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\n \n\n \n \n \n \n \n \n Thioflavin T Interaction with Acetylcholinesterase: New Evidence of 1:1 Binding Stoichiometry Obtained with Samples Prepared by Equilibrium Microdialysis.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n ACS Chemical Neuroscience, 9(7): 1793-1801. 2018.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Thioflavin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n 2017\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Partially Assembled Nucleosome Structures at Atomic Detail.\n \n \n \n \n\n\n \n Rychkov, G.; Ilatovskiy, A.; Nazarov, I.; Shvetsov, A.; Lebedev, D.; Konev, A.; Isaev-Ivanov, V.; and Onufriev, A.\n\n\n \n\n\n\n Biophysical Journal, 112(3): 460-472. 2017.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Partially$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Rychkov2017460,\r\nauthor={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.},\r\ntitle={Partially Assembled Nucleosome Structures at Atomic Detail},\r\njournal={Biophysical Journal},\r\nyear={2017},\r\nvolume={112},\r\nnumber={3},\r\npages={460-472},\r\ndoi={10.1016/j.bpj.2016.10.041},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009290748&doi=10.1016%2fj.bpj.2016.10.041&partnerID=40&md5=11a123be201359b0889bc6505c1b6dc0},\r\naffiliation={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},\r\nabstract={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},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)obr-i 14-24-01103},\r\nfunding_details={Ministry of Education and Science of the Russian Federation8482 07.09.2012},\r\nfunding_details={Russian Science Foundation14-50-00068},\r\nfunding_details={National Institutes of HealthR01 GM099450, GM076121},\r\n}

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\n \n 2016\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochimie, 121: 5-12. 2016.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"AFM$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase.\n \n \n \n \n\n\n \n Schmidt, A.; Shvetsov, A.; Kuklin, A.; Lebedev, D.; Surzhik, M.; Sergeev, V.; and Isaev-Ivanov, V.\n\n\n \n\n\n\n Crystallography Reports, 61(1): 149-152. 2016.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Small-angle$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Schmidt2016149,\r\nauthor={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.},\r\ntitle={Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase},\r\njournal={Crystallography Reports},\r\nyear={2016},\r\nvolume={61},\r\nnumber={1},\r\npages={149-152},\r\ndoi={10.1134/S1063774516010223},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955578899&doi=10.1134%2fS1063774516010223&partnerID=40&md5=ec97b1e534a5b01b73f260682af7ee41},\r\naffiliation={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},\r\nabstract={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.},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)14-24-01103 ofi-m},\r\n}

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\n \n\n \n \n \n \n \n \n The method of integrated kinetics and its applicability to the exo-glycosidase-catalyzed hydrolyses of p-nitrophenyl glycosides.\n \n \n \n \n\n\n \n Borisova, A.; Reddy, S.; Ivanen, D.; Bobrov, K.; Eneyskaya, E.; Rychkov, G.; Sandgren, M.; Stålbrand, H.; Sinnott, M.; Kulminskaya, A.; and Shabalin, K.\n\n\n \n\n\n\n Carbohydrate Research, 412: 43-49. 2015.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Borisova201543,\r\nauthor={Borisova, A.S. and Reddy, S.K. and Ivanen, D.R. and Bobrov, K.S. and Eneyskaya, E.V. and Rychkov, G.N. and Sandgren, M. and Stålbrand, H. and Sinnott, M.L. and Kulminskaya, A.A. and Shabalin, K.A.},\r\ntitle={The method of integrated kinetics and its applicability to the exo-glycosidase-catalyzed hydrolyses of p-nitrophenyl glycosides},\r\njournal={Carbohydrate Research},\r\nyear={2015},\r\nvolume={412},\r\npages={43-49},\r\ndoi={10.1016/j.carres.2015.03.021},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929649802&doi=10.1016%2fj.carres.2015.03.021&partnerID=40&md5=f216c9f632b9a6d57c20a434a9dbc525},\r\naffiliation={National Research Center Kurchatov Institute, B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Orlova roscha, 188300, Russian Federation; Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Biochemistry and Structural Biology, Lund University, Lund, S-221 00, Sweden; Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom; St. Petersburg State Polytechnical University, 29 Politekhnicheskaya st., St. Petersburg, 195251, Russian Federation},\r\nabstract={In the present work we suggest an efficient method, using the whole time course of the reaction, whereby parameters k<inf>cat</inf>, K<inf>m</inf> and product K<inf>I</inf> for the hydrolysis of a p-nitrophenyl glycoside by an exo-acting glycoside hydrolase can be estimated in a single experiment. Its applicability was demonstrated for three retaining exo-glycoside hydrolases, β-xylosidase from Aspergillus awamori, β-galactosidase from Penicillium sp. and α-galactosidase from Thermotoga maritima (TmGalA). During the analysis of the reaction course catalyzed by the TmGalA enzyme we had observed that a non-enzymatic process, mutarotation of the liberated α-d-galactose, affected the reaction significantly. © 2015 Elsevier Ltd. All rights reserved.},\r\nauthor_keywords={Integrated kinetics;  Mutarotation;  Retaining glycoside hydrolase},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)12-08-00813-a},\r\n}

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\n \n\n \n \n \n \n \n \n α-Galactobiosyl units: Thermodynamics and kinetics of their formation by transglycosylations catalysed by the GH36 α-galactosidase from Thermotoga maritima.\n \n \n \n \n\n\n \n Borisova, A.; Ivanen, D.; Bobrov, K.; Eneyskaya, E.; Rychkov, G.; Sandgren, M.; Kulminskaya, A.; Sinnott, M.; and Shabalin, K.\n\n\n \n\n\n\n Carbohydrate Research, 401: 115-121. 2015.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"α-Galactobiosyl$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Borisova2015115,\r\nauthor={Borisova, A.S. and Ivanen, D.R. and Bobrov, K.S. and Eneyskaya, E.V. and Rychkov, G.N. and Sandgren, M. and Kulminskaya, A.A. and Sinnott, M.L. and Shabalin, K.A.},\r\ntitle={α-Galactobiosyl units: Thermodynamics and kinetics of their formation by transglycosylations catalysed by the GH36 α-galactosidase from Thermotoga maritima},\r\njournal={Carbohydrate Research},\r\nyear={2015},\r\nvolume={401},\r\npages={115-121},\r\ndoi={10.1016/j.carres.2014.11.003},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84918807980&doi=10.1016%2fj.carres.2014.11.003&partnerID=40&md5=a72be071ed1f9fe275f7d4cc1bf43ce0},\r\naffiliation={National Research Center Kurchatov Institute, B.P. Konstantinov Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, 188300, Russian Federation; Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden; St. Petersburg State Polytechnical University, 29 Politechnicheskaya str., St. Petersburg, 195251, Russian Federation; Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom},\r\nabstract={Broad regioselectivity of α-galactosidase from Thermotoga maritima (TmGal36A) is a limiting factor for application of the enzyme in the directed synthesis of oligogalactosides. However, this property can be used as a convenient tool in studies of thermodynamics of a glycosidic bond. Here, a novel approach to energy difference estimation is suggested. Both transglycosylation and hydrolysis of three types of galactosidic linkages were investigated using total kinetics of formation and hydrolysis of pNP-galactobiosides catalysed by monomeric glycoside hydrolase family 36 α-galactosidase from T. maritima, a retaining exo-acting glycoside hydrolase. We have estimated transition state free energy differences between the 1,2- and 1,3-linkage (ΔΔG‡0 values were equal 5.34 ± 0.85 kJ/mol) and between 1,6-linkage and 1,3-linkage (ΔΔG‡0 = 1.46 ± 0.23 kJ/mol) in pNP-galactobiosides over the course of the reaction catalysed by TmGal36A. Using the free energy difference for formation and hydrolysis of glycosidic linkages (ΔΔG‡F - ΔΔG‡H), we found that the 1,2-linkage was 2.93 ± 0.47 kJ/mol higher in free energy than the 1,3-linkage, and the 1,6-linkage 4.44 ± 0.71 kJ/mol lower. © 2014 Elsevier Ltd. All rights reserved.},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)12-08-00813-a},\r\n}

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\n \n\n \n \n \n \n \n \n Knotted proteins.\n \n \n \n \n\n\n \n Stepanenko, O.; Bublikov, G.; Stepanenko, O.; Rychkov, G.; Povarova, O.; Verkhusha, V.; Turoverov, K.; and Kuznetsova, I.\n\n\n \n\n\n\n Tsitologiia, 57(3): 177-183. 2015.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Knotted$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Stepanenko2015177,\r\nauthor={Stepanenko, O.V. and Bublikov, G.S. and Stepanenko, O.V. and Rychkov, G.N. and Povarova, O.I. and Verkhusha, V.V. and Turoverov, K.K. and Kuznetsova, I.M.},\r\ntitle={Knotted proteins},\r\njournal={Tsitologiia},\r\nyear={2015},\r\nvolume={57},\r\nnumber={3},\r\npages={177-183},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930793234&partnerID=40&md5=908504c6118c04c2e88f54d1769b8280},\r\nabstract={For a long time the presence of knots in a protein structure was not admitted. However, the existence of proteins with various types of knots has now been proven. The functional significance of knotted topology remains unclear despite numerous assumptions. Studing the structure of knots in proteins and their impact on the acquisition of native structure of proteins is important for the understanding of protein folding as a whole. We review the types of knots in the proteins discovered to date, including trefoil knot, figure-of-eight knot, and more complex knots with 5 and 6 crossings of polypeptide chain. We survey the folding of knotted proteins as well.},\r\nissn={00413771},\r\npubmed_id={26021166},\r\nlanguage={Russian},\r\nabbrev_source_title={Tsitologiia},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives.\n \n \n \n \n\n\n \n Akimova, A.; Rychkov, G.; Grin, M.; Filippova, N.; Golovina, G.; Durandin, N.; Vinogradov, A.; Kokrashvili, T.; Mironov, A.; Shtil, A.; and Kuzmin, V.\n\n\n \n\n\n\n Acta Naturae, 7(1): 109-116. 2015.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Interaction$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Akimova2015109,\r\nauthor={Akimova, A.V. and Rychkov, G.N. and Grin, M.A. and Filippova, N.A. and Golovina, G.V. and Durandin, N.A. and Vinogradov, A.M. and Kokrashvili, T.A. and Mironov, A.F. and Shtil, A.A. and Kuzmin, V.A.},\r\ntitle={Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives},\r\njournal={Acta Naturae},\r\nyear={2015},\r\nvolume={7},\r\nnumber={1},\r\npages={109-116},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929151488&partnerID=40&md5=e7ed874dcbf45f3d9b63552e1b6293d5},\r\naffiliation={N.M. Emanuel Institute of Biochemical Physics, Kosygina Str., 4, Moscow, 119334, Russian Federation; Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, Leningrad district, 188300, Russian Federation; St.Petersburg State Polytechnical University, Politekhnicheskaya Str., 29, St. Petersburg, 195251, Russian Federation; M.V. Lomonosov Moscow State University of Fine Chemical Technologies, Prospekt Vernadskogo, 86, Moscow, 119571, Russian Federation; N.N. Blokhin Russian Cancer Research Center, Kashirskoe Shosse, 24, Moscow, 115478, Russian Federation; Georgian Technical University, Kostava Str., 77, Tbilisi, 0175, Georgia},\r\nabstract={Optimization of the chemical structure of antitumor photosensitizers (PSs) is aimed at increasing their affinity to a transport protein, albumin and irreversible light-induced tumor cell damage. Bacteriopurpurinimide derivatives are promising PSs thanks to their ability to absorb light in the near infrared spectral region. Using spectrophotometry, we show that two new bacteriopurpurinimide derivatives with different substituents at the N atoms of the imide exocycle and the pyrrole ring A are capable of forming non-covalent complexes with human serum albumin (HSA). The association constant (calculated with the Benesi-Hildebrand equation) for N-ethoxybacteriopurpurinimide ethyloxime (compound 1) is higher than that for the methyl ether of methoxybacteriopurpurinimide (compound 2) (1.18×105 M-1 vs. 1.26×104 M-1, respectively). Molecular modeling provides details of the atomic interactions between 1 and 2 and amino acid residues in the FA1 binding site of HSA. The ethoxy group stabilizes the position of 1 within this site due to hydrophobic interaction with the protein. The higher affinity of 1 for HSA makes this compound more potent than 2 in photodynamic therapy for cultured human colon carcinoma cells. Photoactivation of 1 and 2 in cells induces rapid (within a few minutes of irradiation) necrosis. This mechanism of cell death may be efficient for eliminating tumors resistant to other therapies. © 2015 Park-media, Ltd.},\r\nauthor_keywords={Albumin;  Association constant;  Cancer;  Necrosis;  Photodynamic therapy;  Photosensitizers},\r\ncorrespondence_address1={Akimova, A.V.; N.M. Emanuel Institute of Biochemical Physics, Kosygina Str., 4, Russian Federation; email: alexa_karpenko@mail.ru},\r\npublisher={Russian Federation Agency for Science and Innovation},\r\nissn={20758251},\r\nlanguage={English},\r\nabbrev_source_title={Acta Naturae},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Introduction of additional thiol groups into glucoamylase in Aspergillus Awamori and their effect on the thermal stability and catalytic activity of the enzyme.\n \n \n \n \n\n\n \n Surzhik, M.; Schmidt, A.; Glazunov, E.; Firsov, D.; and Petukhov, M.\n\n\n \n\n\n\n Applied Biochemistry and Microbiology, 50(2): 118-124. 2014.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Introduction$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Surzhik2014118,\r\nauthor={Surzhik, M.A. and Schmidt, A.E. and Glazunov, E.A. and Firsov, D.L. and Petukhov, M.G.},\r\ntitle={Introduction of additional thiol groups into glucoamylase in Aspergillus Awamori and their effect on the thermal stability and catalytic activity of the enzyme},\r\njournal={Applied Biochemistry and Microbiology},\r\nyear={2014},\r\nvolume={50},\r\nnumber={2},\r\npages={118-124},\r\ndoi={10.1134/S0003683814020185},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897790640&doi=10.1134%2fS0003683814020185&partnerID=40&md5=71e70330501a996dfb4ab4ef6c53ceda},\r\naffiliation={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},\r\nabstract={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.},\r\ncorrespondence_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},\r\nissn={00036838},\r\nlanguage={English},\r\nabbrev_source_title={Appl. Biochem. Microbiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n [Introduction of additional thiol groups into glucoamylase in Aspergillus awamori and their effect on the thermal stability and catalytic activity of the enzyme].\n \n \n \n \n\n\n \n Surzhik, M.; Shmidt, A.; Glazunov, E.; Firsov, D.; and Petukhov, M.\n\n\n \n\n\n\n Prikladnaia biokhimiia i mikrobiologiia, 50(2): 139-146. 2014.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"[Introduction$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Surzhik2014139,\r\nauthor={Surzhik, M.A. and Shmidt, A.E. and Glazunov, E.A. and Firsov, D.L. and Petukhov, M.G.},\r\ntitle={[Introduction of additional thiol groups into glucoamylase in Aspergillus awamori and their effect on the thermal stability and catalytic activity of the enzyme].},\r\njournal={Prikladnaia biokhimiia i mikrobiologiia},\r\nyear={2014},\r\nvolume={50},\r\nnumber={2},\r\npages={139-146},\r\ndoi={10.7868/S0555109914020184},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907611887&doi=10.7868%2fS0555109914020184&partnerID=40&md5=803c85902077bd96a64585bd0d293a98},\r\nabstract={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.},\r\ncorrespondence_address1={Surzhik, M.A.},\r\nissn={05551099},\r\npubmed_id={25272730},\r\nlanguage={Russian},\r\nabbrev_source_title={Prikl. Biokhim. Mikrobiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n De novo design of stable α-helices.\n \n \n \n \n\n\n \n Yakimov, A.; Rychkov, G.; and Petukhov, M.\n\n\n \n\n\n\n Methods in Molecular Biology, 1216: 1-14. 2014.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"De$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Yakimov20141,\r\nauthor={Yakimov, A. and Rychkov, G. and Petukhov, M.},\r\ntitle={De novo design of stable α-helices},\r\njournal={Methods in Molecular Biology},\r\nyear={2014},\r\nvolume={1216},\r\npages={1-14},\r\ndoi={10.1007/978-1-4939-1486-9_1},\r\nnote={cited By 6},\r\nurl={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},\r\naffiliation={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},\r\nabstract={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.},\r\nauthor_keywords={Sequence optimization;  Solubility;  Stability;  α-Helix},\r\nfunding_details={Russian Foundation for Basic Research12-04-91444-NIH_a},\r\npublisher={Humana Press Inc.},\r\nissn={10643745},\r\npubmed_id={25213408},\r\nlanguage={English},\r\nabbrev_source_title={Methods Mol. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Novel derivatives of bacteriochlorophyll a: Complex formation with albumin and the mechanism of tumor cell photodamage.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Doklady Biochemistry and Biophysics, 454(1): 17-20. 2014.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Novel$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n 2013\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Exosomes are natural carriers of exogenous siRNA to human cells in vitro.\n \n \n \n \n\n\n \n Shtam, T.; Kovalev, R.; Varfolomeeva, E.; Makarov, E.; Kil, Y.; and Filatov, M.\n\n\n \n\n\n\n Cell Communication and Signaling, 11(1). 2013.\n cited By 160\n\n\n\n
\n\n\n\n \n \n $\"Exosomes$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Shtam2013,\r\nauthor={Shtam, T.A. and Kovalev, R.A. and Varfolomeeva, E.Y. and Makarov, E.M. and Kil, Y.V. and Filatov, M.V.},\r\ntitle={Exosomes are natural carriers of exogenous siRNA to human cells in vitro},\r\njournal={Cell Communication and Signaling},\r\nyear={2013},\r\nvolume={11},\r\nnumber={1},\r\ndoi={10.1186/1478-811X-11-88},\r\nart_number={88},\r\nnote={cited By 160},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84887703287&doi=10.1186%2f1478-811X-11-88&partnerID=40&md5=da53d624b8be3bfd1494f309cb115de5},\r\naffiliation={Division of Molecular and Radiation Biophysics, SFBI Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, United Kingdom; Department of Biophysics, St. Petersburg State Polytechnical University, St.-Petersburg 195251, Russian Federation},\r\nabstract={Background: Exosomes are nano-sized vesicles of endocytic origin that are involved in cell-to-cell communication including shuttle RNA, mainly mRNA and microRNA. As exosomes naturally carry RNA between cells, these particles might be useful in gene cancer therapy to deliver therapeutic short interfering RNA (siRNA) to the target cells. Despite the promise of RNA interference (RNAi) for use in therapy, several technical obstacles must be overcome. Exogenous siRNA is prone to degradation, has a limited ability to cross cell membranes and may induce an immune response. Naturally occurring RNA carriers, such as exosomes, might provide an untapped source of effective delivery strategies. Results: This study demonstrates that exosomes can deliver siRNA to recipient cells in vitro. The different strategies were used to introduce siRNAs into human exosomes of various origins. The delivery of fluorescently labeled siRNA via exosomes to cells was confirmed using confocal microscopy and flow cytometry. Two different siRNAs against RAD51 and RAD52 were used to transfect into the exosomes for therapeutic delivery into target cells. The exosome-delivered siRNAs were effective at causing post-transcriptional gene silencing in recipient cells. Moreover, the exosome-delivered siRNA against RAD51 was functional and caused the massive reproductive cell death of recipient cancer cells. Conclusions: The results strongly suggest that exosomes effectively delivered the siRNA into the target cells. The therapeutic potential of exosome-mediated siRNA delivery was demonstrated in vitro by the strong knockdown of RAD51, a prospective therapeutic target for cancer cells. The results give an additional evidence of the ability to use human exosomes as vectors in cancer therapy, including RNAi-based gene therapy. © 2013 Shtam et al.; licensee BioMed Central Ltd.},\r\nauthor_keywords={Cancer therapy;  Drug delivery system;  Exosomes;  RAD51;  RNA interference (RNAi)},\r\ncorrespondence_address1={Filatov, M.V.; Division of Molecular and Radiation Biophysics, SFBI Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; email: filatov@omrb.pnpi.spb.ru},\r\nissn={1478811X},\r\npubmed_id={24245560},\r\nlanguage={English},\r\nabbrev_source_title={Cell Commun. Signal.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Improvement of the efficiency of transglycosylation catalyzed by α-galactosidase from Thermotoga maritima by protein engineering.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemistry (Moscow), 78(10): 1112-1123. 2013.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"Improvement$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Differential binding preference of methylpheophorbide a and its diboronated derivatives to albumin and low density lipoproteins.\n \n \n \n \n\n\n \n Golovina, G.; Rychkov, G.; Ol'shevskaya, V.; Zaitsev, A.; Kalinin, V.; Kuzmin, V.; and Shtil, A.\n\n\n \n\n\n\n Anti-Cancer Agents in Medicinal Chemistry, 13(4): 639-646. 2013.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Differential$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Golovina2013639,\r\nauthor={Golovina, G.V. and Rychkov, G.N. and Ol'shevskaya, V.A. and Zaitsev, A.V. and Kalinin, V.N. and Kuzmin, V.A. and Shtil, A.A.},\r\ntitle={Differential binding preference of methylpheophorbide a and its diboronated derivatives to albumin and low density lipoproteins},\r\njournal={Anti-Cancer Agents in Medicinal Chemistry},\r\nyear={2013},\r\nvolume={13},\r\nnumber={4},\r\npages={639-646},\r\ndoi={10.2174/1871520611313040012},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84876711965&doi=10.2174%2f1871520611313040012&partnerID=40&md5=333724dbe983dd768e1fe5e937dedd6e},\r\naffiliation={Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russian Federation; Petersburg Nuclear Physics Institute, National Research Center, The Kurchatov Institute Orlova Roscha, Gatchina 188300, Russian Federation; Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Street, Moscow 119991, Russian Federation; Blokhin Cancer Center, Russian Academy of Medical Sciences, 24 Kashirskoye shosse, Moscow 115478, Russian Federation; St. Petersburg State Polytechnical University, 29 Polytechnicheskaya Street, St. Petersburg 195251, Russian Federation},\r\nabstract={The tetrapyrrolic macrocycle and the functional groups at its periphery allow for a variety of modifications aimed at multifunctional therapeutic compounds. In particular, conjugation of boron polyhedra yields dual efficacy antitumor photo/radiosensitizers. Structural optimization of these agents presumes the identification of macromolecules that bind and transport boronated tetrapyrroles. Using spectroscopic methods we demonstrated that methylpheophorbide a forms complexes with serum albumin and low density lipoproteins (LDL) whereas two diboronated derivatives, 13(2),17(3)-[di(o-carboran-1-yl)methoxycarbonyl]pheophorbide a and 13(2),17(3)-[di(1-carba-closo-dodecaboran-1-yl)methoxycarbonyl]pheophorbide a, were capable of binding to LDL but not to albumin. Molecular modeling showed a mode of interaction of methylpheophorbide a with the amino acid residues in the albumin's hemin binding site. In contrast, for diboronated derivatives such interactions are sterically hindered by boron polyhedra, in line with experimentally determined lack of complex formation with albumin. These data strongly suggest that LDL might be the preferred carrier for polycarborane containing methylpheophorbide a derivatives. © 2013 Bentham Science Publishers.},\r\nauthor_keywords={Albumin;  Carborane;  Low density lipoproteins;  Methylpheophorbide a;  Molecular modeling},\r\ncorrespondence_address1={Golovina, G. V.; Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russian Federation; email: golovinagalina@yandex.ru},\r\nissn={18715206},\r\npubmed_id={23343083},\r\nlanguage={English},\r\nabbrev_source_title={Anti-Cancer Agents Med. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2012\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Structural insights into interaction between mammalian methionine sulfoxide reductase B1 and thioredoxin.\n \n \n \n \n\n\n \n Dobrovolska, O.; Rychkov, G.; Shumilina, E.; Nerinovski, K.; Schmidt, A.; Shabalin, K.; Yakimov, A.; and Dikiy, A.\n\n\n \n\n\n\n Journal of Biomedicine and Biotechnology, 2012. 2012.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Dobrovolska2012,\r\nauthor={Dobrovolska, O. and Rychkov, G. and Shumilina, E. and Nerinovski, K. and Schmidt, A. and Shabalin, K. and Yakimov, A. and Dikiy, A.},\r\ntitle={Structural insights into interaction between mammalian methionine sulfoxide reductase B1 and thioredoxin},\r\njournal={Journal of Biomedicine and Biotechnology},\r\nyear={2012},\r\nvolume={2012},\r\ndoi={10.1155/2012/586539},\r\nart_number={586539},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859726670&doi=10.1155%2f2012%2f586539&partnerID=40&md5=d880f44788e267595adc09bd0e60cd97},\r\naffiliation={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},\r\nabstract={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.},\r\ncorrespondence_address1={Dikiy, A.; Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway; email: alex.dikiy@biotech.ntnu.no},\r\nissn={11107243},\r\ncoden={JBBOA},\r\npubmed_id={22505815},\r\nlanguage={English},\r\nabbrev_source_title={J. Biomed. Biotechnol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2010\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase.\n \n \n \n \n\n\n \n Surzhik, M.; Churkina, S.; Shmidt, A.; Shvetsov, A.; Kozhina, T.; Firsov, D.; Firsov, L.; and Petukhov, M.\n\n\n \n\n\n\n Applied Biochemistry and Microbiology, 46(2): 206-211. 2010.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Surzhik2010206,\r\nauthor={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.},\r\ntitle={The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase},\r\njournal={Applied Biochemistry and Microbiology},\r\nyear={2010},\r\nvolume={46},\r\nnumber={2},\r\npages={206-211},\r\ndoi={10.1134/S0003683810020134},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77952311178&doi=10.1134%2fS0003683810020134&partnerID=40&md5=32c7917eb15ba2847a518a070ad3cb0e},\r\naffiliation={Konstantinov Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina Leningrad oblast, 188300, Russian Federation},\r\nabstract={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.},\r\nfunding_details={RNP.2.2.1.1.4663},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)07 04 00785},\r\n}

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\n \n\n \n \n \n \n \n \n The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase.\n \n \n \n \n\n\n \n Surzhik, M.; Churkina, S.; Shmidt, A.; Shvetsov, A.; Kozhina, T.; Firsov, D.; Firsov, L.; and Petukhov, M.\n\n\n \n\n\n\n Prikladnaia biokhimiia i mikrobiologiia, 46(2): 221-227. 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Surzhik2010221,\r\nauthor={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.},\r\ntitle={The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase},\r\njournal={Prikladnaia biokhimiia i mikrobiologiia},\r\nyear={2010},\r\nvolume={46},\r\nnumber={2},\r\npages={221-227},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953272021&partnerID=40&md5=a730cf407f3b139bfb854b3e7c51ced9},\r\nabstract={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.},\r\ncorrespondence_address1={Surzhik, M.A.},\r\nissn={05551099},\r\npubmed_id={20391767},\r\nlanguage={Russian},\r\nabbrev_source_title={Prikl. Biokhim. Mikrobiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2009\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Expression of gene recA of Deinococcus radiodurans in Escherichia coli cells.\n \n \n \n \n\n\n \n Verbenko, V.; Kuznetsova, L.; Krup'ian, E.; and Shalguev, V.\n\n\n \n\n\n\n Genetika, 45(10): 1353-1360. 2009.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Expression$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Verbenko20091353,\r\nauthor={Verbenko, V.N. and Kuznetsova, L.V. and Krup'ian, E.P. and Shalguev, V.I.},\r\ntitle={Expression of gene recA of Deinococcus radiodurans in Escherichia coli cells},\r\njournal={Genetika},\r\nyear={2009},\r\nvolume={45},\r\nnumber={10},\r\npages={1353-1360},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-73349118464&partnerID=40&md5=0982146a8c365f4d90432d5fff68959e},\r\nabstract={Plasmids pKS5 and pKSrec30 carrying normal and mutant alleles of Deinococcus radiodurans recA gene controlled by the lactose promoter slightly increase radioresistance of Escherichia coli cells with mutations at genes recA and ssb. The RecA protein of D. radiodurans is expressed in E. coli cells, and its synthesis can be supplementary induced. The radioprotective effect of the xenologic protein does not exceed 1.5 times and is essentially to the contribution of plasmid pUC 19-recA1.1 harboring the E. coli recA+ gene in the recovery of resistance of the deltarecA deletion mutant. These data suggest that the expression of D. radiodurans recA gene in E. coli cells does not complement mutations at gene recA in the chromosome possibly due to structural and functional peculiarities of the D. radiodurans RecA protein.},\r\ncorrespondence_address1={Verbenko, V.N.},\r\nissn={00166758},\r\npubmed_id={19947546},\r\nlanguage={Russian},\r\nabbrev_source_title={Genetika},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Expression of recA gene of deinococcus radiodurans in escherichia coli cells.\n \n \n \n \n\n\n \n Verbenko, V.; Kuznetsova, L.; Krupyan, E.; and Shalguev, V.\n\n\n \n\n\n\n Russian Journal of Genetics, 45(10): 1192-1199. 2009.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Expression$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Verbenko20091192,\r\nauthor={Verbenko, V.N. and Kuznetsova, L.V. and Krupyan, E.P. and Shalguev, V.I.},\r\ntitle={Expression of recA gene of deinococcus radiodurans in escherichia coli cells},\r\njournal={Russian Journal of Genetics},\r\nyear={2009},\r\nvolume={45},\r\nnumber={10},\r\npages={1192-1199},\r\ndoi={10.1134/S1022795409100068},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70350418440&doi=10.1134%2fS1022795409100068&partnerID=40&md5=c041f97f88493f292939082071122e9e},\r\naffiliation={St. Petersburg Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina 188300, Russian Federation},\r\nabstract={Plasmids pKS5 and pKSrec30 carrying normal and mutant alleles of the Deinococcus recA gene controlled by the lactose promoter slightly increase radioresistance of Escherichia coli cells with mutations in genes recA and ssb. The RecA protein of D. radiodurans is expressed in E. coli cells, and its synthesis can be supplementary induced. The radioprotective effect of the xenologic protein does not exceed 1.5 fold and yields essentially to the contribution of plasmid pUC19-recA1.1 harboring the E. coli recA+ gene in the recovery of resistance of the ΔrecA deletion mutant. These data suggest that the expression of D. radiodurans recA gene in E. coli cells does not complement mutations at gene recA in the chromosome possibly due to structural and functional peculiarities of the D. radiodurans RecA protein. © Pleiades Publishing, Inc., 2009.},\r\ncorrespondence_address1={Verbenko, V. N.; St. Petersburg Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina 188300, Russian Federation; email: verbenko@omrb.pnpi.spb.ru},\r\nissn={10227954},\r\nlanguage={English},\r\nabbrev_source_title={Russ. J. Gen.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2008\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Destabilization and stabilization of poly(A) • poly(U) structure by platinum(II) compounds.\n \n \n \n \n\n\n \n Bogdanov, A.; Ivanov, Y.; Kasyanenko, N.; Potekhin, S.; Surzhik, M.; Timkovskii, A.; Feofanov, S.; Khusainova, R.; and Yakoblev, K.\n\n\n \n\n\n\n Biophysics, 53(5): 341-343. 2008.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Destabilization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Bogdanov2008341,\r\nauthor={Bogdanov, A.A. and Ivanov, Yu.V. and Kasyanenko, N.A. and Potekhin, S.A. and Surzhik, M.A. and Timkovskii, A.L. and Feofanov, S.A. and Khusainova, R.S. and Yakoblev, K.I.},\r\ntitle={Destabilization and stabilization of poly(A) • poly(U) structure by platinum(II) compounds},\r\njournal={Biophysics},\r\nyear={2008},\r\nvolume={53},\r\nnumber={5},\r\npages={341-343},\r\ndoi={10.1134/S0006350908050035},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-59849113492&doi=10.1134%2fS0006350908050035&partnerID=40&md5=c78d7a84eb36d3a25a361100d8b9e942},\r\naffiliation={St. Petersburg State University, St. Petersburg, Russian Federation; Konstantinov Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad oblast, Russian Federation; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russian Federation; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russian Federation; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russian Federation; St. Petersburg State Chemicopharmaceutical Academy, St. Petersburg, Russian Federation},\r\nabstract={A methodology for analyzing the intramolecular structural order of the polynucleotide duplex poly(A) • poly(U) has been developed on the basis of molecular biophysics. The combination of circular dichroism spectroscopy and differential scanning calorimetry was shown to be an optimal approach. It ensures the screening of a wide set of substances and interaction conditions and the choice of compound(s) capable of stabilizing the structure and increasing the biological activity of this duplex. The study is aimed at obtaining a new and highly active antiviral drug. © 2008 Pleiades Publishing, Ltd.},\r\nauthor_keywords={Polynucleotide interferon inducers;  Structure-activity relationships},\r\ncorrespondence_address1={Bogdanov, A. A.; St. Petersburg State University, St. Petersburg, Russian Federation},\r\nissn={00063509},\r\nlanguage={English},\r\nabbrev_source_title={Biophysics},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Destabilization and stabilization of poly(A).poly(U) structure by platinum(II) compounds.\n \n \n \n \n\n\n \n Bogdanov, A.; Ivanov, I.; Kas'ianenko, N.; Potekhin, S.; Surzhik, M.; Timkovskiǐ, A.; Feofanov, S.; Khusainova, R.; and Iakovlev, K.\n\n\n \n\n\n\n Biofizika, 53(5): 740-743. 2008.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Destabilization$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Bogdanov2008740,\r\nauthor={Bogdanov, A.A. and Ivanov, I.V. and Kas'ianenko, N.A. and Potekhin, S.A. and Surzhik, M.A. and Timkovskiǐ, A.L. and Feofanov, S.A. and Khusainova, R.S. and Iakovlev, K.I.},\r\ntitle={Destabilization and stabilization of poly(A).poly(U) structure by platinum(II) compounds},\r\njournal={Biofizika},\r\nyear={2008},\r\nvolume={53},\r\nnumber={5},\r\npages={740-743},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-56149093279&partnerID=40&md5=406b8bf0b46870a0b4952ba3d022e203},\r\nabstract={On the basis of molecular biophysics, a methodology for the analysis of intramolecular structural order of the polynucleotide duplex poly(A).poly(U) has been developed. It was shown that the combination of circular dichroism spectroscopy with differential scanning calorimetry is an optimal approach, which ensures the screening of a wide set of substances and interaction conditions and the choice of compound(s) that can stabilize the structure and increase the biological activity of this duplex. The study is aimed at obtaining a new and highly active antiviral remedy.},\r\ncorrespondence_address1={Bogdanov, A.A.},\r\nissn={00063029},\r\npubmed_id={18953999},\r\nlanguage={Russian},\r\nabbrev_source_title={Biofizika},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Two RecA protein types that mediate different modes of hyperrecombination.\n \n \n \n \n\n\n \n Baitin, D.; Bakhlanova, I.; Chervyakova, D.; Kil, Y.; Lanzov, V.; and Cox, M.\n\n\n \n\n\n\n Journal of Bacteriology, 190(8): 3036-3045. 2008.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Two$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Baitin20083036,\r\nauthor={Baitin, D.M. and Bakhlanova, I.V. and Chervyakova, D.V. and Kil, Y.V. and Lanzov, V.A. and Cox, M.M.},\r\ntitle={Two RecA protein types that mediate different modes of hyperrecombination},\r\njournal={Journal of Bacteriology},\r\nyear={2008},\r\nvolume={190},\r\nnumber={8},\r\npages={3036-3045},\r\ndoi={10.1128/JB.01006-07},\r\nnote={cited By 8},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41949126064&doi=10.1128%2fJB.01006-07&partnerID=40&md5=5622b294633bb84eb4f32efcb2976eb8},\r\naffiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation; Research-Education Center Biophysics, St. Petersburg State Polytechnic University, St. Petersburg 194021, Russian Federation; Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706-1544, United States},\r\nabstract={RecAX53 is a chimeric variant of the Escherichia coli RecA protein (RecAEc) that contains a part of the central domain of Pseudomonas aeruginosa RecA (RecAPa), encompassing a region that differs from RecAEc at 12 amino acid positions. Like RecAPa, this chimera exhibits hyperrecombination activity in E. coli cells, increasing the frequency of recombination exchanges per DNA unit length (FRE). RecAX53 confers the largest increase in FRE observed to date. The contrasting properties of RecAX53 and RecAPa are manifested by in vivo differences in the dependence of the FRE value on the integrity of the mutS gene and thus in the ratio of conversion and crossover events observed among their hyperrecombination products. In strains expressing the RecAPa or RecAEc protein, crossovers are the main mode of hyperrecombination. In contrast, conversions are the primary result of reactions promoted by RecAX53. The biochemical activities of RecAX53 and its ancestors, RecAEc and RecAPa, have been compared. Whereas RecAPa generates a RecA presynaptic complex (PC) that is more stable than that of RecAEc, RecAX53 produces a more dynamic PC (relative to both RecAEc and RecAPa). The properties of RecAX53 result in a more rapid initiation of the three-strand exchange reaction but an inability to complete the four-strand transfer. This indicates that RecAX53 can form heteroduplexes rapidly but is unable to convert them into crossover configurations. A more dynamic RecA activity thus translates into an increase in conversion events relative to crossovers. Copyright © 2008, American Society for Microbiology. All Rights Reserved.},\r\ncorrespondence_address1={Cox, M. M.; Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706-1544, United States; email: cox@biochem.wisc.edu},\r\nissn={00219193},\r\ncoden={JOBAA},\r\npubmed_id={18296520},\r\nlanguage={English},\r\nabbrev_source_title={J. Bacteriol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Large-scale structure of RecA protein from Deinococcus radiodurance and its complexes in solution.\n \n \n \n \n\n\n \n Karelov, D.; Lebedev, D.; Suslov, A.; Shalguev, V.; Kuklin, A.; Islamov, A.; Lauter, H.; Lanzov, V.; and Isaev-Ivanov, V.\n\n\n \n\n\n\n Journal of Physics Condensed Matter, 20(10). 2008.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Large-scale$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Karelov2008,\r\nauthor={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.},\r\ntitle={Large-scale structure of RecA protein from Deinococcus radiodurance and its complexes in solution},\r\njournal={Journal of Physics Condensed Matter},\r\nyear={2008},\r\nvolume={20},\r\nnumber={10},\r\ndoi={10.1088/0953-8984/20/10/104215},\r\nart_number={104215},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41849107564&doi=10.1088%2f0953-8984%2f20%2f10%2f104215&partnerID=40&md5=ad0548b44c3c670e7599d7037610244b},\r\naffiliation={Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Joint Institute for Nuclear Research, Dubna, Russian Federation; Institute Max von Laue Paul Langevin, Grenoble, France},\r\nabstract={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.},\r\ncorrespondence_address1={Karelov, D. V.; Petersburg Nuclear Physics Institute, Gatchina, Russian Federation},\r\nissn={09538984},\r\ncoden={JCOME},\r\nlanguage={English},\r\nabbrev_source_title={J Phys Condens Matter},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2007\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Selective functionalization of semiconductor quantum dots with short peptides and integrins of cancer cells for biophotonic applications.\n \n \n \n \n\n\n \n Bairamov, B.; Toporov, V.; Bayramov, F.; Petukhov, M.; Glazunov, E.; Lanzov, V.; Li, Y.; Ramadurai, D.; Shi, P.; Dutta, M.; Stroscio, M.; and Irmer, G.\n\n\n \n\n\n\n 2007.\n 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\n\n\n\n
\n\n\n\n \n \n $\"Selective$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@CONFERENCE{Bairamov2007511,\r\nauthor={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.},\r\ntitle={Selective functionalization of semiconductor quantum dots with short peptides and integrins of cancer cells for biophotonic applications},\r\njournal={Proceedings of the International Conference on Physics, Chemistry and Application of Nanostructures, NANOMEETING 2007 - Reviews and Short Notes},\r\nyear={2007},\r\npages={511-515},\r\nnote={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},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884371405&partnerID=40&md5=fb3a3a043ff10b75ae7615cecd4b9d86},\r\naffiliation={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},\r\nabstract={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.},\r\ncorrespondence_address1={A.F. Ioffe Physico-Technical Institute, RAS, 194021 St. Petersburg, Russian Federation},\r\naddress={Minsk},\r\nisbn={9812705996; 9789812705990},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Int. Conf. Phys., Chem. Appl. Nanostructures, NANOMEETING - Rev. Short Notes},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Joint neighbors approximation of macromolecular solvent accessible surface area.\n \n \n \n \n\n\n \n Rychkov, G.; and Petukhov, M.\n\n\n \n\n\n\n Journal of Computational Chemistry, 28(12): 1974-1989. 2007.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"Joint$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Rychkov20071974,\r\nauthor={Rychkov, G. and Petukhov, M.},\r\ntitle={Joint neighbors approximation of macromolecular solvent accessible surface area},\r\njournal={Journal of Computational Chemistry},\r\nyear={2007},\r\nvolume={28},\r\nnumber={12},\r\npages={1974-1989},\r\ndoi={10.1002/jcc.20550},\r\nnote={cited By 10},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547336672&doi=10.1002%2fjcc.20550&partnerID=40&md5=b62368763022b295011b31eb80b79244},\r\naffiliation={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},\r\nabstract={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.},\r\nauthor_keywords={Analytical gradients;  Analytical surface area;  Folded and unfolded proteins;  Hydration;  Solvent-accessible surface area},\r\ncorrespondence_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},\r\nissn={01928651},\r\ncoden={JCCHD},\r\npubmed_id={17407094},\r\nlanguage={English},\r\nabbrev_source_title={J. Comput. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo.\n \n \n \n \n\n\n \n Lebedev, D.; Monkenbusch, M.; Shalguev, V.; Lantsov, V.; and Isaev-Ivanov, V.\n\n\n \n\n\n\n Biofizika, 52(5): 799-803. 2007.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Dynamic$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Lebedev2007799,\r\nauthor={Lebedev, D.V. and Monkenbusch, M. and Shalguev, V.I. and Lantsov, V.A. and Isaev-Ivanov, V.V.},\r\ntitle={Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo},\r\njournal={Biofizika},\r\nyear={2007},\r\nvolume={52},\r\nnumber={5},\r\npages={799-803},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-38449083418&partnerID=40&md5=abda3d7f880a7a4897704b162f0695db},\r\nabstract={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.},\r\ncorrespondence_address1={Lebedev, D.V.},\r\nissn={00063029},\r\npubmed_id={17969911},\r\nlanguage={Russian},\r\nabbrev_source_title={Biofizika},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2006\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Conformational flexibility of RecA protein filament: Transitions between compressed and stretched states.\n \n \n \n \n\n\n \n Petukhov, M.; Lebedev, D.; Shalguev, V.; Islamov, A.; Kuklin, A.; Lanzov, V.; and Isaev-Ivanov, V.\n\n\n \n\n\n\n Proteins: Structure, Function and Genetics, 65(2): 296-304. 2006.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Conformational$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Petukhov2006296,\r\nauthor={Petukhov, M. and Lebedev, D. and Shalguev, V. and Islamov, A. and Kuklin, A. and Lanzov, V. and Isaev-Ivanov, V.},\r\ntitle={Conformational flexibility of RecA protein filament: Transitions between compressed and stretched states},\r\njournal={Proteins: Structure, Function and Genetics},\r\nyear={2006},\r\nvolume={65},\r\nnumber={2},\r\npages={296-304},\r\ndoi={10.1002/prot.21116},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749025273&doi=10.1002%2fprot.21116&partnerID=40&md5=dfc8701e07f6ab357a9c0657907dfbe9},\r\naffiliation={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},\r\nabstract={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.},\r\nauthor_keywords={Homologous recombination;  Molecular modeling;  RecA filament helix pitch;  RecA mobile N-terminal domain;  SANS},\r\ncorrespondence_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},\r\nissn={08873585},\r\ncoden={PSFGE},\r\npubmed_id={16909421},\r\nlanguage={English},\r\nabbrev_source_title={Proteins Struct. Funct. Genet.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Distinguishing characteristics of hyperrecombinogenic RecA protein from Pseudomonas aeruginosa acting in escherichia coli.\n \n \n \n \n\n\n \n Baitin, D.; Bakhlanova, I.; Kil, Y.; Cox, M.; and Lanzov, V.\n\n\n \n\n\n\n Journal of Bacteriology, 188(16): 5812-5820. 2006.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Distinguishing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Baitin20065812,\r\nauthor={Baitin, D.M. and Bakhlanova, I.V. and Kil, Y.V. and Cox, M.M. and Lanzov, V.A.},\r\ntitle={Distinguishing characteristics of hyperrecombinogenic RecA protein from Pseudomonas aeruginosa acting in escherichia coli},\r\njournal={Journal of Bacteriology},\r\nyear={2006},\r\nvolume={188},\r\nnumber={16},\r\npages={5812-5820},\r\ndoi={10.1128/JB.00358-06},\r\nnote={cited By 7},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748638384&doi=10.1128%2fJB.00358-06&partnerID=40&md5=a527bb9dfb3d913fd90639271dd73f9e},\r\naffiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, St. Petersburg 188300, Russian Federation; Research-Education Center Biophysics, St. Petersburg State Polytechnic University, St. Petersburg 194021, Russian Federation; Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544, United States; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation},\r\nabstract={In Escherichia coli, a relatively low frequency of recombination exchanges (FRE) is predetermined by the activity of RecA protein, as modulated by a complex regulatory program involving both autoregulation and other factors. The RecA protein of Pseudomonas aeruginosa (RecAPa) exhibits a more robust recombinase activity than its E. coli counterpart (RecAEc). Low-level expression of RecAPa in E. coli cells results in hyperrecombination (an increase of FRE) even in the presence of RecA Ec. This genetic effect is supported by the biochemical finding that the RecAPa protein is more efficient in filament formation than RecA K72R, a mutant protein with RecAEc-like DNA-binding ability. Expression of RecAPa also partially suppresses the effects of recF, recO, and recR mutations. In concordance with the latter, RecAPa filaments initiate recombination equally from both the 5′ and 3′ ends. Besides, these filaments exhibit more resistance to disassembly from the 5′ ends that makes the ends potentially appropriate for initiation of strand exchange. These comparative genetic and biochemical characteristics reveal that multiple levels are used by bacteria for a programmed regulation of their recombination activities. Copyright © 2006, American Society for Microbiology. All Rights Reserved.},\r\ncorrespondence_address1={Lanzov, V.A.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation; email: val@bpc.spbstu.ru},\r\nissn={00219193},\r\ncoden={JOBAA},\r\npubmed_id={16885449},\r\nlanguage={English},\r\nabbrev_source_title={J. Bacteriol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Improved RecA-assisted fluorescence assay for DNA strand exchange reaction.\n \n \n \n \n\n\n \n Kaboev, O.; Luchkina, L.; Shalguev, V.; Andreichuk, Y.; Kulikov, V.; Kozarenko, A.; and Lanzov, V.\n\n\n \n\n\n\n BioTechniques, 40(6): 736-738. 2006.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Improved$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Kaboev2006736,\r\nauthor={Kaboev, O. and Luchkina, L. and Shalguev, V. and Andreichuk, Y. and Kulikov, V. and Kozarenko, A. and Lanzov, V.},\r\ntitle={Improved RecA-assisted fluorescence assay for DNA strand exchange reaction},\r\njournal={BioTechniques},\r\nyear={2006},\r\nvolume={40},\r\nnumber={6},\r\npages={736-738},\r\ndoi={10.2144/000112195},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33746499205&doi=10.2144%2f000112195&partnerID=40&md5=24cadceda33d4d9a0f4578734a32647d},\r\naffiliation={Petersburg Nuclear Physics Institute of RAS, Gatchina, Russian Federation; HELIX Research Company, St. Petersburg, Russian Federation; Petersburg Nuclear Physics Institute RAS, 188300, Gatchina, Russian Federation},\r\ncorrespondence_address1={Kaboev, O.; Petersburg Nuclear Physics Institute RAS, 188300, Gatchina, Russian Federation; email: kaboev@omrb.pnpi.spb.ru},\r\nissn={07366205},\r\ncoden={BTNQD},\r\npubmed_id={16774116},\r\nlanguage={English},\r\nabbrev_source_title={BioTechniques},\r\ndocument_type={Short Survey},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2005\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Identification of Rad51 protein from Chlamydomonas reinhardtii: Recombinational characteristics.\n \n \n \n \n\n\n \n Shalguev, V.; Kaboev, O.; Sizova, I.; Hegemann, P.; and Lanzov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 39(1): 112-119. 2005.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Identification$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Shalguev2005112,\r\nauthor={Shalguev, V.I. and Kaboev, O.K. and Sizova, I.A. and Hegemann, P. and Lanzov, V.A.},\r\ntitle={Identification of Rad51 protein from Chlamydomonas reinhardtii: Recombinational characteristics},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={2005},\r\nvolume={39},\r\nnumber={1},\r\npages={112-119},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-21244474443&partnerID=40&md5=709da542bb9b29c04ab3585eaec056f1},\r\naffiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/Sankt-Petersburg, 188300, Russian Federation; St. Petersburg State University, Sankt-Petersburg, 198904, Russian Federation; Institute für Biochemie, Genetik, and Microbiologie, Universität Regensburg, Germany},\r\nabstract={The unicellular green microalga Chlamydomonas reinhardtii is a perspective model object for basic and applied research. However, its homologous recombination (HR) system which lies in the basis of double-strand DNA break repair have still not been studied. Last years the program of C. reinhardtii nuclear genome sequence is realized and different nucleotide repeats in the genome structure have been revealed that can explain a low level of HR relative to nonhomologous recombination events. Analyses of the C. reinhardtii EST (Expressed Sequence Tag)- and genome libraries permitted us to reconstruct and clone cDNA of the RAD51 gene. In present work, the cDNA was expressed, its product was purified and some basal biochemical activities were studied. The results show that Rad51 protein from lower eukaryote C. reinhardtii is identified as typical representative of the Rad51C-like subfamily of higher eukaryotes.},\r\ncorrespondence_address1={Shalguev, V.I.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/Sankt-Petersburg, 188300, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={15773555},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Identification of Chlamydomonas reinhardtii Rad51C: Recombinational characteristics.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Molecular Biology, 39(1): 98-104. 2005.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Identification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Characteristic thermodependence of the RadA recombinase from the hyperthermophilic archaeon Desulfurococcus amylolyticus.\n \n \n \n \n\n\n \n Kil, Y.; Glazunov, E.; and Lanzov, V.\n\n\n \n\n\n\n Journal of Bacteriology, 187(7): 2555-2557. 2005.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Characteristic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Kil20052555,\r\nauthor={Kil, Y.V. and Glazunov, E.A. and Lanzov, V.A.},\r\ntitle={Characteristic thermodependence of the RadA recombinase from the hyperthermophilic archaeon Desulfurococcus amylolyticus},\r\njournal={Journal of Bacteriology},\r\nyear={2005},\r\nvolume={187},\r\nnumber={7},\r\npages={2555-2557},\r\ndoi={10.1128/JB.187.7.2555-2557.2005},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-15244356831&doi=10.1128%2fJB.187.7.2555-2557.2005&partnerID=40&md5=675792b5d3bcdba89f146e5c0e34dba7},\r\naffiliation={Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation},\r\nabstract={The Desulfurococcus amylolyticus RadA protein (RadADa) promotes recombination at temperatures approaching the DNA melting point. Here, analyzing ATPase of the RadADa presynaptic complex, we described other distinguishing characteristics of RadADa. These include sensitivity to NaCl, preference for lengthy single-stranded DNA as a cofactor, protein activity at temperatures of over 100°C, and bimodal ATPase activity. These characteristics suggest that RadADa is a founding member of a new class of archaeal recombinases. Copyright © 2005, American Society for Microbiology. All Rights Reserved.},\r\ncorrespondence_address1={Lanzov, V.A.; Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation; email: vlanzov@bpc.spbstu.ru},\r\nissn={00219193},\r\ncoden={JOBAA},\r\npubmed_id={15774902},\r\nlanguage={English},\r\nabbrev_source_title={J. Bacteriol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2004\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Rad51 protein from the thermotolerant yeast Pichia angusta as a typical but thermodependent member of the Rad51 family.\n \n \n \n \n\n\n \n Shalguev, V.; Kil, Y.; Yurchenko, L.; Namsaraev, E.; and Lanzov, V.\n\n\n \n\n\n\n Eukaryotic Cell, 3(6): 1567-1573. 2004.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Rad51$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Shalguev20041567,\r\nauthor={Shalguev, V.I. and Kil, Y.V. and Yurchenko, L.V. and Namsaraev, E.A. and Lanzov, V.A.},\r\ntitle={Rad51 protein from the thermotolerant yeast Pichia angusta as a typical but thermodependent member of the Rad51 family},\r\njournal={Eukaryotic Cell},\r\nyear={2004},\r\nvolume={3},\r\nnumber={6},\r\npages={1567-1573},\r\ndoi={10.1128/EC.3.6.1567-1573.2004},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-11144347802&doi=10.1128%2fEC.3.6.1567-1573.2004&partnerID=40&md5=5cfd5b5995b6dfb61cd75461e59763ba},\r\naffiliation={Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, United States},\r\nabstract={The Rad51 protein from the methylotrophic yeast Pichia angusta (Rad51 Pa) of the taxonomic complex Hansenula polymorpha is a homolog of the RecA-RadA-Rad51 protein superfamily, which promotes homologous recombination and recombination repair in prokaryotes and eukaryotes. We cloned the RAD51 gene from the cDNA library of the thermotolerant P. angusta strain BKM Y1397. Induction of this gene in a rad51-deficient Saccharomyces cerevisiae strain partially complemented the survival rate after ionizing radiation. Purified Rad51Pa protein exhibited properties typical of the superfamily, including the stoichiometry of binding to single-stranded DNA (ssDNA) (one protomer of Rad51Pa per 3 nucleotides) and DNA specificity for ssDNA-dependent ATP hydrolysis [poly(dC) &gt; poly(dT) &gt; φX174 ssDNA &gt; poly(dA) &gt; double-stranded M13 DNA]. An inefficient ATPase and very low cooperativity for ATP interaction position Rad51Pa closer to Rad51 than to RecA. Judging by thermoinactivation, Rad51Pa alone was 20-fold more thermostable at 37°C than its S. cerevisiae homolog (Rad51 Sc). Moreover, it maintained ssDNA-dependent ATPase and DNA transferase activities up to 52 to 54°C, whereas Rad51Sc was completely inactive at 47°C. A quick nucleation and an efficient final-product formation in the strand exchange reaction promoted by Rad51 Pa occurred only at temperatures above 42°C. These reaction characteristics suggest that Rad51Pa is dependent on high temperatures for activity.},\r\ncorrespondence_address1={Lanzov, V.A.; Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russian Federation; email: vlanzov@bpc.spbstu.ru},\r\nissn={15359778},\r\ncoden={ECUEA},\r\npubmed_id={15590830},\r\nlanguage={English},\r\nabbrev_source_title={Eukaryotic Cell},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Structural properties and dynamics of low-energy collective excitations of water and lisozyme.\n \n \n \n \n\n\n \n Bayramov, F.; Toporov, V.; Petukhov, M.; Glazunov, E.; and Bairamov, B.\n\n\n \n\n\n\n 2004.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@CONFERENCE{Bayramov20043134,\r\nauthor={Bayramov, F.B. and Toporov, V.V. and Petukhov, M. and Glazunov, E.A. and Bairamov, B.H.},\r\ntitle={Structural properties and dynamics of low-energy collective excitations of water and lisozyme},\r\njournal={Physica Status Solidi C: Conferences},\r\nyear={2004},\r\nvolume={1},\r\nnumber={11},\r\npages={3134-3137},\r\ndoi={10.1002/pssc.200405368},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-11044233665&doi=10.1002%2fpssc.200405368&partnerID=40&md5=029557f29cc4058ba8997681f60e3107},\r\naffiliation={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},\r\nabstract={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.},\r\ncorrespondence_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},\r\nissn={16101634},\r\nlanguage={English},\r\nabbrev_source_title={Phys. Status Solidi C Conf.},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n H-bonding in protein hydration revisited.\n \n \n \n \n\n\n \n Petukhov, M.; Rychkov, G.; Firsov, L.; and Serrano, L.\n\n\n \n\n\n\n Protein Science, 13(8): 2120-2129. 2004.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"H-bonding$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Petukhov20042120,\r\nauthor={Petukhov, M. and Rychkov, G. and Firsov, L. and Serrano, L.},\r\ntitle={H-bonding in protein hydration revisited},\r\njournal={Protein Science},\r\nyear={2004},\r\nvolume={13},\r\nnumber={8},\r\npages={2120-2129},\r\ndoi={10.1110/ps.04748404},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-3342882423&doi=10.1110%2fps.04748404&partnerID=40&md5=0d9ff327ae21af729ffa5435ab512b9d},\r\naffiliation={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},\r\nabstract={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.},\r\nauthor_keywords={H-bonding;  Hydration;  Protein;  Solvent-accessible surface area;  Water},\r\ncorrespondence_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},\r\nissn={09618368},\r\ncoden={PRCIE},\r\npubmed_id={15238635},\r\nlanguage={English},\r\nabbrev_source_title={Protein Sci.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2003\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Expression, isolation, purification, and biochemical properties of trehalose-6-phosphate hydrolase from thermoresistant strain Bacillus sp. GP16.\n \n \n \n \n\n\n \n Karelov, D.; Krasikov, V.; Surzhik, M.; and Firsov, L.\n\n\n \n\n\n\n Biokhimiya, 68(9): 1238-1246. 2003.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Expression,$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Karelov20031238,\r\nauthor={Karelov, D.V. and Krasikov, V.V. and Surzhik, M.A. and Firsov, L.M.},\r\ntitle={Expression, isolation, purification, and biochemical properties of trehalose-6-phosphate hydrolase from thermoresistant strain Bacillus sp. GP16},\r\njournal={Biokhimiya},\r\nyear={2003},\r\nvolume={68},\r\nnumber={9},\r\npages={1238-1246},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0346151621&partnerID=40&md5=7e1598371f69b6b4fb4a6639cc1bd935},\r\naffiliation={Inst. of Nuclear Physics, RAS, Gatchina, Leningrad Region, 188350, Russian Federation},\r\nabstract={In the paper, cloning, expression, and purification of the enzyme trehalose-6-phosphate hydrolase from thermoresistant strain Bacillus sp. GP16 is described. Principal biochemical properties of the enzyme at different pH and temperature values were determined. Entropy and enthalpy of activation of the enzyme for substrates trehalose-6-phosphate and p-nitrophenyl glucoside were calculated, and the dependence of the kinetic parameters from ionic strength was established.},\r\nauthor_keywords={Catalysis;  Cloning of a gene;  Determination of Michaelis constants;  Gene expression;  Temperature dependence;  Trehalose-6-phosphate hydrolase},\r\ncorrespondence_address1={Karelov, D.V.; Inst. of Nuclear Physics, RAS, Gatchina, Leningrad Region, 188350, Russian Federation},\r\nissn={03209725},\r\ncoden={BIOHA},\r\nlanguage={Russian},\r\nabbrev_source_title={Biokhim.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Analytical model for determination of parameters of helical structures in solution by small angle scattering: Comparison of RecA structures by SANS.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n FEBS Letters, 537(1-3): 182-186. 2003.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Analytical$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2002\n \n \n (2)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Temperature dependence of HpRad51, the central protein of the homological recombination in the yeast Hansenula polymorpha.\n \n \n \n \n\n\n \n Shalguev, V.; Kil', Y.; Yurchenko, L.; and Lantsov, V.\n\n\n \n\n\n\n Doklady. Biochemistry and biophysics, 387: 328-330. 2002.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Temperature$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Shalguev2002328,\r\nauthor={Shalguev, V.I. and Kil', Y. and Yurchenko, L.V. and Lantsov, V.A.},\r\ntitle={Temperature dependence of HpRad51, the central protein of the homological recombination in the yeast Hansenula polymorpha.},\r\njournal={Doklady. Biochemistry and biophysics},\r\nyear={2002},\r\nvolume={387},\r\npages={328-330},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037823481&partnerID=40&md5=b907f9788af9ac970a8623625f839063},\r\naffiliation={Konstantinov Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Leningrad Oblast, Russia, 188350, Russian Federation},\r\ncorrespondence_address1={Shalguev, V.I.},\r\nissn={16076729},\r\npubmed_id={12577614},\r\nlanguage={English},\r\nabbrev_source_title={Dokl. Biochem. Biophys.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Thermodependence of the main protein of homologous recombination Rad51 in Hansenula polymorpha.\n \n \n \n \n\n\n \n Shalguev, V.; Kil', Y.; Yurchenko, L.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 387(5): 694-697. 2002.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Thermodependence$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Shalguev2002694,\r\nauthor={Shalguev, V.I. and Kil', Yu.V. and Yurchenko, L.V. and Lantsov, V.A.},\r\ntitle={Thermodependence of the main protein of homologous recombination Rad51 in Hansenula polymorpha},\r\njournal={Doklady Akademii Nauk},\r\nyear={2002},\r\nvolume={387},\r\nnumber={5},\r\npages={694-697},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036963024&partnerID=40&md5=6c07b5ac115e87d150d1ee9cdd984cc4},\r\npublisher={National Academy of Sciences},\r\nissn={08695652},\r\ncoden={DAKNE},\r\nabbrev_source_title={Dokl Akad Nauk},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n\n\n\n

\n

\n \n 2001\n \n \n (2)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Two types of thermodependence for homologous recombinases in Archaesa properties of recombinase from Desulfurococcus amylolyticus.\n \n \n \n \n\n\n \n Glazunov, E.; Kil', Y.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 379(5): 708-712. 2001.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Two$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Glazunov2001708,\r\nauthor={Glazunov, E.A. and Kil', Yu.V. and Lantsov, V.A.},\r\ntitle={Two types of thermodependence for homologous recombinases in Archaesa properties of recombinase from Desulfurococcus amylolyticus},\r\njournal={Doklady Akademii Nauk},\r\nyear={2001},\r\nvolume={379},\r\nnumber={5},\r\npages={708-712},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035548025&partnerID=40&md5=c96ea115272dcf22c69e6b67addd3de0},\r\nissn={08695652},\r\ncoden={DAKNE},\r\nabbrev_source_title={Dokl Akad Nauk},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

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\n \n\n \n \n \n \n \n \n Two types of temperature dependence of homologous recombinases in archaea: the properties of the Desulfurococcus amylolyticus recombinase.\n \n \n \n \n\n\n \n Glazunov, E.; Kil, Y.; and Lantsov, V.\n\n\n \n\n\n\n Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections / translated from Russian, 379: 389-392. 2001.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Two$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Glazunov2001389,\r\nauthor={Glazunov, E.A. and Kil, Y. and Lantsov, V.A.},\r\ntitle={Two types of temperature dependence of homologous recombinases in archaea: the properties of the Desulfurococcus amylolyticus recombinase.},\r\njournal={Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections / translated from Russian},\r\nyear={2001},\r\nvolume={379},\r\npages={389-392},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0141992527&partnerID=40&md5=9d3dde9efcea04155403d1aa63dc28e8},\r\naffiliation={Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Russia, 188350, Russian Federation},\r\ncorrespondence_address1={Glazunov, E.A.},\r\nissn={00124966},\r\npubmed_id={12918383},\r\nlanguage={English},\r\nabbrev_source_title={Dokl. Biol. Sci.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2000\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n The RadA protein from a hyperthermophilic archaeon Pyrobaculum islandicum is a DNA-dependent ATPase that exhibits two disparate catalytic modes, with a transition temperature at 75 °C.\n \n \n \n \n\n\n \n Spies, M.; Kil, Y.; Masui, R.; Kato, R.; Kujo, C.; Ohshima, T.; Kuramitsu, S.; and Lanzov, V.\n\n\n \n\n\n\n European Journal of Biochemistry, 267(4): 1125-1137. 2000.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Spies20001125,\r\nauthor={Spies, M. and Kil, Y. and Masui, R. and Kato, R. and Kujo, C. and Ohshima, T. and Kuramitsu, S. and Lanzov, V.},\r\ntitle={The RadA protein from a hyperthermophilic archaeon Pyrobaculum islandicum is a DNA-dependent ATPase that exhibits two disparate catalytic modes, with a transition temperature at 75 °C},\r\njournal={European Journal of Biochemistry},\r\nyear={2000},\r\nvolume={267},\r\nnumber={4},\r\npages={1125-1137},\r\ndoi={10.1046/j.1432-1327.2000.01108.x},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033952524&doi=10.1046%2fj.1432-1327.2000.01108.x&partnerID=40&md5=39ffd8272231ee93b715ed3af8098efd},\r\naffiliation={Dept. of Molec. and Radiat. Biophys., Petersburg Nucl. Physics Institute, Russian Academy of Sciences, St Petersburg, Russian Federation; Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan},\r\nabstract={The radA gene is an archaeal homolog of bacterial recA and eukaryotic RAD51 genes, which are critical components in homologous recombination and recombinational DNA repair. We cloned the radA gene from a hyperthermophilic archaeon, Pyrobaculum islandicum, overproduced the radA gene product in Escherichia coli and purified it to homogeneity. The purified P. islandicum RadA protein maintained its secondary structure and activities in vitro at high temperatures, up to 87 °C. It also showed high stability of 18.3 kcal·mol-1 (76.5 kJ·mol-1) at 25 °C and neutral pH. P. islandicum RadA exhibited activities typical of the family of RecA-like proteins, such as the ability to bind ssDNA, to hydrolyze ATP in a DNA-dependent manner and to catalyze DNA strand exchange. At 75 °C, all DNAs tested stimulated ATPase activity of the RadA. The protein exhibited a break in the Arrhenius plot of ATP hydrolysis at 75 °C. The cooperativity of ATP hydrolysis and ssDNA- binding ability of the protein above 75 °C were higher than at lower temperatures, and the activation energy of ATP hydrolysis was lower above this break point temperature. These results suggest that the ssDNA-dependent ATPase activity of P. islandicum RadA displays a temperature-dependent capacity to exist in two different catalytic modes, with 75 °C being the critical threshold temperature.},\r\nauthor_keywords={Arrhenius plot;  DNA-dependent ATPase;  Homologous genetic recombination;  Pyrobaculum islandicum;  RadA},\r\ncorrespondence_address1={Kuramitsu, S.; Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; email: kuramitu@bio.sci.osaka.u.ac.jp},\r\nissn={00142956},\r\ncoden={EJBCA},\r\npubmed_id={10672022},\r\nlanguage={English},\r\nabbrev_source_title={Eur. J. Biochem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Efficient strand transfer by the RadA recombinase from the hyperthermophilic archaeon Desulfurococcus amylolyticus.\n \n \n \n \n\n\n \n Kil, Y.; Baitin, D.; Masui, R.; Bonch-Osmolovskaya, E.; Kuramitsu, S.; and Lanzov, V.\n\n\n \n\n\n\n Journal of Bacteriology, 182(1): 130-134. 2000.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"Efficient$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kil2000130,\r\nauthor={Kil, Y.V. and Baitin, D.M. and Masui, R. and Bonch-Osmolovskaya, E.A. and Kuramitsu, S. and Lanzov, V.A.},\r\ntitle={Efficient strand transfer by the RadA recombinase from the hyperthermophilic archaeon Desulfurococcus amylolyticus},\r\njournal={Journal of Bacteriology},\r\nyear={2000},\r\nvolume={182},\r\nnumber={1},\r\npages={130-134},\r\ndoi={10.1128/JB.182.1.130-134.2000},\r\nnote={cited By 18},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033987061&doi=10.1128%2fJB.182.1.130-134.2000&partnerID=40&md5=146501195ab2c595fbd2a44ed6fa559a},\r\naffiliation={Div. of Molec. and Radiat. Biophys., Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188350, Russian Federation; Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Institute of Microbiology, Russian Academy of Sciences, Moskow 117811, Russian Federation; Petersburg Nuclear Physics Institute, RAS, Gatchina/St. Petersburg 188350, Russian Federation},\r\nabstract={The radA gene predicted to be responsible for homologous recombination in a hyperthermophilic archaeon, Desulfurococcus amylolyticus, was cloned, sequenced, and overexpressed in Escherichia coli cells. The deduced amino acid sequence of the gene product, RadA, was more similar to the human Rad51 protein (65% homology) than to the E. coli RecA protein (35%). A highly purified RadA protein was shown to exclusively catalyze single-stranded DNA- dependent ATP hydrolysis, which monitored presynaptic recombinational complex formation, at temperatures above 65°C (catalytic rate constant of 1.2 to 2.5 min-1 at 80 to 95°C). The RadA protein alone efficiently promoted the strand exchange reaction at the range of temperatures from 80 to 90°C, i.e., at temperatures approaching the melting point of DNA. It is noteworthy that both ATP hydrolysis and strand exchange are very efficient at temperatures optimal for host cell growth (90 to 92°C).},\r\ncorrespondence_address1={Lanzov, V.A.; Petersburg Nuclear Physics Institute, RAS, Gatchina/St. Petersburg 188350, Russian Federation; email: lanzov@lnpi.spb.su},\r\npublisher={American Society for Microbiology},\r\nissn={00219193},\r\ncoden={JOBAA},\r\npubmed_id={10613871},\r\nlanguage={English},\r\nabbrev_source_title={J. Bacteriol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n\n\n\n\n\n

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\n \n 1999\n \n \n (3)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n The catalysis of polyriboadenylate synthesis and phosphorolysis by polynucleotide phosphorylase immobilized on a new type of carrier.\n \n \n \n \n\n\n \n Platonova, G.; Surzhik, M.; Tennikova, T.; Vlasov, G.; and Timkovskii, A.\n\n\n \n\n\n\n Bioorganicheskaya Khimiya, 25(3): 193-194. 1999.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Platonova1999193,\r\nauthor={Platonova, G.A. and Surzhik, M.A. and Tennikova, T.B. and Vlasov, G.P. and Timkovskii, A.L.},\r\ntitle={The catalysis of polyriboadenylate synthesis and phosphorolysis by polynucleotide phosphorylase immobilized on a new type of carrier},\r\njournal={Bioorganicheskaya Khimiya},\r\nyear={1999},\r\nvolume={25},\r\nnumber={3},\r\npages={193-194},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0043231093&partnerID=40&md5=03850c6da4eef1eabf58b8cbda01cea4},\r\naffiliation={Inst. of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31, St. Petersburg, 199004, Russian Federation; Konstantinov Nucl. Phys. Inst., S., Russian Academy of Sciences, Gatchina, Leningrad oblast, 188350, Russian Federation},\r\nabstract={Polynucleotide phosphorylase from Thermus thermophilus was immobilized on monolithic-type polymeric carriers with an optimal pore size and a certain level of hydrophilic-hydrophobic balance (CIM-Disks), which had been recently developed and used for the preparation of highly selective affinity immunosorbents. This enzymic preparation was placed in a flow-type bioreactor and examined for the ability to synthesize polyriboad-enylate from ADP and to carry out its reverse phosphorolysis. The Michaelis constants of the direct and reverse reactions and the dependence of both types of activity on pH and the concentration of magnesium ions were determined for immobilized and soluble polynucleotide phosphorylase. The immobilization on porous monolithic carriers was shown to reinforce differences in the specificity of the enzyme interaction with high-and low-molecular-mass substrates. The productivity of the reactor was retained for six months at 65°C with repeated renewal of the substrate mixture.},\r\nauthor_keywords={CIM-Disk;  Immobilization;  Polynucleotide phosphorylase;  Porous materials;  Solid phase carrier},\r\ncorrespondence_address1={Platonova, G.A.; Inst. of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31, St. Petersburg, 199004, Russian Federation; email: tim@bird.macro.ru},\r\nissn={01323423},\r\nlanguage={English},\r\nabbrev_source_title={Bioorganicheskaya Khim.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The catalysis of polyriboadenylate synthesis and phosphorolysis by polynucleotide phosphorylase immobilized on a new type of carrier.\n \n \n \n \n\n\n \n Platonova, G.; Surzhik, M.; Tennikova, T.; Vlasov, G.; and Timkovskii, A.\n\n\n \n\n\n\n Russian Journal of Bioorganic Chemistry, 25(3): 166-171. 1999.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Platonova1999166,\r\nauthor={Platonova, G.A. and Surzhik, M.A. and Tennikova, T.B. and Vlasov, G.P. and Timkovskii, A.L.},\r\ntitle={The catalysis of polyriboadenylate synthesis and phosphorolysis by polynucleotide phosphorylase immobilized on a new type of carrier},\r\njournal={Russian Journal of Bioorganic Chemistry},\r\nyear={1999},\r\nvolume={25},\r\nnumber={3},\r\npages={166-171},\r\nnote={cited By 11},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-22644448619&partnerID=40&md5=0e4f3b237ac06b9fedb4ba9a9448ad55},\r\naffiliation={Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi pr. 31, St. Petersburg, 199004, Russian Federation; Konstantinov Nuclear Physics Institute, St. Petersburg, Russian Academy of Sciences, Gatchina, Leningrad oblast, 188350, Russian Federation},\r\nabstract={Polynucleotide phosphorylase from Thermus thermophilus was immobilized on monolithic-type polymeric carriers with an optimal pore size and a certain level of hydrophilic-hydrophobic balance (CIM-Disks), which had been recently developed and used for the preparation of highly selective affinity immunosorbents. This enzymic preparation was placed in a flow-type bioreactor and examined for the ability to synthesize polyriboadenylate from ADP and to carry out its reverse phosphorolysis. The Michaelis constants of the direct and reverse reactions and the dependence of both types of activity on pH and the concentration of magnesium ions were determined for immobilized and soluble polynucleotide phosphorylase. The immobilization on porous monolithic carriers was shown to reinforce differences in the specificity of the enzyme interaction with high- and low-molecular-mass substrates. The productivity of the reactor was retained for six months at 65°C with repeated renewal of the substrate mixture. © 1999 MAEe cyrillic signK "Hayκa/Interperiodica".},\r\nauthor_keywords={CIM-Disk;  Immobilization;  Polynucleotide phosphorylase;  Porous materials;  Solid phase carrier},\r\ncorrespondence_address1={Platonova, G.A.; Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi pr. 31, St. Petersburg, 199004, Russian Federation; email: tim@bird.macro.ru},\r\nissn={10681620},\r\nlanguage={English},\r\nabbrev_source_title={Russ. J. Bioorg. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Comment on a paper by Facchiano et al. (1998).\n \n \n \n \n\n\n \n Petukhov, M.; Kil, Y.; Lanzov, V.; Facchiano, A.; Colonna, G.; and Ragone, R.\n\n\n \n\n\n\n Protein Engineering, 12(6): 437-438. 1999.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Comment$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Petukhov1999437,\r\nauthor={Petukhov, M. and Kil, Y. and Lanzov, V. and Facchiano, A.M. and Colonna, G. and Ragone, R.},\r\ntitle={Comment on a paper by Facchiano et al. (1998)},\r\njournal={Protein Engineering},\r\nyear={1999},\r\nvolume={12},\r\nnumber={6},\r\npages={437-438},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033037566&partnerID=40&md5=d6c4cff51abb5758347d15da2ee9ac90},\r\naffiliation={European Molecular Biology Lab., Heidelberg 69012, Germany},\r\ncorrespondence_address1={Petukhov, M.; European Molecular Biology Lab., Heidelberg 69012, Germany},\r\npublisher={Oxford University Press},\r\nissn={02692139},\r\ncoden={PRENE},\r\npubmed_id={10388838},\r\nlanguage={English},\r\nabbrev_source_title={Protein Eng.},\r\ndocument_type={Note},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1998\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Optimal rigidity of protein structure: Three classes of rigidity in the reca protein family of eubacteria.\n \n \n \n \n\n\n \n Petukhov, M.; Baitin, D.; Kil', Y.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 362(1): 118-121. 1998.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Optimal$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Petukhov1998118,\r\nauthor={Petukhov, M.G. and Baitin, D.M. and Kil', Yu.V. and Lantsov, V.A.},\r\ntitle={Optimal rigidity of protein structure: Three classes of rigidity in the reca protein family of eubacteria},\r\njournal={Doklady Akademii Nauk},\r\nyear={1998},\r\nvolume={362},\r\nnumber={1},\r\npages={118-121},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032151784&partnerID=40&md5=6d2be933783417861956ca60fff1a5e6},\r\nissn={08695652},\r\ncoden={DAKNE},\r\npubmed_id={9858990},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl. Akad. Nauk},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Tn5/IS50 target recognition.\n \n \n \n \n\n\n \n Goryshin, I.; Miller, J.; Kil, Y.; Lanzov, V.; and Reznikoff, W.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 95(18): 10716-10721. 1998.\n cited By 91\n\n\n\n
\n\n\n\n \n \n $\"Tn5/IS50$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Goryshin199810716,\r\nauthor={Goryshin, I.Y. and Miller, J.A. and Kil, Y.V. and Lanzov, V.A. and Reznikoff, W.S.},\r\ntitle={Tn5/IS50 target recognition},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={1998},\r\nvolume={95},\r\nnumber={18},\r\npages={10716-10721},\r\ndoi={10.1073/pnas.95.18.10716},\r\nnote={cited By 91},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032168013&doi=10.1073%2fpnas.95.18.10716&partnerID=40&md5=1bdf50cb3b1bed008f4f5e44275fde96},\r\naffiliation={Department of Biochemistry, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, United States; Molecular Genetics Laboratory, St. Petersburg Nucl. Phys. Institute, Gatchina/St. Petersburg, 188350, Russian Federation},\r\nabstract={This communication reports an analysis of Tn5/IS50 target site selection by using an extensive collection of Tn5 and IS50 insertions in two relatively small regions of DNA (less than 1 kb each). For both regions data were collected resulting from in vitro and in vivo transposition events. Since the data sets are consistent and transposase was the only protein present in vitro, this demonstrates that target selection is a property of only transposase. There appear to be two factors governing target selection. A target consensus sequence, which presumably reflects the target selection of individual pairs of Tn5/IS50 bound transposase protomers, was deduced by analyzing all insertion sites. The consensus Tn5/IS50 target site is A- GNTYWRANC-T. However, we observed that independent insertion sites tend to form groups of closely located insertions (clusters), and insertions very often were spaced in a 5-bp periodic fashion. This suggests that Tn5/IS50 target selection is facilitated by more than two transposase protomers binding to the DNA, and, thus, for a site to be a good target, the overlapping neighboring DNA should be a good target, too. Synthetic target sequences were designed and used to test and confirm this model.},\r\nauthor_keywords={Composite transposons;  Escherichia coli;  Insertion specificity},\r\ncorrespondence_address1={Reznikoff, W.S.; Department of Biochemistry, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, United States; email: reznikoff@biochem.wisc.edu},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={9724770},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Template-dependent biosynthesis of poly(G)·poly(C) and its antiviral activity in vitro and in vivo.\n \n \n \n \n\n\n \n Surzhik, M.; Vilner, L.; Katchurin, A.; and Timkovskii, A.\n\n\n \n\n\n\n Antiviral Research, 38(2): 131-140. 1998.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Template-dependent$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Surzhik1998131,\r\nauthor={Surzhik, M.A. and Vilner, L.M. and Katchurin, A.L. and Timkovskii, A.L.},\r\ntitle={Template-dependent biosynthesis of poly(G)·poly(C) and its antiviral activity in vitro and in vivo},\r\njournal={Antiviral Research},\r\nyear={1998},\r\nvolume={38},\r\nnumber={2},\r\npages={131-140},\r\ndoi={10.1016/S0166-3542(98)00018-7},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031816538&doi=10.1016%2fS0166-3542%2898%2900018-7&partnerID=40&md5=03d8b4a10254ed0aaf6c11191377a550},\r\naffiliation={Laboratory of Biopolymers, Div. Molec. Radiat. Biophys., P., Leningrad District, 188 350, Russian Federation; Inst. Poliomyelitis Viral E., Russian Academy of Medical Sciences, Moscow District, 142 782, Russian Federation},\r\nabstract={Experimental conditions for poly(G) synthesis from GTP on a poly(C) template with the aid of Escherichia coli DNA-dependent RNA polymerase were investigated. The reaction product was purified without the use of RNase. On the basis of spectral data, gel permeation chromatography, affinity adsorption and electron microscopic visualization, the poly(G)·poly(C) product was assumed to possess a high degree of structural regularity. Its in vitro and in vivo antiviral activities were compared with those of traditional poly(G)·poly(C) and poly(I)·poly(C). Template-dependent poly(G)·poly(C was similar in its in vitro activity to poly(I)·poly(C) or even surpassed it, whereas the 'traditional' poly(G)·poly(C) was only slightly active in vitro. However, 'traditional poly(G)·poly(C) and poly(I)·poly(C) had similar activity in vivo, whereas template-dependent poly(G)·poly(C) was much less active in vivo. The role of intramolecular structural regularity in the in vitro and in vivo antiviral activity of polyribonucleotide duplexes is discussed.},\r\nauthor_keywords={Antiviral activity;  In vitro;  Poly(G)·poly(C);  Polyribonucleotide duplexes;  Structure;  Template biosynthesis},\r\ncorrespondence_address1={Timkovskii, A.L.; Laboratory of Biopolymers, Molecular/Radiation Biophysics Div., Petersburg Nuclear Physics Institute, Gatchina, Leningrad District 188350, Russian Federation; email: ALT@virus.iem.ras.spb.ru},\r\nissn={01663542},\r\ncoden={ARSRD},\r\npubmed_id={9707375},\r\nlanguage={English},\r\nabbrev_source_title={Antiviral Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n\n\n\n\n\n

\n

\n \n 1997\n \n \n (4)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Specific Features of Synthesis of the Poly(C, U) Copolymer by Mesophilic and Thermophilic Polynucleotide Phosphorylases.\n \n \n \n \n\n\n \n Glazunov, E.; Surzhik, M.; and Dyatlova, N.\n\n\n \n\n\n\n Prikladnaya Biokhimiya i Mikrobiologiya, 33(4): 396. 1997.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Specific$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Glazunov1997396,\r\nauthor={Glazunov, E.A. and Surzhik, M.A. and Dyatlova, N.G.},\r\ntitle={Specific Features of Synthesis of the Poly(C, U) Copolymer by Mesophilic and Thermophilic Polynucleotide Phosphorylases},\r\njournal={Prikladnaya Biokhimiya i Mikrobiologiya},\r\nyear={1997},\r\nvolume={33},\r\nnumber={4},\r\npages={396},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0347703285&partnerID=40&md5=d3157a876306c9247e21f540dc7f90da},\r\nabstract={The syntheses of poly(C, U) copolymer by polynucleotide phosphorylases isolated from two microbial species (Escherichia coli and Thermus thermophilus) was studied. Relationships between compositions of substrate mixtures (in a broad range of concentration ratios of these bases) and the composition of the product synthesized by either free or immobilized enzymes were determined. Knowledge of these dependences can be important for biotechnological production of large amounts of copolymerized polyribonucleotides of a required composition.},\r\nissn={05551099},\r\nlanguage={Russian},\r\nabbrev_source_title={Prikl. Biokhim. Mikrobiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n On the nature of protein thermoresistence: Stability of α-hilices of recA proteins from thermophilic bacteria.\n \n \n \n \n\n\n \n Petukhov, M.; Kil', Y.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 356(2): 267-271. 1997.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"On$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Petukhov1997267,\r\nauthor={Petukhov, M.G. and Kil', Yu.V. and Lantsov, V.A.},\r\ntitle={On the nature of protein thermoresistence: Stability of α-hilices of recA proteins from thermophilic bacteria},\r\njournal={Doklady Akademii Nauk},\r\nyear={1997},\r\nvolume={356},\r\nnumber={2},\r\npages={267-271},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748733991&partnerID=40&md5=afe6cfaffd9b5b5e3010e684441ce589},\r\nissn={08695652},\r\ncoden={DAKNE},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl. Akad. Nauk},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Insights into thermal resistance of proteins from the intrinsic stability of their α-helices.\n \n \n \n \n\n\n \n Petukhov, M.; Kil, Y.; Kuramitsu, S.; and Lanzov, V.\n\n\n \n\n\n\n Proteins: Structure, Function and Genetics, 29(3): 309-320. 1997.\n cited By 44\n\n\n\n
\n\n\n\n \n \n $\"Insights$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Petukhov1997309,\r\nauthor={Petukhov, M. and Kil, Y. and Kuramitsu, S. and Lanzov, V.},\r\ntitle={Insights into thermal resistance of proteins from the intrinsic stability of their α-helices},\r\njournal={Proteins: Structure, Function and Genetics},\r\nyear={1997},\r\nvolume={29},\r\nnumber={3},\r\npages={309-320},\r\ndoi={10.1002/(SICI)1097-0134(199711)29:3<309::AID-PROT5>3.0.CO;2-5},\r\nnote={cited By 44},\r\nurl={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},\r\naffiliation={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},\r\nabstract={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.},\r\nauthor_keywords={α-helix stability;  Aspartate aminotransferases;  L lactate dehydrogenases;  Protein thermostability;  RecA protein family;  Seryl-tRNA synthetases},\r\ncorrespondence_address1={Petukhov, M.; European Molec. Biology Laboratory, Meyerhofstrasse 1, Postfach 10.2209, 69012 Heidelberg, Germany},\r\nissn={08873585},\r\ncoden={PSFGE},\r\npubmed_id={9365986},\r\nlanguage={English},\r\nabbrev_source_title={PROTEINS STRUCT. FUNCT. GENET.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n

\n 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.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Specific features of synthesis of the poly(C,U) copolymer by mesophilic and thermophilic polynucleotide phosphorylases.\n \n \n \n \n\n\n \n Glazunov, E.; Surzhik, M.; and Dyatlova, N.\n\n\n \n\n\n\n Applied Biochemistry and Microbiology, 33(4): 349-352. 1997.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Specific$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Glazunov1997349,\r\nauthor={Glazunov, E.A. and Surzhik, M.A. and Dyatlova, N.G.},\r\ntitle={Specific features of synthesis of the poly(C,U) copolymer by mesophilic and thermophilic polynucleotide phosphorylases},\r\njournal={Applied Biochemistry and Microbiology},\r\nyear={1997},\r\nvolume={33},\r\nnumber={4},\r\npages={349-352},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031503936&partnerID=40&md5=1e31e773006c86b0d9602969a3b31a95},\r\nabstract={The syntheses of poly(C,U) copolymer by polynucleotide phosphorylases isolated from two microbial species (Escherichia coli and Thermus thermophilus) was studied. Relationships between compositions of substrate mixtures (in a broad range of concentration ratios of these bases) and the composition of the product synthesized by either free or immobilized enzymes were determined. Knowledge of these dependences can be important for biotechnological production of large amounts of copolymerized polyribonucleotides of a desired composition.},\r\nissn={00036838},\r\nlanguage={English},\r\nabbrev_source_title={Appl. Biochem. Microbiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n

\n \n 1994\n \n \n (1)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n DNA length, bending, and twisting constraints on IS50 transposition.\n \n \n \n \n\n\n \n Goryshin, I.; Kil, Y.; and Reznikoff, W.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 91(23): 10834-10838. 1994.\n cited By 32\n\n\n\n
\n\n\n\n \n \n $\"DNA$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Goryshin199410834,\r\nauthor={Goryshin, I.Y. and Kil, Y.V. and Reznikoff, W.S.},\r\ntitle={DNA length, bending, and twisting constraints on IS50 transposition},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={1994},\r\nvolume={91},\r\nnumber={23},\r\npages={10834-10838},\r\ndoi={10.1073/pnas.91.23.10834},\r\nnote={cited By 32},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027962511&doi=10.1073%2fpnas.91.23.10834&partnerID=40&md5=8e02c169dd3e5e7c24d45b2c5fd6b3b8},\r\naffiliation={Department of Biochemistry, Coll. of Agric. and Life Sciences, University of Wisconsin, Madison, WI 53706-1569, United States; Molecular Genetics Laboratory, St. Petersburg Nucl. Phys. Institute, 188350 Gatchina, Leningrad District, Russian Federation},\r\nabstract={Transposition is a multistep process in which a transposable element DNA sequence moves from its original genetic location to a new site. Early steps in this process include the formation of a transposition complex in which the end sequences of the transposable element are brought together in a structurally precise fashion through the action of the element-encoded transposase protein and the cleavage of the element free from the adjoining DNA. If transposition complex formation must precede DNA cleavage (or nicking), then changing the length of the donor DNA between closely spaced ends should have dramatic effects on the frequency of the transposition. This question has been examined by studying the effects of altering donor DNA length on IS50 transposition. Donor DNA ≤ 64 bp severely impaired transposition. Donor DNA ≥ 200 bp demonstrated high transposition frequencies with only modest length dependencies. Constructs with donor DNA lengths between 66 and 174 bp demonstrated a dramatic periodic effect on transposition (periodicity ≃ 10.5 bp).},\r\ncorrespondence_address1={Reznikoff, W.S.; Department of Biochemistry, Agricultural/Life Sciences College, University of Wisconsin, Madison, WI 53706-1569, United States},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={7971970},\r\nlanguage={English},\r\nabbrev_source_title={PROC. NATL. ACAD. SCI. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1993\n \n \n (1)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Interrelationship between the chain length of poly-L-lysine and the degree of protection of polyribonucleotide interferon inducers from human blood nucleases [Vzaimosviaz' mezhdu dlinoǐ tsepi ékraniruiushchego poli-L-lizina i stepen'iu zashchity poliribonukleotidnykh induktorob interferona ot nukleas krovi cheloveka.].\n \n \n \n \n\n\n \n Surzhik, M.; Duks, A.; Diatlova, N.; Glazunov, E.; Feldmane, G.; and Timkovskiǐ, A.\n\n\n \n\n\n\n Antibiotiki i Khimioterapiya, 38(7): 21-25. 1993.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Interrelationship$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Surzhik199321,\r\nauthor={Surzhik, M.A. and Duks, A.E. and Diatlova, N.G. and Glazunov, E.A. and Feldmane, G.I. and Timkovskiǐ, A.L.},\r\ntitle={Interrelationship between the chain length of poly-L-lysine and the degree of protection of polyribonucleotide interferon inducers from human blood nucleases [Vzaimosviaz' mezhdu dlinoǐ tsepi ékraniruiushchego poli-L-lizina i stepen'iu zashchity poliribonukleotidnykh induktorob interferona ot nukleas krovi cheloveka.]},\r\njournal={Antibiotiki i Khimioterapiya},\r\nyear={1993},\r\nvolume={38},\r\nnumber={7},\r\npages={21-25},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027631606&partnerID=40&md5=cd5fd07f76af4766f1ce55f00e95e2fc},\r\nabstract={The action of the human total blood serum on polynucleotide interferon inducers, larifan and ridostin (natural double-stranded RNAs) and poly(I).poly(C) (a double-stranded complex of synthetic polyribonucleotides) used both in the free state and in the state shielded with poly-L-lysine was studied. The rate of the accumulation of the acid soluble products was compared with the residual interferon-inducing activity in mice. All the unshielded inducers were shown to completely loose their activity after a 4-hour contact with the serum. The protective activity of poly-L-lysine increased in parallel with the increase of its molecular weight and was maximal for the preparation with the molecular weight of 12300 +/- 1000 Da. Differences in the structure of the inducers and the mechanism of their biosynthesis and degradation must be taken into account.},\r\ncorrespondence_address1={Surzhik, M.A.},\r\nissn={02352990},\r\npubmed_id={8161271},\r\nlanguage={Russian},\r\nabbrev_source_title={Antibiot Khimioter},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1992\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Riboflavin operon of Bacillus subtilis: unusual symmetric arrangement of the regulatory region.\n \n \n \n \n\n\n \n Kil, Y.; Mironovi, V.; Gorishin, I.; Kreneva, R.; and Perumov, D.\n\n\n \n\n\n\n MGG Molecular & General Genetics, 233(3): 483-486. 1992.\n cited By 55\n\n\n\n
\n\n\n\n \n \n $\"Riboflavin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Kil1992483,\r\nauthor={Kil, Y.V. and Mironovi, V.N. and Gorishin, I.Yu. and Kreneva, R.A. and Perumov, D.A.},\r\ntitle={Riboflavin operon of Bacillus subtilis: unusual symmetric arrangement of the regulatory region},\r\njournal={MGG Molecular & General Genetics},\r\nyear={1992},\r\nvolume={233},\r\nnumber={3},\r\npages={483-486},\r\ndoi={10.1007/BF00265448},\r\nnote={cited By 55},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026632334&doi=10.1007%2fBF00265448&partnerID=40&md5=229405cbf898604bba7b431fec915367},\r\naffiliation={Department of Molecular and Radiation Biophysics, Leningrad Nuclear Physics Institute of the Academy of Sciences of the USSR, Gatchina, Leningrad District, 188350, Russia; Centre of Bioengineering, Institute of Molecular Biology of the Academy of Sciences of the USSR, Moscow, 117984, Russia},\r\nabstract={Seventeen cis-dominant mutations leading to riboflavin overproduction in Bacillus subtilis were localized to the region between nucleotides + 37 and + 159 relative to the transcription initiation site of the riboflavin operon. This region displays an unusual structure for regulatory sequences. The main part of it represents clusters of A/T and G/Grich sequences that symmetrically blank a short inverted repeat. © 1992 Springer-Verlag.},\r\nauthor_keywords={Bacillus subtilis;  Regulatory mutants;  Riboflavin operon},\r\ncorrespondence_address1={Perumov, D.A.; Department of Molecular and Radiation Biophysics, Leningrad Nuclear Physics Institute of the Academy of Sciences of the USSR, Gatchina, Leningrad District, 188350, Russia},\r\npublisher={Springer-Verlag},\r\nissn={00268925},\r\ncoden={MGGEA},\r\npubmed_id={1620102},\r\nlanguage={English},\r\nabbrev_source_title={Molec. Gen. Genet.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Resistance of natural and synthetic polyribonucleotide inductors of interferon to human blood ribonucleases.\n \n \n \n \n\n\n \n Surzhik, M.; Dyatlova, N.; Glazunov, E.; Timkovsky, A.; Vlasov, G.; and Kozhevnikova Yu., N.\n\n\n \n\n\n\n Antibiotiki i Khimioterapiya, 37(1): 21-23. 1992.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Resistance$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Surzhik199221,\r\nauthor={Surzhik, M.A. and Dyatlova, N.G. and Glazunov, E.A. and Timkovsky, A.L. and Vlasov, G.P. and Kozhevnikova Yu., N.},\r\ntitle={Resistance of natural and synthetic polyribonucleotide inductors of interferon to human blood ribonucleases},\r\njournal={Antibiotiki i Khimioterapiya},\r\nyear={1992},\r\nvolume={37},\r\nnumber={1},\r\npages={21-23},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026609858&partnerID=40&md5=dcbb9c42f9c485c009156613babb8656},\r\naffiliation={Institute of Nuclear Physics, USSR Academy of Sciences, St. Petersburg, Russia},\r\ncorrespondence_address1={Surzhik, M.A.; Institute of Nuclear Physics, USSR Academy of Sciences, St. Petersburg, Russia},\r\nissn={02352990},\r\ncoden={ANKHE},\r\npubmed_id={1530353},\r\nlanguage={Russian},\r\nabbrev_source_title={ANTIBIOT. KHIMIOTER.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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