptibility χ, and EPR spectra have been studied for the insulator polycrystalline manganite Pr2/3Ca1/3MnO3 undergoing the orbital (O) and charge (C) orderings below TCO   250 K that lead to antiferromagnetic (AF) ordering below TN ≈ 155 K. Above TC   110 K, the χ′(T) dependence indicates that the sample contains a phase undergoing a second-order transition from the paramagnetic to ferromagnetic state. In the vicinity of TC, the colossal magnetoresistance effect is observed. The EPR spectrum characteristics are sensitive to the development of the O/C and AF orderings, and they show peculiarities at TCO and TN. Between TCO and TN, the temperature dependence of the g factor exhibits a characteristic point that can be related to the appearance of the electric polarization revealed in manganites of this class. © 2011 Pleiades Publishing, Ltd.

@ARTICLE{Dudkina2011546,
author={Dudkina, A.V. and Shvetsov, A.V. and Bakhlanova, I.V. and Baǐtin, D.M.},
title={[Changing of filamentation dynamics of RecA protein, induced by D112R amino acid substitution or ATP to dATP replacement, results in filament steadiness TO THE RecX protein action].},
journal={Molekuliarnaia biologiia},
year={2011},
volume={45},
number={3},
pages={546-553},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052357874&partnerID=40&md5=5664bbb02e2093d8985e4c4b873aaca5},
abstract={It is known that RecX is a negative regulator of RecA protein. We found that the mutant RecA D112R protein exhibits increased resistance to RecX protein comparatively to wild-type RecA protein in vitro and in vivo. Using molecular modeling we showed, that amino acid located in position 112 can not approach RecX closer than 25-28 angstroms. Thus, direct contact between amino acid and RecX is impossible. RecA D112R protein more actively competes with SSB protein for the binding sites on ssDNA and, therefore, differs from the wild-type RecA protein by dynamics of filamentation on ssDNA. On the other hand, after the replacement of ATP by dATP, the wild-type RecA protein, changing the dynamics of filamentation on ssDNA, also becomes more resistant to RecX. Based on these data it is concluded that the dynamics of filamentation has a great, if not dominant role in the stability of RecA filament to RecX relative to the role of RecA-RecX protein-protein interactions discussed earlier. We also propose an improved model of regulation of RecA by RecX protein, where RecA filament elongation along ssDNA is blocked by RecX protein on the ssDNA region, located outside the filament.},
correspondence_address1={Dudkina, A.V.},
issn={00268984},
pubmed_id={21790018},
language={Russian},
abbrev_source_title={Mol. Biol. (Mosk.)},
document_type={Article},
source={Scopus},
}

It is known that RecX is a negative regulator of RecA protein. We found that the mutant RecA D112R protein exhibits increased resistance to RecX protein comparatively to wild-type RecA protein in vitro and in vivo. Using molecular modeling we showed, that amino acid located in position 112 can not approach RecX closer than 25-28 angstroms. Thus, direct contact between amino acid and RecX is impossible. RecA D112R protein more actively competes with SSB protein for the binding sites on ssDNA and, therefore, differs from the wild-type RecA protein by dynamics of filamentation on ssDNA. On the other hand, after the replacement of ATP by dATP, the wild-type RecA protein, changing the dynamics of filamentation on ssDNA, also becomes more resistant to RecX. Based on these data it is concluded that the dynamics of filamentation has a great, if not dominant role in the stability of RecA filament to RecX relative to the role of RecA-RecX protein-protein interactions discussed earlier. We also propose an improved model of regulation of RecA by RecX protein, where RecA filament elongation along ssDNA is blocked by RecX protein on the ssDNA region, located outside the filament.

@ARTICLE{Alekseev20111292,
author={Alekseev, K.O. and Luginya, V.S. and Kiselev, I.A.},
title={Typical features of measurement of the flow rate of biological fluid in hemodialysis machines},
journal={Measurement Techniques},
year={2011},
volume={53},
number={11},
pages={1292-1298},
doi={10.1007/s11018-011-9656-5},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79954606102&doi=10.1007%2fs11018-011-9656-5&partnerID=40&md5=d3688f7ca2d6149a3cb9e37329a50b1e},
affiliation={Laser Systems Company, St. Petersburg, Russian Federation},
abstract={We consider the typical features of application of the laser Doppler method for determination of blood flow rate in hemodialysis machines. We have analyzed the scattering characteristics of blood and blood flow in the blood tubing. We have obtained estimates of the basic parameters of the Doppler signal and we present the optical layout of the flowmeter. © 2011 Springer Science+Business Media, Inc.},
author_keywords={biological fluid;  flow rate;  flowmeter;  hemodialysis;  laser diagnostics;  optical Doppler effect;  radiation scattering},
}

We consider the typical features of application of the laser Doppler method for determination of blood flow rate in hemodialysis machines. We have analyzed the scattering characteristics of blood and blood flow in the blood tubing. We have obtained estimates of the basic parameters of the Doppler signal and we present the optical layout of the flowmeter. © 2011 Springer Science+Business Media, Inc.

We present the results a study of structure by neutron diffraction and data on the magnetic prop- erties (linear and nonlinear (second and third order) susceptibilities) of polycrystalline La0.88MnO2.95. This compound exhibits an insulator-metal (IM) phase transition at TIM̃253 K (above the Curie temperature, TC̃244 K) and reveals colossal magnetoresistance. The crystal structure is found to be rhombohedral, and the space group is R3c. Analysis of magnetic properties shows that at T*̃258 K > TC, isolated paramagnetic clusters occur in the paramagnetic matrix; their concentration increases upon cooling. We observed no noticeable differences between the temperature evolution of the clustered state of this manganite with its insulator-metal transition and in the insulator La0.88MnO2.91. Possible scenarios of the paramagnet-ferro- magnet and I-M transitions in a self-organized clustered structure are discussed. © Allerton Press, Inc., 2011.

@CONFERENCE{Egorov2011,
author={Egorov, V.V. and Garmay, Y.P. and Shaldzhyan, A.A. and Lebedev, D.V. and Vasin, A.V. and Grudinina, N.A. and Kiselev, O.I.},
title={Modeling of self-organization of two-dimensional ordered structures},
journal={Journal of Physics: Conference Series},
year={2011},
volume={291},
number={1},
doi={10.1088/1742-6596/291/1/012005},
art_number={012005},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79959399030&doi=10.1088%2f1742-6596%2f291%2f1%2f012005&partnerID=40&md5=43c4d7b268b8f96c5c81742edd1d1e2b},
affiliation={Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, Prof. Popova st. 15/17, St-Petersburg, Russian Federation; Department of Molecular, Radiation Biophysics Petersburg Nuclear Physics Institute, Russian Academy of Science, Orlova Roscha, Gatchina, Leningrad Region, Russian Federation; Institute of Experimental Medicine, North-Western Branch, Russian Academy of Medical Science, Akademika Pavlova st., 12, St-Petersburg, Russian Federation},
abstract={The problem of the search of biostructures capable to self-organization is quite urgent considering the prospects of application of nanostructured biomaterials as components of composite materials in transplantology and optics as well as "scaffolds" for the synthesis of nanostructured materials based on inorganic particles. The given study focuses on modeling of the growth of structures using the cellular automata with a set of states of the two values (0 and 1), with the value corresponding to the state is determined by the contribution of "the closest neighbor" (by the probability of induction of the state of the nextgeneration in the direction of the interaction) and the geometry of the field isdetermined by the vector of the direction of the particle and the direction of the interaction. © Published under licence by IOP Publishing Ltd.},
correspondence_address1={Egorov, V. V.; Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, Prof. Popova st. 15/17, St-Petersburg, Russian Federation; email: toizeg@gmail.com},
publisher={Institute of Physics Publishing},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

The problem of the search of biostructures capable to self-organization is quite urgent considering the prospects of application of nanostructured biomaterials as components of composite materials in transplantology and optics as well as "scaffolds" for the synthesis of nanostructured materials based on inorganic particles. The given study focuses on modeling of the growth of structures using the cellular automata with a set of states of the two values (0 and 1), with the value corresponding to the state is determined by the contribution of "the closest neighbor" (by the probability of induction of the state of the nextgeneration in the direction of the interaction) and the geometry of the field isdetermined by the vector of the direction of the particle and the direction of the interaction. © Published under licence by IOP Publishing Ltd.

Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription. © 2010 Springer Science+Business Media, LLC.

@ARTICLE{Ryzhov2011485,
author={Ryzhov, V.A. and Lazuta, A.V. and Smirnov, O.P. and Khavronin, V.P. and Molkanov, P.L. and Mukovskii, Ya.M. and Chichkov, V.I.},
title={Behavior of clustered state above the curie temperature in La 0.78Ca0.22MnO3 single crystal},
journal={Solid State Phenomena},
year={2011},
volume={168-169},
pages={485-488},
doi={10.4028/www.scientific.net/SSP.168-169.485},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951915871&doi=10.4028%2fwww.scientific.net%2fSSP.168-169.485&partnerID=40&md5=daafd42ad9c95d35cf2d50723271d25e},
affiliation={Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; State Technological University, Moscow Steel and Alloys Institute (MISIS), Moscow, 119049, Russian Federation},
abstract={The results of structural neutron diffraction study and the data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the La0.88Ca 0.22MnO3 single crystal. This compound has the orthorhombic Pbnm space group, showing no structural transformations between 90 K and 300 K. It exhibits the paramagnetferromagnet (P-F) (TC ≈ 186 K) and insulator - metal (I-M) (TIM ≈ 201 K > TC) phase transitions. The measurements of the second harmonic of the magnetization in the parallel ac and dc H magnetic fields, M2(H,T), showed that below T* ≈ 252 K, the FM clusters appear in the PI matrix undergoing the second-order transition. The concentration of the FM clusters increases with cooling so that it is above the percolative threshold value below T IM, and the sample exhibits metallic behavior. The M2(H) hysteresis loops possess a high sensitivity to the I-M transition. Their usual central symmetry is broken in the vicinity of TIM and the loops become asymmetric. This effect is attributed to cluster link nucleation-and-growth process.},
author_keywords={Magnetization dynamics;  Magnetization reversal mechanisms;  Phase transitions},
correspondence_address1={Ryzhov, V. A.; Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; email: ryzhov@omrb.pnpi.spb.ru},
publisher={Trans Tech Publications Ltd},
issn={10120394},
isbn={9783037850213},
coden={DDBPE},
language={English},
abbrev_source_title={Diffus Def Data Pt B},
document_type={Conference Paper},
source={Scopus},
}

The results of structural neutron diffraction study and the data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the La0.88Ca 0.22MnO3 single crystal. This compound has the orthorhombic Pbnm space group, showing no structural transformations between 90 K and 300 K. It exhibits the paramagnetferromagnet (P-F) (TC ≈ 186 K) and insulator - metal (I-M) (TIM ≈ 201 K > TC) phase transitions. The measurements of the second harmonic of the magnetization in the parallel ac and dc H magnetic fields, M2(H,T), showed that below T* ≈ 252 K, the FM clusters appear in the PI matrix undergoing the second-order transition. The concentration of the FM clusters increases with cooling so that it is above the percolative threshold value below T IM, and the sample exhibits metallic behavior. The M2(H) hysteresis loops possess a high sensitivity to the I-M transition. Their usual central symmetry is broken in the vicinity of TIM and the loops become asymmetric. This effect is attributed to cluster link nucleation-and-growth process.

@ARTICLE{Lazuta2011457,
author={Lazuta, A.V. and Ryzhov, V.A. and Kurbakov, A.I. and Khavronin, V.P. and Molkanov, P.L. and Mukovskii, Ya.M. and Pestun, A.E. and Privezentsev, R.V.},
title={Inhomogeneous magnetic state above the Curie temperature of the doped cobaltite La1-xSrxCoO3},
journal={Solid State Phenomena},
year={2011},
volume={168-169},
pages={457-460},
doi={10.4028/www.scientific.net/SSP.168-169.457},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951903073&doi=10.4028%2fwww.scientific.net%2fSSP.168-169.457&partnerID=40&md5=a5559a3ece06727f18b24d6e079e4eae},
affiliation={Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; State Technological University, Moscow Steel and Alloys Institute (MISIS), Moscow 119049, Russian Federation},
abstract={Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are reported for the La1-xSrxCoO 3 (x = 0.18 and 0.2) polycrystals. The data on the linear and third-order susceptibilities show indications of a long - range ferromagnetic ordering with the Curie temperature (TC) about 180 K. Measurements of the second harmonic of the magnetization in the parallel ac and steady (H) magnetic fields (M2(H,T)) reveal the appearance of ferromagnetic clusters in a paramagnetic matrix below some temperature (T*) above T C. The characteristics of this clustered state and the stages of its temperature evolution are reliably determined since the non-ferromagnetic matrix affects weakly this state. It is found that a spontaneous nucleation of the ferromagnetic clusters occurs below T*, and their concentration increases sharply on cooling. Upon further decreasing temperature, the isolated clusters coalesce, leading to a percolative - type origination of a ferromagnetism. The M2(H,T) response of isolated clusters and its T-variation, including the onset of the coalescence, are very close to those found in the doped manganites, which supports an assumption on a common origin of the clustered state in these compounds.},
author_keywords={Clustered state;  Cobaltites;  Phase separation;  Phase transitions},
correspondence_address1={Lazuta, A. V.; Petersburg Nuclear Physics Institute, RAS, Gatchina, St.Petersburg, 188300, Russian Federation; email: Alexandr@VL9467.spb.edu},
publisher={Trans Tech Publications Ltd},
issn={10120394},
isbn={9783037850213},
coden={DDBPE},
language={English},
abbrev_source_title={Diffus Def Data Pt B},
document_type={Conference Paper},
source={Scopus},
}

Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are reported for the La1-xSrxCoO 3 (x = 0.18 and 0.2) polycrystals. The data on the linear and third-order susceptibilities show indications of a long - range ferromagnetic ordering with the Curie temperature (TC) about 180 K. Measurements of the second harmonic of the magnetization in the parallel ac and steady (H) magnetic fields (M2(H,T)) reveal the appearance of ferromagnetic clusters in a paramagnetic matrix below some temperature (T*) above T C. The characteristics of this clustered state and the stages of its temperature evolution are reliably determined since the non-ferromagnetic matrix affects weakly this state. It is found that a spontaneous nucleation of the ferromagnetic clusters occurs below T*, and their concentration increases sharply on cooling. Upon further decreasing temperature, the isolated clusters coalesce, leading to a percolative - type origination of a ferromagnetism. The M2(H,T) response of isolated clusters and its T-variation, including the onset of the coalescence, are very close to those found in the doped manganites, which supports an assumption on a common origin of the clustered state in these compounds.

@CONFERENCE{Vasin2011,
author={Vasin, A.V. and Sandybaev, N.T. and Plotnikova, M.A. and Klotchenko, S.A. and Chervyakova, O.V. and Strochkov, V.M. and Taylakova, E.T. and Elpaeva, E.A. and Komissarov, A.B. and Egorov, V.V. and Koshemetov, J.K. and Kiselev, O.I. and Mamadaliev, S.M.},
title={Multisegment one-step RT-PCR fluorescent labeling of influenza A virus genome for use in diagnostic microarray applications},
journal={Journal of Physics: Conference Series},
year={2011},
volume={291},
number={1},
doi={10.1088/1742-6596/291/1/012006},
art_number={012006},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79959409260&doi=10.1088%2f1742-6596%2f291%2f1%2f012006&partnerID=40&md5=f611236222dfac466be1bc100121b414},
affiliation={Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg, Russian Federation; Research Institute for Biological Safety Problems, RK NBC/SC MEandS RK, Gvardeiskiy, Kazakhstan},
abstract={Microarray technology is one of the most challenging methods of influenza A virus subtyping, which is based on the antigenic properties of viral surface glycoproteins - hemagglutinin and neuraminidase. On the example of biochip for detection of influenza A/H5N1 virus we showed the possibility of using multisegment RTPCR method for amplification of fluorescently labeled cDNA of all possible influenza A virus subtypes with a single pair of primers in influenza diagnostic microarrays. © Published under licence by IOP Publishing Ltd.},
correspondence_address1={Vasin, A. V.; Research Institute of Influenza, Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg, Russian Federation; email: vasin@influenza.spb.ru},
publisher={Institute of Physics Publishing},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

Microarray technology is one of the most challenging methods of influenza A virus subtyping, which is based on the antigenic properties of viral surface glycoproteins - hemagglutinin and neuraminidase. On the example of biochip for detection of influenza A/H5N1 virus we showed the possibility of using multisegment RTPCR method for amplification of fluorescently labeled cDNA of all possible influenza A virus subtypes with a single pair of primers in influenza diagnostic microarrays. © Published under licence by IOP Publishing Ltd.

@CONFERENCE{Malkov2010,
author={Malkov, V.M. and Kiselev, I.A. and Orlov, A.E. and Shatalov, I.V.},
title={Improving of flow optical quality in COIL resonator cavity as result of operation of pressure recovery system developed on base of active diffuser},
journal={Proceedings of SPIE - The International Society for Optical Engineering},
year={2010},
volume={7751},
doi={10.1117/12.879797},
art_number={77510Q},
note={cited By 1; Conference of 18th International Symposium on Gas Flow, Chemical Lasers, and High-Power Lasers ; Conference Date: 30 August 2010 Through 3 September 2010;  Conference Code:84460},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953237852&doi=10.1117%2f12.879797&partnerID=40&md5=5bc37ec070bc6b632d1a11068ddbc45a},
affiliation={Laser Systems Ltd., St.-Petersburg, Russian Federation},
abstract={Active diffuser- AD has been developed by blowing in the high pressure gas from small scale nozzles along the laser chamber walls. Blowing has stabilized boundary layers, decreased its thickness and prevented its separation. So AD operating has stabilized the gas flow parameters in resonator and localized the zone of slow down of laser flow - pseudoshock - after laser chamber. So regular shock - wave structures (X-type shocks) that could degrade the flow optical quality don't appear in resonator. The use of AD allows developing PRS on base of single-stage ejector with high ejection coefficient (usually ground -based COIL PRS consist from passive diffuser and two-stage ejector and has low ejection coefficient). © 2010 Copyright SPIE - The International Society for Optical Engineering.},
author_keywords={diffuser;  nozzle bank;  numerical simulation;  optical quality of flow;  supersonic chemical laser},
correspondence_address1={Malkov, V. M.; Laser Systems Ltd., St.-Petersburg, Russian Federation; email: office@lsystems.ru},
sponsors={EOARD; Bulgarian Academy of Sciences; Institute of Electronics; National Science Fund of Bulgaria; The Society of Photo-Optical Instrumentation Engineers (SPIE)},
address={Sofia},
issn={0277786X},
isbn={9780819482426},
coden={PSISD},
language={English},
abbrev_source_title={Proc SPIE Int Soc Opt Eng},
document_type={Conference Paper},
source={Scopus},
}

Active diffuser- AD has been developed by blowing in the high pressure gas from small scale nozzles along the laser chamber walls. Blowing has stabilized boundary layers, decreased its thickness and prevented its separation. So AD operating has stabilized the gas flow parameters in resonator and localized the zone of slow down of laser flow - pseudoshock - after laser chamber. So regular shock - wave structures (X-type shocks) that could degrade the flow optical quality don't appear in resonator. The use of AD allows developing PRS on base of single-stage ejector with high ejection coefficient (usually ground -based COIL PRS consist from passive diffuser and two-stage ejector and has low ejection coefficient). © 2010 Copyright SPIE - The International Society for Optical Engineering.

@ARTICLE{Lazuta201011,
author={Lazuta, A.V. and Ryzhov, V.A. and Khavronin, V.P. and Chernenkov, Y.P. and Smirnov, O.P. and Molkanov, P.L. and Troyanchuk, I.O. and Khomchenko, V.A.},
title={Paramagnet-to-ferromagnet and insulator-to-metal phase transitions in La0.88Mno2.95},
journal={Functional Materials},
year={2010},
volume={17},
number={1},
pages={11-17},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951879985&partnerID=40&md5=2cb92aae019f403f0e3b91d30ec53706},
affiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, 188300 St.Petersburg, Russian Federation; Institute of Solid State and Semiconductor Physics, National Academy of Sciences of Belarus, 17 P.Brovki St, 220072 Minsk, Belarus},
abstract={Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the metallic polycrystal La0.88Mn02.95. This above compound exhibits the paramagnet-ferromagnet (P-F, Tc ≈ 244 K) and insulator-metal (I-M, TIM ≈ 253 K > Tc) phase transitions, and reveals a colossal magnetoresistance near TIM. An analysis of the diffraction data is performed using the rhombohedral space group (R3c) in the temperature range 4-300 K. Below T*≈258 K, the FM clusters appear in the PI matrix undergoing a second-order transition. In contract to the traditionally doped analogs, this compound reveals the clustered state in the high symmetrical rhombohedral phase. The concentration of FM clusters increases under cooling, so that it exceeds the percolative threshold value below TIM, and the sample exhibits a metallic behavior. The T-evolution of the clustered state is unexpectedly found to be very close to that of the insulating La0.88MnO2.91 with the F ground state. It is shown that this leads to a certain restriction on a structure of a FM percolative network forming at TIM. The critical behavior of this system has a complicated character due mainly to the origination of the FM infinite cluster below TIM and its interaction with the PI matrix. © 2010 - STC Institute for Single Crystals.},
correspondence_address1={Troyanchuk, I.O.; Institute of Solid State and Semiconductor Physics, National Academy of Sciences of Belarus, 17 P.Brovki St, 220072 Minsk, Belarus},
issn={10275495},
language={English},
abbrev_source_title={Funct. Mater.},
document_type={Article},
source={Scopus},
}

Results of structural neutron diffraction study and data on the transport and magnetic properties (the linear and nonlinear (second and third order) susceptibilities) are presented for the metallic polycrystal La0.88Mn02.95. This above compound exhibits the paramagnet-ferromagnet (P-F, Tc ≈ 244 K) and insulator-metal (I-M, TIM ≈ 253 K > Tc) phase transitions, and reveals a colossal magnetoresistance near TIM. An analysis of the diffraction data is performed using the rhombohedral space group (R3c) in the temperature range 4-300 K. Below T*≈258 K, the FM clusters appear in the PI matrix undergoing a second-order transition. In contract to the traditionally doped analogs, this compound reveals the clustered state in the high symmetrical rhombohedral phase. The concentration of FM clusters increases under cooling, so that it exceeds the percolative threshold value below TIM, and the sample exhibits a metallic behavior. The T-evolution of the clustered state is unexpectedly found to be very close to that of the insulating La0.88MnO2.91 with the F ground state. It is shown that this leads to a certain restriction on a structure of a FM percolative network forming at TIM. The critical behavior of this system has a complicated character due mainly to the origination of the FM infinite cluster below TIM and its interaction with the PI matrix. © 2010 - STC Institute for Single Crystals.

We present the results from studying the magnetic properties (linear and nonlinear susceptibilities and the depolarization of polarized neutrons) of Nd1 - x Ba x MnO3 manganite, x = 0.3, with Curie temperature T C ≈ 140 K and dielectric-to-metal transition temperature T DM ≈ 129 K. Its critical behavior corresponds to that of an isotropic 3-D ferromagnet at temperatures above T≈ 144 K, but a strong nonlinear response in weak magnetic fields and depolarization are observed at temperatures below T. It is shown that this nontraditional behavior is related to the generation of ferromagnetic clusters in the paramagnetic matrix that form a conducting percolative network at temperatures near T DM. © 2010 Allerton Press, Inc.

@ARTICLE{Isaev-Ivanov20101063,
author={Isaev-Ivanov, V.V. and Lebedev, D.V. and Lauter, H. and Pantina, R.A. and Kuklin, A.I. and Islamov, A.K. and Filatov, M.V.},
title={Comparative analysis of the nucleosome structure of cell nuclei by small-angle neutron scattering},
journal={Physics of the Solid State},
year={2010},
volume={52},
number={5},
pages={1063-1073},
doi={10.1134/S1063783410050379},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77952334920&doi=10.1134%2fS1063783410050379&partnerID=40&md5=b7266c4aa86093bcd4dc258952790714},
affiliation={Konstantinov Petersburg Nuclear Physics Institute, Russian Academy of Sciences, ul. Orlova Roshcha 1, Gatchina, Leningradskaya oblast 188300, Russian Federation; Research and Educational Center Biophysics of the St. Petersburg State Polytechnical University, Konstantinov Petersburg Nuclear Physics Institute of the Russian Academy of Sciences, St. Petersburg 195251, Russian Federation; Institut Laue-Langevin, BP 156, Grenoble 38042, France; Joint Institute for Nuclear Research, ul. Joliot-Curie 6, Dubna, Moscow oblast 141980, Russian Federation},
abstract={The nucleosome structure in native nuclei of normal (chicken erythrocyte and rat leukocyte nuclei) and anomalously proliferating (the human cervical adenocarcinoma cell line HeLa and the Chinese hamster fibroblast cell line A238) cells has been investigated using small-angle neutron scattering. The experimental results obtained allow one to make the inference that the parameters of the nucleosome structure for the chicken erythrocyte and rat leukocyte nuclei (on average over the nucleus) are close to the universally accepted values and that the distance distribution function is bimodal. The bimodality of the distance distribution function reflects a narrow distribution of distances between nucleosomes (on average over the nucleus) at the fibril level of the chromatin organization. The histone core of the nucleosome structure in the nuclei of the HeLa and A238 cells (on average over the nucleus) is considerably less compact than that in the chicken erythrocyte and rat leukocyte nuclei, and the distance distribution function does not exhibit indications of the bimodality. © 2010 Pleiades Publishing, Ltd.},
correspondence_address1={Filatov, M. V.; Konstantinov Petersburg Nuclear Physics Institute, Russian Academy of Sciences, ul. Orlova Roshcha 1, Gatchina, Leningradskaya oblast 188300, Russian Federation; email: filatov@omrb.pnpi.spb.ru},
issn={10637834},
language={English},
abbrev_source_title={Phys. Solid State},
document_type={Article},
source={Scopus},
}

The nucleosome structure in native nuclei of normal (chicken erythrocyte and rat leukocyte nuclei) and anomalously proliferating (the human cervical adenocarcinoma cell line HeLa and the Chinese hamster fibroblast cell line A238) cells has been investigated using small-angle neutron scattering. The experimental results obtained allow one to make the inference that the parameters of the nucleosome structure for the chicken erythrocyte and rat leukocyte nuclei (on average over the nucleus) are close to the universally accepted values and that the distance distribution function is bimodal. The bimodality of the distance distribution function reflects a narrow distribution of distances between nucleosomes (on average over the nucleus) at the fibril level of the chromatin organization. The histone core of the nucleosome structure in the nuclei of the HeLa and A238 cells (on average over the nucleus) is considerably less compact than that in the chicken erythrocyte and rat leukocyte nuclei, and the distance distribution function does not exhibit indications of the bimodality. © 2010 Pleiades Publishing, Ltd.

@ARTICLE{Surzhik2010206,
author={Surzhik, M.A. and Churkina, S.V. and Shmidt, A.E. and Shvetsov, A.V. and Kozhina, T.N. and Firsov, D.L. and Firsov, L.M. and Petukhov, M.G.},
title={The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase},
journal={Applied Biochemistry and Microbiology},
year={2010},
volume={46},
number={2},
pages={206-211},
doi={10.1134/S0003683810020134},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77952311178&doi=10.1134%2fS0003683810020134&partnerID=40&md5=32c7917eb15ba2847a518a070ad3cb0e},
affiliation={Konstantinov Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina Leningrad oblast, 188300, Russian Federation},
abstract={Conformational flexibility of α-helices in glucoamylase of the fungus Aspergillus awamori was studied by molecular dynamics methods. Several amino acid substitutions (G127A, P128A, I136L, G137A, and G139A) optimizing intrinsic interactions in one of the α-helices (D) within the hydrophobic core of this protein were constructed and studied. It was found that these point mutations had different effects on the glucoamylase thermal inactivation constant. Unlike amino acid substitution P128A and substitutions G137A and A246C, I136L and G139A displayed a pronounced additive thermostabilizing effect. © 2010 Pleiades Publishing, Ltd.},
funding_details={RNP.2.2.1.1.4663},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)07 04 00785},
}

Conformational flexibility of α-helices in glucoamylase of the fungus Aspergillus awamori was studied by molecular dynamics methods. Several amino acid substitutions (G127A, P128A, I136L, G137A, and G139A) optimizing intrinsic interactions in one of the α-helices (D) within the hydrophobic core of this protein were constructed and studied. It was found that these point mutations had different effects on the glucoamylase thermal inactivation constant. Unlike amino acid substitution P128A and substitutions G137A and A246C, I136L and G139A displayed a pronounced additive thermostabilizing effect. © 2010 Pleiades Publishing, Ltd.

@ARTICLE{Surzhik2010221,
author={Surzhik, M.A. and Churkina, S.V. and Shmidt, A.E. and Shvetsov, A.V. and Kozhina, T.N. and Firsov, D.L. and Firsov, L.M. and Petukhov, M.G.},
title={The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase},
journal={Prikladnaia biokhimiia i mikrobiologiia},
year={2010},
volume={46},
number={2},
pages={221-227},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953272021&partnerID=40&md5=a730cf407f3b139bfb854b3e7c51ced9},
abstract={Conformational flexibility of alpha-helices in glucoamylase of the fungus Aspergillus awamori was studied by molecular dynamics methods. Several amino acid substitutions (G127A, P128A, I136L, G137A, and G139A) optimizing intrinsic interactions in one of the alpha-helices (D) within the hydrophobic core of this protein were constructed and studied. It was found that these point mutations had different effects on the glucoamylase thermal inactivation constant. Unlike amino acid substitution P128A and substitutions G137A and A246C, I136L and G139A displayed a pronounced additive thermostabilizing effect.},
correspondence_address1={Surzhik, M.A.},
issn={05551099},
pubmed_id={20391767},
language={Russian},
abbrev_source_title={Prikl. Biokhim. Mikrobiol.},
document_type={Article},
source={Scopus},
}

Conformational flexibility of alpha-helices in glucoamylase of the fungus Aspergillus awamori was studied by molecular dynamics methods. Several amino acid substitutions (G127A, P128A, I136L, G137A, and G139A) optimizing intrinsic interactions in one of the alpha-helices (D) within the hydrophobic core of this protein were constructed and studied. It was found that these point mutations had different effects on the glucoamylase thermal inactivation constant. Unlike amino acid substitution P128A and substitutions G137A and A246C, I136L and G139A displayed a pronounced additive thermostabilizing effect.

@ARTICLE{Ogneva2010418,
author={Ogneva, I.V. and Lebedev, D.V. and Shenkman, B.S.},
title={Transversal stiffness and young's modulus of single fibers from rat soleus muscle probed by atomic force microscopy},
journal={Biophysical Journal},
year={2010},
volume={98},
number={3},
pages={418-424},
doi={10.1016/j.bpj.2009.10.028},
note={cited By 40},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-76249126880&doi=10.1016%2fj.bpj.2009.10.028&partnerID=40&md5=acace22581df43f29b787704025108d6},
affiliation={State Scientific Center of Russian Federation, Institute for Biomedical Problems of Russian Academy of Sciences, Moscow, Russian Federation; Petersburg Nuclear Physics Institute, Gatchina, Russian Federation},
abstract={The structural integrity of striated muscle is determined by extra-sarcomere cytoskeleton that includes structures that connect the Z-disks and M-bands of a sarcomere to sarcomeres of neighbor myofibrils or to sarcolemma. Mechanical properties of these structures are not well characterized. The surface structure and transversal stiffness of single fibers from soleus muscle of the rat were studied with atomic force microscopy in liquid. We identified surface regions that correspond to projections of the Z-disks, M-bands, and structures between them. Transversal stiffness of the fibers was measured in each of these three regions. The stiffness was higher in the Z-disk regions, minimal between the Z-disks and the M-bands, and intermediate in the M-band regions. The stiffness increased twofold when relaxed fibers were maximally activated with calcium and threefold when they were transferred to rigor (ATP-free) solution. Transversal stiffness of fibers heavily treated with Triton X-100 was about twice higher than that of the permeabilized ones, however, its regional difference and the dependence on physiological state of the fiber remained the same. The data may be useful for understanding mechanics of muscle fibers when it is subjected to both axial and transversal strain and stress. © 2010 by the Biophysical Society.},
correspondence_address1={Ogneva, I. V.; State Scientific Center of Russian Federation, Institute for Biomedical Problems of Russian Academy of Sciences, Moscow, Russian Federation; email: iogneva@yandex.ru},
publisher={Biophysical Society},
issn={00063495},
coden={BIOJA},
language={English},
abbrev_source_title={Biophys. J.},
document_type={Article},
source={Scopus},
}

The structural integrity of striated muscle is determined by extra-sarcomere cytoskeleton that includes structures that connect the Z-disks and M-bands of a sarcomere to sarcomeres of neighbor myofibrils or to sarcolemma. Mechanical properties of these structures are not well characterized. The surface structure and transversal stiffness of single fibers from soleus muscle of the rat were studied with atomic force microscopy in liquid. We identified surface regions that correspond to projections of the Z-disks, M-bands, and structures between them. Transversal stiffness of the fibers was measured in each of these three regions. The stiffness was higher in the Z-disk regions, minimal between the Z-disks and the M-bands, and intermediate in the M-band regions. The stiffness increased twofold when relaxed fibers were maximally activated with calcium and threefold when they were transferred to rigor (ATP-free) solution. Transversal stiffness of fibers heavily treated with Triton X-100 was about twice higher than that of the permeabilized ones, however, its regional difference and the dependence on physiological state of the fiber remained the same. The data may be useful for understanding mechanics of muscle fibers when it is subjected to both axial and transversal strain and stress. © 2010 by the Biophysical Society.

@CONFERENCE{Kurbakov2010,
author={Kurbakov, A.I. and Lazuta, A.V. and Ryzhov, V.A.},
title={Phase diagram of Sm1-xSrxMnO3 perovskite manganites},
journal={Journal of Physics: Conference Series},
year={2010},
volume={200},
number={SECTION 1},
doi={10.1088/1742-6596/200/1/012099},
art_number={012099},
note={cited By 11},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957098417&doi=10.1088%2f1742-6596%2f200%2f1%2f012099&partnerID=40&md5=595154be2fe2c9857bcaa0d0c299aac5},
affiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Leningrad region, 188300 Gatchina, Russian Federation},
abstract={We present the electronic, structural and magnetic phase diagram of the colossal magnetoresistive Sm1-xSrxMnO3 (0.16≤x≤0.67) perovskite manganites, constructed on the basis of their regular investigations by high-resolution neutron powder diffraction, temperature magnetic and transport measurements. It is shown, that a real pattern of the physical phenomena in Sm-Sr manganites is considerably more various and is interesting than it was followed from macromeasurements. The tendency of researched system to formation of the phase-separated states on crystallographic as well as, in the even greater extent, on magnetic level is demonstrated. It is shown that there is a clear correlation between fine specific features and temperature evolution of crystal structures and the corresponding types of low-temperature magnetic ordering. © 2010 IOP Publishing Ltd.},
correspondence_address1={Kurbakov, A. I.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Leningrad region, 188300 Gatchina, Russian Federation; email: kurbakov@pnpi.spb.ru},
sponsors={},
publisher={Institute of Physics Publishing},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

We present the electronic, structural and magnetic phase diagram of the colossal magnetoresistive Sm1-xSrxMnO3 (0.16≤x≤0.67) perovskite manganites, constructed on the basis of their regular investigations by high-resolution neutron powder diffraction, temperature magnetic and transport measurements. It is shown, that a real pattern of the physical phenomena in Sm-Sr manganites is considerably more various and is interesting than it was followed from macromeasurements. The tendency of researched system to formation of the phase-separated states on crystallographic as well as, in the even greater extent, on magnetic level is demonstrated. It is shown that there is a clear correlation between fine specific features and temperature evolution of crystal structures and the corresponding types of low-temperature magnetic ordering. © 2010 IOP Publishing Ltd.

@ARTICLE{Ogneva2009365,
author={Ogneva, I.V. and Lebedev, D.V. and Shenkman, B.S.},
title={Lateral mechanics of muscle fibers and its role in signaling},
journal={Biophysics},
year={2009},
volume={54},
number={3},
pages={365-369},
doi={10.1134/S0006350909030208},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70350417132&doi=10.1134%2fS0006350909030208&partnerID=40&md5=be71f89f80283893e24add9ab882014c},
affiliation={Institute for Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russian Federation; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, 188300, Russian Federation},
abstract={The minireview considers some aspects of the lateral mechanics of muscle fibers, such as the available data on transverse stiffness of intact muscle cells, skinned fibers, and isolated myofibrils under various conditions and at different differentiation stages; the mechanisms whereby extrasarcomeric cytoskeletal proteins are involved in forming the structural basis of transverse stiffness; and their possible signaling role. © Pleiades Publishing, Inc., 2009.},
author_keywords={Lateral mechanics;  Muscle fiber;  Transverse stiffness},
correspondence_address1={Ogneva, I. V.; Institute for Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russian Federation},
issn={00063509},
language={English},
abbrev_source_title={Biophysics},
document_type={Review},
source={Scopus},
}

The minireview considers some aspects of the lateral mechanics of muscle fibers, such as the available data on transverse stiffness of intact muscle cells, skinned fibers, and isolated myofibrils under various conditions and at different differentiation stages; the mechanisms whereby extrasarcomeric cytoskeletal proteins are involved in forming the structural basis of transverse stiffness; and their possible signaling role. © Pleiades Publishing, Inc., 2009.

@ARTICLE{Petukhov2009359,
author={Petukhov, M. and Tatsu, Y. and Tamaki, K. and Murase, S. and Uekawa, H. and Yoshikawa, S. and Serrano, L. and Yumoto, N.},
title={Design of stable α-helices using global sequence optimization},
journal={Journal of Peptide Science},
year={2009},
volume={15},
number={5},
pages={359-365},
doi={10.1002/psc.1122},
note={cited By 10},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-67649171707&doi=10.1002%2fpsc.1122&partnerID=40&md5=ee949545d1639a86bef8ca445e875365},
affiliation={Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, 188300 Gatchina, Russian Federation; National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan; CRG-EMBL Systems Biology Unit, Centre de Regulacio Genomica, Dr Aiguader 88, 08003 Barcelona, Spain},
abstract={The rational design of peptide and protein helices is not only of practical importance for protein engineering but also is a useful approach in attempts to improve our understanding of protein folding. Recent modifications of theoreticalmodels of helix-coil transitions allow accurate predictions of the helix stability of monomeric peptides in water and provide new possibilities for protein design. We report here a new method for the design of α-helices in peptides and proteins using AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides and the tunneling algorithm of global optimization of multidimensional functions for optimization of amino acid sequences. CD measurements of helical content of peptides with optimized sequences indicate that the helical potential of protein amino acids is high enough to allow formation of stable α-helices in peptides as short as of 10 residues in length. The results show the maximum achievable helix content (HC) of short peptides with fully optimized sequences at 5 °C is expected to be ∼70-75%. Under certain conditions the method can be a powerful practical tool for protein engineering. Unlike traditional approaches that are often used to increase protein stability by adding a few favorable interactions to the protein structure, this method deals with all possible sequences of protein helices and selects the best one from them. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.},
author_keywords={α-helix;  AGADIR;  Design;  Sequence optimization;  Tunneling algorithm},
correspondence_address1={Petukhov, M.; Department of Molecular and Radiation Biophysics, Petersburg Institute of Nuclear Physics, RAS, Orlovarosha, Gatchina 88300, Russian Federation; email: michael.petukhov@gmail.com},
issn={10752617},
coden={JPSIE},
pubmed_id={19222027},
language={English},
abbrev_source_title={J. Pept. Sci.},
document_type={Article},
source={Scopus},
}

The rational design of peptide and protein helices is not only of practical importance for protein engineering but also is a useful approach in attempts to improve our understanding of protein folding. Recent modifications of theoreticalmodels of helix-coil transitions allow accurate predictions of the helix stability of monomeric peptides in water and provide new possibilities for protein design. We report here a new method for the design of α-helices in peptides and proteins using AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides and the tunneling algorithm of global optimization of multidimensional functions for optimization of amino acid sequences. CD measurements of helical content of peptides with optimized sequences indicate that the helical potential of protein amino acids is high enough to allow formation of stable α-helices in peptides as short as of 10 residues in length. The results show the maximum achievable helix content (HC) of short peptides with fully optimized sequences at 5 °C is expected to be ∼70-75%. Under certain conditions the method can be a powerful practical tool for protein engineering. Unlike traditional approaches that are often used to increase protein stability by adding a few favorable interactions to the protein structure, this method deals with all possible sequences of protein helices and selects the best one from them. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.

@ARTICLE{Ogneva2009522,
author={Ogneva, I.V. and Lebedev, D.V. and Shenkman, B.S.},
title={Lateral mechanics of muscle fibres and its role in signaling},
journal={Biofizika},
year={2009},
volume={54},
number={3},
pages={522-528},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-68349102079&partnerID=40&md5=3106f7ed14c5ef140769306f40f28ac1},
abstract={Different aspects of the lateral mechanics of muscle fibres have been considered. The current data on the transverse stiffness of intact muscle cells, demenbranized muscle fibres, and isolated myofibrils under various conditions and at different stages of the differentiation of myofibers. The signaling role of cytoskeleton proteins and possible mechanisms of their involvement in the structural basis of transverse stiffness are dissussed.},
correspondence_address1={Ogneva, I.V.},
issn={00063029},
pubmed_id={19569516},
language={Russian},
abbrev_source_title={Biofizika},
document_type={Review},
source={Scopus},
}

Different aspects of the lateral mechanics of muscle fibres have been considered. The current data on the transverse stiffness of intact muscle cells, demenbranized muscle fibres, and isolated myofibrils under various conditions and at different stages of the differentiation of myofibers. The signaling role of cytoskeleton proteins and possible mechanisms of their involvement in the structural basis of transverse stiffness are dissussed.

@ARTICLE{Ilatovskiy2009555,
author={Ilatovskiy, A. and Petukhov, M.},
title={Genome-wide search for local DNA segments with anomalous GC-content},
journal={Journal of Computational Biology},
year={2009},
volume={16},
number={4},
pages={555-564},
doi={10.1089/cmb.2008.0159},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-64749115060&doi=10.1089%2fcmb.2008.0159&partnerID=40&md5=a81d9b2e4dcfbcb0892eec3bcf030e12},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; Research and Education Centre Biophysics PNPI RAS, St. Petersburg State Polytecnic University, St. Petersburg, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Orlova roscha, Gatchina /St. Petersburg, 188300, Russian Federation},
abstract={An anomalous (i.e., significantly different from genome-average) GC-content is often used as one of the markers to reveal the events of horizontal gene transfer (HGT). Unfortunately, results obtained by the traditional fixed-length window analysis strongly depend on an arbitrary selection of DNA window length. Here we present a new method for genome-wide statistical analysis of GC-content without that drawback. The method is based on a set of nonparametric statistical tests and is capable of providing reliable estimations of both a local and global GC-content, and thus can identify small local areas (as short as 30bp) with anomalous GC-content in a bacterial genome. The tests, applied to a well-studied bacterial genome of Escherichia coli K-12, show that approximately 21% of the genome belongs to the anomalous GC-content areas. Among top 23 anomalous GC-content areas, seven correspond to the annotated prophages, four to Rhs elements, and two to IS elements. A remaining 10 areas contain putative horizontally transferred DNA and genes with still unknown functions. Software is available at http://mml.spbstu.ru/gcstat. © Copyright 2009 Mary Ann Liebert, Inc.},
author_keywords={GC-content;  Genome;  Horizontal gene transfer;  Sequence analysis},
correspondence_address1={Ilatovskiy, A.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; email: andreyi@omrb.pnpi.spb.ru},
issn={10665277},
coden={JCOBE},
pubmed_id={19361327},
language={English},
abbrev_source_title={J. Comput. Biol.},
document_type={Article},
source={Scopus},
}

An anomalous (i.e., significantly different from genome-average) GC-content is often used as one of the markers to reveal the events of horizontal gene transfer (HGT). Unfortunately, results obtained by the traditional fixed-length window analysis strongly depend on an arbitrary selection of DNA window length. Here we present a new method for genome-wide statistical analysis of GC-content without that drawback. The method is based on a set of nonparametric statistical tests and is capable of providing reliable estimations of both a local and global GC-content, and thus can identify small local areas (as short as 30bp) with anomalous GC-content in a bacterial genome. The tests, applied to a well-studied bacterial genome of Escherichia coli K-12, show that approximately 21% of the genome belongs to the anomalous GC-content areas. Among top 23 anomalous GC-content areas, seven correspond to the annotated prophages, four to Rhs elements, and two to IS elements. A remaining 10 areas contain putative horizontally transferred DNA and genes with still unknown functions. Software is available at http://mml.spbstu.ru/gcstat. © Copyright 2009 Mary Ann Liebert, Inc.

@ARTICLE{Rutberg2009325,
author={Rutberg, P.G. and Kolikov, V. and Snetov, V. and Stogov, A. and Noskin, L. and Landa, S. and Arutjunan, A. and Egorov, V. and Sirotkin, A.},
title={Uppermolecule complexes of oxide nanostructures and albumins formation},
journal={High Temperature Material Processes},
year={2009},
volume={13},
number={3-4},
pages={325-334},
doi={10.1615/HighTempMatProc.v13.i3-4.60},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-76649096972&doi=10.1615%2fHighTempMatProc.v13.i3-4.60&partnerID=40&md5=b13904e357dc4fcc8c145fa052c1ea10},
affiliation={Institute for Electrophysics and Electric Power Russian Academy of Sciences (IEE RAS), Dvortsovaya nab. 18, 191186 St.-Petersburg, Russian Federation; Institute for Nuclear Physics Russian Academy of Science, 188300 Gatchina, Russian Federation; Institute for Nuclear Physics Russian Academy of Science, Gatchina; Unstitute for Influenza Russian Academy of Medicine Science, 197376, prof. Popov st. 15, St. Petersburg, Russian Federation},
abstract={Possible employment of oxide nanostructures in medicine demands elucidation of their negative effects on various systems of a human organism. In particular, in this paper the experimental results of investigation of interaction of Ag, Cu, Fe, and Pt nanostructures water dispersions (NWD), which were produced by means the treatment of water by pulsed electric discharges (PED), with serum of human blood (HBS), are presented. The goal of the investigation was to determine connection between the properties of the nanostructures and peculiarities of their interactions with the human blood serum (HBS) as highly concentrated solutions of macromolecules. It was found that albuminous and lipoprotein structures of HBS are agglutinated on surface of the nanoparticles, forming upper molecule complexes. Thus, the higher the concentration of nanoparticles in joint dispersion is, the larger complexes are formed. At early stages of the process rather small complexes of albuminous and immunoglobulins are formed, then lipoproteins are agglutinated, and finally, large complexes of hydrodynamic radius (Rh) more than 2 m are formed.},
author_keywords={Ag;  Cu;  Fe;  Human blood serum (HBS);  Nanoparticles;  Nanostructures;  Pt},
correspondence_address1={Rutberg, P. G.; Institute for Electrophysics and Electric Power Russian Academy of Sciences (IEE RAS), Dvortsovaya nab. 18, 191186 St.-Petersburg, Russian Federation},
publisher={Begell House Inc.},
issn={10933611},
language={English},
abbrev_source_title={High Temp. Mater. Processes},
document_type={Article},
source={Scopus},
}

Possible employment of oxide nanostructures in medicine demands elucidation of their negative effects on various systems of a human organism. In particular, in this paper the experimental results of investigation of interaction of Ag, Cu, Fe, and Pt nanostructures water dispersions (NWD), which were produced by means the treatment of water by pulsed electric discharges (PED), with serum of human blood (HBS), are presented. The goal of the investigation was to determine connection between the properties of the nanostructures and peculiarities of their interactions with the human blood serum (HBS) as highly concentrated solutions of macromolecules. It was found that albuminous and lipoprotein structures of HBS are agglutinated on surface of the nanoparticles, forming upper molecule complexes. Thus, the higher the concentration of nanoparticles in joint dispersion is, the larger complexes are formed. At early stages of the process rather small complexes of albuminous and immunoglobulins are formed, then lipoproteins are agglutinated, and finally, large complexes of hydrodynamic radius (Rh) more than 2 m are formed.

@ARTICLE{Ogneva2008604,
author={Ogneva, I.V. and Lebedev, D.V. and Isaev-Ivanov, V.V. and Shenkman, B.S.},
title={Spatial distribution of the transverse stiffness of relaxed and activated rat soleus muscle fibers},
journal={Biophysics},
year={2008},
volume={53},
number={6},
pages={604-607},
doi={10.1134/S0006350908060250},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-62149147592&doi=10.1134%2fS0006350908060250&partnerID=40&md5=fe2978f4a4ddb2be34d9e923018e2d0c},
affiliation={Institute of Biomedical Problems, Russian Academy of Sciences, Moscow 123007, Russian Federation; Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Orlova roshcha, Gatchina, Leningrad oblast, Russian Federation},
abstract={The transverse stiffness of glycerinated and demembranated fibers from the soleus muscle of Wistar rats in different functional states was measured by atomic force microscopy. It was demonstrated that the transverse stiffness of relaxed fibers near the Z disk is approximately twofold higher as compared with the M-line region. However, the stiffness of glycerinated fibers in the Z-disk and M-line regions is considerably lower than that of demembranated fibers. The values of mechanical parameters of activated fibers are significantly higher as compared with the relaxed fibers. However, the stiffness of activated glycerinated fibers near the Z disk approximately doubled as compared with the relaxed state, whereas the stiffness of the Z-disk region in demembranated fibers increased more than fourfold. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold. © 2008 Pleiades Publishing, Ltd.},
author_keywords={Atomic force microscopy;  Cytoskeleton;  Muscle fiber;  Transverse stiffness},
funding_details={6006/4},
}

The transverse stiffness of glycerinated and demembranated fibers from the soleus muscle of Wistar rats in different functional states was measured by atomic force microscopy. It was demonstrated that the transverse stiffness of relaxed fibers near the Z disk is approximately twofold higher as compared with the M-line region. However, the stiffness of glycerinated fibers in the Z-disk and M-line regions is considerably lower than that of demembranated fibers. The values of mechanical parameters of activated fibers are significantly higher as compared with the relaxed fibers. However, the stiffness of activated glycerinated fibers near the Z disk approximately doubled as compared with the relaxed state, whereas the stiffness of the Z-disk region in demembranated fibers increased more than fourfold. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold. © 2008 Pleiades Publishing, Ltd.

@ARTICLE{Ogneva200869,
author={Ogneva, I.V. and Lebedev, D.V. and Shenkman, B.S.},
title={Transverse stiffness of muscular fibers. Methods of measuring and physiological foundations},
journal={Aviakosmicheskaya i Ekologicheskaya Meditsina},
year={2008},
volume={42},
number={3},
pages={69-74},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-58149308817&partnerID=40&md5=7914fa76fa9d80a10398c36d7fccaf14},
abstract={The article contains the data about transverse stiffness of both native and demembraned fibers of different muscles. Under consideration is atomic force microscopy as the most promising method of investigating the cell and molecular mechanic properties of living objects.},
issn={0233528X},
pubmed_id={19055017},
language={Russian},
abbrev_source_title={Aviakosmicheskaya Ekol. Med.},
document_type={Article},
source={Scopus},
}

The article contains the data about transverse stiffness of both native and demembraned fibers of different muscles. Under consideration is atomic force microscopy as the most promising method of investigating the cell and molecular mechanic properties of living objects.

@ARTICLE{Ogneva20081073,
author={Ogneva, I.V. and Lebedev, D.V. and Isaev-Ivanov, V.V. and Shenkman, B.S.},
title={Spatial distribution of transverse stiffness of relaxed and activated rat soleus myofibers},
journal={Biofizika},
year={2008},
volume={53},
number={6},
pages={1073-1077},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-61549140069&partnerID=40&md5=6958c445d300a2d319de6ae11cb4c0ec},
abstract={The transverse stiffness of isolated glycerinated and demembranized muscle fibers from soleus muscle of Wistar rat were measured in different functional states by atomic force microscopy. It was shown that transverse stiffness of relaxed fibers near the Z-disk projection is approximately twice as high as near the M-line. The transverse stiffness of demembranized fibers is much higher than that of glycerinated fibers for both the Z-disk and M-line. The activation of the fiber resulted in a significant increase in transverse stiffness. However, while the stiffness of activated glycerinated fibers near the Z-disk increased about twofold, demembranized fibers showed a more than fourfold increase in transverse stiffness compared to relaxed fibers. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold.},
correspondence_address1={Ogneva, I.V.},
issn={00063029},
pubmed_id={19137695},
language={Russian},
abbrev_source_title={Biofizika},
document_type={Article},
source={Scopus},
}

The transverse stiffness of isolated glycerinated and demembranized muscle fibers from soleus muscle of Wistar rat were measured in different functional states by atomic force microscopy. It was shown that transverse stiffness of relaxed fibers near the Z-disk projection is approximately twice as high as near the M-line. The transverse stiffness of demembranized fibers is much higher than that of glycerinated fibers for both the Z-disk and M-line. The activation of the fiber resulted in a significant increase in transverse stiffness. However, while the stiffness of activated glycerinated fibers near the Z-disk increased about twofold, demembranized fibers showed a more than fourfold increase in transverse stiffness compared to relaxed fibers. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold.

@ARTICLE{Karelov2008,
author={Karelov, D.V. and Lebedev, D.V. and Suslov, A.V. and Shalguev, V.I. and Kuklin, A.I. and Islamov, A.Kh. and Lauter, H. and Lanzov, V.A. and Isaev-Ivanov, V.V.},
title={Large-scale structure of RecA protein from Deinococcus radiodurance and its complexes in solution},
journal={Journal of Physics Condensed Matter},
year={2008},
volume={20},
number={10},
doi={10.1088/0953-8984/20/10/104215},
art_number={104215},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41849107564&doi=10.1088%2f0953-8984%2f20%2f10%2f104215&partnerID=40&md5=ad0548b44c3c670e7599d7037610244b},
affiliation={Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Joint Institute for Nuclear Research, Dubna, Russian Federation; Institute Max von Laue Paul Langevin, Grenoble, France},
abstract={Different conformational states of the filaments formed by RecA protein from a radiation resistant strain Deinococcus radiodurance (RecADr) in solution were investigated using small angle neutron scattering. Scattering by the protein self-polymer was consistent with a long helix model, with the pitch of the helix being lower than that in the crystal structure. Compared to those of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, helical filaments of RecA from D.radiodurance exhibited a lower helical pitch and lower stability at low Mg2+ concentrations or under conditions of elevated ionic strength in the absence of ATP (adenosine triphosphate). Formation of an active filament upon binding of ATPγS and either single-or double-stranded DNA brought about a significant increase in the helix pitch and a moderate decrease in the cross-sectional gyration radius, but resulted in little change in the number of monomers per helix turn. The helix pitch value of the RecA Dr presynaptic complex was conservative and close to that found for other RecA proteins and their analogs. © IOP Publishing Ltd.},
correspondence_address1={Karelov, D. V.; Petersburg Nuclear Physics Institute, Gatchina, Russian Federation},
issn={09538984},
coden={JCOME},
language={English},
abbrev_source_title={J Phys Condens Matter},
document_type={Article},
source={Scopus},
}

Different conformational states of the filaments formed by RecA protein from a radiation resistant strain Deinococcus radiodurance (RecADr) in solution were investigated using small angle neutron scattering. Scattering by the protein self-polymer was consistent with a long helix model, with the pitch of the helix being lower than that in the crystal structure. Compared to those of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, helical filaments of RecA from D.radiodurance exhibited a lower helical pitch and lower stability at low Mg2+ concentrations or under conditions of elevated ionic strength in the absence of ATP (adenosine triphosphate). Formation of an active filament upon binding of ATPγS and either single-or double-stranded DNA brought about a significant increase in the helix pitch and a moderate decrease in the cross-sectional gyration radius, but resulted in little change in the number of monomers per helix turn. The helix pitch value of the RecA Dr presynaptic complex was conservative and close to that found for other RecA proteins and their analogs. © IOP Publishing Ltd.

@ARTICLE{Lebedev2008110,
author={Lebedev, D.V. and Filatov, M.V. and Kuklin, A.I. and Islamov, A.Kh. and Stellbrink, J. and Pantina, R.A. and Denisov, Yu.Yu. and Toperverg, B.P. and Isaev-Ivanov, V.V.},
title={Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization},
journal={Crystallography Reports},
year={2008},
volume={53},
number={1},
pages={110-115},
doi={10.1134/S1063774508010136},
note={cited By 18},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-38749093755&doi=10.1134%2fS1063774508010136&partnerID=40&md5=cfa0e3cb31cc3b6a1cf7674af5cbbbbf},
affiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, ul. Orlova Roshcha 1, Gatchina, Leningrad oblast 188300, Russian Federation; Biofizika Research and Education Center, St. Petersburg State Polytechnic University, Russian Academy of Sciences, St. Petersburg 195251, Russian Federation; Joint Institute of Nuclear Research, ul. Zholio-Kyuri 6, Dubna, Moscow Oblast 141980, Russian Federation; Research Centre Jülich, Jülich 52425, Germany},
abstract={The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 × 10-1 to 10-4 Å-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm. © 2008 Pleiades Publishing, Inc.},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)02-04-49259-a},
funding_details={Ministry of Education and Science of the Russian FederationRNP 2.2.1.1.4663},
funding_details={Ministry of Education and Science of the Russian Federation40.012.1.1.1149},
}

The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 × 10-1 to 10-4 Å-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm. © 2008 Pleiades Publishing, Inc.

@ARTICLE{Boreysho2007561,
author={Boreysho, A.S. and Druzhinin, S.L. and Malkov, V.M. and Kiselev, I.A. and Morozov, A.V. and Orlov, A.E. and Savin, A.V. and Shatalov, I.V. and Zapryagaev, V.I. and Sobolev, A.V.},
title={Pressure recovery system for a high-power HF/DF laser: Implementation practice},
journal={Thermophysics and Aeromechanics},
year={2007},
volume={14},
number={4},
pages={561-576},
doi={10.1134/S0869864307040075},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-49149100074&doi=10.1134%2fS0869864307040075&partnerID=40&md5=87a1be70861b1730e9ff98b252b70837},
affiliation={Laser Systems Scientific Production Association, St. Petersburg, Russian Federation; Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russian Federation},
abstract={The matter of development of a high-performance pressure recovery system (PRS) for a high-power HF/DF laser is discussed. A sequence of design steps is proposed, which involves estimation of basic characteristics of PRS components with the help of one-dimensional integral and semi-empirical procedures; simulation, to be performed using three-dimensional non-stationary Navier - Stokes equations; experimental modelling aimed at verification of the calculation procedures and at refinement of obtained parameters; and a fullscale experiment. An ejector-type system providing for recovery of pressure from 12 Torr to atmospheric pressure in the gas-dynamic system of an HF/DF laser of several-tens-kilowatt power is developed. Matching conditions for parameters of individual PRS components as well as joint functioning of the PRS with a continuous chemical laser in an integral complex are analysed. Conditions for minimization of mass-dimensional characteristics of the laser-PRS complex necessary for the development of ground-based mobile systems are identified. © 2007 Pleiades Publishing, Ltd.},
correspondence_address1={Boreysho, A. S.; Laser Systems Scientific Production Association, St. Petersburg, Russian Federation},
issn={08698643},
language={English},
abbrev_source_title={Thermophys. Aeromech.},
document_type={Article},
source={Scopus},
}

The matter of development of a high-performance pressure recovery system (PRS) for a high-power HF/DF laser is discussed. A sequence of design steps is proposed, which involves estimation of basic characteristics of PRS components with the help of one-dimensional integral and semi-empirical procedures; simulation, to be performed using three-dimensional non-stationary Navier - Stokes equations; experimental modelling aimed at verification of the calculation procedures and at refinement of obtained parameters; and a fullscale experiment. An ejector-type system providing for recovery of pressure from 12 Torr to atmospheric pressure in the gas-dynamic system of an HF/DF laser of several-tens-kilowatt power is developed. Matching conditions for parameters of individual PRS components as well as joint functioning of the PRS with a continuous chemical laser in an integral complex are analysed. Conditions for minimization of mass-dimensional characteristics of the laser-PRS complex necessary for the development of ground-based mobile systems are identified. © 2007 Pleiades Publishing, Ltd.

@CONFERENCE{Bairamov2007511,
author={Bairamov, B.H. and Toporov, V.V. and Bayramov, F.B. and Petukhov, M. and Glazunov, E.A. and Lanzov, V. and Li, Y. and Ramadurai, D. and Shi, P. and Dutta, M. and Stroscio, M.A. and Irmer, G.},
title={Selective functionalization of semiconductor quantum dots with short peptides and integrins of cancer cells for biophotonic applications},
journal={Proceedings of the International Conference on Physics, Chemistry and Application of Nanostructures, NANOMEETING 2007 - Reviews and Short Notes},
year={2007},
pages={511-515},
note={cited By 2; Conference of International Conference on Physics, Chemistry and Application of Nanostructures, NANOMEETING 2007 ; Conference Date: 22 May 2007 Through 25 May 2007;  Conference Code:99437},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884371405&partnerID=40&md5=fb3a3a043ff10b75ae7615cecd4b9d86},
affiliation={A.F. Ioffe Physico-Technical Institute, RAS, 194021 St. Petersburg, Russian Federation; Petersburg Nuclear Physics Institute, RAS, 188300 Gatchina, Russian Federation; Department of Electrical and Computer Engineering, University of Illinois, Chicago, IL 60607, United States; Department of Bioengineering, University of Illinois, Chicago, IL 60607, United States; Department of Physics, University of Illinois, Chicago, IL 60607, United States; Department of Bioengineering and Physics, University of Illinois, Chicago, IL 60607, United States; Institute of Theoretical Physics, University of Mining and Technology, D-09596 Freiberg, Germany},
abstract={We discuss our results on study of structural properties of the nanoscale integrated colloidal semiconductor quantum dots (SQDs) such as CdS and ZnS-capped CdSe conjugated with biomolecules such as short peptides and integrins of cancer MDA-MB- 435 cells for biomedical applications. We study chemically prepared CdS SQDs functionalized with peptides composed of the following aminoacid chains: CGGGRGDS, CGGGRVDS, CGGIKVAV, and CGGGLDV. The effective diameter of the CdS SQDs is 3 nm. The cysteine (C) aminoacid links to CdS SQDs via the thiol link, the GGG sequences of glycine (G) amino acid, provide a spacer in the amino acid chain. The RGDS, RVDS, IKAV, and LDV sequences have selective affinities to specialized transmembrane cellular structures known as integrins of neurons and MDA-MB-435 cancer cells, respectively. We also studied a role of water and other bioenvironments in stability, surface properties, dynamical and structural characteristics of these systems.},
correspondence_address1={A.F. Ioffe Physico-Technical Institute, RAS, 194021 St. Petersburg, Russian Federation},
address={Minsk},
isbn={9812705996; 9789812705990},
language={English},
abbrev_source_title={Proc. Int. Conf. Phys., Chem. Appl. Nanostructures, NANOMEETING - Rev. Short Notes},
document_type={Conference Paper},
source={Scopus},
}

We discuss our results on study of structural properties of the nanoscale integrated colloidal semiconductor quantum dots (SQDs) such as CdS and ZnS-capped CdSe conjugated with biomolecules such as short peptides and integrins of cancer MDA-MB- 435 cells for biomedical applications. We study chemically prepared CdS SQDs functionalized with peptides composed of the following aminoacid chains: CGGGRGDS, CGGGRVDS, CGGIKVAV, and CGGGLDV. The effective diameter of the CdS SQDs is 3 nm. The cysteine (C) aminoacid links to CdS SQDs via the thiol link, the GGG sequences of glycine (G) amino acid, provide a spacer in the amino acid chain. The RGDS, RVDS, IKAV, and LDV sequences have selective affinities to specialized transmembrane cellular structures known as integrins of neurons and MDA-MB-435 cancer cells, respectively. We also studied a role of water and other bioenvironments in stability, surface properties, dynamical and structural characteristics of these systems.

@ARTICLE{Lebedev2007799,
author={Lebedev, D.V. and Monkenbusch, M. and Shalguev, V.I. and Lantsov, V.A. and Isaev-Ivanov, V.V.},
title={Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo},
journal={Biofizika},
year={2007},
volume={52},
number={5},
pages={799-803},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-38449083418&partnerID=40&md5=abda3d7f880a7a4897704b162f0695db},
abstract={Bacterial RecA protein is the key enzyme in the processes of homologous recombination, post-replication repair and induction of SOS-repair functions. While a significant amount of data on the structure of RecA protein and its functional analogs has been obtained, there is little information about the molecular dynamics of this protein. In this work we present the results of neutron spin-echo measurements of the relaxation kinetics of filaments formed by RecA proteins from E. coli and P. aeruginosa. The results suggest that the protein filaments exhibit both diffusion and internal relaxation modes, which change during the formation of complexes of these proteins with ATP and single-stranded DNA.},
correspondence_address1={Lebedev, D.V.},
issn={00063029},
pubmed_id={17969911},
language={Russian},
abbrev_source_title={Biofizika},
document_type={Article},
source={Scopus},
}

Bacterial RecA protein is the key enzyme in the processes of homologous recombination, post-replication repair and induction of SOS-repair functions. While a significant amount of data on the structure of RecA protein and its functional analogs has been obtained, there is little information about the molecular dynamics of this protein. In this work we present the results of neutron spin-echo measurements of the relaxation kinetics of filaments formed by RecA proteins from E. coli and P. aeruginosa. The results suggest that the protein filaments exhibit both diffusion and internal relaxation modes, which change during the formation of complexes of these proteins with ATP and single-stranded DNA.

@ARTICLE{Rychkov20071974,
author={Rychkov, G. and Petukhov, M.},
title={Joint neighbors approximation of macromolecular solvent accessible surface area},
journal={Journal of Computational Chemistry},
year={2007},
volume={28},
number={12},
pages={1974-1989},
doi={10.1002/jcc.20550},
note={cited By 10},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547336672&doi=10.1002%2fjcc.20550&partnerID=40&md5=b62368763022b295011b31eb80b79244},
affiliation={Division of Molecular and Radiation Biophysics, St. Petersburg Nuclear Physics Institute, Russian Academy of Sciences (PNPI RAS), Gatchina, St. Petersburg 188300, Russian Federation; Biophysics, Research and Education Center, PNPI RAS, St. Petersburg State Polytechnic University, St. Petersburg, 194021, Russian Federation},
abstract={A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 Å2, while for unfolded protein conformations it varies from 1.65 to 1.87 Å2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today. © 2007 Wiley Periodicals, Inc.},
author_keywords={Analytical gradients;  Analytical surface area;  Folded and unfolded proteins;  Hydration;  Solvent-accessible surface area},
correspondence_address1={Rychkov, G.; Division of Molecular and Radiation Biophysics, St. Petersburg Nuclear Physics Institute, Russian Academy of Sciences (PNPI RAS), Gatchina, St. Petersburg 188300, Russian Federation; email: georgy-rychkov@yandex.ru},
issn={01928651},
coden={JCCHD},
pubmed_id={17407094},
language={English},
abbrev_source_title={J. Comput. Chem.},
document_type={Article},
source={Scopus},
}

A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 Å2, while for unfolded protein conformations it varies from 1.65 to 1.87 Å2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today. © 2007 Wiley Periodicals, Inc.

@ARTICLE{Egorov2007152,
author={Egorov, V.V. and Garmaj, Yu.P. and Solovyov, K.V. and Grudinina, N.A. and Aleinikova, T.D. and Sirotkin, A.K. and Kiselev, O.I. and Shawlovsky, M.M.},
title={Amyloidogenic peptide homologous to β-domain region of α-lactalbumin},
journal={Doklady Biochemistry and Biophysics},
year={2007},
volume={414},
number={1},
pages={152-154},
doi={10.1134/S1607672907030167},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547337506&doi=10.1134%2fS1607672907030167&partnerID=40&md5=8f751c777b6aa0e8fc8285dbed8b8df6},
affiliation={Institute of Experimental Medicine, Russian Academy of Medical Sciences, ul. Professora Popova 12, St. Petersburg, 197376, Russian Federation; Influenza Research Institute, Russian Academy of Medical Sciences, ul. Akademika Pavlova 15/17, St. Petersburg, 197376, Russian Federation},
correspondence_address1={Egorov, V.V.; Institute of Experimental Medicine, Russian Academy of Medical Sciences, ul. Professora Popova 12, St. Petersburg, 197376, Russian Federation},
issn={16076729},
pubmed_id={17695325},
language={English},
abbrev_source_title={Doklad. Biochem. Biophys.},
document_type={Article},
source={Scopus},
}

@ARTICLE{Egorov2007471,
author={Egorov, V.V. and Solovyov, K.V. and Grudinina, N.A. and Lebedev, D.V. and Isaev-Ivanov, V.V. and Kiselev, O.I. and Shawlovsky, M.M.},
title={Atomic force microscopy study of peptides homologous to beta-domain of alpha-lactalbumins},
journal={Protein and Peptide Letters},
year={2007},
volume={14},
number={5},
pages={471-474},
doi={10.2174/092986607780782858},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34249743235&doi=10.2174%2f092986607780782858&partnerID=40&md5=b627ff86500ddc6e21422c29aeab5a55},
affiliation={Institute for Experimental Medicine RAMS, 12, Akad. Pavlova St., Saint Petersburg, Russian Federation; Petersburg Nuclear Physics Institute RAS, Orlova Roscha, Gatchina, Russian Federation; Influenza Institute RAMS, 15/17 Prof. Popova St., Saint Petersburg, Russian Federation},
abstract={Symmetrical peptide GYDTQAIVENNESTEYG (WT, Wild Type) identical to 35-51 aminoacid residues of human alpha-lactalbumin (HLA) and peptide GYDTQTVVNNNGHTDYG (ID, IDeal symmetry) homologous to beta-domain of mammalian alpha-lactalbumins can form amyloid-like fibrils in conditions required for fibrillogenesis of HLA. The latter peptide can also form fibrils in deionized water. Fibrils formed by these peptides can cause forming of HLA amyloid-like aggregates in physiological conditions. These results provide an evidence for presence of amyloidogenic determinant in beta-domain of alpha-lactalbumin. Thus, symmetry in the primary structure may play the role in fibrillogenesis of proteins. © 2007 Bentham Science Publishers Ltd.},
author_keywords={Alpha-lactalbumin;  Atomic force microscopy;  Fibrillogenesis;  GYDTQAIVENNESTEYG;  GYDTQTVVNNNGHTDYG;  Symmetry},
correspondence_address1={Egorov, V.V.; Institute for Experimental Medicine RAMS, 12, Akad. Pavlova St., Saint Petersburg, Russian Federation; email: olivejra@yahoo.com},
issn={09298665},
coden={PPELE},
pubmed_id={17584173},
language={English},
abbrev_source_title={Protein Pept. Lett.},
document_type={Article},
source={Scopus},
}

Symmetrical peptide GYDTQAIVENNESTEYG (WT, Wild Type) identical to 35-51 aminoacid residues of human alpha-lactalbumin (HLA) and peptide GYDTQTVVNNNGHTDYG (ID, IDeal symmetry) homologous to beta-domain of mammalian alpha-lactalbumins can form amyloid-like fibrils in conditions required for fibrillogenesis of HLA. The latter peptide can also form fibrils in deionized water. Fibrils formed by these peptides can cause forming of HLA amyloid-like aggregates in physiological conditions. These results provide an evidence for presence of amyloidogenic determinant in beta-domain of alpha-lactalbumin. Thus, symmetry in the primary structure may play the role in fibrillogenesis of proteins. © 2007 Bentham Science Publishers Ltd.

@ARTICLE{Petukhov2006296,
author={Petukhov, M. and Lebedev, D. and Shalguev, V. and Islamov, A. and Kuklin, A. and Lanzov, V. and Isaev-Ivanov, V.},
title={Conformational flexibility of RecA protein filament: Transitions between compressed and stretched states},
journal={Proteins: Structure, Function and Genetics},
year={2006},
volume={65},
number={2},
pages={296-304},
doi={10.1002/prot.21116},
note={cited By 6},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749025273&doi=10.1002%2fprot.21116&partnerID=40&md5=dfc8701e07f6ab357a9c0657907dfbe9},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; Research and Education Center Biophysics, PNPI RAS, St. Petersburg State Polytechnical University, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, 188300, St. Petersburg, Russian Federation},
abstract={RecA protein is a central enzyme in homologous DNA recombination, repair and other forms of DNA metabolism in bacteria. It functions as a flexible helix-shaped filament bound on stretched single-stranded or double-stranded DNA in the presence of ATP. In this work, we present an atomic level model for conformational transitions of the RecA filament. The model describes small movements of the RecA N-terminal domain due to coordinated rotation of main chain dihedral angles of two amino acid residues (Psi/Lys23 and Phi/Gly24), while maintaining unchanged the RecA intersubunit interface. The model is able to reproduce a wide range of observed helix pitches in transitions between compressed and stretched conformations of the RecA filament. Predictions of the model are in agreement with Small Angle Neutron Scattering (SANS) measurements of the filament helix pitch in ReCA::ADP-AlF 4 complex at various salt concentrations. © 2006 Wiley-Liss, Inc.},
author_keywords={Homologous recombination;  Molecular modeling;  RecA filament helix pitch;  RecA mobile N-terminal domain;  SANS},
correspondence_address1={Petukhov, M.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, 188300, St. Petersburg, Russian Federation; email: pmg@omrb.pnpi.spb.ru},
issn={08873585},
coden={PSFGE},
pubmed_id={16909421},
language={English},
abbrev_source_title={Proteins Struct. Funct. Genet.},
document_type={Article},
source={Scopus},
}

RecA protein is a central enzyme in homologous DNA recombination, repair and other forms of DNA metabolism in bacteria. It functions as a flexible helix-shaped filament bound on stretched single-stranded or double-stranded DNA in the presence of ATP. In this work, we present an atomic level model for conformational transitions of the RecA filament. The model describes small movements of the RecA N-terminal domain due to coordinated rotation of main chain dihedral angles of two amino acid residues (Psi/Lys23 and Phi/Gly24), while maintaining unchanged the RecA intersubunit interface. The model is able to reproduce a wide range of observed helix pitches in transitions between compressed and stretched conformations of the RecA filament. Predictions of the model are in agreement with Small Angle Neutron Scattering (SANS) measurements of the filament helix pitch in ReCA::ADP-AlF 4 complex at various salt concentrations. © 2006 Wiley-Liss, Inc.

@ARTICLE{Pal20066279,
author={Pal, P. and Lebedev, D. and Salim, S. and Knauf, P.A.},
title={Substrates induce conformational changes in human anion exchanger 1 (hAE1) as observed by fluorescence resonance energy transfer},
journal={Biochemistry},
year={2006},
volume={45},
number={20},
pages={6279-6295},
doi={10.1021/bi051916r},
note={cited By 5},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33646894111&doi=10.1021%2fbi051916r&partnerID=40&md5=f2da086a938612c1b281b0d2de4acb18},
affiliation={Department of Biochemistry and Biophysics, University of Rochester, Box 712, 601 Elmwood Avenue, Rochester, NY 14642, United States; Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, United States; St. Petersburg Nuclear Physics Institute, RAS Gatchina, Leningrad, District 188300, Russian Federation},
abstract={The one-for-one exchange of Cl- and HCO3- ions is catalyzed by human erythrocyte anion exchanger 1 (hAE1) through a ping-pong mechanism whereby the protein exists in two main conformations, with the single anion-binding site exposed at either the cytoplasmic (inner) side (Ei) or the extracellular side (Eo), with interconversion between the two states being possible only after anion binding. Steady-state and time-resolved resonance energy transfer (FRET) techniques were used to determine the distance of the binding site for diTBA (bis-(1,3- diethylthiobarbituric acid)trimethine oxonol), a high affinity fluorescent oxonol inhibitor of hAE1, from a benchmark site (probably Lys-430) labeled by external fluorescein maleimide (FM). Using red cell ghost membranes, energy transfer distances were measured in media containing different anions between FM as the donor, covalently attached to one monomer, and diTBA as the acceptor, reversibly bound to the adjacent monomer of a hAE1 dimer. Energy transfer increased significantly in chloride or bicarbonate buffers relative to conditions where no transportable anions were present, that is, in citrate buffer. These differences in transfer efficiencies were interpreted in light of the conformational distributions of hAE1 in various buffers and the possible effects of diTBA itself on the distribution. The analysis indicates that the diTBA binding site comes closer to the FM site by ∼7 Å in chloride buffer as compared to that in citrate (or equivalent changes in diTBA orientation occur) because of the effects of anion binding. This provides the first direct physical evidence for structural changes in hAE1 induced by substrates. © 2006 American Chemical Society.},
correspondence_address1={Pal, P.; Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, United States; email: ppal@med.unc.edu},
issn={00062960},
coden={BICHA},
pubmed_id={16700540},
language={English},
abbrev_source_title={Biochemistry},
document_type={Article},
source={Scopus},
}

The one-for-one exchange of Cl- and HCO3- ions is catalyzed by human erythrocyte anion exchanger 1 (hAE1) through a ping-pong mechanism whereby the protein exists in two main conformations, with the single anion-binding site exposed at either the cytoplasmic (inner) side (Ei) or the extracellular side (Eo), with interconversion between the two states being possible only after anion binding. Steady-state and time-resolved resonance energy transfer (FRET) techniques were used to determine the distance of the binding site for diTBA (bis-(1,3- diethylthiobarbituric acid)trimethine oxonol), a high affinity fluorescent oxonol inhibitor of hAE1, from a benchmark site (probably Lys-430) labeled by external fluorescein maleimide (FM). Using red cell ghost membranes, energy transfer distances were measured in media containing different anions between FM as the donor, covalently attached to one monomer, and diTBA as the acceptor, reversibly bound to the adjacent monomer of a hAE1 dimer. Energy transfer increased significantly in chloride or bicarbonate buffers relative to conditions where no transportable anions were present, that is, in citrate buffer. These differences in transfer efficiencies were interpreted in light of the conformational distributions of hAE1 in various buffers and the possible effects of diTBA itself on the distribution. The analysis indicates that the diTBA binding site comes closer to the FM site by ∼7 Å in chloride buffer as compared to that in citrate (or equivalent changes in diTBA orientation occur) because of the effects of anion binding. This provides the first direct physical evidence for structural changes in hAE1 induced by substrates. © 2006 American Chemical Society.

@ARTICLE{Ryzhov2006,
author={Ryzhov, V.A. and Lazuta, A.V. and Kiselev, I.A. and Khavronin, V.P. and Molkanov, P.L. and Troaynchuk, I.O. and Trukhanov, S.V.},
title={Unusual peculiarities of paramagnet to ferromagnet phase transition in La0.88MnO2.91},
journal={Journal of Magnetism and Magnetic Materials},
year={2006},
volume={300},
number={1},
pages={e159-e162},
doi={10.1016/j.jmmm.2005.10.173},
note={cited By 10; Conference of Third International Symposium on Magnetism 2005 ; Conference Date: 26 June 2005 Through 30 June 2005;  Conference Code:66801},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33644651864&doi=10.1016%2fj.jmmm.2005.10.173&partnerID=40&md5=a7a47b935db064f08233dce6d369b809},
affiliation={Petersburg Nuclear Physics Institute, RAS, Gatchina, St. Petersburg, 188300, Russian Federation; Institute of Physics of Solids and Semiconductors, National Academy of Sciences, ul. P. Brovki 17, 220072, Minsk, Belarus},
abstract={Study of the linear and nonlinear magnetic responses as well as electron spin resonance (ESR) is presented for insulating La0.88MnO 2.91 with TC≈216K. According to the data on the second harmonic of magnetization (M2), this compound exhibits an unconventional paramagnet to ferromagnet (PF) phase transition. A critical behavior of the system is found to agree with a prediction for a 3D isotropic ferromagnet in the P-region above T*≈247 K. Below T*, an anomalous phase develops whose properties differ radically from those of a magnet exhibiting an usual PF transition. This phase originates in a ferromagnetically ordered state and reveals a strong nonlinear behavior in the weak fields. The ESR data, which are obtained in the essentially higher field and frequency than those in the M 2 measurements, agree with the conventional critical behavior above 225 K, indicating a strong suppression of the anomalous response by the field. These peculiarities are close to those found in the usually doped Nd 1-xBaxMnO3 (x=0.23, 0.25) manganites. It supports an assumption on universal character of this phenomenon, namely, formation of a heterogeneous magnetic state with the coexistence of the anomalous and traditional phases. Since this compound is near a border of a metal to insulator transition, the anomalous phase is assumed to exhibit a ferromagnetic metallic state whereas the traditional one is a ferromagnetic insulator. Formation of this nontrivial state is attributed to a strong coupling of the orbital, Jahn-Teller phonons and charge degrees of freedom with the magnetic ones. © 2005 Elsevier B.V. All rights reserved.},
author_keywords={Electron paramagnetic resonance;  Magnetically ordered materials;  Nonlinear response;  Phase transition},
correspondence_address1={Ryzhov, V.A.; Petersburg Nuclear Physics Institute, RAS, Gatchina, St. Petersburg, 188300, Russian Federation; email: ryzhov@omrb.pnpi.spb.ru},
editor={Perov N.},
issn={03048853},
coden={JMMMD},
language={English},
abbrev_source_title={J Magn Magn Mater},
document_type={Article},
source={Scopus},
}

Study of the linear and nonlinear magnetic responses as well as electron spin resonance (ESR) is presented for insulating La0.88MnO 2.91 with TC≈216K. According to the data on the second harmonic of magnetization (M2), this compound exhibits an unconventional paramagnet to ferromagnet (PF) phase transition. A critical behavior of the system is found to agree with a prediction for a 3D isotropic ferromagnet in the P-region above T*≈247 K. Below T*, an anomalous phase develops whose properties differ radically from those of a magnet exhibiting an usual PF transition. This phase originates in a ferromagnetically ordered state and reveals a strong nonlinear behavior in the weak fields. The ESR data, which are obtained in the essentially higher field and frequency than those in the M 2 measurements, agree with the conventional critical behavior above 225 K, indicating a strong suppression of the anomalous response by the field. These peculiarities are close to those found in the usually doped Nd 1-xBaxMnO3 (x=0.23, 0.25) manganites. It supports an assumption on universal character of this phenomenon, namely, formation of a heterogeneous magnetic state with the coexistence of the anomalous and traditional phases. Since this compound is near a border of a metal to insulator transition, the anomalous phase is assumed to exhibit a ferromagnetic metallic state whereas the traditional one is a ferromagnetic insulator. Formation of this nontrivial state is attributed to a strong coupling of the orbital, Jahn-Teller phonons and charge degrees of freedom with the magnetic ones. © 2005 Elsevier B.V. All rights reserved.

@ARTICLE{Lazuta200644,
author={Lazuta, A.V. and Ryzhov, V.A. and Smirnov, O.P. and Kiselev, I.A. and Chernenkov, Y.P. and Borisov, S.A. and Troaynchuk, I.O. and Khalyavin, D.D.},
title={Neutron diffraction and ESR studies of pseudocubic Nd0.75Ba 0.25MnO3 and its unusual critical behavior above T C},
journal={Journal of Magnetism and Magnetic Materials},
year={2006},
volume={300},
number={1},
pages={44-47},
doi={10.1016/j.jmmm.2005.10.029},
note={cited By 2; Conference of Third International Symposium on Magnetism 2005 ; Conference Date: 26 June 2005 Through 30 June 2005;  Conference Code:66801},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33644638929&doi=10.1016%2fj.jmmm.2005.10.029&partnerID=40&md5=2a9e0685091307a3472c31d1894d5cd8},
affiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciencies, Gatchina, St. Petersburg 188300, Russian Federation; Institute of Physics of Solids and Semiconductors, National Academy of Sciences, ul. P. Brovki 17, 220072 Minsk, Belarus},
abstract={Results of structural neutron diffraction study and electron spin resonance (ESR) measurements are presented for insulating Nd1- xBaxMnO3 (x=0.25) with the Curie temperature TC≈129K. Its pseudocubic structure reveals the definite distortions to a lower symmetry. Detailed analysis of the data is performed in the frame of Pbnm space group in a temperature range 4.2-300 K. The compound is found to exhibit the Jahn-Teller (JT) transition at TJT≈250 K. Character of the coherent JT distortions and their temperature evolution differ from those of the x=0.23 manganite. The ESR results correspond to behavior of a 3D isotropic ferromagnet above T*≈143K (τ*≈0.12≤τ<1, τ=(T-TC)/TC). It is shown that an anisotropic exchange coupling of the Mn and Nd magnetic moments may give a substantial contribution in ESR linewidth masking its critical enhancement. The different temperature treatments (slow/fast cooling/heating with/without external magnetic field) of the sample reveal a temperature hysteresis of the ESR spectra below T* indicating an anomalous response in the paramagnetic region. The study of the magnetic phase transition in the x=0.23 and 0.25 NdBa manganites suggests a change in its character from the second to first order at T*. The conventional free energy including the magnetization and magnetic field failed to describe this first-order transition. The unconventional critical behavior is attributed to an orbital liquid metallic phase that begins to coexist with the initial orbital-ordered phases below T*. © 2005 Elsevier B.V. All rights reserved.},
author_keywords={Electron paramagnetic resonance;  Magnetically ordered materials;  Neutron scattering;  Phase transitions},
correspondence_address1={Lazuta, A.V.; Petersburg Nuclear Physics Institute, Russian Academy of Sciencies, Gatchina, St. Petersburg 188300, Russian Federation; email: alexandr@VL9467.spb.edu},
editor={Perov N.},
issn={03048853},
coden={JMMMD},
language={English},
abbrev_source_title={J Magn Magn Mater},
document_type={Article},
source={Scopus},
}

Results of structural neutron diffraction study and electron spin resonance (ESR) measurements are presented for insulating Nd1- xBaxMnO3 (x=0.25) with the Curie temperature TC≈129K. Its pseudocubic structure reveals the definite distortions to a lower symmetry. Detailed analysis of the data is performed in the frame of Pbnm space group in a temperature range 4.2-300 K. The compound is found to exhibit the Jahn-Teller (JT) transition at TJT≈250 K. Character of the coherent JT distortions and their temperature evolution differ from those of the x=0.23 manganite. The ESR results correspond to behavior of a 3D isotropic ferromagnet above T*≈143K (τ*≈0.12≤τ<1, τ=(T-TC)/TC). It is shown that an anisotropic exchange coupling of the Mn and Nd magnetic moments may give a substantial contribution in ESR linewidth masking its critical enhancement. The different temperature treatments (slow/fast cooling/heating with/without external magnetic field) of the sample reveal a temperature hysteresis of the ESR spectra below T* indicating an anomalous response in the paramagnetic region. The study of the magnetic phase transition in the x=0.23 and 0.25 NdBa manganites suggests a change in its character from the second to first order at T*. The conventional free energy including the magnetization and magnetic field failed to describe this first-order transition. The unconventional critical behavior is attributed to an orbital liquid metallic phase that begins to coexist with the initial orbital-ordered phases below T*. © 2005 Elsevier B.V. All rights reserved.

@ARTICLE{Solovyov2006543,
author={Solovyov, K.V. and Gasteva, A.A. and Egorov, V.V. and Aleinikova, T.D. and Sirotkin, A.K. and Shvartsman, A.L. and Shavlovsky, M.M.},
title={Role of the C-terminal fragment of human transthyretin in abnormal fibrillogenesis},
journal={Biochemistry (Moscow)},
year={2006},
volume={71},
number={5},
pages={543-549},
doi={10.1134/S0006297906050129},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33744522336&doi=10.1134%2fS0006297906050129&partnerID=40&md5=03b58d785fea6a3cd0dc686f204c3ddd},
affiliation={Department of Molecular Genetics, Institute of Experimental Medicine, Russian Academy of Medical Sciences, ul. Akademika Pavlova 12, 197376 St. Petersburg, Russian Federation; Institute of Influenza, Russian Academy of Medical Sciences, ul. Professora Popova 15/17, 196376 St. Petersburg, Russian Federation},
abstract={Polypeptide chain fragments of recombinant transthyretin (TTR) with leucine-55 substituted by proline (L55P), which are involved in abnormal fibrillogenesis of this protein, were studied. No fibrils were produced in purified preparations of TTR(L55P) under the optimum conditions for fibrillogenesis but in absence of protease inhibitors. The ability of TTR for fibrillogenesis was lost because of a limited proteolysis resulting in detachment of the TTR polypeptide chain C-terminal fragment of ∼ 18 amino acid residues in length. This proteolysis seemed to occur with involvement of a bacterial serine endopeptidase sohB (EC 3.4.21), which was identified in TTR preparations by the MALDI-TOF method. The presence of the C-terminal fragment of the TTR polypeptide chain seems to be crucial for production of abnormal fibrils. © Pleiades Publishing, Inc., 2006.},
author_keywords={Aggregations;  Amyloidoses;  Fibrillogenesis;  Transthyretin;  TTR (L55P)},
correspondence_address1={Solovyov, K.V.; Department of Molecular Genetics, Institute of Experimental Medicine, Russian Academy of Medical Sciences, ul. Akademika Pavlova 12, 197376 St. Petersburg, Russian Federation; email: kak-nikak@mail.ru},
issn={00062979},
coden={BIORA},
pubmed_id={16732734},
language={English},
abbrev_source_title={Biochemistry Moscow},
document_type={Article},
source={Scopus},
}

Polypeptide chain fragments of recombinant transthyretin (TTR) with leucine-55 substituted by proline (L55P), which are involved in abnormal fibrillogenesis of this protein, were studied. No fibrils were produced in purified preparations of TTR(L55P) under the optimum conditions for fibrillogenesis but in absence of protease inhibitors. The ability of TTR for fibrillogenesis was lost because of a limited proteolysis resulting in detachment of the TTR polypeptide chain C-terminal fragment of ∼ 18 amino acid residues in length. This proteolysis seemed to occur with involvement of a bacterial serine endopeptidase sohB (EC 3.4.21), which was identified in TTR preparations by the MALDI-TOF method. The presence of the C-terminal fragment of the TTR polypeptide chain seems to be crucial for production of abnormal fibrils. © Pleiades Publishing, Inc., 2006.

@ARTICLE{Lebedev200525,
author={Lebedev, D.V.},
title={On influence of uncertainty of the inertia matrix upon microsatellite stabilization},
journal={Journal of Automation and Information Sciences},
year={2005},
volume={37},
number={12},
pages={25-34},
doi={10.1615/J Automat Inf Scien.v37.i12.40},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33644949694&doi=10.1615%2fJ+Automat+Inf+Scien.v37.i12.40&partnerID=40&md5=b89b776a3840e597bfe0c5362ad47812},
abstract={For a space vehicle of the microsatellite type, which revolves along a circular orbit and is equipped with a magnetic attitude and stabilization control system, the influence of uncertainty of information about values of the elements of the inertia matrix upon its orbital orientation is investigated. © 2005 by Begell House, Inc.},
author_keywords={Control system;  Inertia matrix;  Satellite;  Stabilization;  Uncertainty},
issn={10642315},
language={English},
abbrev_source_title={J Autom Inform Sci},
document_type={Conference Paper},
source={Scopus},
}

For a space vehicle of the microsatellite type, which revolves along a circular orbit and is equipped with a magnetic attitude and stabilization control system, the influence of uncertainty of information about values of the elements of the inertia matrix upon its orbital orientation is investigated. © 2005 by Begell House, Inc.

@ARTICLE{Danilova200543,
author={Danilova, I.G. and Shevelev, I.V. and Isaev-Ivanov, V.V. and Noskin, L.A.},
title={Molecular bases of regulation of the enzymatic activity of bovine pancreatic deoxyribonuclease I as determined by laser correlation and fluorescence spectroscopy},
journal={Biophysics},
year={2005},
volume={50},
number={1},
pages={43-55},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750521132&partnerID=40&md5=98a38229da090f2c54a7c8f095264f53},
affiliation={Konstantinov St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad Region, 188300, Russian Federation},
abstract={The effect of activating divalent and inhibiting monovalent cations on the interactions of bovine pancreatic deoxyribonuclease I with phage M13 circular single-stranded DNA was studied. The effect of the monovalent cations on the DNA-binding site and the active site of the enzyme was determined, and disturbance of the formation of an enzyme-substrate complex in the presence of these ions was detected. The totality of the results obtained proved that the protein molecule undergoes much more significant conformational changes that those expected from the previously published x-ray diffraction data. Copyright © 2005 by MAIK "Nauka/Interperiodica".},
author_keywords={Bovine pancreatic deoxyribonuclease I;  Fluorescence spectroscopy;  Laser correlation spectroscopy;  Protein-DNA interactions},
correspondence_address1={Danilova, I.G.; Konstantinov St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad Region, 188300, Russian Federation},
issn={00063509},
language={English},
abbrev_source_title={Biophysics},
document_type={Article},
source={Scopus},
}

The effect of activating divalent and inhibiting monovalent cations on the interactions of bovine pancreatic deoxyribonuclease I with phage M13 circular single-stranded DNA was studied. The effect of the monovalent cations on the DNA-binding site and the active site of the enzyme was determined, and disturbance of the formation of an enzyme-substrate complex in the presence of these ions was detected. The totality of the results obtained proved that the protein molecule undergoes much more significant conformational changes that those expected from the previously published x-ray diffraction data. Copyright © 2005 by MAIK "Nauka/Interperiodica".

@ARTICLE{Kurbakov2005,
author={Kurbakov, A.I. and Lazuta, A.V. and Ryzhov, V.A. and Trounov, V.A. and Larionov, I.I. and Martin, C. and Maignan, A. and Hervieu, M.},
title={Crystal structure and magnetic and transport properties of Sm0.5154Sr0.5MnO3: A-type antiferromagnetic phase and ferromagnetic polarons},
journal={Physical Review B - Condensed Matter and Materials Physics},
year={2005},
volume={72},
number={18},
doi={10.1103/PhysRevB.72.184432},
art_number={184432},
note={cited By 27},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-29644445737&doi=10.1103%2fPhysRevB.72.184432&partnerID=40&md5=40a7f9806cb5918b8fb488391b39671a},
affiliation={Petersburg Nuclear Physics Institute RAS, Gatchina, St. Petersburg 188300, Russian Federation; Laboratoire CRISMAT, UMR 6508 ISMRA, Universite de Caen, Boulevard de Marechal Juin, 14050 Caen, France},
abstract={Structural investigations (neutron diffraction and electron microscopy), as well as data on resistance, magnetization, and second harmonic of magnetization, are presented for Sm0.5154Sr0.5MnO3 manganite. The neutron diffraction studies reveal a structural phase transition at Tst≈135K from a high-temperature Pbnm space group to a mixture of two Pbnm phases, which are coherently coupled by atomic positions but differ in cell parameters. Above Tst, this compound is a paramagnetic insulator. At room temperature, a strained and complex nanostructure state is observed in the high-resolution electron microscopy images. In the Pbnm structure it is generated by the coexistence of twinning domains and a small deviation from orthorhombicity for a monoclinic structure. Below Tst, both structural phases begin to exhibit coherent Jahn-Teller distortions, which are different in the two phases. The structural transition is accompanied by the development of a magnetic ordering, so that the ground state is a mixture of ferromagnetism (F) and A-type antiferromagnetism (AF-A). The AF-A order develops in the new low-temperature structural phase II, whereas the F moment is related to the high-temperature structure I. The several variants of the magnetic ordering are considered for phase I. A more physically justified scenario is that this phase does not possess an AF-A component and exhibits F ordering with an F moment of 1.9(1)μB Mn at 1.5K. In this case, the AF moment of phase II is found to be 4.1(1)μB Mn at 1.5K. This unexpected result is attributed to the formation of ferromagnetic polarons in connection with a new electronic structure proposed for the AF-A state. A metalliclike behavior is only observed below 50K and is related to the F phase. The AF-A phase is expected to be insulating. It can exhibit a short-range charge ordering that is observed by electron diffraction at 92K. A field hysteresis of the second harmonic is found above TC∼TN≈Tst, which is associated with AF-A regions in the paramagnetic matrix which possess a weak ferromagnetism. © 2005 The American Physical Society.},
correspondence_address1={Kurbakov, A.I.; Petersburg Nuclear Physics Institute RAS, Gatchina, St. Petersburg 188300, Russian Federation},
issn={10980121},
coden={PRBMD},
language={English},
abbrev_source_title={Phys. Rev. B Condens. Matter Mater. Phys.},
document_type={Article},
source={Scopus},
}

Structural investigations (neutron diffraction and electron microscopy), as well as data on resistance, magnetization, and second harmonic of magnetization, are presented for Sm0.5154Sr0.5MnO3 manganite. The neutron diffraction studies reveal a structural phase transition at Tst≈135K from a high-temperature Pbnm space group to a mixture of two Pbnm phases, which are coherently coupled by atomic positions but differ in cell parameters. Above Tst, this compound is a paramagnetic insulator. At room temperature, a strained and complex nanostructure state is observed in the high-resolution electron microscopy images. In the Pbnm structure it is generated by the coexistence of twinning domains and a small deviation from orthorhombicity for a monoclinic structure. Below Tst, both structural phases begin to exhibit coherent Jahn-Teller distortions, which are different in the two phases. The structural transition is accompanied by the development of a magnetic ordering, so that the ground state is a mixture of ferromagnetism (F) and A-type antiferromagnetism (AF-A). The AF-A order develops in the new low-temperature structural phase II, whereas the F moment is related to the high-temperature structure I. The several variants of the magnetic ordering are considered for phase I. A more physically justified scenario is that this phase does not possess an AF-A component and exhibits F ordering with an F moment of 1.9(1)μB Mn at 1.5K. In this case, the AF moment of phase II is found to be 4.1(1)μB Mn at 1.5K. This unexpected result is attributed to the formation of ferromagnetic polarons in connection with a new electronic structure proposed for the AF-A state. A metalliclike behavior is only observed below 50K and is related to the F phase. The AF-A phase is expected to be insulating. It can exhibit a short-range charge ordering that is observed by electron diffraction at 92K. A field hysteresis of the second harmonic is found above TC∼TN≈Tst, which is associated with AF-A regions in the paramagnetic matrix which possess a weak ferromagnetism. © 2005 The American Physical Society.

@ARTICLE{Trukhanov20056495,
author={Trukhanov, S.V. and Lobanovski, L.S. and Bushinsky, M.V. and Fedotova, V.V. and Troyanchuk, I.O. and Trukhanov, A.V. and Ryzhov, V.A. and Szymczak, H. and Szymczak, R. and Baran, M.},
title={Study of A-site ordered PrBaMn2O6-δ manganite properties depending on the treatment conditions},
journal={Journal of Physics Condensed Matter},
year={2005},
volume={17},
number={41},
pages={6495-6506},
doi={10.1088/0953-8984/17/41/019},
note={cited By 49},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-26444470912&doi=10.1088%2f0953-8984%2f17%2f41%2f019&partnerID=40&md5=4f380f1bb37172ef8aa934ea28dd317e},
affiliation={Institute of Solids and Semiconductor Physics of NASB, P Brovka Street 17, 220072 Minsk, Belarus; Chemistry Department, Vitebsk State University, Moscow Avenue 33, 210036 Vitebsk, Belarus; Petersburg Nuclear Physics Institute RAS, Gatchina, St Petersburg 188300, Russian Federation; Institute of Physics, PAS, Lotnikov street 32/46, 02-668 Warsaw, Poland},
abstract={The effect of treatment conditions on the magnetic and magnetotransport properties of A-site ordered PrBaMn2O6-δ manganites is examined. The parent oxygen-stoichiometric A-site ordered PrBaMn 2O6 samples were prepared from oxygen-stoichiometric A-site disordered Pr0.50Ba0.50MnO3 ones by using a 'two-step' synthesis method. The most significant structural feature of the A-site ordered manganites is that the MnO2 sublattice is sandwiched by two kinds of rock-salt layers, PrOx and BaO. The oxygen-stoichiometric A-site ordered PrBaMn2O6 demonstrates a ferromagnetic metal to paramagnetic insulator transition with the Curie point at about 320 K. These compounds are stable in air up to 1300 °C. The A-site ordered PrBaMn2O6 samples were next reduced in flowing argon as well as being treated under high pressure conditions. The reduction of the A-site ordered PrBaMn2O6 samples leads to the appearance of an antiferromagnetic state with a Néel point of about 140 K, while the A-site order remains. Upon high pressure treatment the degree of A-site order decreases, which reduces TC to 180 K. The magnetotransport properties of A-site ordered manganites treated under different conditions are discussed in terms of the manganese valence, oxygen content and degree of A-site order. © 2005 IOP Publishing Ltd.},
correspondence_address1={Trukhanov, S.V.; Institute of Solids and Semiconductor Physics of NASB, P Brovka Street 17, 220072 Minsk, Belarus},
issn={09538984},
coden={JCOME},
language={English},
abbrev_source_title={J Phys Condens Matter},
document_type={Review},
source={Scopus},
}

The effect of treatment conditions on the magnetic and magnetotransport properties of A-site ordered PrBaMn2O6-δ manganites is examined. The parent oxygen-stoichiometric A-site ordered PrBaMn 2O6 samples were prepared from oxygen-stoichiometric A-site disordered Pr0.50Ba0.50MnO3 ones by using a 'two-step' synthesis method. The most significant structural feature of the A-site ordered manganites is that the MnO2 sublattice is sandwiched by two kinds of rock-salt layers, PrOx and BaO. The oxygen-stoichiometric A-site ordered PrBaMn2O6 demonstrates a ferromagnetic metal to paramagnetic insulator transition with the Curie point at about 320 K. These compounds are stable in air up to 1300 °C. The A-site ordered PrBaMn2O6 samples were next reduced in flowing argon as well as being treated under high pressure conditions. The reduction of the A-site ordered PrBaMn2O6 samples leads to the appearance of an antiferromagnetic state with a Néel point of about 140 K, while the A-site order remains. Upon high pressure treatment the degree of A-site order decreases, which reduces TC to 180 K. The magnetotransport properties of A-site ordered manganites treated under different conditions are discussed in terms of the manganese valence, oxygen content and degree of A-site order. © 2005 IOP Publishing Ltd.

@CONFERENCE{Malkov2005164,
author={Malkov, V.M. and Savin, A.V. and Kiselev, I.A.},
title={Diffusera of COIL and DF-lasers},
journal={Proceedings of SPIE - The International Society for Optical Engineering},
year={2005},
volume={5777},
number={PART I},
pages={164-169},
doi={10.1117/12.611004},
art_number={29},
note={cited By 7; Conference of XV International Symposium on Gas Flow, Chemical Lasers, and High-Power Lasers, GCL/HPL 2004 ; Conference Date: 30 August 2004 Through 3 September 2004;  Conference Code:65752},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-26444580270&doi=10.1117%2f12.611004&partnerID=40&md5=2cbf60aefad6d937025c86c57ba00e97},
affiliation={Laser Systems Ltd, 1st Krasnoarmeyskaya, 1, St.- Petersburg 190005, Russian Federation},
abstract={The slow down process of supersonic flow in channel of chemical lasers - DF-lasers and COIL - is discussed. Particularity of these processes in case of chemical laser is determined by heat generation existing in the active laser medium. Heat generation is determined by physics of laser and lead to reduction of slow down zone - pseudo-shock zone. So diffuser of chemical lasers must be shorter than traditional diffuser.},
author_keywords={Chemical laser;  Diffuser;  Pseudo-shock;  Shock;  Slow down of supersonic flow},
correspondence_address1={Malkov, V.M.; Laser Systems Ltd, 1st Krasnoarmeyskaya, 1, St.- Petersburg 190005, Russian Federation; email: office@lsystems.ru},
editor={Kodymova J.},
sponsors={SPIE - The Int. Society for Optical Engineering; EOARD, AFOSR,US Airforce Research Laboratory},
address={Prague},
issn={0277786X},
coden={PSISD},
language={English},
abbrev_source_title={Proc SPIE Int Soc Opt Eng},
document_type={Conference Paper},
source={Scopus},
}

The slow down process of supersonic flow in channel of chemical lasers - DF-lasers and COIL - is discussed. Particularity of these processes in case of chemical laser is determined by heat generation existing in the active laser medium. Heat generation is determined by physics of laser and lead to reduction of slow down zone - pseudo-shock zone. So diffuser of chemical lasers must be shorter than traditional diffuser.

@ARTICLE{Ryzhov2005,
author={Ryzhov, V.A. and Lazuta, A.V. and Smirnov, O.P. and Kiselev, I.A. and Chernenkov, Yu.P. and Borisov, S.A. and Troaynchuk, I.O. and Khalyavin, D.D.},
title={Neutron diffraction, magnetization, and ESR studies of pseudocubic Nd0.75Ba0.25MnO3 and its critical behavior above TC},
journal={Physical Review B - Condensed Matter and Materials Physics},
year={2005},
volume={72},
number={13},
doi={10.1103/PhysRevB.72.134427},
art_number={134427},
note={cited By 15},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-29844451322&doi=10.1103%2fPhysRevB.72.134427&partnerID=40&md5=8a1450f7f6e80b6470f4695a7fd9090e},
affiliation={Petersburg Nuclear Physics Institute, Leningrad District, Gatchina, 188300, Russian Federation; Institute of Physics of Solids and Semiconductors, National Academy of Sciences, ul. P. Brovki street 17, Minsk, 220072, Belarus},
abstract={Results of structural neutron diffraction study, magnetization, and electron spin resonance (ESR) measurements are presented for insulating Nd1-xBaxMnO3(x=0.25) with the Curie temperature TC129K. Detailed analysis of the data is performed by using Pbnm space group in a temperature range 4.2-300 K. The compound is found to exhibit the Jahn-Teller (JT) transition at TJT∼250K. The character of the coherent JT distortions and their temperature evolution differ from those of the x=0.23 manganite. The field cooled magnetization data are in reasonable agreement with the predictions for a three-dimensional (3D) isotropic ferromagnet above TC. These measurements, however, reveal a difference between the field cooled and zero field cooled data in the paramagnetic region. The ESR results also correspond with behavior of a 3D isotropic ferromagnet above T*143K[τ*0.12≤τ<1, τ=(T-TC)TC]. The T-dependence of the ESR linewidth is found to be proportional to [Tχ(T)]-1, where χ(T) is the susceptibility. This uncritical behavior results from the anisotropic spin interactions that can be attributed to the Dzyaloshinsky-Moria (DM) coupling. The critical enhancement is not observed. It can be explained by the strong uncritical contribution to the linewidth, and suppression of the critical enhancement by a magnetic field. The different temperature treatments (slow/fast cooling/heating, with/without external magnetic field) of the sample reveal a temperature hysteresis of the ESR spectra below T* indicating an anomalous response in the paramagnetic region. The study of the magnetic phase transition in the x=0.23 and 0.25 manganites suggests change in its character from second to first order at T*. The conventional free energy including the magnetization and magnetic field is not found to describe this first order transition. This suggests that the charge, orbital, and JT phonon degrees of freedom, in addition to magnetization, may be the critical variables, the unusual character of the transition being determined by their coupling. The unconventional critical behavior is attributed to an orbital liquid metallic phase that begins to coexist with the initial orbital ordered phase below T*. © 2005 The American Physical Society.},
correspondence_address1={Ryzhov, V.A.; Petersburg Nuclear Physics Institute, Leningrad District, Gatchina, 188300, Russian Federation},
issn={10980121},
coden={PRBMD},
language={English},
abbrev_source_title={Phys. Rev. B Condens. Matter Mater. Phys.},
document_type={Article},
source={Scopus},
}

Results of structural neutron diffraction study, magnetization, and electron spin resonance (ESR) measurements are presented for insulating Nd1-xBaxMnO3(x=0.25) with the Curie temperature TC129K. Detailed analysis of the data is performed by using Pbnm space group in a temperature range 4.2-300 K. The compound is found to exhibit the Jahn-Teller (JT) transition at TJT∼250K. The character of the coherent JT distortions and their temperature evolution differ from those of the x=0.23 manganite. The field cooled magnetization data are in reasonable agreement with the predictions for a three-dimensional (3D) isotropic ferromagnet above TC. These measurements, however, reveal a difference between the field cooled and zero field cooled data in the paramagnetic region. The ESR results also correspond with behavior of a 3D isotropic ferromagnet above T*143K[τ*0.12≤τ<1, τ=(T-TC)TC]. The T-dependence of the ESR linewidth is found to be proportional to [Tχ(T)]-1, where χ(T) is the susceptibility. This uncritical behavior results from the anisotropic spin interactions that can be attributed to the Dzyaloshinsky-Moria (DM) coupling. The critical enhancement is not observed. It can be explained by the strong uncritical contribution to the linewidth, and suppression of the critical enhancement by a magnetic field. The different temperature treatments (slow/fast cooling/heating, with/without external magnetic field) of the sample reveal a temperature hysteresis of the ESR spectra below T* indicating an anomalous response in the paramagnetic region. The study of the magnetic phase transition in the x=0.23 and 0.25 manganites suggests change in its character from second to first order at T*. The conventional free energy including the magnetization and magnetic field is not found to describe this first order transition. This suggests that the charge, orbital, and JT phonon degrees of freedom, in addition to magnetization, may be the critical variables, the unusual character of the transition being determined by their coupling. The unconventional critical behavior is attributed to an orbital liquid metallic phase that begins to coexist with the initial orbital ordered phase below T*. © 2005 The American Physical Society.

@ARTICLE{Trukhanov20051123,
author={Trukhanov, S.V. and Troyanchuk, I.O. and Fedotova, V.V. and Ryzhov, V.A. and Maignan, A. and Flahaut, D. and Szymczak, H. and Szymczak, R.},
title={Magnetic properties of the nonstoichiometric Sr-doped manganites},
journal={Physica Status Solidi (B) Basic Research},
year={2005},
volume={242},
number={5},
pages={1123-1131},
doi={10.1002/pssb.200402143},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-17444421211&doi=10.1002%2fpssb.200402143&partnerID=40&md5=b1fd333d8500a2d528512d37f00cfd68},
affiliation={Lab. of Nonmetallic Ferromagnets, Inst. Solids and Semiconduct. Phys., Natl. Academy of Sciences of Belarus, P. Brovka str. 17, 220072 Minsk, Belarus; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, St. Petersburg 188300, Russian Federation; Laboratoire CRISMAT, ISMRA, 6 Boulevard du Marrechal Juin, 14050 Caen Cedex, France; Institute of Physics, Polish Academy of Sciences, Lotnikov str. 32/46, 02-668 Warsaw, Poland},
abstract={The chemical phase content, crystal structure, and magnetization for the doped anion-deficient La1-xSrxMnO3-x/2 (x = 0, 0.05, 0.10, 0.20, 0.30) manganites have been studied. The samples undergo the structural phase transition from the O'-orthorhombic to the rhombohedric unit cell at x > 0.10. As doping level and oxygen deficiency increase the samples show a number of magnetic transitions. In the region of 0.05 ≤ x ≤ 0.20 the samples are inhomogeneous ferromagnets while at x = 0.30 they are cluster spin glasses. The temperature of the magnetic moment freezing is ∼45 K. The concentration dependences of the spontaneous magnetization and coercivity as well as magnetic phase diagram have been constructed. The magnetic properties of the anion-deficient Sr-doped samples may be interpreted on the basis of competition of the positive Mn3+(6)-O-Mn3+(6) and negative Mn3+(5)-O-Mn3+(6) isotropic superexchange interactions and impurity phase separation models. © 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
correspondence_address1={Trukhanov, S.V.; Lab. of Nonmetallic Ferromagnets, Inst. Solids and Semiconduct. Phys., Natl. Academy of Sciences of Belarus, P. Brovka str. 17, 220072 Minsk, Belarus; email: truhanov@ifttp.bas-net.by},
issn={03701972},
language={English},
abbrev_source_title={Phys. Status Solidi B Basic Res.},
document_type={Article},
source={Scopus},
}

The chemical phase content, crystal structure, and magnetization for the doped anion-deficient La1-xSrxMnO3-x/2 (x = 0, 0.05, 0.10, 0.20, 0.30) manganites have been studied. The samples undergo the structural phase transition from the O'-orthorhombic to the rhombohedric unit cell at x > 0.10. As doping level and oxygen deficiency increase the samples show a number of magnetic transitions. In the region of 0.05 ≤ x ≤ 0.20 the samples are inhomogeneous ferromagnets while at x = 0.30 they are cluster spin glasses. The temperature of the magnetic moment freezing is ∼45 K. The concentration dependences of the spontaneous magnetization and coercivity as well as magnetic phase diagram have been constructed. The magnetic properties of the anion-deficient Sr-doped samples may be interpreted on the basis of competition of the positive Mn3+(6)-O-Mn3+(6) and negative Mn3+(5)-O-Mn3+(6) isotropic superexchange interactions and impurity phase separation models. © 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 μm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales. © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

@ARTICLE{Danilova200549,
author={Danilova, I.G. and Shevelev, I.V. and Isaev-Ivanov, V.V. and Noskin, L.A.},
title={Molecular reasons for the regulation of the enzymatic activity of bovine pancreatic deoxyribonuclease I as studied by dynamic light scattering and fluorescent spectroscopy},
journal={Biofizika},
year={2005},
volume={50},
number={1},
pages={49-61},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-18244386022&partnerID=40&md5=b9503753f0af12d8374b93c11af984ea},
abstract={The effect of catalytic bivalent and inhibitory monovalent cations on the interactions of bovine pancreatic deoxyribonuclease I with the circle single-stranded DNA of M13 phase was studied. It was found that monovalent cations affect the site of binding to DNA and the active center of the enzyme; in their presence, a break of the formation of the enzyme-substrate complex occurs. The results provide evidence that conformational changes of the protein molecule in all cases are more substantial that it could be expected from X-ray data published earlier.},
correspondence_address1={Danilova, I.G.},
issn={00063029},
pubmed_id={15759502},
language={Russian},
abbrev_source_title={Biofizika},
document_type={Article},
source={Scopus},
}

The effect of catalytic bivalent and inhibitory monovalent cations on the interactions of bovine pancreatic deoxyribonuclease I with the circle single-stranded DNA of M13 phase was studied. It was found that monovalent cations affect the site of binding to DNA and the active center of the enzyme; in their presence, a break of the formation of the enzyme-substrate complex occurs. The results provide evidence that conformational changes of the protein molecule in all cases are more substantial that it could be expected from X-ray data published earlier.

@CONFERENCE{Bayramov20043134,
author={Bayramov, F.B. and Toporov, V.V. and Petukhov, M. and Glazunov, E.A. and Bairamov, B.H.},
title={Structural properties and dynamics of low-energy collective excitations of water and lisozyme},
journal={Physica Status Solidi C: Conferences},
year={2004},
volume={1},
number={11},
pages={3134-3137},
doi={10.1002/pssc.200405368},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-11044233665&doi=10.1002%2fpssc.200405368&partnerID=40&md5=029557f29cc4058ba8997681f60e3107},
affiliation={Ioffe Physico-Technical Institute, Department of Solid State Physics, RAS, 26 Polytekhnicheskaya ul., 194021 St. Petersburg, Russian Federation; Department of Molecular Biophysics, Petersburg Inst. of Nuclear Physics, RAS, Leningrad region, 188300 Gatchina, Russian Federation},
abstract={We performed inelastic light scattering measurements of the high purity double distilled and deionized water and lysozyme macromolecules in aqueous solutions to reveal the spectral indication of structural disorder of constantly changing hydrogen bonded three-dimensional network. By comparing spectra of lysozyme solution pure water, we find a drastic increase of the central component, indicating corresponding decrease of relaxation time, as well as a strong enhancement of the background scattering. The appearance of the background is correlated with hydrogen bonding in the pure water and different charged molecules in the lysozyme solution. © 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
correspondence_address1={Bayramov, F.B.; Ioffe Physico-Technical Institute, Department of Solid State Physics, RAS, 26 Polytekhnicheskaya ul., 194021 St. Petersburg, Russian Federation; email: farid@cellmedia.com},
issn={16101634},
language={English},
abbrev_source_title={Phys. Status Solidi C Conf.},
document_type={Conference Paper},
source={Scopus},
}

We performed inelastic light scattering measurements of the high purity double distilled and deionized water and lysozyme macromolecules in aqueous solutions to reveal the spectral indication of structural disorder of constantly changing hydrogen bonded three-dimensional network. By comparing spectra of lysozyme solution pure water, we find a drastic increase of the central component, indicating corresponding decrease of relaxation time, as well as a strong enhancement of the background scattering. The appearance of the background is correlated with hydrogen bonding in the pure water and different charged molecules in the lysozyme solution. © 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

We suggest measuring the nuclear-spin-dependent P-odd amplitude in the transitions between hyperfine structure sublevels in the ground state of potassium isotopes. Since the main contribution to this amplitude is due to the anapole moment of the nucleus, such measurements of the P-odd spin-dependent effects may provide new information about weak interactions. It is established that the measurement of such effects with a statistical error within 1% can be performed for approximately 1 h. © 2004 MAIK "Nauka/ Interperiodica".

@ARTICLE{Petukhov20042120,
author={Petukhov, M. and Rychkov, G. and Firsov, L. and Serrano, L.},
title={H-bonding in protein hydration revisited},
journal={Protein Science},
year={2004},
volume={13},
number={8},
pages={2120-2129},
doi={10.1110/ps.04748404},
note={cited By 22},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-3342882423&doi=10.1110%2fps.04748404&partnerID=40&md5=0d9ff327ae21af729ffa5435ab512b9d},
affiliation={Div. Molec./Radiat. Biophys. (OMRB), St. Petersburg Nucl. Phys. Institute, RAS, Gatchina, 188350, St. Petersburg, Russian Federation; Europ. Molec. Biol. Lab. (EMBL), Meyerhofstrasse 1, Heidelberg D-69117, Germany},
abstract={H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water-protein H-bonding at any given protein conformation. The free energy of water-protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.},
author_keywords={H-bonding;  Hydration;  Protein;  Solvent-accessible surface area;  Water},
correspondence_address1={Petukhov, M.; Div. Molec./Radiat. Biophys. (OMRB), St. Petersburg Nucl. Phys. Institute, RAS, Gatchina, 188350, St. Petersburg, Russian Federation; email: pmg@omrb.pnpi.spb.ru},
issn={09618368},
coden={PRCIE},
pubmed_id={15238635},
language={English},
abbrev_source_title={Protein Sci.},
document_type={Article},
source={Scopus},
}

H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water-protein H-bonding at any given protein conformation. The free energy of water-protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.

The data on the resistance and magnetoresistance (MR) as well as measurements of the linear and nonlinear susceptibilities are presented for a Nd0.75Ba0.25MnO3 single crystal with the Curie temperature TC≈129K. Although this compound remains insulating in the ferromagnetic state, its resistance has an anomaly near TC and it reveals the colossal magnetoresistance. The data on the magnetic response are well described by the dynamic scaling theory for 3D isotropic ferromagnets in the paramagnetic critical region at τ≥τ*≈0.11, τ=(T-TC)/TC. Below τ* an anomalous critical behavior is found that suggests the coexistence of two magnetic phases. This behavior is discussed in terms of a phase separation which can occur in the moderately doped manganites exhibiting an orbital ordering. © 2004 Elsevier Ltd. All rights reserved.

Structural neutron diffraction study and electron spin resonance (ESR) measurements are presented for insulating Nd0.77Ba 0.23MnO3 with the Curie temperature TC≈124 K. Its pseudocubic structure exhibits the definite distortions to a low symmetry. A detailed analysis of the data is given for a Pbnm space group in the temperature range 4.2-500 K. A systematic transformation of the crystalline structure, which is accompanied by the peculiarities in the temperature variations of structural parameters, is found. The ESR data are in agreement with the predictions for 3D isotropic ferromagnets in the paramagnetic critical region at τ*≈0.2≤τ<1,τ=(T-TC)/T C. The main disagreement observed below τ* is that the ESR linewidth reveals no the characteristic critical enhancement. The anomalous critical behavior, which is found in the present and our previous studies in this range, is consistent with the development of some structural changes. Different temperature treatments (slow/fast cooling/heating, with/without external magnetic field) of the sample, which usually reveal the possible hysteretic phenomena, have a little effect on the ESR spectra. These results present a challenge to the understanding of the magnetic phase transition in these manganites. © 2003 Elsevier Ltd. All rights reserved.

@ARTICLE{Lazuta2003315,
author={Lazuta, A.V. and Ryzhov, V.A. and Kurbukov, A.I. and Trounov, V.A. and Larionov, I.I. and Gorbenko, O. and Kaul, A.},
title={Magic hole doped composition of 152Sm1-xSrxMnO3 manganite: Crystal structure and unusual magnetic properties in paramagnetic phase at x = 0.45},
journal={Journal of Magnetism and Magnetic Materials},
year={2003},
volume={258-259},
pages={315-318},
doi={10.1016/S0304-8853(02)01153-8},
note={cited By 13; Conference of Second Moscow International Symposium on Magnetism (MISM) ; Conference Date: 20 June 2001 Through 24 June 2001;  Conference Code:60839},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-18544406248&doi=10.1016%2fS0304-8853%2802%2901153-8&partnerID=40&md5=ca977bf2f888c1c2b0f503eb0f078648},
affiliation={Petersburg Nuclear Physics Institute, Gatchina 188350, Russian Federation; Department of Chemistry, Moskow State University, Moskow 119899, Russian Federation},
abstract={Neutron diffraction investigations and data on second harmonic of magnetization are presented for 152Sm0.55Sr0.45MnO3 manganite. The coherent Jahn-Teller distortions are found to occur just below 300 K, collapse at TC∼125 K, and exhibit a rather complicated temperature behavior between these points. Temperature dependence of a spontaneous magnetization evidences the first-order transition at TC and a homogeneous ferromagnetic phase below TC with practically full ferromagnetic alignment at T∼1.5 K. A field hysteresis of the second harmonic is observed above TC that is associated with the CE-type antiferromagnetic regions possessing a weak ferromagnetism, as well as with the ferromagnetic domains. Interconnection of spin and Jahn-Teller phonons degrees of freedom is supposed to account for the inhomogeneous paramagnetic phase with the nontrivial properties. © 2002 Elsevier Science B.V. All rights reserved.},
author_keywords={Jahn-Teller distortion;  Manganite;  Nonlinear response;  Phase separation},
correspondence_address1={Lazuta, A.V.; Petersburg Nuclear Physics Institute, Gatchina 188350, Russian Federation; email: alexandr@vl9467.spb.edu},
editor={Perov N},
address={Moscow},
issn={03048853},
coden={JMMMD},
language={English},
abbrev_source_title={J Magn Magn Mater},
document_type={Conference Paper},
source={Scopus},
}

Neutron diffraction investigations and data on second harmonic of magnetization are presented for 152Sm0.55Sr0.45MnO3 manganite. The coherent Jahn-Teller distortions are found to occur just below 300 K, collapse at TC∼125 K, and exhibit a rather complicated temperature behavior between these points. Temperature dependence of a spontaneous magnetization evidences the first-order transition at TC and a homogeneous ferromagnetic phase below TC with practically full ferromagnetic alignment at T∼1.5 K. A field hysteresis of the second harmonic is observed above TC that is associated with the CE-type antiferromagnetic regions possessing a weak ferromagnetism, as well as with the ferromagnetic domains. Interconnection of spin and Jahn-Teller phonons degrees of freedom is supposed to account for the inhomogeneous paramagnetic phase with the nontrivial properties. © 2002 Elsevier Science B.V. All rights reserved.

The filament structures of the self-polymers of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, their complexes with ATPγS, phage M13 single-stranded DNA (ssDNA) and the tertiary complexes RecA::ATPγS::ssDNA were compared by small angle neutron scattering. A model was developed that allowed for an analytical solution for small angle scattering on a long helical filament, making it possible to obtain the helical pitch and the mean diameter of the protein filament from the scattering curves. The results suggest that the structure of the filaments formed by these two RecA proteins, and particularly their complexes with ATPγS, is conservative. © 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

@ARTICLE{Tarbutt20025013,
author={Tarbutt, M.R. and Hudson, J.J. and Sauer, B.E. and Hinds, E.A. and Ryzhov, V.A. and Ryabov, V.L. and Ezhov, V.F.},
title={A jet beam source of cold YbF radicals},
journal={Journal of Physics B: Atomic, Molecular and Optical Physics},
year={2002},
volume={35},
number={24},
pages={5013-5022},
doi={10.1088/0953-4075/35/24/306},
note={cited By 38},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037192089&doi=10.1088%2f0953-4075%2f35%2f24%2f306&partnerID=40&md5=09d1bc0df964ea307b5b895b81e9b347},
affiliation={Blackett Laboratory, Imperial College, London SW7 2BW, United Kingdom; Petersburg Nuclear Physics Institute, Gatchina, Leningrad 188300, Russian Federation},
abstract={We have developed a pulsed supersonic beam of slow, cold YbF molecular radicals with an intensity of 1.4 × 109 YbF molecules per steradian per pulse in the X 2∑+(v = 0, N = 0) ground state. The translational and rotational temperatures of the beam are equal. The lowest temperature produced was 1.4 K and the slowest centre-of-mass velocity was 290 K. We show that YbF can be made either by ablating Yb metal into a fluorine-bearing carrier gas or by ablating solid precursors into a pure inert carrier gas. This source is suitable for injecting a molecule decelerator and for high-resolution laser-rf-double-resonance studies such as the measurement of the electron electric dipole moment.},
correspondence_address1={Tarbutt, M.R.; Blackett Laboratory, Imperial College, London SW7 2BW, United Kingdom; email: ed.hinds@ic.ac.uk},
issn={09534075},
coden={JPAPE},
language={English},
abbrev_source_title={J Phys B At Mol Opt Phys},
document_type={Article},
source={Scopus},
}

We have developed a pulsed supersonic beam of slow, cold YbF molecular radicals with an intensity of 1.4 × 109 YbF molecules per steradian per pulse in the X 2∑+(v = 0, N = 0) ground state. The translational and rotational temperatures of the beam are equal. The lowest temperature produced was 1.4 K and the slowest centre-of-mass velocity was 290 K. We show that YbF can be made either by ablating Yb metal into a fluorine-bearing carrier gas or by ablating solid precursors into a pure inert carrier gas. This source is suitable for injecting a molecule decelerator and for high-resolution laser-rf-double-resonance studies such as the measurement of the electron electric dipole moment.

@ARTICLE{Petukhov2002766,
author={Petukhov, M. and Uegaki, K. and Yumoto, N. and Serrano, L.},
title={Amino acid intrinsic α-helical propensities III: Positional dependence at several positions of C terminus},
journal={Protein Science},
year={2002},
volume={11},
number={4},
pages={766-777},
doi={10.1110/ps.2610102},
note={cited By 36},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036127566&doi=10.1110%2fps.2610102&partnerID=40&md5=283c9bfbf0cfe8939651d097c7bb4327},
affiliation={European Molecular Biology Laboratory (EMBL), Heidelberg, D-69012, Germany; Division of Molecular and Radiation Biology, St. Petersburg Nuclear Physics Institute, RAS, Gatchina, 188350, St. Petersburg, Russian Federation; Osaka National Research Institute, AIST, Ikeda, Osaka 563, Japan; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg D-69117, Germany},
abstract={In this study, we have analyzed experimentally the helical intrinsic propensities of noncharged and nonaromatic residues at different C-terminal positions (C1, C2, C3) of an Ala-based peptide. The effect was found to be complex, resulting in extra stabilization or destabilization, depending on guest amino acid and position under consideration. Polar (Ser, Thr, Cys, Asn, and Gln) amino acids and Gly were found to have significantly larger helical propensities at several C-terminal positions compared with the α-helix center (-1.0 kcal/mole in some cases). Some of the nonpolar residues, especially β-branched ones (Val and Ile) are significantly more favorable at position C3 (-0.3 to -0.4 kcal/mole), although having minor differences at other C-terminal positions compared with the α-helix center. Leu has moderate (-0.1 to -0.2 kcal/mole) stabilization effects at position C2 and C3, whereas being relatively neutral at C1. Finally, Met was found to be unfavorable at C1 and C2 (+0.2 kcal/mole) and favorable at C3 (-0.2 kcal/mole). Thus, significant differences found between the intrinsic helical propensities at the C-terminal positions and those in the α-helix center must be accounted for in helix/coil transition theories and in protein design.},
author_keywords={α-helix;  C terminus;  Folding;  Secondary structure},
correspondence_address1={Serrano, L.; European Molec. Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany; email: serrano@EMBL-Heidelberg.de},
issn={09618368},
coden={PRCIE},
pubmed_id={11910021},
language={English},
abbrev_source_title={Protein Sci.},
document_type={Article},
source={Scopus},
}

In this study, we have analyzed experimentally the helical intrinsic propensities of noncharged and nonaromatic residues at different C-terminal positions (C1, C2, C3) of an Ala-based peptide. The effect was found to be complex, resulting in extra stabilization or destabilization, depending on guest amino acid and position under consideration. Polar (Ser, Thr, Cys, Asn, and Gln) amino acids and Gly were found to have significantly larger helical propensities at several C-terminal positions compared with the α-helix center (-1.0 kcal/mole in some cases). Some of the nonpolar residues, especially β-branched ones (Val and Ile) are significantly more favorable at position C3 (-0.3 to -0.4 kcal/mole), although having minor differences at other C-terminal positions compared with the α-helix center. Leu has moderate (-0.1 to -0.2 kcal/mole) stabilization effects at position C2 and C3, whereas being relatively neutral at C1. Finally, Met was found to be unfavorable at C1 and C2 (+0.2 kcal/mole) and favorable at C3 (-0.2 kcal/mole). Thus, significant differences found between the intrinsic helical propensities at the C-terminal positions and those in the α-helix center must be accounted for in helix/coil transition theories and in protein design.

The second magnetization harmonic was studied for a moderately doped Nd0.77Ba0.23MnO3 neodymium manganite single crystal in parallel constant and harmonic magnetic fields in the critical paramagnetic region. According to the neutron and X-ray diffraction data, the crystal was crystallographically single-phase and had a pseudocubic structure both at room temperature and below the Curie point Tc = 124.1 K. Although the specific resistance of this compound had a singularity near T c and exhibited giant magnetoresistance, it remained an insulator in the ferromagnetic state. Nonlinear response measurements in the Tc < T < T* ≈ 146.7 K paramagnetic region were indicative of the existence of two magnetic phases. Above T*, the crystal was magnetically single-phase, and its critical behavior was well described by dynamical similarity theory for isotropic 3D ferromagnets. The unexpected appearance of a new magnetic phase in the structurally homogeneous crystal was discussed based on phase separation ideas; such a phase separation could occur in moderately doped cubic manganites experiencing orbital ordering. © 2002 MAIK "Nauka/Interperiodica".

Genetic analysis of RecA protein chimeras and their ancestors, RecAEc (from Escherichia coli) and RecAPa (Pseudomonas aeruginosa) had allowed us to place these proteins with respect to their recombinogenic activities in the following order: RecAPa %#62; RecAX21 %#62; RecAX20 = RecAEc. While RecAX20 differs from RecAEc in five amino acid residues with two substitutions ([S25A] and [126V]) at the interface of subunit interactions in the RecA polymer, RecAX20 and RecAX21 differ only by a single substitution [L29M] present at the interface. Here, we present an analysis of the biochemical properties considered important for the recombinogenic activity of all four RecA proteins. While RecAX20 was very similar to RecAEc by all activities analysed, RecAX21 differed from RecAEc in several respects. These differences included an increased affinity for double-stranded DNA, a more active displacement of SSB protein from single-stranded DNA (ssDNA), a decreased end-dependent RecAX21 protein dissociation from a presynaptic complex, and a greater accumulation of intermediate products relative to the final product in the strandexchange reaction. RecAPa was more tolerant than RecAX21 only to the end-dependent RecA protein dissociation. In addition, RecAPa was more resistant to temperature and salt concentrations in its ability to form a presynaptic RecAPa::ATP::ssDNA filament. Calculations of conformational energy revealed that the [L29M] substitution in RecAX21 polymer caused an increase in its flexibility. This led us to conclude that even a small change in the flexibility of the RecA presynaptic complex could profoundly affect its recombinogenic properties. © 2001 Academic Press.

@ARTICLE{Ryzhov2001,
author={Ryzhov, V.A. and Luzyanin, I.D. and Lazuta, A.V. and Khavronin, V.P. and Larionov, I.I. and Troyanchuk, I.O. and Khalyavin, D.D.},
title={Critical linear and nonlinear responses and evidence for two-phase coexistence in a Nd0.77Ba0.23MnO3 single crystal},
journal={Physics of Metals and Metallography},
year={2001},
volume={91},
number={1 SUPPL.},
pages={S185-S189},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035566675&partnerID=40&md5=d52985033255dc3cb04194c197480f9d},
affiliation={Petersburg Nucl. Phys. Institute RAS, Gatchina, St. Petersburg, 620219, Russian Federation; Inst. Phys. Solids Semiconductors, National Academy of Sciences, ul. P. Brovki 17, 220072, Minsk, Belarus},
abstract={We present the data on dynamic linear and nonlinear susceptibilities (second and third harmonics of magnetization) in the critical paramagnetic region for weakly doped manganite Nd0.77Ba0.23MnO3. It has a pseudocubic structure both at room temperature and below the Curie temperature, remaining in an insulating state below TC. The coexistence of two magnetic phases is found below T ≈ 146.7 K > TC ≈ 124.1 K. The critical behavior of the major phase is in good quantitative agreement with the scaling theory for Heisenberg ferromagnets. The second phase is found to spontaneously magnetize. The unexpected appearance of the new phase in the paramagnetic region is discussed on the basis of recent ideas on phase separation in the weakly and moderately doped manganites.},
correspondence_address1={Ryzhov, V.A.; Petersburg Nucl. Phys. Institute RAS, Gatchina, St. Petersburg, 620219, Russian Federation},
issn={0031918X},
language={English},
abbrev_source_title={Phys. Met. Metallogr.},
document_type={Article},
source={Scopus},
}

We present the data on dynamic linear and nonlinear susceptibilities (second and third harmonics of magnetization) in the critical paramagnetic region for weakly doped manganite Nd0.77Ba0.23MnO3. It has a pseudocubic structure both at room temperature and below the Curie temperature, remaining in an insulating state below TC. The coexistence of two magnetic phases is found below T ≈ 146.7 K > TC ≈ 124.1 K. The critical behavior of the major phase is in good quantitative agreement with the scaling theory for Heisenberg ferromagnets. The second phase is found to spontaneously magnetize. The unexpected appearance of the new phase in the paramagnetic region is discussed on the basis of recent ideas on phase separation in the weakly and moderately doped manganites.

@ARTICLE{Luzyanin2001,
author={Luzyanin, I.D. and Ryzhov, V.A. and Chernyshov, D.Yu. and Kurbakov, A.I. and Trounov, V.A. and Lazuta, A.V. and Khavronin, V.P. and Larionov, I.I. and Dunaevsky, S.M.},
title={Crystal structure and magnetic properties of the unique 154Sm0.6Sr0.4MnO3 Jahn-Teller system},
journal={Physics of Metals and Metallography},
year={2001},
volume={91},
number={1 SUPPL.},
pages={S179-S184},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035562196&partnerID=40&md5=6db154118153bcaf41f5470822af2991},
affiliation={Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, 620219, Russian Federation},
abstract={Structural neutron diffraction investigations, as well as the data on the resistance, linear susceptibility, and second harmonic of magnetization, are presented for 154Sm0.6Sr0.4MnO3 manganite. Structural studies reveal the unique Jahn-Teller (JT) character of this compound, which is found to exhibit the Pbnm space group. Unusually large coherent JT distortions are found to develop below TJT ≈ 180 K and remain even in the metallic ferromagnetic phase below the Curie point TC ≈ 120 K. In the paramagnetic region, the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above TC. This is evidence of the existence of macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, the temperature dependence of the linear susceptibility reveals a plateau at T > TC. These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with antiferromagnetic regions with weak ferromagnetism.},
correspondence_address1={Luzyanin, I.D.; Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, 620219, Russian Federation},
issn={0031918X},
language={English},
abbrev_source_title={Phys. Met. Metallogr.},
document_type={Article},
source={Scopus},
}

Structural neutron diffraction investigations, as well as the data on the resistance, linear susceptibility, and second harmonic of magnetization, are presented for 154Sm0.6Sr0.4MnO3 manganite. Structural studies reveal the unique Jahn-Teller (JT) character of this compound, which is found to exhibit the Pbnm space group. Unusually large coherent JT distortions are found to develop below TJT ≈ 180 K and remain even in the metallic ferromagnetic phase below the Curie point TC ≈ 120 K. In the paramagnetic region, the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above TC. This is evidence of the existence of macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, the temperature dependence of the linear susceptibility reveals a plateau at T > TC. These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with antiferromagnetic regions with weak ferromagnetism.

@ARTICLE{Luzyanin2001944321,
author={Luzyanin, I.D. and Ryzhov, V.A. and Chernyshov, D.Yu. and Kurbakov, A.I. and Trounov, V.A. and Lazuta, A.V. and Khavronin, V.P. and Larionov, I. and Dunaevsky, S.M.},
title={Crystal structure and magnetic properties of the unique Jahn-Teller system 154Sm0.6Sr0.4MnO3},
journal={Physical Review B - Condensed Matter and Materials Physics},
year={2001},
volume={64},
number={9},
pages={944321-9443211},
art_number={094432},
note={cited By 32},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035449122&partnerID=40&md5=0b12bdbce484ce55c1a88c6d0301a110},
affiliation={Petersburg Nuclear Physics Institute, Gatchina 188350, St. Petersburg, Russian Federation},
abstract={Structural neutron diffraction investigations as well as data on resistance, linear susceptibility, and second harmonic of magnetization are presented for 154Sm0.6Sr0.4MnO3 manganite. The structural studies reveal the unique Jahn-Teller (JT) character of this compound which is established to exhibit a Pbmn space group. Unusual large coherent JT distortions are found to develop below TJT≈180 K and remain even in a metallic ferromagnetic phase below the Curie point Tc≈120 K. In the paramagnetic region the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above Tc. This evidences the existence of the macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, temperature dependence of the linear susceptibility reveals a plateau at T>Tc. These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with the antiferromagnetic regions possessing a weak ferromagnetism. The ordered regions appear as a result of first order transition at T≈160 K, destroy at T*≈137.5 K and reveal a characteristic three-critical behavior for T→T*+0. Change in a balance between the ferromagnetic double exchange hopping of eg electrons and the antiferromagnetic interactions of t2g spins, which caused by the cooperative JT effect, and the charge ordering correlations are supposed to account for the anomalous magnetic behavior above Tc.},
correspondence_address1={Luzyanin, I.D.; Petersburg Nuclear Physics Institute, Gatchina 188350, St. Petersburg, Russian Federation},
issn={01631829},
coden={PRBMD},
language={English},
abbrev_source_title={Phys. Rev. B Condens. Matter Mater. Phys.},
document_type={Article},
source={Scopus},
}

Structural neutron diffraction investigations as well as data on resistance, linear susceptibility, and second harmonic of magnetization are presented for 154Sm0.6Sr0.4MnO3 manganite. The structural studies reveal the unique Jahn-Teller (JT) character of this compound which is established to exhibit a Pbmn space group. Unusual large coherent JT distortions are found to develop below TJT≈180 K and remain even in a metallic ferromagnetic phase below the Curie point Tc≈120 K. In the paramagnetic region the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above Tc. This evidences the existence of the macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, temperature dependence of the linear susceptibility reveals a plateau at T>Tc. These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with the antiferromagnetic regions possessing a weak ferromagnetism. The ordered regions appear as a result of first order transition at T≈160 K, destroy at T*≈137.5 K and reveal a characteristic three-critical behavior for T→T*+0. Change in a balance between the ferromagnetic double exchange hopping of eg electrons and the antiferromagnetic interactions of t2g spins, which caused by the cooperative JT effect, and the charge ordering correlations are supposed to account for the anomalous magnetic behavior above Tc.

The behavior of the linear and nonlinear dynamic susceptibilities of a Nd0.77Ba0.23MnO3 single crystal is studied with the aim to verify whether sealing theory is applicable for describing the critical phenomena in manganites with cubic symmetry. The experimental results obtained for the exchange temperature region (4πχ ≪ 1) agree well with the theoretical predictions, whereas the appearance of magnetically ordered formations in the paramagnetic phase is presumably due to the orbital ordering. © 2001 MAIK "Nauka/Interperiodica".

@ARTICLE{Malkov2001419,
author={Malkov, V.M. and Boreysho, A.S. and Savin, A.V. and Kiselev, I.A. and Orlov, A.E.},
title={About choice of working parameters of pressure recovery systems for high power gas flow chemical lasers},
journal={Proceedings of SPIE - The International Society for Optical Engineering},
year={2001},
volume={4184},
pages={419-422},
doi={10.1117/12.413965},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035044602&doi=10.1117%2f12.413965&partnerID=40&md5=7135fb615d5512c057b4f7cb8428ba7d},
affiliation={Institute of Theoretical and Applied Mechanics, Novosibirsk, Russian Federation; Baltic State Technical University, St. Petersburg, Russian Federation},
abstract={The working parameters of supersonic diffuser (SD) and supersonic ejector (EJ) in pressure recovery system (PRS) of continuous wave chemical lasers (CCL) were discussed. The scheme solution of PRS and the working parameters of system were determined by output parameters of installation. The supersonic diffuser was analyzed in PRS for slowdown of supersonic flow coming out of resonator cavity. The process of slowdown of supersonic flow in a channel required interaction of oblique shocks with the boundary layers. The subsonic laser flow increased along the channel due to turbulence, gradually catching a flow core.},
issn={0277786X},
language={English},
abbrev_source_title={Proc SPIE Int Soc Opt Eng},
document_type={Article},
source={Scopus},
}

The working parameters of supersonic diffuser (SD) and supersonic ejector (EJ) in pressure recovery system (PRS) of continuous wave chemical lasers (CCL) were discussed. The scheme solution of PRS and the working parameters of system were determined by output parameters of installation. The supersonic diffuser was analyzed in PRS for slowdown of supersonic flow coming out of resonator cavity. The process of slowdown of supersonic flow in a channel required interaction of oblique shocks with the boundary layers. The subsonic laser flow increased along the channel due to turbulence, gradually catching a flow core.

@ARTICLE{Luzyanin2001,
author={Luzyanin, I.D. and Ryzhov, V.A. and Chernyshov, D.Y. and Kurbakov, A.I. and Trounov, V.A. and Lazuta, A.V. and Khavronin, V.P. and Larionov, I. and Dunaevsky, S.M.},
title={Crystal structure and magnetic properties of the unique Jahn-Teller system (formula presented)},
journal={Physical Review B - Condensed Matter and Materials Physics},
year={2001},
volume={64},
number={9},
page_count={11},
doi={10.1103/PhysRevB.64.094432},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038298474&doi=10.1103%2fPhysRevB.64.094432&partnerID=40&md5=9409b1e4034d450e2df89ea2f238fbba},
affiliation={Petersburg Nuclear Physics Institute, Gatchina 188350, St. Petersburg, Russian Federation},
abstract={Structural neutron diffraction investigations as well as data on resistance, linear susceptibility, and second harmonic of magnetization are presented for (formula presented) manganite. The structural studies reveal the unique Jahn-Teller (JT) character of this compound which is established to exhibit a (formula presented) space group. Unusual large coherent JT distortions are found to develop below (formula presented) and remain even in a metallic ferromagnetic phase below the Curie point (formula presented). In the paramagnetic region the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above (formula presented) This evidences the existence of the macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, temperature dependence of the linear susceptibility reveals a plateau at (formula presented) These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with the antiferromagnetic regions possessing a weak ferromagnetism. The ordered regions appear as a result of first order transition at (formula presented) destroy at (formula presented) and reveal a characteristic three-critical behavior for (formula presented). Change in a balance between the ferromagnetic double exchange hopping of (formula presented) electrons and the antiferromagnetic interactions of (formula presented) spins, which caused by the cooperative JT effect, and the charge ordering correlations are supposed to account for the anomalous magnetic behavior above (formula presented)© 2001 The American Physical Society.},
issn={10980121},
language={English},
abbrev_source_title={Phys. Rev. B Condens. Matter Mater. Phys.},
document_type={Article},
source={Scopus},
}

Structural neutron diffraction investigations as well as data on resistance, linear susceptibility, and second harmonic of magnetization are presented for (formula presented) manganite. The structural studies reveal the unique Jahn-Teller (JT) character of this compound which is established to exhibit a (formula presented) space group. Unusual large coherent JT distortions are found to develop below (formula presented) and remain even in a metallic ferromagnetic phase below the Curie point (formula presented). In the paramagnetic region the resistance is consistent with polaron hopping. A field hysteresis of the second harmonic is observed above (formula presented) This evidences the existence of the macroscopic ferromagnetic regions in the paramagnetic matrix. In contrast, temperature dependence of the linear susceptibility reveals a plateau at (formula presented) These conflicting peculiarities of the magnetic properties can be explained by assuming the ferromagnetic behavior to be associated with the antiferromagnetic regions possessing a weak ferromagnetism. The ordered regions appear as a result of first order transition at (formula presented) destroy at (formula presented) and reveal a characteristic three-critical behavior for (formula presented). Change in a balance between the ferromagnetic double exchange hopping of (formula presented) electrons and the antiferromagnetic interactions of (formula presented) spins, which caused by the cooperative JT effect, and the charge ordering correlations are supposed to account for the anomalous magnetic behavior above (formula presented)© 2001 The American Physical Society.

The method for separation of emission (EM) and excitation (EX) spectra of a protein into EM and EX spectra of its tyrosine (Tyr) and tryptophan (Trp) residues was described. The method was applied to analysis of Escherichia coli RecA protein and its complexes with Mg2+, ATPγS or ADP, and single-stranded DNA (ssDNA). RecA consists of a C-terminal domain containing two Trp and two Tyr residues, a major domain with five Tyr residues, and an N-terminal domain without these residues (R. M. Story, I. T. Weber, and T. A. Steitz (1992) Nature (London) 355, 374-376). Because the fluorescence of Tyr residues in the C-terminal domain was shown to be quenched by energy transfer to Trp residues, Trp and Tyr fluorescence of RecA was provided by the C-terminal and the major domains, respectively. Spectral analysis of Trp and Tyr constituents revealed that a relative spatial location of the C-terminal and the major domains in RecA monomers was different for their complexes with either ATPγS or ADP, whereas this location did not change upon additional interaction of these complexes with ssDNA. Homogeneous (that is, independent of EX wavelength) and nonhomogeneous (dependent on EX wavelength) types of Tyr and Trp fluorescence quenching were analyzed for RecA and its complexes with nucleotide cofactors and ssDNA. The former was expected to result from singlet-singlet energy transfer from these residues to adenine of ATPγS or ADP. By analogy, the latter was suggested to proceed through energy transfer from high vibrational levels of the excited state of Trp and Tyr residues to the adenine. In this case, for correct calculation of the overlap integral, Trp and Tyr donor emission spectra were substituted by the spectral function of convolution of emission and excitation spectra that resulted in a significant increase of the overlap integral and gave an explanation of the nonhomogeneous quenching of Trp residues in the C-terminal domain. (C) 2000 Academic Press.

Results are presented of studies of the dynamic magnetic susceptibility of CuO, Cu1-xZnxO (x ≈ 1.5%), and Cu1-xLxO (x ≈ 1%) single crystals. The orientational dependence of the ESR spectra was investigated at room temperature. The results for CuO are analyzed using a model of a quasi-one-dimensional antiferromagnet (S = 1/2) with anisotropic exchange interaction between Cu2+ spins in the chains and exchange coupling between the chains allowing for one-dimensional spin diffusion and spinon excitations. The estimated line width is of the same order of magnitude as the experimental data. Substituting Cu with Zn scarcely alters the spin dynamics of the Cu2+ ions, as in weakly diluted magnets. Lithium doping substantially increases the ESR line width and this is attributed to excess holes forming rapidly relaxing spin complexes with copper ions. © 2000 MAIK "Nauka/Interperiodica".

The temperature and field behaviors of the linear and nonlinear responses to a weak ac magnetic field in the Sm1-x SrxMnO3 manganites with x = 0.25, 0.3, and 0.4 have been investigated. It is found that the hysteresis of the second harmonic of magnetization in the dc magnetic field arises in the far-paramagnetic range at T ≤ 180 K, whereas the hystereses of the linear susceptibility and the dc resistivity are observed at lower temperatures. This phenomenon is associated with the formation of macroscopic ferromagnetic (ferrimagnetic) domains in the paramagnetic matrix. The shape of the temperature dependence of the linear susceptibility at T > Tc is determined by the degree of doping, and the susceptibility itself nonmonotonically depends on x. ©2000 MAIK "Nauka/Interperiodica".

@ARTICLE{Dulin1999698,
author={Dulin, S.K. and Kiselev, I.A.},
title={Structurization of knowledge in monitoring systems},
journal={Journal of Computer and Systems Sciences International},
year={1999},
volume={38},
number={5},
pages={698-703},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33747396595&partnerID=40&md5=9737e03479adb17042cfaf3e6fa5624e},
affiliation={Computing Center, Russian Academy of Sciences, ul. Vavilova 40, GSP-1, Moscow, 117967, Russian Federation},
abstract={Problems associated with the creation of an expert knowledge base for monitoring tasks that require operative processing of incoming data and, as a result, restructuring of the knowledge base are considered. The procedures reducing the search for an optimal consonant state of mutually related elements of a knowledge base are proposed. An approach to the estimation of the interrelations of weakly structured objects such as text documents and informational messages is developed. A practical implementation of this approach, the operating "Resonance" system, is described. Copyright & 1999 by "MAK Haya/Interperiodica".},
correspondence_address1={Dulin, S.K.; Computing Center, Russian Academy of Sciences, ul. Vavilova 40, GSP-1, Moscow, 117967, Russian Federation},
issn={10642307},
coden={JSSIE},
language={English},
abbrev_source_title={J Comput Syst Sci Int},
document_type={Article},
source={Scopus},
}

Problems associated with the creation of an expert knowledge base for monitoring tasks that require operative processing of incoming data and, as a result, restructuring of the knowledge base are considered. The procedures reducing the search for an optimal consonant state of mutually related elements of a knowledge base are proposed. An approach to the estimation of the interrelations of weakly structured objects such as text documents and informational messages is developed. A practical implementation of this approach, the operating "Resonance" system, is described. Copyright & 1999 by "MAK Haya/Interperiodica".

@ARTICLE{Isaev-Ivanov1999552,
author={Isaev-Ivanov, V.V. and Lantsov, V.A.},
title={Conformational change in bacterial reca protein in the course of its interaction with ligands: Differential spectrofluorometry of tyrosine and tryptophan residius},
journal={Doklady Akademii Nauk},
year={1999},
volume={366},
number={4},
pages={552-556},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033143857&partnerID=40&md5=40c4d0bba6dcb05c94049b7efeec37cc},
issn={08695652},
coden={DAKNE},
pubmed_id={10439915},
language={Russian},
abbrev_source_title={Dokl. Akad. Nauk},
document_type={Article},
source={Scopus},
}

@ARTICLE{Petukhov19991982,
author={Petukhov, M. and Cregut, D. and Soares, C.M. and Serrano, L.},
title={Local water bridges and protein conformational stability},
journal={Protein Science},
year={1999},
volume={8},
number={10},
pages={1982-1989},
doi={10.1110/ps.8.10.1982},
note={cited By 55},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032860932&doi=10.1110%2fps.8.10.1982&partnerID=40&md5=cdcd87f17a7d1d483d03af7570fa5eb2},
affiliation={Europ. Molecular Biology Laboratory, Meyerhofstrasse I, Heidelberg D-69117, Germany; Inst. de Tecn. Quimica e Biologica, UNL, Apartado 127, 2780 Oeiras, Portugal},
abstract={Recent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif - the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).},
author_keywords={Local water structure;  Protein conformational stability;  Solvation potential},
correspondence_address1={Petukhov, M.; European Molec. Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany; email: Petukhov@EMBL-Heidelberg.de},
publisher={Cambridge University Press},
issn={09618368},
coden={PRCIE},
pubmed_id={10548043},
language={English},
abbrev_source_title={Protein Sci.},
document_type={Article},
source={Scopus},
}

Recent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif - the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).

@ARTICLE{Petukhov19992144,
author={Petukhov, M. and Uegaki, K. and Yumoto, N. and Yoshikawa, S. and Serrano, L.},
title={Position dependence of amino acid intrinsic helical propensities II: Non-charged polar residues: Ser, Thr, Asn, and Gln},
journal={Protein Science},
year={1999},
volume={8},
number={10},
pages={2144-2150},
doi={10.1110/ps.8.10.2144},
note={cited By 44},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032869079&doi=10.1110%2fps.8.10.2144&partnerID=40&md5=ef9c8fae19a5f8dd01faf745e46917f7},
affiliation={Europ. Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69012, Germany; Osaka National Research Institute, AIST, Ikeda, Osaka 563, Japan; Europ. Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany},
abstract={The assumption that the intrinsic α-helical propensities of the amino acids are position independent was critical in several helix/coil transition theories. In the first paper of these series, we reported that this is not the case for Gly and nonpolar aliphatic amino acids (Val, Leu, Met, and Ile). Here we have analyzed the helical intrinsic propensities of noncharged polar residues (Ser, Thr, Asn, and Gln) at different positions of a model polyalanine-based peptide. We found that Thr is more favorable (by ~0.3 kcal/mol) at positions N1 and N2 than in the helix center, although for Ser, Asn, and Gln the differences are smaller (±0.2 kcal/mol), and in many cases within the experimental error. There is a reasonable agreement (±0.2 kcal/mol) between the calculated free energies, using the ECEPP/2 force field equipped with a hydration potential, and the experimental data, except at position N1.},
author_keywords={Entropy;  Folding;  Hydration;  Secondary structure;  Stability;  α-helix},
correspondence_address1={Petukhov, M.; European Molec. Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany; email: Petukhov@EMBL-Heidelberg.de},
publisher={Cambridge University Press},
issn={09618368},
coden={PRCIE},
pubmed_id={10548060},
language={English},
abbrev_source_title={Protein Sci.},
document_type={Article},
source={Scopus},
}

The assumption that the intrinsic α-helical propensities of the amino acids are position independent was critical in several helix/coil transition theories. In the first paper of these series, we reported that this is not the case for Gly and nonpolar aliphatic amino acids (Val, Leu, Met, and Ile). Here we have analyzed the helical intrinsic propensities of noncharged polar residues (Ser, Thr, Asn, and Gln) at different positions of a model polyalanine-based peptide. We found that Thr is more favorable (by  0.3 kcal/mol) at positions N1 and N2 than in the helix center, although for Ser, Asn, and Gln the differences are smaller (±0.2 kcal/mol), and in many cases within the experimental error. There is a reasonable agreement (±0.2 kcal/mol) between the calculated free energies, using the ECEPP/2 force field equipped with a hydration potential, and the experimental data, except at position N1.

@ARTICLE{Petukhov1999437,
author={Petukhov, M. and Kil, Y. and Lanzov, V. and Facchiano, A.M. and Colonna, G. and Ragone, R.},
title={Comment on a paper by Facchiano et al. (1998)},
journal={Protein Engineering},
year={1999},
volume={12},
number={6},
pages={437-438},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033037566&partnerID=40&md5=d6c4cff51abb5758347d15da2ee9ac90},
affiliation={European Molecular Biology Lab., Heidelberg 69012, Germany},
correspondence_address1={Petukhov, M.; European Molecular Biology Lab., Heidelberg 69012, Germany},
publisher={Oxford University Press},
issn={02692139},
coden={PRENE},
pubmed_id={10388838},
language={English},
abbrev_source_title={Protein Eng.},
document_type={Note},
source={Scopus},
}

@ARTICLE{Dulin1998780,
author={Dulin, S.K. and Kiselev, I.A.},
title={About one approach to data expert analysis in the intranet},
journal={Journal of Computer and Systems Sciences International},
year={1998},
volume={37},
number={5},
pages={780-787},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33746417092&partnerID=40&md5=b84e4dea034714ed4b177dad3d4d5f48},
affiliation={Computer Center, Russian Academy of Sciences, Moscow, Russian Federation},
abstract={In this paper, stages of analytical expert activity are considered. The main tools and instruments used for a subject information search on the Intranet under the conditions of large information distribution and data type diversity are analyzed. The design of a specific model of subject field for rearrangement of the knowledge structure of local analysts is proposed as one of the methods for solution of this problem. The capabilities of a demonstration dummy are briefly described. Copyright © 1998 by MAK Haya/Interperiodica Publishing.},
correspondence_address1={Dulin, S.K.; Computer Center, Russian Academy of Sciences, Moscow, Russian Federation},
issn={10642307},
coden={JSSIE},
language={English},
abbrev_source_title={J Comput Syst Sci Int},
document_type={Article},
source={Scopus},
}

In this paper, stages of analytical expert activity are considered. The main tools and instruments used for a subject information search on the Intranet under the conditions of large information distribution and data type diversity are analyzed. The design of a specific model of subject field for rearrangement of the knowledge structure of local analysts is proposed as one of the methods for solution of this problem. The capabilities of a demonstration dummy are briefly described. Copyright © 1998 by MAK Haya/Interperiodica Publishing.

@ARTICLE{Rizvi1998137,
author={Rizvi, T.Z. and Petukhov, M. and Tatsu, Y. and Yoshikawa, S.},
title={Stabilization of helix-turn-helix motif in short peptides},
journal={Journal of Chemical Society of Pakistan},
year={1998},
volume={20},
number={2},
pages={137-140},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032334773&partnerID=40&md5=d5487d3a9ceae1a5682cd3b3f41a3240},
affiliation={Applied Chemistry Research Centre, PCSIR Laboratories Complex, Lahore, Pakistan; Biomolecular Engineering Laboratory, Department of Organic Materials, Osaka National Research Institute, Osaka, Japan},
abstract={Effective De novo designing of proteins is a great challenge and a critical test of our knowledge of protein structure. The main problem is the attainment of a protein with a defined fold for its specific function. This paper reports the synthesis and characterization of a series of helix - turn - helix (h-t-h) peptides with stable secondary and tertiary structures. In the order to optimize the stability of the anti-parallel coiled-coil structure of alpha helical hairpin peptides, all peplides with the same interacting helical regions but different number and sequences of residues in the turn region was examined. The turn region was incorporated between g and e2 of leucine zipper heptnd CD measurements showed that a four residue turn region was the best of stabilizing coiled coil structure in these peptides. The four residue turn sequence selected from h-t-h motifs of DNA binding proteins showed the highest helix stabilization in a short peptide of twenty nine amino acid residues.},
correspondence_address1={Rizvi, T.Z.; Applied Chemistry Research Centre, PCSIR Laboratories Complex, Lahore, Pakistan},
issn={02535106},
language={English},
abbrev_source_title={J. Chem. Soc. Pak.},
document_type={Article},
source={Scopus},
}

Effective De novo designing of proteins is a great challenge and a critical test of our knowledge of protein structure. The main problem is the attainment of a protein with a defined fold for its specific function. This paper reports the synthesis and characterization of a series of helix - turn - helix (h-t-h) peptides with stable secondary and tertiary structures. In the order to optimize the stability of the anti-parallel coiled-coil structure of alpha helical hairpin peptides, all peplides with the same interacting helical regions but different number and sequences of residues in the turn region was examined. The turn region was incorporated between g and e2 of leucine zipper heptnd CD measurements showed that a four residue turn region was the best of stabilizing coiled coil structure in these peptides. The four residue turn sequence selected from h-t-h motifs of DNA binding proteins showed the highest helix stabilization in a short peptide of twenty nine amino acid residues.

@ARTICLE{Petukhov1998118,
author={Petukhov, M.G. and Baitin, D.M. and Kil', Yu.V. and Lantsov, V.A.},
title={Optimal rigidity of protein structure: Three classes of rigidity in the reca protein family of eubacteria},
journal={Doklady Akademii Nauk},
year={1998},
volume={362},
number={1},
pages={118-121},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032151784&partnerID=40&md5=6d2be933783417861956ca60fff1a5e6},
issn={08695652},
coden={DAKNE},
pubmed_id={9858990},
language={Russian},
abbrev_source_title={Dokl. Akad. Nauk},
document_type={Article},
source={Scopus},
}

@ARTICLE{Kachurin19981183,
author={Kachurin, A.M. and Protasenya, S.V. and Shabalin, K.A. and Isaev-Ivanov, V.V. and Golubev, A.M. and Neustroev, K.N.},
title={Tryptophan residues in α-galactosidase from Trichoderma reesei},
journal={Biochemistry (Moscow)},
year={1998},
volume={63},
number={10},
pages={1183-1190},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032175116&partnerID=40&md5=27f87fcfbac7ed8407da523139b06a4a},
affiliation={St. Petersburg Konstantinov N.P.I., Orlova rosbcha, Gatchina 188351, Russian Federation},
abstract={Tryptophan residues in α-galactosidase were modified with bromosuccinimide. The fact that galactose, a specific inhibitor of α-galactosidase, does not prevent this modification demonstrates that tryptophan residues are not located in galactose binding sites. Analysis of the inactivation kinetics revealed two groups of Trp residues (8.5 and 7.5 residues) with different accessibility for N-bromosuccinimide. We studied specific quenching of α-galactosidase fluorescence resulting from modification of an sulfhydryl group in the active site of the enzyme with Hg2+ and Ag+ ions. The specific quenching is due to conformational changes of the enzyme. Forster's radii were determined for various protein-chromophore complexes. Dynamic quenching of α-galactosidase fluorescence was investigated. To describe abnormal dynamic quenching in α-galactosidase, a modification of the Stern-Volmer equation is suggested.},
author_keywords={α-galactosidase;  Enzyme active site;  Fluorescence spectroscopy;  Sulfhydryl group;  Trichoderma reesei},
correspondence_address1={Neustroev, K.N.; St. Petersburg Konstantinov N.P.I., Orlova rosbcha, Gatchina 188351, Russian Federation; email: neustk@omrb.pnpi.spb.ru},
issn={00062979},
coden={BIORA},
pubmed_id={9864453},
language={English},
abbrev_source_title={Biochemistry Moscow},
document_type={Article},
source={Scopus},
}

Tryptophan residues in α-galactosidase were modified with bromosuccinimide. The fact that galactose, a specific inhibitor of α-galactosidase, does not prevent this modification demonstrates that tryptophan residues are not located in galactose binding sites. Analysis of the inactivation kinetics revealed two groups of Trp residues (8.5 and 7.5 residues) with different accessibility for N-bromosuccinimide. We studied specific quenching of α-galactosidase fluorescence resulting from modification of an sulfhydryl group in the active site of the enzyme with Hg2+ and Ag+ ions. The specific quenching is due to conformational changes of the enzyme. Forster's radii were determined for various protein-chromophore complexes. Dynamic quenching of α-galactosidase fluorescence was investigated. To describe abnormal dynamic quenching in α-galactosidase, a modification of the Stern-Volmer equation is suggested.

@ARTICLE{Dulin1998780,
author={Dulin, S.K. and Kiselev, I.A.},
title={About one approach to data expert analysis in the intranet},
journal={Izvestiya Akademii Nauk. Teoriya i Sistemy Upravleniya},
year={1998},
volume={37},
number={5},
pages={780},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032161076&partnerID=40&md5=93fabf0fdd8efd77d7cb37bc234b1d59},
affiliation={Computer Cent of Russian Acad of, Sciences, Moscow, Russian Federation},
abstract={In this paper, stages of analytical expert activity are considered. The main tools and instruments used for a subject information search on the Intranet under the conditions of large information distribution and data type diversity are analyzed. The design of a specific model of subject field for rearrangement of the knowledge structure of local analysts is proposed as one of the methods for solution of this problem. The capabilities of a demonstration dummy are briefly described.},
correspondence_address1={Dulin, S.K.; Computer Cent of Russian Acad of, Sciences, Moscow, Russian Federation},
publisher={Mezhdunarodnaya Kniga, Moscow, Russian Federation},
issn={00023388},
coden={IATKA},
language={Russian},
abbrev_source_title={Izv Akad Nauk Teh Kibern},
document_type={Article},
source={Scopus},
}

In this paper, stages of analytical expert activity are considered. The main tools and instruments used for a subject information search on the Intranet under the conditions of large information distribution and data type diversity are analyzed. The design of a specific model of subject field for rearrangement of the knowledge structure of local analysts is proposed as one of the methods for solution of this problem. The capabilities of a demonstration dummy are briefly described.

Until now and based on the success of the helix/coil transition theory it has been assumed that the α-helical propensities of the amino acids are position independent. This has been critical to derive the set of theoretical parameters for the 20 natural amino acids. Here, we have analyzed the behavior of several non-polar residues, Val, Ile, Leu, Met and Gly at the N-cap, at each position of the first helical turn and at a central helical position of a 16-residue peptide model system that starts with eight consecutive alanine residues. We have interpreted the results from these experiments with the model of the helix/coil transition (AGADIR), that indicates that the intrinsic helical propensity is position dependent. Gly, Val and Ile are more favorable at the first turn than in the middle of the α-helix, while for Leu and Met we observe the opposite behavior. The differences between the observed helical propensities are as large as 1.0 kcal/mol in some cases. Molecular modeling calculations using the ECEPP/2 force-field equipped with a hydration potential show that this effect can be explained by the combination of three factors: (a) the side-chains in the first helix turn are more solvent-exposed; (b) they have fewer intramolecular van der Waals' contacts; and (c) they posses higher configurational entropy than that in the central position of an α-helix. The position-dependent results of the calculations are in reasonable agreement with the experimental estimates and with the intrinsic propensities of the amino acids derived from the statistical analysis of the protein structure database.

@ARTICLE{Lebedev1998,
author={Lebedev, D.V. and Shearer, S. and Knauf, P.A.},
title={Volume-sensitive amino acid transport during Regulatory Volume Decrease (RVD) in HL-60 cells},
journal={FASEB Journal},
year={1998},
volume={12},
number={5},
pages={A1023},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749332327&partnerID=40&md5=ebb384cc7bd32ca75a267c2bf7cb0f78},
affiliation={Univ. of Rochester Med. Ctr., Rochester, NY 14642, United States},
abstract={RVD in promyelocytic leukemic HL-60 cells is accomplished primarily by K+ and Cl- loss triggered by opening of volume-sensitive Cl channels. To evaluate the involvement of other transport processes in RVD. we have measured RVD in medium with the [K]o[Cl]o product set to approximate [K]i[Cl]i. Triple-label radioisotope measurements of cell water and Cl content indicate that under these conditions cells swollen in 50% tonicity medium still show approximately 40% of the normal volume recovery, even though cell Cl content remains unchanged. Volume recovery is inhibited by 50μM DIDS, which inhibits volume-sensitive Cl efflux during normal RVD. There was a significant (over 5 fold) increase in the rate of release of ninhydrin-positive substances (very likely amino acids) under hypotonic conditions. Both amino acid release and unidirectional 36Cl efflux were inhibited by an oxonol dye WW781 (IC50 = 4.5±1.3μM and 2.1±0.3μM, respectively); the differential effects of WW781 on Cl- and amino acid efflux fit a model with more than one pathway for amino acid transport. This is supported by evidence that external ATP (10 mM) has different effects on 36Cl efflux and on 3H-D-aspartate efflux in hypotonic medium, implying that part of the volume-sensitive amino acid efflux goes via a different pathway than chloride.},
correspondence_address1={Lebedev, D.V.; Univ. of Rochester Med. Ctr., Rochester, NY 14642, United States},
issn={08926638},
coden={FAJOE},
language={English},
abbrev_source_title={FASEB J.},
document_type={Article},
source={Scopus},
}

RVD in promyelocytic leukemic HL-60 cells is accomplished primarily by K+ and Cl- loss triggered by opening of volume-sensitive Cl channels. To evaluate the involvement of other transport processes in RVD. we have measured RVD in medium with the [K]o[Cl]o product set to approximate [K]i[Cl]i. Triple-label radioisotope measurements of cell water and Cl content indicate that under these conditions cells swollen in 50% tonicity medium still show approximately 40% of the normal volume recovery, even though cell Cl content remains unchanged. Volume recovery is inhibited by 50μM DIDS, which inhibits volume-sensitive Cl efflux during normal RVD. There was a significant (over 5 fold) increase in the rate of release of ninhydrin-positive substances (very likely amino acids) under hypotonic conditions. Both amino acid release and unidirectional 36Cl efflux were inhibited by an oxonol dye WW781 (IC50 = 4.5±1.3μM and 2.1±0.3μM, respectively); the differential effects of WW781 on Cl- and amino acid efflux fit a model with more than one pathway for amino acid transport. This is supported by evidence that external ATP (10 mM) has different effects on 36Cl efflux and on 3H-D-aspartate efflux in hypotonic medium, implying that part of the volume-sensitive amino acid efflux goes via a different pathway than chloride.

We report a study of the second order dynamic susceptibility in parallel static and alternating magnetic fields of three lightly oxygenated single crystals of La2CuO4+x (x < 0.03) with different TN (TN1 ≈ 222 K, TN2 ≈ 272 K and TN3 ≈ 243 K). The response of all the samples reveals common features which are characteristic of an antiferromagnet with a weak ferromagnetism (WF). These new magnetic properties are attributed to the oxygen-rich phase forming in the course of the phase separation. We show that the WF can be related to out-of CuO2 plane ordering (staging) of the interstitial oxygen. The response of crystals N1 and N3 is observed in the vicinity of TN and exhibits a critical enhancement. A simple model of WF domain is presented which allows us to describe quantitatively the H-dependence of the signal of crystal N3 above TN. It provides a basis for a comparative analysis of the data on N1 and N3 crystals. The response of crystal N2 is found below TN. In this case its peculiarities reflect change and destruction of initial magnetic ordering in the forming oxygen-rich phase. © 1998 Elsevier Science B.V.

@ARTICLE{Kachurin19981391,
author={Kachurin, A.M. and Protasenya, S.V. and Shabalin, K.A. and Isaev-Ivanov, V.V. and Golubev, A.M. and Neustroev, K.N.},
title={Tryptophan residues in alpha-galactosidase from trichoderma reesei},
journal={Dadianji Jishu/Large Electric Machine and Hydraulic Turbine},
year={1998},
number={6},
pages={1391-1399},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031611457&partnerID=40&md5=d9ae959df025d35c167a594525ac6d14},
affiliation={St. Petersburg Konstantinov Nuclear, Physics Inst, Gatchina, Russian Federation},
abstract={Tryptophan residues in alpha-galactosidase were modified with bromosuccinimide. The fact that galactose, a specific inhibitor of alpha-galactosidase, does not prevent this modification demonstrates that tryptophan residues are not located in galactose binding sites. Analysis of the inactivation kinetics revealed two groups of Trp residues (8.5 and 7.5 residues) with different accessibility for N-bromosuccinimide. We studied specific quenching of alpha-galactosidase fluorescence resulting from modification of an sulfhydryl group in the active site of the enzyme with Hg2+ and Ag+ ions. The specific quenching is due to conformational changes of the enzyme. Forster's radii were determined for various protein - chromophore complexes. Dynamic quenching of alpha-galactosidase fluorescence was investigated. To describe abnormal dynamic quenching in alpha-galactosidase, a modification of the Stern - Volmer equation is suggested.},
correspondence_address1={Kachurin, A.M.; St. Petersburg Konstantinov Nuclear, Physics Inst, Gatchina, Russian Federation},
publisher={Scientific Publishing House, Beijing, China},
issn={10003983},
coden={DAJIF},
language={Russian},
abbrev_source_title={Dadianji Jishu},
document_type={Article},
source={Scopus},
}

Tryptophan residues in alpha-galactosidase were modified with bromosuccinimide. The fact that galactose, a specific inhibitor of alpha-galactosidase, does not prevent this modification demonstrates that tryptophan residues are not located in galactose binding sites. Analysis of the inactivation kinetics revealed two groups of Trp residues (8.5 and 7.5 residues) with different accessibility for N-bromosuccinimide. We studied specific quenching of alpha-galactosidase fluorescence resulting from modification of an sulfhydryl group in the active site of the enzyme with Hg2+ and Ag+ ions. The specific quenching is due to conformational changes of the enzyme. Forster's radii were determined for various protein - chromophore complexes. Dynamic quenching of alpha-galactosidase fluorescence was investigated. To describe abnormal dynamic quenching in alpha-galactosidase, a modification of the Stern - Volmer equation is suggested.

@ARTICLE{Dulin1997692,
author={Dulin, S.K. and Kiselev, I.A.},
title={Knowledge base simulation in document databases},
journal={Journal of Computer and Systems Sciences International},
year={1997},
volume={36},
number={5},
pages={692-696},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33747942520&partnerID=40&md5=22fe7e1a54756ee8f834689fb0a7458f},
affiliation={Computer Center of the Russian Academy of Sciences, Moscow, Russian Federation},
abstract={One of the most contemporary systems based on semiotic modeling is the active knowledge base [1] supplied with a special concordance mechanism of structural consistency. Such method is especially actual when we deal with different document databases, where rule records do not have any structure, and relations between them are hidden. This paper covers some problems of creating models of subject area and deals with an active knowledge base condition considered by means of connections structure analysis of knowledge base components. Thereby, the dominant attribute of any component is supposed to be the connections structure of knowledge base component (object). A set of objects with connections that have a binary existence estimate is examined. Consonant, dissonant, and assonant sets are distinguished, depending on the satisfiability of the consonance criterion. An algorithm is proposed and realized for reducing assonant and dissonant sets to a consonance state with minimum expenditures in the sense of the general number variable estimates of the connections. Interactive systems DISSON and RESTRUCTOR have been developed to realize this algorithm for consistency of knowledge base components. © 1997 by MAHK HayKa/lnterperiodicâ Publishing.},
correspondence_address1={Computer Center of the Russian Academy of Sciences, Moscow, Russian Federation},
issn={10642307},
coden={JSSIE},
language={English},
abbrev_source_title={J Comput Syst Sci Int},
document_type={Article},
source={Scopus},
}

One of the most contemporary systems based on semiotic modeling is the active knowledge base [1] supplied with a special concordance mechanism of structural consistency. Such method is especially actual when we deal with different document databases, where rule records do not have any structure, and relations between them are hidden. This paper covers some problems of creating models of subject area and deals with an active knowledge base condition considered by means of connections structure analysis of knowledge base components. Thereby, the dominant attribute of any component is supposed to be the connections structure of knowledge base component (object). A set of objects with connections that have a binary existence estimate is examined. Consonant, dissonant, and assonant sets are distinguished, depending on the satisfiability of the consonance criterion. An algorithm is proposed and realized for reducing assonant and dissonant sets to a consonance state with minimum expenditures in the sense of the general number variable estimates of the connections. Interactive systems DISSON and RESTRUCTOR have been developed to realize this algorithm for consistency of knowledge base components. © 1997 by MAHK HayKa/lnterperiodicâ Publishing.

@ARTICLE{Petukhov1997267,
author={Petukhov, M.G. and Kil', Yu.V. and Lantsov, V.A.},
title={On the nature of protein thermoresistence: Stability of α-hilices of recA proteins from thermophilic bacteria},
journal={Doklady Akademii Nauk},
year={1997},
volume={356},
number={2},
pages={267-271},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748733991&partnerID=40&md5=afe6cfaffd9b5b5e3010e684441ce589},
issn={08695652},
coden={DAKNE},
language={Russian},
abbrev_source_title={Dokl. Akad. Nauk},
document_type={Article},
source={Scopus},
}

@ARTICLE{Petukhov1997309,
author={Petukhov, M. and Kil, Y. and Kuramitsu, S. and Lanzov, V.},
title={Insights into thermal resistance of proteins from the intrinsic stability of their α-helices},
journal={Proteins: Structure, Function and Genetics},
year={1997},
volume={29},
number={3},
pages={309-320},
doi={10.1002/(SICI)1097-0134(199711)29:3<309::AID-PROT5>3.0.CO;2-5},
note={cited By 44},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030781507&doi=10.1002%2f%28SICI%291097-0134%28199711%2929%3a3%3c309%3a%3aAID-PROT5%3e3.0.CO%3b2-5&partnerID=40&md5=55e18041b80f0fc6ca174f9bf849ae33},
affiliation={Pac. Inst. of Bioorganic Chemistry, RAS, Vladivostok, Russian Federation; Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, RAS, Gatchina/St. Petersburg, Russian Federation; Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan; Europ. Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany},
abstract={To investigate the role of u helices in protein thermostability, we compared energy characteristics of a helices from thermophilic and mesophilic proteins belonging to four protein families of known three-dimensional structure, for at least one member of each family. The changes in intrinsic free energy of α-helix formation were estimated using the statistical mechanical theory for describing helix/coil transitions in peptide helices [Munoz, V., Serrano, L. Nature Struc. Biol. 1:399-409, 1994; Munoz, V., Serrano, L. J. Mol. Biol. 245:275-296, 1995; Munoz, V., Serrano, L. J. Mol. Biol. 245:297-308, 1995]. Based on known sequences of mesophilic and thermophilic RecA proteins we found that (1) a high stability of a helices is necessary but is not a sufficient condition for thermostability of RecA proteins, (2) the total helix stability, rather than that of individual helices, is the factor determining protein thermostability, and (3) two facets of intrahelical interactions, the intrinsic helical propensities of amino acids and the side chainside chain interactions, are the main contributors to protein thermostability. Similar analysis applied to families of L-lactate dehydrogenases, seryl-tRNA synthetases, and aspartate amino transferases led us to conclude that an enhanced total stability of a helices is a general feature of many thermophilic proteins. The magnitude of the observed decrease in intrinsic free energy on α-helix formation of several thermoresistant proteins was found to be sufficient to explain the experimentally determined increase of their thermostability. Free energies of intrahelical interactions of different RecA proteins calculated at three temperatures that are thought to be close to its normal environmental conditions were found to be approximately equal. This indicates that certain flexibility of RecA protein structure is an essential factor for protein function. All RecA proteins analyzed fell into three temperature-dependent classes of similar α-helix stability (ΔG(int) = 45.0 ± 2.0 kcal/mol). These classes were consistent with the natural origin of the proteins. Based on the sequences of protein a helices with optimized arrangement of stabilizing interactions, a natural reserve of RecA protein thermoresistance was estimated to be sufficient for conformational stability of the protein at nearly 200°C.},
author_keywords={α-helix stability;  Aspartate aminotransferases;  L lactate dehydrogenases;  Protein thermostability;  RecA protein family;  Seryl-tRNA synthetases},
correspondence_address1={Petukhov, M.; European Molec. Biology Laboratory, Meyerhofstrasse 1, Postfach 10.2209, 69012 Heidelberg, Germany},
issn={08873585},
coden={PSFGE},
pubmed_id={9365986},
language={English},
abbrev_source_title={PROTEINS STRUCT. FUNCT. GENET.},
document_type={Article},
source={Scopus},
}

To investigate the role of u helices in protein thermostability, we compared energy characteristics of a helices from thermophilic and mesophilic proteins belonging to four protein families of known three-dimensional structure, for at least one member of each family. The changes in intrinsic free energy of α-helix formation were estimated using the statistical mechanical theory for describing helix/coil transitions in peptide helices [Munoz, V., Serrano, L. Nature Struc. Biol. 1:399-409, 1994; Munoz, V., Serrano, L. J. Mol. Biol. 245:275-296, 1995; Munoz, V., Serrano, L. J. Mol. Biol. 245:297-308, 1995]. Based on known sequences of mesophilic and thermophilic RecA proteins we found that (1) a high stability of a helices is necessary but is not a sufficient condition for thermostability of RecA proteins, (2) the total helix stability, rather than that of individual helices, is the factor determining protein thermostability, and (3) two facets of intrahelical interactions, the intrinsic helical propensities of amino acids and the side chainside chain interactions, are the main contributors to protein thermostability. Similar analysis applied to families of L-lactate dehydrogenases, seryl-tRNA synthetases, and aspartate amino transferases led us to conclude that an enhanced total stability of a helices is a general feature of many thermophilic proteins. The magnitude of the observed decrease in intrinsic free energy on α-helix formation of several thermoresistant proteins was found to be sufficient to explain the experimentally determined increase of their thermostability. Free energies of intrahelical interactions of different RecA proteins calculated at three temperatures that are thought to be close to its normal environmental conditions were found to be approximately equal. This indicates that certain flexibility of RecA protein structure is an essential factor for protein function. All RecA proteins analyzed fell into three temperature-dependent classes of similar α-helix stability (ΔG(int) = 45.0 ± 2.0 kcal/mol). These classes were consistent with the natural origin of the proteins. Based on the sequences of protein a helices with optimized arrangement of stabilizing interactions, a natural reserve of RecA protein thermoresistance was estimated to be sufficient for conformational stability of the protein at nearly 200°C.

@ARTICLE{Dulin199743,
author={Dulin, S.K. and Kiselev, I.A.},
title={Knowledge base simulation in document databases},
journal={Izvestiya Akademii Nauk. Teoriya i Sistemy Upravleniya},
year={1997},
volume={36},
number={5},
pages={43-47},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031224804&partnerID=40&md5=375562a17f3304c623a4fb59c15c2129},
affiliation={Computer Cent of the Russian Acad of, Sciences, Moscow, Russian Federation},
abstract={One of the most contemporary systems based on semiotic modeling is the active knowledge base supplied with a special concordance mechanism of structural consistency. Such method is especially actual when we deal with different document databases, where rule records do not have any structure, and relations between them are hidden. This paper covers some problems of creating models of subject area and deals with an active knowledge base condition considered by means of connections structure analysis of knowledge base components. Thereby, the dominant attribute of any component is supposed to be the connections structure of knowledge base component (object). A set of objects with connections that have a binary existence estimate is examined. Consonant, dissonant, and assonant sets are distinguished, depending on the satisfiability of the consonance criterion. An algorithm is proposed and realized for reducing assonant and dissonant sets to a consonance state with minimum expenditures in the sense of the general number variable estimates of the connections. Interactive systems DISSON and RESTRUCTOR have been developed to realize this algorithm for consistency of knowledge base components.},
correspondence_address1={Dulin, S.K.; Computer Cent of the Russian Acad of, Sciences, Moscow, Russian Federation},
issn={00023388},
coden={IATKA},
language={Russian},
abbrev_source_title={Izv Akad Nauk Teh Kibern},
document_type={Article},
source={Scopus},
}

One of the most contemporary systems based on semiotic modeling is the active knowledge base supplied with a special concordance mechanism of structural consistency. Such method is especially actual when we deal with different document databases, where rule records do not have any structure, and relations between them are hidden. This paper covers some problems of creating models of subject area and deals with an active knowledge base condition considered by means of connections structure analysis of knowledge base components. Thereby, the dominant attribute of any component is supposed to be the connections structure of knowledge base component (object). A set of objects with connections that have a binary existence estimate is examined. Consonant, dissonant, and assonant sets are distinguished, depending on the satisfiability of the consonance criterion. An algorithm is proposed and realized for reducing assonant and dissonant sets to a consonance state with minimum expenditures in the sense of the general number variable estimates of the connections. Interactive systems DISSON and RESTRUCTOR have been developed to realize this algorithm for consistency of knowledge base components.

@ARTICLE{Petukhov1997268,
author={Petukhov, M.G. and Kil', I.V. and Lantsov, V.A.},
title={Nature of protein thermal resistance: stability of alpha-helices of RecA proteins of the thermophilic bacteria [O prirode termoresistentnosti belkov: stabil'nost' al'fa-spiralei belkov RecA termofil'nykh bakterii.]},
journal={Doklady Akademii nauk / [Rossiiskaia akademii nauk]},
year={1997},
volume={356},
number={2},
pages={268-271},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031227170&partnerID=40&md5=6bf80b2fc248d2a41e00e72643c239db},
correspondence_address1={Petukhov, M.G.},
issn={08695652},
pubmed_id={9376806},
language={Russian},
abbrev_source_title={Dokl. Akad. Nauk.},
document_type={Article},
source={Scopus},
}

@ARTICLE{Lazuta1997275,
author={Lazuta, A.V. and Ryzhov, V.A. and Larionov, I.I. and Arbuzova, T.I.},
title={Second harmonic of magnetization and Cu magnetic system behavior at phase separation in moderately oxygenated single crystals of La2CuO4+x},
journal={Applied Magnetic Resonance},
year={1997},
volume={12},
number={2-3},
pages={275-285},
doi={10.1007/BF03162194},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031484255&doi=10.1007%2fBF03162194&partnerID=40&md5=d66837d052acdba5ee4ff76b04652afe},
affiliation={Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, Russian Federation; Institute of Metal Physics, Ekaterinburg, Russian Federation; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, St. Petersburg 188350, Russian Federation},
abstract={The results on the nonlinear longitudinal response (second order uniform dynamic susceptibility χ2(ω)) of two moderately doped La2CuO4+x single crystals in the temperature region of the phase separation of extra oxygen are reported. Large 2D-fragments (l ≃ 7·103 Å) of stoichiometric La2CuO4 are shown to be responsible for the signal in sample with Tps ≥ TN ≃ 243 K. The signal of the crystal with Tps < TN ≃ 272 K is due to oxygen-rich phase. Its peculiarities are related either to change and destruction of magnetic ordering in the course of the phase separation or to the ordering of the extra oxygen. © Springer-Verlag 1997 Printed in Austria.},
correspondence_address1={Lazuta, A.V.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, St. Petersburg 188350, Russian Federation},
publisher={Springer New York},
issn={09379347},
coden={APMRE},
language={English},
abbrev_source_title={Appl. Magn. Reson.},
document_type={Article},
source={Scopus},
}

The results on the nonlinear longitudinal response (second order uniform dynamic susceptibility χ2(ω)) of two moderately doped La2CuO4+x single crystals in the temperature region of the phase separation of extra oxygen are reported. Large 2D-fragments (l ≃ 7·103 Å) of stoichiometric La2CuO4 are shown to be responsible for the signal in sample with Tps ≥ TN ≃ 243 K. The signal of the crystal with Tps < TN ≃ 272 K is due to oxygen-rich phase. Its peculiarities are related either to change and destruction of magnetic ordering in the course of the phase separation or to the ordering of the extra oxygen. © Springer-Verlag 1997 Printed in Austria.

@ARTICLE{Ryzhov1996620,
author={Ryzhov, V.A. and Larionov, I.I. and Fomichev, V.N.},
title={On the spurious signal in the longitudinal nonlinear magnetic susceptibility of magnets at the second harmonic of the excitation frequency},
journal={Technical Physics},
year={1996},
volume={41},
number={6},
pages={620-626},
note={cited By 14},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030486467&partnerID=40&md5=f927e6f61fa3282cdacfd5c49c7cda2b},
affiliation={B. P. Konstantinov St. Petersburg I., Russian Academy of Sciences, Gatchina, Leningrad District, Russian Federation},
abstract={The physical nature of the spurious signal that limits the sensitivity in measurements of the longitudinal nonlinear response of magnets at the second harmonic of the magnetization in the radio-frequency region is elucidated. Its cause is the presence of magnetic impurities (Ni, Fe, oxides of Fe) in the constituent materials of the rf elements of the excitation and detection modes of the two-frequency resonance system of the apparatus. An experimental apparatus is described for which the spurious signal is suppressed to the level of the thermal noise of the detector in a detection band Δf=1 kHz, and the sensitivity achieved is close to the theoretical. The maximum amount of magnetic impurities that can be present in the working volume of the ac magnetic field coil without preventing the attainment of this sensitivity is found to be mNimax≃0.6×10-12 g, mFemax≃2.5×10-12 g, and moxmax≃0.9×10-6 g at Δf=1 Hz. The high sensitivity to these impurities shows that this method can be used as a sensitive and inexpensive means of real-time monitoring for them in pure materials. It is shown that the given apparatus can be used to study the homogeneous dynamic magnetic susceptibility of La2CuO4+δ - a member of a new class of high-Tc superconductors which do not have an observable EPR signal from the copper magnetic system. © 1996 American Institute of Physics.},
correspondence_address1={Ryzhov, V.A.; B. P. Konstantinov St. Petersburg I., Russian Academy of Sciences, Gatchina, Leningrad District, Russian Federation},
issn={10637842},
language={English},
abbrev_source_title={Tech. Phys.},
document_type={Article},
source={Scopus},
}

The physical nature of the spurious signal that limits the sensitivity in measurements of the longitudinal nonlinear response of magnets at the second harmonic of the magnetization in the radio-frequency region is elucidated. Its cause is the presence of magnetic impurities (Ni, Fe, oxides of Fe) in the constituent materials of the rf elements of the excitation and detection modes of the two-frequency resonance system of the apparatus. An experimental apparatus is described for which the spurious signal is suppressed to the level of the thermal noise of the detector in a detection band Δf=1 kHz, and the sensitivity achieved is close to the theoretical. The maximum amount of magnetic impurities that can be present in the working volume of the ac magnetic field coil without preventing the attainment of this sensitivity is found to be mNimax≃0.6×10-12 g, mFemax≃2.5×10-12 g, and moxmax≃0.9×10-6 g at Δf=1 Hz. The high sensitivity to these impurities shows that this method can be used as a sensitive and inexpensive means of real-time monitoring for them in pure materials. It is shown that the given apparatus can be used to study the homogeneous dynamic magnetic susceptibility of La2CuO4+δ - a member of a new class of high-Tc superconductors which do not have an observable EPR signal from the copper magnetic system. © 1996 American Institute of Physics.

@ARTICLE{Petukhov1996387,
author={Petukhov, M. and Yumoto, N. and Murase, S. and Onmura, R. and Yoshikawa, S.},
title={Factors that affect the stabilization of α-helices in short peptides by a capping box},
journal={Biochemistry},
year={1996},
volume={35},
number={2},
pages={387-397},
doi={10.1021/bi9513766},
note={cited By 36},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030071921&doi=10.1021%2fbi9513766&partnerID=40&md5=e5946410c79eb5d1c8ebda51e275d70d},
affiliation={Pac. Inst. of Bioorganic Chemistry, RAS, Vladivostok 690022, Russian Federation; Osaka National Research Institute, AIST, Ikeda, Osaka 563, Japan; Department of Organic Materials, Osaka National Research Institute, Japan},
abstract={It was reported recently that the capping box sequences of four N-terminal residues are very important for the stabilization of α-helices in proteins and peptides. To elucidate factors that affect the stabilization of α- helices in short peptides by this motif, we analyzed conformational properties of side chains of five N-terminal residues in several analogs of neuropeptide Y (NPY). The analysis revealed three previously unreported factors that appear to be important for stabilization of an α-helix: (a) a second capping box hydrogen bond for the side chains of Ser, Thr, and Cys; (b) long-range electrostatic interactions between the first (N-cap) and fifth (N4) residues; and (c) capping interactions of α-amino groups with the N4 residue. These factors were incorporated into the parameter set of a recently published, statistical mechanics approach that showed excellent accuracy in the prediction of the helical propensities of short peptides in water [Munoz, V., and Serrano, L. (1995) J. Mol. Biol. 245, 275-296, 297-308]. A significant improvement in the agreement between theoretical predictions and experimental data was achieved. The present results also clarify the nature of capping box stabilization of α-helices in peptides and proteins, indicating that the total influence of hydrogen bonding, local interactions between side chains, helix macrodipole-charge/dipole interactions, and solvation possibilities must all be taken into account. All these factors are associated with approximately the same energy, but with different residues at the N-cap position, they may have opposite effects on the helix stability of peptides. Thus, a delicate balance of interactions of different types controls the stabilization properties of N-cap residues in α-helices.},
correspondence_address1={Yoshikawa, S.; Department of Organic Materials, Osaka National Research Institute, AIST, Ikeda, Osaka 563, Japan},
issn={00062960},
coden={BICHA},
pubmed_id={8555208},
language={English},
abbrev_source_title={BIOCHEMISTRY},
document_type={Article},
source={Scopus},
}

It was reported recently that the capping box sequences of four N-terminal residues are very important for the stabilization of α-helices in proteins and peptides. To elucidate factors that affect the stabilization of α- helices in short peptides by this motif, we analyzed conformational properties of side chains of five N-terminal residues in several analogs of neuropeptide Y (NPY). The analysis revealed three previously unreported factors that appear to be important for stabilization of an α-helix: (a) a second capping box hydrogen bond for the side chains of Ser, Thr, and Cys; (b) long-range electrostatic interactions between the first (N-cap) and fifth (N4) residues; and (c) capping interactions of α-amino groups with the N4 residue. These factors were incorporated into the parameter set of a recently published, statistical mechanics approach that showed excellent accuracy in the prediction of the helical propensities of short peptides in water [Munoz, V., and Serrano, L. (1995) J. Mol. Biol. 245, 275-296, 297-308]. A significant improvement in the agreement between theoretical predictions and experimental data was achieved. The present results also clarify the nature of capping box stabilization of α-helices in peptides and proteins, indicating that the total influence of hydrogen bonding, local interactions between side chains, helix macrodipole-charge/dipole interactions, and solvation possibilities must all be taken into account. All these factors are associated with approximately the same energy, but with different residues at the N-cap position, they may have opposite effects on the helix stability of peptides. Thus, a delicate balance of interactions of different types controls the stabilization properties of N-cap residues in α-helices.

@ARTICLE{Murase199637,
author={Murase, S. and Yumoto, N. and Petukhov, M.G. and Yoshikawa, S.},
title={Acylation of the α-amino group in neuropeptide Y (12-36) increases binding affinity for the Y2 receptor},
journal={Journal of Biochemistry},
year={1996},
volume={119},
number={1},
pages={37-41},
doi={10.1093/oxfordjournals.jbchem.a021213},
note={cited By 16},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029671190&doi=10.1093%2foxfordjournals.jbchem.a021213&partnerID=40&md5=bca99fd604be4a051355237c6e6854fa},
affiliation={Osaka National Research Institute, AIST, 1-8-31 Midorigaoka, Ikeda, Osaka 563, Japan},
abstract={Competition assays using three series of analogs of neuropeptide Y (NPY) ([Xaa11]NPY(11-36), [Xaa12]NPY(12-36), and [Xaa13]NPY(13-36)) revealed that the binding affinity for the Y2 receptor was considerably lowered by truncation of residue 11. Upon acetylation or succinylation of the α-amino group, the binding affinity of [Xaa12]NPY(12-36) recovered to a level similar to that of [Xaa11]NPY(11-36). No significant difference was observed between the increases caused by acetylation and those caused by succinylation, suggesting that the increase in binding affinity cannot be explained by the change in the net charge at the N-terminus as a consequence of the modification. The scattered data points on a plot of the α-helix content vs. IC50 of all these analogs revealed the absence of any apparent relationship, an indication that prior formation of the α-helix is not necessary for binding to the Y2 receptor. It has been widely accepted that fewer than 12 residues from the C-terminus are directly involved in binding of NPY to the Y2 receptor, while the remaining part of NPY only assists in the adoption of a favorable conformation by the C-terminal hexapeptide for recognition by the receptor. However, the present results suggest that the region around residue 12 does not project from the Y2 receptor.},
author_keywords={Acylation;  Binding affinity;  Neuropeptide Y;  Y2 receptor;  α-helix stability},
correspondence_address1={Yoshikawa, S.; Osaka National Research Institute, AIST, 1-8-31 Midorigaoka, Ikeda, Osaka 563, Japan},
publisher={Japanese Biochemical Society},
issn={0021924X},
coden={JOBIA},
pubmed_id={8907173},
language={English},
abbrev_source_title={J. Biochem.},
document_type={Article},
source={Scopus},
}

Competition assays using three series of analogs of neuropeptide Y (NPY) ([Xaa11]NPY(11-36), [Xaa12]NPY(12-36), and [Xaa13]NPY(13-36)) revealed that the binding affinity for the Y2 receptor was considerably lowered by truncation of residue 11. Upon acetylation or succinylation of the α-amino group, the binding affinity of [Xaa12]NPY(12-36) recovered to a level similar to that of [Xaa11]NPY(11-36). No significant difference was observed between the increases caused by acetylation and those caused by succinylation, suggesting that the increase in binding affinity cannot be explained by the change in the net charge at the N-terminus as a consequence of the modification. The scattered data points on a plot of the α-helix content vs. IC50 of all these analogs revealed the absence of any apparent relationship, an indication that prior formation of the α-helix is not necessary for binding to the Y2 receptor. It has been widely accepted that fewer than 12 residues from the C-terminus are directly involved in binding of NPY to the Y2 receptor, while the remaining part of NPY only assists in the adoption of a favorable conformation by the C-terminal hexapeptide for recognition by the receptor. However, the present results suggest that the region around residue 12 does not project from the Y2 receptor.

@ARTICLE{Basavappa1996764,
author={Basavappa, S. and Huang, C.-C. and Mangel, A.W. and Lebedev, D.V. and Knauf, P.A. and Ellory, J.C.},
title={Swelling-activated amino acid efflux in the human neuroblastoma cell line CHP-100},
journal={Journal of Neurophysiology},
year={1996},
volume={76},
number={2},
pages={764-769},
doi={10.1152/jn.1996.76.2.764},
note={cited By 32},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029813762&doi=10.1152%2fjn.1996.76.2.764&partnerID=40&md5=6062bad593f7a224da629e608419d38a},
affiliation={Department of Physiology, University of Oxford, Parks Road, Oxford OX1 3PT, United Kingdom},
abstract={1. The effects of hypoosmotic stress on cell volume and amino acid efflux were evaluated in the human neuroblastoma cell line CHP-100 with the Coulter Counter Multisizer and radiolabeled amino acid efflux, respectively. 2. CHP-100 cells swelled by ~35 ± 5% (means ± SE) when the osmolarity of the solution was decreased from 290 to 190 mOsm/kg H2O. The rapid swelling was followed by a biphasic regulatory volume decrease (RVD). 3. In cells loaded with 14C-taurine, hypoosmotic stress induced a 300 ± 22% (n = 23. P < 0.05) increase in taurine efflux compared with controls. This efflux was inhibited by the chloride channel blockers 5-nitro-2-(3-phenylpropylamino)- benzoic acid (NPPB). 4,4'-diisothio-cyanostilbene-2,2'-disulfonic acid (DIDS), niflumic acid and by the volume activated anion channel blocker tamoxifen. In addition, the swelling-activated taurine efflux was dependent upon extracellular calcium. 4. Similarly, in cells loaded with 14C-glycine, hypoosmotic stress significantly increased glycine efflux, which was also sensitive to NPPB. In contrast, efflux of 3H-glutamate was not significantly altered after hypoosmotic stress. 5. With the use of patch clamp recording techniques, Cl- channels were activated in cell attached patches after exposure to hypoosmotic solutions. 6. In nystatin perforated patches, permeability of the hypoosmotically activated anion channel was observed to be SCN > I > Br > Cl >> Glutamate. 7. It is concluded that in CHP-100 cells, anion channels are activated during hypoosmotic stress and these channels represent a pathway for efflux of amino acids.},
correspondence_address1={Basavappa, S.; Department of Physiology, University of Oxford, Parks Road, Oxford OX1 3PT, United Kingdom},
publisher={American Physiological Society},
issn={00223077},
coden={JONEA},
pubmed_id={8871197},
language={English},
abbrev_source_title={J. NEUROPHYSIOL.},
document_type={Article},
source={Scopus},
}

1. The effects of hypoosmotic stress on cell volume and amino acid efflux were evaluated in the human neuroblastoma cell line CHP-100 with the Coulter Counter Multisizer and radiolabeled amino acid efflux, respectively. 2. CHP-100 cells swelled by  35 ± 5% (means ± SE) when the osmolarity of the solution was decreased from 290 to 190 mOsm/kg H2O. The rapid swelling was followed by a biphasic regulatory volume decrease (RVD). 3. In cells loaded with 14C-taurine, hypoosmotic stress induced a 300 ± 22% (n = 23. P < 0.05) increase in taurine efflux compared with controls. This efflux was inhibited by the chloride channel blockers 5-nitro-2-(3-phenylpropylamino)- benzoic acid (NPPB). 4,4'-diisothio-cyanostilbene-2,2'-disulfonic acid (DIDS), niflumic acid and by the volume activated anion channel blocker tamoxifen. In addition, the swelling-activated taurine efflux was dependent upon extracellular calcium. 4. Similarly, in cells loaded with 14C-glycine, hypoosmotic stress significantly increased glycine efflux, which was also sensitive to NPPB. In contrast, efflux of 3H-glutamate was not significantly altered after hypoosmotic stress. 5. With the use of patch clamp recording techniques, Cl- channels were activated in cell attached patches after exposure to hypoosmotic solutions. 6. In nystatin perforated patches, permeability of the hypoosmotically activated anion channel was observed to be SCN > I > Br > Cl >> Glutamate. 7. It is concluded that in CHP-100 cells, anion channels are activated during hypoosmotic stress and these channels represent a pathway for efflux of amino acids.

@ARTICLE{Petukhov199541,
author={Petukhov, M.G. and Mazur, A.K. and Elyakova, L.A.},
title={Investigation of the conformational properties of a β-(1 → 3) branched β-(1 → 6) heptasaccharide elicitor and its analogues by internal coordinate stochastic dynamics},
journal={Carbohydrate Research},
year={1995},
volume={279},
number={C},
pages={41-57},
doi={10.1016/0008-6215(95)00277-4},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029562237&doi=10.1016%2f0008-6215%2895%2900277-4&partnerID=40&md5=241bb6542b1e89256b00245238e27e83},
affiliation={Pacific Institute of Bioorganic Chemistry, The Russian Academy of Sciences, 690022 Vladivostok, Russian Federation},
abstract={A series of β-(1 → 3) branched β-(1 → 6) oligosaccharides that are known to take part in switching immune reactions in plants was studied by a molecular dynamics approach. A novel technique was applied which recently proved to be very efficient in polypeptide simulations. Molecular dynamics is simulated in internal rather than Cartesian coordinates with dramatically reduced numbers of degrees of freedom and a time step ten-fold larger than usual values. Comparison and classification of most populated conformational states revealed a few conformational motifs that are frequently adopted by highly active oligosaccharides and are not populated in an inactive analogue. As a result a putative biologically active conformation of the oligosaccharides is proposed. © 1995.},
author_keywords={Branched oligosaccharides;  Conformational states;  Internal coordinate stochastic dynamics},
correspondence_address1={Petukhov, M.G.; Pacific Institute of Bioorganic Chemistry, The Russian Academy of Sciences, 690022 Vladivostok, Russian Federation},
issn={00086215},
coden={CRBRA},
pubmed_id={8593632},
language={English},
abbrev_source_title={Carbohydr. Res.},
document_type={Article},
source={Scopus},
}

A series of β-(1 → 3) branched β-(1 → 6) oligosaccharides that are known to take part in switching immune reactions in plants was studied by a molecular dynamics approach. A novel technique was applied which recently proved to be very efficient in polypeptide simulations. Molecular dynamics is simulated in internal rather than Cartesian coordinates with dramatically reduced numbers of degrees of freedom and a time step ten-fold larger than usual values. Comparison and classification of most populated conformational states revealed a few conformational motifs that are frequently adopted by highly active oligosaccharides and are not populated in an inactive analogue. As a result a putative biologically active conformation of the oligosaccharides is proposed. © 1995.

@ARTICLE{Masterov199417,
author={Masterov, V.F. and Isaev-Ivanov, V.V. and Patrina, I.B.},
title={A new ESR spectrum in the Y-Ca-Ba-La-Cu-O high-Tcsuperconductor system},
journal={Superconductor Science and Technology},
year={1994},
volume={7},
number={1},
pages={17-18},
doi={10.1088/0953-2048/7/1/004},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028320736&doi=10.1088%2f0953-2048%2f7%2f1%2f004&partnerID=40&md5=cbc3e7fec142e710758ff709939687dd},
affiliation={State Technical University, 29 Polytekhnicheskaya st, St Petersburg, 195251, Russian Federation; Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad, 188350, Russian Federation; Institute of Silicate Chemistry, Russian Academy of Sciences, St Petersburg, 199034, Russian Federation},
abstract={Electron spin resonance spectra (ESR) of YBa1.5La0.5Cu3O7.21and Y0.7Ca0.3Ba1.5La0.5Ca3O7.08high-Tcsuperconductors (HTSC) were obtained using 3 cm and 2 mm ESR spectrometers. A nearly isotropic Lorentz line with a g factor of 2.0065+or-0.0005 was observed and interpreted as being due to the electron located near a diamagnetic atom in the HTSC lattice. © 1994 IOP Publishing Ltd. © 1994 IOP Publishing Ltd.},
issn={09532048},
language={English},
abbrev_source_title={Supercond Sci Technol},
document_type={Article},
source={Scopus},
}

Electron spin resonance spectra (ESR) of YBa1.5La0.5Cu3O7.21and Y0.7Ca0.3Ba1.5La0.5Ca3O7.08high-Tcsuperconductors (HTSC) were obtained using 3 cm and 2 mm ESR spectrometers. A nearly isotropic Lorentz line with a g factor of 2.0065+or-0.0005 was observed and interpreted as being due to the electron located near a diamagnetic atom in the HTSC lattice. © 1994 IOP Publishing Ltd. © 1994 IOP Publishing Ltd.

@ARTICLE{Ryzhov19941573,
author={Ryzhov, V.A. and Lazuta, A.V. and Larionov, I.I. and Arbuzova, T.I. and Kurnevich, L.A.},
title={Second harmonic of magnetization and novel peculiarities of phase separation in lightly-oxygenated single crystals of La2CuO4+x.},
journal={Physica C: Superconductivity and its applications},
year={1994},
volume={235-240},
number={PART 3},
pages={1573-1574},
doi={10.1016/0921-4534(94)92012-5},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0346842185&doi=10.1016%2f0921-4534%2894%2992012-5&partnerID=40&md5=1ff1c4da81f57dcb8b90a33df4665535},
affiliation={Petersburg Nuclear Physics Institute, 188350 Gatchina St. Petersburg, Russian Federation; Institute of Metal Physics, 620219 Ekaterinburg, Russian Federation; Institute of Physics of Solids and Semiconductors, 220072 Minsk Belorussia, Russian Federation},
abstract={First results of investigations of nonlinear response of three lightly-oxygenated crystals of La2CuO4+x in the excess-oxygen phase separation (PS) region are reported. It is argued that the peculiarities of response are due to domains formed at PS which possess weak ferromagnetism. The estimations of domain sizes are obtained: LII≈4.5·103 Å in CuO2 - plane and L⊥≥260Å in orthogonal direction. © 1994.},
correspondence_address1={Ryzhov, V.A.; Petersburg Nuclear Physics Institute, 188350 Gatchina St. Petersburg, Russian Federation},
issn={09214534},
coden={PHYCE},
language={English},
abbrev_source_title={Phys C Supercond Appl},
document_type={Article},
source={Scopus},
}

First results of investigations of nonlinear response of three lightly-oxygenated crystals of La2CuO4+x in the excess-oxygen phase separation (PS) region are reported. It is argued that the peculiarities of response are due to domains formed at PS which possess weak ferromagnetism. The estimations of domain sizes are obtained: LII≈4.5·103 Å in CuO2 - plane and L⊥≥260Å in orthogonal direction. © 1994.

@ARTICLE{Dulin19931,
author={Dulin, S.K. and Kiselev, I.A.},
title={Management of structural matching in a knowledge base},
journal={Journal of Computer and Systems Sciences International},
year={1993},
volume={31},
number={1},
pages={1-9},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027266567&partnerID=40&md5=e9f07c9aa8dc60994b15d9f7ef327aaa},
affiliation={Computer Cent of the Acad of, Sciences, Moscow, Russian Federation},
abstract={This paper examines approach to modelling structural mismatching in a knowledge base by means of a character-based relational matrix. The algorithm developed to reduce mismatching is implemented as a resident module in the DISSON interactive structural matching management system. A description of the package is given together with the primary performance characteristics of a demonstration example of the DISSON system.},
correspondence_address1={Dulin, S.K.; Computer Cent of the Acad of, Sciences, Moscow, Russian Federation},
issn={10642307},
coden={00097},
language={English},
abbrev_source_title={J Comput Syst Sci Int},
document_type={Article},
source={Scopus},
}

This paper examines approach to modelling structural mismatching in a knowledge base by means of a character-based relational matrix. The algorithm developed to reduce mismatching is implemented as a resident module in the DISSON interactive structural matching management system. A description of the package is given together with the primary performance characteristics of a demonstration example of the DISSON system.

@ARTICLE{Petukhov1992154,
author={Petukhov, M.G. and Dorofeyev, V.E. and Abagyan, R.A. and Mazur, A.K.},
title={Total optimization of the conformational energy of oligopeptides using a tunnel algorithm},
journal={Biophysics},
year={1992},
volume={37},
number={2},
pages={154-157},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-44049122910&partnerID=40&md5=b798a8bb9ee3a4bcfdc366fa276b972d},
affiliation={Pacific Ocean Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok, Russian Federation},
abstract={A method is proposed for obtaining low energy conformations of oligopeptides - the tunnel method of overall optimization. Test examples are given to compare the efficacy of the work of the tunnel method and other known approaches to the solution to this problem - grid search, molecular dynamics at a constant temperature. It is shown that for oligopeptides with a length of 3-4 residues the method finds the overall energy minimum more effectively than other methods; for longer oligopeptides the method does not always converge to an overall minimum although in this case it allows the low energy conformations to be sought quite effectively. © 1992.},
correspondence_address1={Petukhov, M.G.; Pacific Ocean Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok, Russian Federation},
issn={00063509},
language={English},
abbrev_source_title={Biophysics},
document_type={Article},
source={Scopus},
}

A method is proposed for obtaining low energy conformations of oligopeptides - the tunnel method of overall optimization. Test examples are given to compare the efficacy of the work of the tunnel method and other known approaches to the solution to this problem - grid search, molecular dynamics at a constant temperature. It is shown that for oligopeptides with a length of 3-4 residues the method finds the overall energy minimum more effectively than other methods; for longer oligopeptides the method does not always converge to an overall minimum although in this case it allows the low energy conformations to be sought quite effectively. © 1992.

@ARTICLE{Petukhov1992226,
author={Petukhov, M.G. and Dorofeev, V.E. and Abagian, R.A. and Mazur, A.K.},
title={Global optimization of the conformational energy of oligopeptides using a tunnel algorithm [Global'naia optimizatsiia konformatsionnoǐ énergii oligopeptidov s pomoshch'iu tunnel'nogo algoritma.]},
journal={Biofizika},
year={1992},
volume={37},
number={2},
pages={226-230},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026840322&partnerID=40&md5=1bed2f2e562b93e5a1c4d89697f53711},
abstract={The tunneling algorithm has been suggested as a method for the searching of the low energy conformations of the oligopeptides. The efficiency of the method has been compared with other global energy minimization methods such as grid search and molecular dynamics. It has been shown that tunneling algorithm reached global minimum of potential energy of the molecule of 3-4 residues more effectively than other methods. Experiments with oligopeptides of more than 4 residues showed that although during reasonable time tunneling algorithm does not reach the global minimum it can very effectively find the low energy minimum.},
correspondence_address1={Petukhov, M.G.},
issn={00063029},
pubmed_id={7578315},
language={Russian},
abbrev_source_title={Biofizika},
document_type={Article},
source={Scopus},
}

The tunneling algorithm has been suggested as a method for the searching of the low energy conformations of the oligopeptides. The efficiency of the method has been compared with other global energy minimization methods such as grid search and molecular dynamics. It has been shown that tunneling algorithm reached global minimum of potential energy of the molecule of 3-4 residues more effectively than other methods. Experiments with oligopeptides of more than 4 residues showed that although during reasonable time tunneling algorithm does not reach the global minimum it can very effectively find the low energy minimum.

@ARTICLE{Petukhov1992292,
author={Petukhov, M.G. and Mazur, A.K.},
title={Modelling of possible binding modes of substrates in the active site of Taka-amylase A},
journal={Molekulyarnaya Biologiya},
year={1992},
volume={26},
number={2},
pages={292-299},
note={cited By 4},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026526131&partnerID=40&md5=2ad6064a59df2e1f8de480b45e012298},
affiliation={Pacific Inst. Bioorganic Chemistry, Russian Academy of Sciences, Vladivostok 690022, Russia},
correspondence_address1={Petukhov, M.G.; Pacific Inst. Bioorganic Chemistry, Russian Academy of Sciences, Vladivostok 690022, Russia},
issn={00268984},
coden={MOBIB},
language={Russian},
abbrev_source_title={MOL. BIOL.},
document_type={Article},
source={Scopus},
}

@ARTICLE{Dulin199129,
author={Dulin, S.K. and Kiselev, I.A.},
title={The control of structured matching in knowledge base},
journal={Izvestiya Akademii Nauk: Tekhnicheskaia Kibernetika},
year={1991},
number={5},
pages={29-39},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026226101&partnerID=40&md5=a9aff1e7fcdebdebb7b9de2e00b78a73},
abstract={The paper deals with the problem of modelling of structured dismasting in knowledge base with the help of sign matrix of cohesiveness. The algorithm of dismatching decreasing is constructed. The matching forming of knowledge system in the process of knowledge acquisition is a very actual problem. Both semantic and structural matching are analyzed. One of the central questions of structured matching analysis is the choice of matching criterion. Evaluation of contents of knowledge base is discussed. Particularly, for solution of this problem authors propose to use the notions of conceptual clustering such as conceptual cohesiveness. The description of the methods and algorithms which have been designed in system 'Disson' is given.},
correspondence_address1={Dulin, S.K.},
coden={IATKA},
language={Russian},
abbrev_source_title={Izv Akad Nauk Teh Kibern},
document_type={Article},
source={Scopus},
}

The paper deals with the problem of modelling of structured dismasting in knowledge base with the help of sign matrix of cohesiveness. The algorithm of dismatching decreasing is constructed. The matching forming of knowledge system in the process of knowledge acquisition is a very actual problem. Both semantic and structural matching are analyzed. One of the central questions of structured matching analysis is the choice of matching criterion. Evaluation of contents of knowledge base is discussed. Particularly, for solution of this problem authors propose to use the notions of conceptual clustering such as conceptual cohesiveness. The description of the methods and algorithms which have been designed in system 'Disson' is given.

@ARTICLE{Mazur1988447,
author={Mazur, A.K. and Petukhov, M.G. and Yelyakova, L.A.},
title={Model of spatial random migration of a depolymerase on interaction with the substrate},
journal={Biophysics},
year={1988},
volume={33},
number={3},
pages={447-452},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-45549115298&partnerID=40&md5=83a962d0c8541a84e59eccbf8f9e022f},
affiliation={Pacific Institute of Bio-Organic Chemistry, U.S.S.R. Academy of Sciences, Vladivostok, Russian Federation},
abstract={The mechanism of splitting of an oligomer by a depolymerase allowing for repeat binding to the substrate is considered. The motion of the molecules is modelled by simple spatial random migration. Numerical evaluations are obtained for the probabilities of repat attack as a function of the chain length of the substrate and bond number. It is concluded that the mechanism considered may describe the repeat attack of α-amylase of A. oryzae. © 1989.},
correspondence_address1={Mazur, A.K.; Pacific Institute of Bio-Organic Chemistry, U.S.S.R. Academy of Sciences, Vladivostok, Russian Federation},
issn={00063509},
language={English},
abbrev_source_title={Biophysics},
document_type={Article},
source={Scopus},
}

The mechanism of splitting of an oligomer by a depolymerase allowing for repeat binding to the substrate is considered. The motion of the molecules is modelled by simple spatial random migration. Numerical evaluations are obtained for the probabilities of repat attack as a function of the chain length of the substrate and bond number. It is concluded that the mechanism considered may describe the repeat attack of α-amylase of A. oryzae. © 1989.

@ARTICLE{Ryzhov1988772,
author={Ryzhov, V.A. and Solov'ev, V.A. and Turutin, V.V. and Fromichev, V.N.},
title={Apparatus for production of modulated electron beam in electromagnet gap of EPR spectrometer for study of radiation chemical reactions in aqueous solutions},
journal={Instruments and experimental techniques New York},
year={1988},
volume={31},
number={3 pt 2},
pages={772-775},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024171727&partnerID=40&md5=c009df5910dcc6f613bb1662a7192302},
affiliation={Acad of Sciences of the USSR, Russian Federation},
abstract={An apparatus for production of an electron beam with an energy of 80 keV in the electromagnet gap of an EPR spectrometer is described. A beam 12 mm in diameter is used to irradiate aqueous solutions in a balanced spin-induction resonator. The electrons are totally absorbed in the specimen and do not reach the resonator, which gets rid of electron current and ionization of the air in the resonator and reduces resonator Q and spurious frequency modulation. The dose absorbed in the working chamber reaches 670 krd/sec for a beam current of ≈40μA. The modulator forms a 100% modulated beam. The beam-current rise and fall times are 20 nsec. The pulse repetition frequency can be varied from 0 to 10 MHz, which allows both stationary and kinetic experiments to be performed.},
correspondence_address1={Ryzhov, V.A.; Acad of Sciences of the USSRRussian Federation},
issn={00204412},
coden={INETA},
language={English},
abbrev_source_title={Instrum Exp Tech},
document_type={Article},
source={Scopus},
}

An apparatus for production of an electron beam with an energy of 80 keV in the electromagnet gap of an EPR spectrometer is described. A beam 12 mm in diameter is used to irradiate aqueous solutions in a balanced spin-induction resonator. The electrons are totally absorbed in the specimen and do not reach the resonator, which gets rid of electron current and ionization of the air in the resonator and reduces resonator Q and spurious frequency modulation. The dose absorbed in the working chamber reaches 670 krd/sec for a beam current of ≈40μA. The modulator forms a 100% modulated beam. The beam-current rise and fall times are 20 nsec. The pulse repetition frequency can be varied from 0 to 10 MHz, which allows both stationary and kinetic experiments to be performed.

@ARTICLE{Petukhov1988152,
author={Petukhov, M.G. and Pershin, V.L.},
title={AB initio investigation of electronic structure of a molecule of α-D-glucose},
journal={Journal of Structural Chemistry},
year={1988},
volume={29},
number={1},
pages={152-153},
doi={10.1007/BF00750190},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0345609358&doi=10.1007%2fBF00750190&partnerID=40&md5=cc33998a6cba180494047256de1057e0},
publisher={Kluwer Academic Publishers-Plenum Publishers},
issn={00224766},
language={English},
abbrev_source_title={J Struct Chem},
document_type={Article},
source={Scopus},
}

@ARTICLE{Bresler1988283,
author={Bresler, V.M. and Isaev-Ivanov, V.V. and Kazbekov, E.N. and Kleiner, A.R. and Orlov Yu., N. and Ostapenko, I.A. and Sukhodolova, A.T. and Fomichev, V.N.},
title={Physico-chemical mechanisms of organic acid transport in vesicles of the apical membrane of the rat kidney proximal channel cells. II. Kinetic parameters of transport and phase state of the lipid bilayer in the Campbell strain rats},
journal={Tsitologiya},
year={1988},
volume={30},
number={3},
pages={283-290},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023975394&partnerID=40&md5=eab4b78d524ce3061c80f7d580bcba4c},
affiliation={Institute of Evolutionary Physiology and Biochemistry of the Academy of Sciences of the USSR, Leningrad, Russian Federation},
issn={00413771},
coden={TSITA},
pubmed_id={2842901},
language={Russian},
abbrev_source_title={TSITOLOGIYA},
document_type={Article},
source={Scopus},
}

@ARTICLE{Bondarev1988212,
author={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kleiner, A.R. and Krasotskaya, G.I. and Fomichev, V.N. and Nezlin, R.S. and Krymov, V.N. and Oransky, L.G. and Bakhmatsky, V.D.},
title={Spin-label tempo-dichlorotriazine distribution in immunoglobulin molecule},
journal={Biofizika},
year={1988},
volume={33},
number={2},
pages={212-215},
note={cited By 3},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023971667&partnerID=40&md5=c70de8dc4324e25f038a8b2c72f72116},
affiliation={B.P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Russian Federation},
issn={00063029},
coden={BIOFA},
pubmed_id={2839241},
language={Russian},
abbrev_source_title={BIOFIZIKA},
document_type={Article},
source={Scopus},
}

@ARTICLE{Bondarev19871655,
author={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kleǐner, A.R. and Krymov, V.N.},
title={Analysis of existing models of spin label movement during spin labeling of biological macromolecules [Analiz sushchestvuiushchikh modeleǐ dvizheniia spinovoǐ metki pri spin-mechenii biologicheskikh makromolekul.]},
journal={Molekulyarnaya Biologiya},
year={1987},
volume={21},
number={6},
pages={1655-1663},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023447664&partnerID=40&md5=4cc5a10ee8f0932ce376d05f1a1ae7a2},
abstract={The spin-labeled bovine serum albumin and IgG were studied in search of an experimental approach for comparison of different models of rotational mobility of spin label. These models are: the model of isotropic motion of spin label together with the macromolecule (IM); the model of highly anisotropic motion of spin label (HAM); and the model of slow isotropic motion of label around the binding site (SIML). The experimental spectra were measured on a common X-band ESR spectrometer and on the unique 140 GHZ (lambda = 2 mm) ESR spectrometer under the same conditions. Theoretical spectra were computer-calculated according to Freed's theory. We have found, that the results of temperature-viscosity experiments in X-band are contradictory to the model of IM both for the BSA and IgG species. The models of HAM and SIML for the BSA give identical X-band spectra. The bovine serum albumin spectra in the 2 mm region strongly contradict to the assumptions of the HAM model. Also, the SIML model fails to describe the experimental spectra in terms of isotropic motion of the spin label around the binding site. X-band spectra of IgG can not be explained by the SIML model, while the same spectra in the 2 mm region can not be explained by the HAM model.},
correspondence_address1={Bondarev, G.N.},
issn={00268984},
pubmed_id={2833690},
language={Russian},
abbrev_source_title={Mol Biol (Mosk)},
document_type={Article},
source={Scopus},
}

The spin-labeled bovine serum albumin and IgG were studied in search of an experimental approach for comparison of different models of rotational mobility of spin label. These models are: the model of isotropic motion of spin label together with the macromolecule (IM); the model of highly anisotropic motion of spin label (HAM); and the model of slow isotropic motion of label around the binding site (SIML). The experimental spectra were measured on a common X-band ESR spectrometer and on the unique 140 GHZ (lambda = 2 mm) ESR spectrometer under the same conditions. Theoretical spectra were computer-calculated according to Freed's theory. We have found, that the results of temperature-viscosity experiments in X-band are contradictory to the model of IM both for the BSA and IgG species. The models of HAM and SIML for the BSA give identical X-band spectra. The bovine serum albumin spectra in the 2 mm region strongly contradict to the assumptions of the HAM model. Also, the SIML model fails to describe the experimental spectra in terms of isotropic motion of the spin label around the binding site. X-band spectra of IgG can not be explained by the SIML model, while the same spectra in the 2 mm region can not be explained by the HAM model.

@ARTICLE{Bresler19871177,
author={Bresler, V.M. and Val'ter, S.N. and Isaev-Ivanov, V.V. and Kazbekov, E.N. and Kleǐner, A.P.},
title={Physico-chemical mechanisms of organic acid transport in the apical membrane cells of the proximal kidney tubules in rats. I. Kinetic transport parameters and effect of the lipid phasic state on transport [Fiziko-khimicheskie mekhanizmy transporta organicheskikh kislot v vezikulakh apikal'noǐ membrany kletok proksimal'nykh kanal'tsev pochki krys. I. Kineticheskie parametry transporta i vliianie fazovogo sostoianiia na transport.]},
journal={Tsitologiya},
year={1987},
volume={29},
number={10},
pages={1177-1184},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023424553&partnerID=40&md5=d99beb72001ade00b15fac8d0e5be47e},
abstract={The kinetics of the transport of 3H-para-aminohippuric acid (PAH) and the influence of the temperature on the initial rate of transport were studied on the vesicles of a purified fraction of the apical membrane isolated from cells of kidney proximal tubules. The PAH transport is accomplished owing to the facilitate diffusion mechanism. The apparent Michaelis constant at 36 degrees C was equal to 7.0 + 1.0 mM, the maximum rate was 15 nmol/min on 1 mg of protein, the inhibition constant for the PAH transport by probenecid being 0.5 mM. At 22 degrees C the apparent Michaelis constant was drastically increased. When the temperature dependence of the initial rate of PAH transport into vesicles was replotted in the form of the Arrhenius plot, there was a turning-point of the line at 28-30 degrees C. The same turning-point is shown on the Arrhenius plot for temperature dependence of alkaline phosphatase activity (a marker enzyme for the apical membrane). The electron paramagnetic resonance spectra analysis of 5-doxylstearate-labeled apical membrane preparation reveals a thermotropic transition near 21-29 degrees C. It is concluded that the function of the carrier and the activity of alkaline phosphatase depend on the phasic state of membrane lipids; the normal function of membrane proteins is possible under the liquid-crystalline state of the lipid bilayer.},
correspondence_address1={Bresler, V.M.},
issn={00413771},
pubmed_id={2829399},
language={Russian},
abbrev_source_title={Tsitologiia},
document_type={Article},
source={Scopus},
}

The kinetics of the transport of 3H-para-aminohippuric acid (PAH) and the influence of the temperature on the initial rate of transport were studied on the vesicles of a purified fraction of the apical membrane isolated from cells of kidney proximal tubules. The PAH transport is accomplished owing to the facilitate diffusion mechanism. The apparent Michaelis constant at 36 degrees C was equal to 7.0 + 1.0 mM, the maximum rate was 15 nmol/min on 1 mg of protein, the inhibition constant for the PAH transport by probenecid being 0.5 mM. At 22 degrees C the apparent Michaelis constant was drastically increased. When the temperature dependence of the initial rate of PAH transport into vesicles was replotted in the form of the Arrhenius plot, there was a turning-point of the line at 28-30 degrees C. The same turning-point is shown on the Arrhenius plot for temperature dependence of alkaline phosphatase activity (a marker enzyme for the apical membrane). The electron paramagnetic resonance spectra analysis of 5-doxylstearate-labeled apical membrane preparation reveals a thermotropic transition near 21-29 degrees C. It is concluded that the function of the carrier and the activity of alkaline phosphatase depend on the phasic state of membrane lipids; the normal function of membrane proteins is possible under the liquid-crystalline state of the lipid bilayer.

@ARTICLE{Ryzhov1983363,
author={Ryzhov, V.A. and Fomichev, V.N.},
title={Resonant nonlinear effects in parallel magnetic fields for solutions of paramagnets in the presence of spin exchange},
journal={Theoretical and Experimental Chemistry},
year={1983},
volume={18},
number={4},
pages={363-371},
doi={10.1007/BF00516984},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34250231745&doi=10.1007%2fBF00516984&partnerID=40&md5=8382455cc84255678fded0813b993d82},
affiliation={B. P. Konstantinov Leningrad Institute of Nuclear Physics, Russian Federation},
correspondence_address1={Ryzhov, V.A.; B. P. Konstantinov Leningrad Institute of Nuclear PhysicsRussian Federation},
publisher={Kluwer Academic Publishers-Plenum Publishers},
issn={00405760},
language={English},
abbrev_source_title={Theor Exp Chem},
document_type={Article},
source={Scopus},
}

@ARTICLE{Isaev-Ivanov1983362,
author={Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kleǐner, A.R. and Odintsov, V.B. and Sidorov, O.I.},
title={Spectral division of conformational states of spin-labeled tRNA Phe from Escherichia coli [Spektral'noe razdelenie konformatsionnykh sostoianiǐ na spin-mechenoǐ tRNK Phe iz Escherichia coli.]},
journal={Molekulyarnaya Biologiya},
year={1983},
volume={17},
number={2},
pages={362-372},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020724858&partnerID=40&md5=2ed571f6fdc7bf24bfde8271a0fd7fec},
abstract={A spectral division method of two conformational states of spin-labeled macromolecules is presented. The method is suitable in conditions of highly anisotropic motion of spin label and is based on titration of experimental spectra of spin-labeled macromolecule by theoretical ones. Theoretical spectra simulation uses the Freed theory and spin-Hamiltonian parameters, derived from independent experiments. Nomogrammes and formula for calculation of order parameter Sz and correlation time tau c in temperature-viscosity experiment are available. The method was applied to spectral division of two conformational states of spin-labeled tRNAPhe from E. coli and spectral parameters Sz and tau c were obtained for both states. ESR spectra of these conformational states at t degree = 20 degrees differ strongly from one another by order parameter Sz. The first conformer, that is characterised by a greater order parameter has no globular conformational transition (in terms of changes of the hydrodynamic macromolecule radius) between 2 degrees and 20 degrees, but local conformational changes take place in this temperature region.},
correspondence_address1={Isaev-Ivanov, V.V.},
issn={00268984},
pubmed_id={6304493},
language={Russian},
abbrev_source_title={Mol Biol (Mosk)},
document_type={Article},
source={Scopus},
}

A spectral division method of two conformational states of spin-labeled macromolecules is presented. The method is suitable in conditions of highly anisotropic motion of spin label and is based on titration of experimental spectra of spin-labeled macromolecule by theoretical ones. Theoretical spectra simulation uses the Freed theory and spin-Hamiltonian parameters, derived from independent experiments. Nomogrammes and formula for calculation of order parameter Sz and correlation time tau c in temperature-viscosity experiment are available. The method was applied to spectral division of two conformational states of spin-labeled tRNAPhe from E. coli and spectral parameters Sz and tau c were obtained for both states. ESR spectra of these conformational states at t degree = 20 degrees differ strongly from one another by order parameter Sz. The first conformer, that is characterised by a greater order parameter has no globular conformational transition (in terms of changes of the hydrodynamic macromolecule radius) between 2 degrees and 20 degrees, but local conformational changes take place in this temperature region.

@ARTICLE{Ryzhov1983674,
author={Ryzhov, V.A. and Fomichev, V.N.},
title={NONLINEAR EFFECTS IN PARALLEL MAGNETIC FIELDS IN SOLUTIONS OF (111) IRON IONS AND VANADYL.},
journal={Soviet physics. Technical physics},
year={1983},
volume={28},
number={6},
pages={674-680},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020763021&partnerID=40&md5=5e6af9cf1b20d2e64c21023f298cff44},
abstract={Nonlinear effects in solutions of vanadyl and (111) iron are studied experimentally in parallel dc and ac linearly polarized magnetic fields; these effects include the absence of an electron paramagnetic resonance (EPR) spectrum due to broadening of the resonant transitions. It is shown that the nonlinear effects are due both to alteration of the relaxation processes by the ac field and to resonant transitions in the parallel fields. When the ac frequency is small compared to the characteristic lattice vibration frequencies (as was the case in the experiment), the relaxation and resonance effects separately.},
correspondence_address1={Ryzhov, V.A.},
issn={00385662},
coden={SPTPA},
language={English},
abbrev_source_title={Sov Phys Tech Phys},
document_type={Article},
source={Scopus},
}

Nonlinear effects in solutions of vanadyl and (111) iron are studied experimentally in parallel dc and ac linearly polarized magnetic fields; these effects include the absence of an electron paramagnetic resonance (EPR) spectrum due to broadening of the resonant transitions. It is shown that the nonlinear effects are due both to alteration of the relaxation processes by the ac field and to resonant transitions in the parallel fields. When the ac frequency is small compared to the characteristic lattice vibration frequencies (as was the case in the experiment), the relaxation and resonance effects separately.

@ARTICLE{Bondarev1982352,
author={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kirillov, S.V. and Kleǐner, A.R.},
title={Study on the conformational state of Escherichia coli tRNA-Phe in solution by ESR-spectometry without modulation [Izuchenie konformatsionnoǐ situatsii v vodnykh rastvorakh spin-mechenoǐ tRNA-Phe iz Escherichia coli bezomduliatsionnym metodom EPR.]},
journal={Molekulyarnaya Biologiya},
year={1982},
volume={16},
number={2},
pages={352-362},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020108887&partnerID=40&md5=737d07719caa6d071f7b656012d89f83},
abstract={ESR-spectrometry without modulation of the magnetic field was used for registering the EST spectral line shape (with shape distortion about 0.1 percent) of spin-labeled Escherichia coli tRNAPhe. The analysis of line shape of two different spin-labels in position 8 (S4U) revealed that tRNAPhe in solution always exists as a mixture of at least two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and the biological state of tRNA (deacylated, aminoacyl- or peptidyl-tRNA). There are no large structural rearrangements upon aminoacylation or peptidylation of tRNA, the observed small changes of spectral line shape are due to the changes in conformational equilibria.},
correspondence_address1={Bondarev, G.N.},
issn={00268984},
pubmed_id={6175894},
language={Russian},
abbrev_source_title={Mol Biol (Mosk)},
document_type={Article},
source={Scopus},
}

ESR-spectrometry without modulation of the magnetic field was used for registering the EST spectral line shape (with shape distortion about 0.1 percent) of spin-labeled Escherichia coli tRNAPhe. The analysis of line shape of two different spin-labels in position 8 (S4U) revealed that tRNAPhe in solution always exists as a mixture of at least two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and the biological state of tRNA (deacylated, aminoacyl- or peptidyl-tRNA). There are no large structural rearrangements upon aminoacylation or peptidylation of tRNA, the observed small changes of spectral line shape are due to the changes in conformational equilibria.

@ARTICLE{Bondarev19821113,
author={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kirillov, S.V. and Kleiner, A.R. and Lepekhin, A.F. and Odinzov, V.B. and Fomichev, V.N.},
title={Study on conformational states of Escherichia coli tRNAPhe in solution by a modulation-free ESR-spectrometer},
journal={Nucleic Acids Research},
year={1982},
volume={10},
number={3},
pages={1113-1126},
doi={10.1093/nar/10.3.1113},
note={cited By 2},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020480097&doi=10.1093%2fnar%2f10.3.1113&partnerID=40&md5=69e930e30c6b63173943f327db31e733},
affiliation={B.P.Konstantinov Nuclear Physics Institute of Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},
abstract={A modulationfree Electron Spin Resonance spectrometer was used for the registration of spectral absorption lines of a spin-labeled Escherichia coli phenylalanine tRNA in solution with low (less than 0.1%) line shape distortion. The analysis of line shape of two different spin-labels introduced into position 8 revealed that phenylalanine tRNA in solution exists as a mixture of two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and functional state of tRNA (deacylated, aminoacylated or peptidylated). There are no overall structural rearrangements upon aminoacylation or peptidylation of tRNA. The observed small changes of spectral line shape can be assigned to shifts in conformational equilibria. © 1982 IRL Press Limited.},
correspondence_address1={Bondarev, G.N.; B.P.Konstantinov Nuclear Physics Institute of Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},
issn={03051048},
coden={NARHA},
pubmed_id={6278435},
language={English},
abbrev_source_title={Nucleic Acids Res.},
document_type={Article},
source={Scopus},
}

A modulationfree Electron Spin Resonance spectrometer was used for the registration of spectral absorption lines of a spin-labeled Escherichia coli phenylalanine tRNA in solution with low (less than 0.1%) line shape distortion. The analysis of line shape of two different spin-labels introduced into position 8 revealed that phenylalanine tRNA in solution exists as a mixture of two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and functional state of tRNA (deacylated, aminoacylated or peptidylated). There are no overall structural rearrangements upon aminoacylation or peptidylation of tRNA. The observed small changes of spectral line shape can be assigned to shifts in conformational equilibria. © 1982 IRL Press Limited.

@ARTICLE{Bondarev1982285,
author={Bondarev, G.N. and Isaev Ivanov, V.V. and Isaeva Ivanova, L.S.},
title={An investigation of the conformational situation in aqueous solutions of spinlabeled tRNA(Phe) from Escherichia coli by the no-modulation EPR method},
journal={Molecular Biology},
year={1982},
volume={16},
number={2 II},
pages={285-293},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020442519&partnerID=40&md5=b67ddab3bb62813db48a07c95bf6a657},
affiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},
issn={00268933},
coden={MOLBB},
language={English},
abbrev_source_title={MOL. BIOL.},
document_type={Article},
source={Scopus},
}

@ARTICLE{ANISIMOV198246,
author={ANISIMOV, G.K. and DEVYATERIKOV, R.P. and ZAVATSKII, E.I. and LAVROV, V.V. and RYZHOV, V.A. and FEL'DMAN, D.M. and FOMICHEV, V.N.},
title={INVESTIGATION OF PARAMAGNETIC SUBSTANCES BY USING NONLINEAREFFECTS IN PARAMAGNETS IN PARALLEL MAGNETIC FIELDS.},
journal={SOV PHYS TECH PHYS},
year={1982},
volume={V 27},
number={N 1},
pages={46-50},
note={cited By 8},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020005772&partnerID=40&md5=df684e0972a91588665767f085dce015},
abstract={THE POSSIBILITY OF STUDYING PARAMAGNETIC SUBSTANCES BY USING NONLINEAR EFFECTS IN THEM IS DISCUSSED. THE THEORETICAL SENSITIVITY OF SUCH A METHOD IS ESTIMATED. THIS SENSITIVITY ISFOUND TO BE SUBSTANTIALLY HIGHER THAN THAT OF ESR FOR SUBSTANCES WITH SHORT PARAMAGNETIC RELAXATION TIMES OR WITH LARGEMAGNETIC-INTERACTION ANISOTROPY. THIS IS OBSERVED FOR FECL//3:6H//2O DISSOLVED IN A 60P AQUEOUS SOLUTION OF SUCROSE. THE BLOCK DIAGRAM OF THE APPARATUS FOR RECORDING THE PHASE COMPONENTS OF THE SECOND HARMONIC OF THE MAGNETIZATION, WITH PROVISION FOR SETTING THE PHASE OF THE REFERENCE VOLTAGE AT RADIO FREQUENCIES (F = 5 AND 15 MHZ), IS DESCRIBED.},
correspondence_address1={ANISIMOV, G.K.},
issn={00385662},
coden={SPTPA},
abbrev_source_title={SOV PHYS TECH PHYS},
document_type={Article},
source={Scopus},
}

THE POSSIBILITY OF STUDYING PARAMAGNETIC SUBSTANCES BY USING NONLINEAR EFFECTS IN THEM IS DISCUSSED. THE THEORETICAL SENSITIVITY OF SUCH A METHOD IS ESTIMATED. THIS SENSITIVITY ISFOUND TO BE SUBSTANTIALLY HIGHER THAN THAT OF ESR FOR SUBSTANCES WITH SHORT PARAMAGNETIC RELAXATION TIMES OR WITH LARGEMAGNETIC-INTERACTION ANISOTROPY. THIS IS OBSERVED FOR FECL//3:6H//2O DISSOLVED IN A 60P AQUEOUS SOLUTION OF SUCROSE. THE BLOCK DIAGRAM OF THE APPARATUS FOR RECORDING THE PHASE COMPONENTS OF THE SECOND HARMONIC OF THE MAGNETIZATION, WITH PROVISION FOR SETTING THE PHASE OF THE REFERENCE VOLTAGE AT RADIO FREQUENCIES (F = 5 AND 15 MHZ), IS DESCRIBED.

@ARTICLE{Anisimov1981589,
author={Anisimov, G.K. and Zavatskii, E.I. and Isaev-Ivanov, V.V. and Lavrov, V.V. and Fomichev, V.N.},
title={ACCURATE LINE-SHAPE MEASUREMENTS OF ESR SIGNALS.},
journal={Soviet physics. Technical physics},
year={1981},
volume={26},
number={5},
pages={589-594},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019563605&partnerID=40&md5=4c3a88493c47e3c60b36e78f4f4f84ef},
abstract={A new method is presented for detecting ESR signals without modulation of the magnetic field. The line shape can be measured accurately by this method without any loss of sensitivity. The principles underlying the method and the spectrometer are described. Experimental results which demonstrate the possibilities of this new modulationless method are reported.},
correspondence_address1={Anisimov, G.K.},
issn={00385662},
coden={SPTPA},
abbrev_source_title={Sov Phys Tech Phys},
document_type={Article},
source={Scopus},
}

A new method is presented for detecting ESR signals without modulation of the magnetic field. The line shape can be measured accurately by this method without any loss of sensitivity. The principles underlying the method and the spectrometer are described. Experimental results which demonstrate the possibilities of this new modulationless method are reported.

@ARTICLE{Isaev-Ivanov1976801,
author={Isaev-Ivanov, V.V. and Fomichev, V.N.},
title={BALANCED RESONATOR FOR ESR RESEARCH.},
journal={Instrum Exp Tech},
year={1976},
volume={19},
number={3 pt 2},
pages={801-803},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016953830&partnerID=40&md5=44ca84e7124b6bf55b06b0a955a5ee4b},
abstract={The principle of operation, the construction, and the results of tests of a resonator with deep frequency-independent balance are described. The principle of operation is based on the spin induction of electrons. The degree of the achieved frequency-independent balance is 50-70 dB. The degree of balance at a fixed frequency is greater than 100 dB. The concentration sensitivity of the ESR spectrometer when a resonator of the given construction is used amounts to 5 multiplied by (times) 10** minus **9 mole/liter for an aqueous solution of MN** plus ** plus salt for a power of the microwave oscillation source equal to 1 W.},
correspondence_address1={Isaev-Ivanov, V.V.},
coden={INETA},
abbrev_source_title={Instrum Exp Tech},
document_type={Article},
source={Scopus},
}

The principle of operation, the construction, and the results of tests of a resonator with deep frequency-independent balance are described. The principle of operation is based on the spin induction of electrons. The degree of the achieved frequency-independent balance is 50-70 dB. The degree of balance at a fixed frequency is greater than 100 dB. The concentration sensitivity of the ESR spectrometer when a resonator of the given construction is used amounts to 5 multiplied by (times) 10** minus **9 mole/liter for an aqueous solution of MN** plus ** plus salt for a power of the microwave oscillation source equal to 1 W.

@ARTICLE{Isaev-Ivanov19751342,
author={Isaev-Ivanov, V.V. and Masterov, V.F. and Nasledov, D.N. and Yarmarkin, V.K.},
title={MOESSBAUER STUDY OF MAGNETIC TRANSITIONS IN GaAs:Fe.},
journal={Sov Phys Solid State},
year={1975},
volume={16},
number={7},
pages={1342-1343},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016443725&partnerID=40&md5=00c477f8abc752856ff16406a01ccb7a},
abstract={Reports the results of a preliminary study of the Moessbauer effect in samples doped with the isotope **5**7Fe and subjected to heat treatments at various temperatures.},
correspondence_address1={Isaev-Ivanov, V.V.},
coden={SPSSA},
abbrev_source_title={Sov Phys Solid State},
document_type={Article},
source={Scopus},
}

Reports the results of a preliminary study of the Moessbauer effect in samples doped with the isotope **5**7Fe and subjected to heat treatments at various temperatures.

@ARTICLE{Isaev-Ivanov19741711,
author={Isaev-Ivanov, V.V. and Kolchanova, N.M. and Masterov, V.F. and Nasledov, D.N. and Talalakin, G.N.},
title={ELECTRON SPIN RESONANCE IN SOME COMPOUNDS OF IRON-GROUP TRANSITION ELEMENTS CONTAINING GROUP VB ELEMENTS.},
journal={Sov Phys Solid State},
year={1974},
volume={15},
number={9},
pages={1711-1714},
note={cited By 0},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016037547&partnerID=40&md5=f5aaaa182bfe61cb6248a0f5aab3f50d},
abstract={The electron spin resonance and the static magnetic susceptibility of TB**V compounds (Fe//xAs//y, Cr//xAs//y, Fe//xSb//y) were investigated in a wide range of temperatures. The results were analyzed bearing in mind the crystal structure of these compounds. The compounds with different stoichiometric compositions but with the same lattice had different magnetic properties. Some of them exhibited magnetic ordering (in the case of CrAs the authors found that T//c was 210 degree K and in the case of FeAs it was 130 degree K); other compounds containing large amounts of B**V showed no magnetic ordering. When the synthesis temperature was raised, the proportion of the phase that could not be ordered increased. One of the possible causes of the anomalous properties of A**I**I**IB**V crystals doped with the iron-group transition elements could be the formation of a magnetic second phase.},
correspondence_address1={Isaev-Ivanov, V.V.},
coden={SPSSA},
abbrev_source_title={Sov Phys Solid State},
document_type={Article},
source={Scopus},
}

The electron spin resonance and the static magnetic susceptibility of TB**V compounds (Fe//xAs//y, Cr//xAs//y, Fe//xSb//y) were investigated in a wide range of temperatures. The results were analyzed bearing in mind the crystal structure of these compounds. The compounds with different stoichiometric compositions but with the same lattice had different magnetic properties. Some of them exhibited magnetic ordering (in the case of CrAs the authors found that T//c was 210 degree K and in the case of FeAs it was 130 degree K); other compounds containing large amounts of B**V showed no magnetic ordering. When the synthesis temperature was raised, the proportion of the phase that could not be ordered increased. One of the possible causes of the anomalous properties of A**I**I**IB**V crystals doped with the iron-group transition elements could be the formation of a magnetic second phase.

@ARTICLE{Isaev-Ivanov1973299,
author={Isaev-Ivanov, V.V. and Kolchanova, N.M. and Masterov, V.F. and Nasledov, D.N. and Talalakin, G.N.},
title={MAGNETIC PROPERTIES OF IRON-DOPED GALLIUM ARSENIDE.},
journal={Sov Phys Semicond},
year={1973},
volume={7},
number={2},
pages={299-300},
note={cited By 8},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0015658135&partnerID=40&md5=9b63d8efa55f1421547507e506eb3222},
abstract={Iron doped (0. 1-10wt%) GaAs crystals grown by the Stockbarger method were studied concerning the electron spin resonance in the 80-300K range. The static magnetic susceptibility was determined in the 80-1000K range.},
correspondence_address1={Isaev-Ivanov, V.V.},
coden={SPSEA},
abbrev_source_title={Sov Phys Semicond},
document_type={Article},
source={Scopus},
}

Iron doped (0. 1-10wt%) GaAs crystals grown by the Stockbarger method were studied concerning the electron spin resonance in the 80-300K range. The static magnetic susceptibility was determined in the 80-1000K range.