Лаборатория моделирования биомолекулярных систем

	Отдел структурной биологии ИБХ РАН

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стартовая / работа / публикации

Наши публикации

2013

Polyansky A.A., Chugunov A.O., Volynsky P.E., Krylov N.A., Nolde D.E., Efremov R.G. (2013). PREDDIMER: a web server for prediction of transmembrane helical dimers. Bioinformatics.
Dubovskii P.V., Konshina A.G., Efremov R.G. (2013). Cobra Cardiotoxins: Membrane Interactions and Pharmacological Potential. Curr. Med. Chem. 21 (3), 270–287.
Chugunov A.O., Pyrkova D.V., Nolde D.E., Polyansky A.A., Pentkovsky V.M., Efremov R.G. (2013). Lipid-II forms potential “landing terrain” for lantibiotics in simulated bacterial membrane. Sci. rep. 3, 1678.
Chugunov A.O., Koromyslova A.D., Berkut A.A., Peigneur S., Tytgat J., Polyansky A.A., Pentkovsky V.M., Vassilevski A.A., Grishin E.V., Efremov R.G. (2013). Modular Organization of α-Toxins from Scorpion Venom Mirrors Domain Structure of Their Targets — Sodium Channels. J. Biol. Chem. 88, 19014-19027.
Volynsky P.E., Polyansky A.A., Fakhrutdinova G.N., Bocharov E.V., Efremov R.G. (2013). Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3. (2013) J. Am. Chem. Soc. 135, 8105-8108.
Krylov N.A., Pentkovsky V.M., Efremov R.G. (2013). Nontrivial Behavior of Water in the Vicinity and Inside Lipid Bilayers as Probed by Molecular Dynamics Simulations. ACS Nano 7(10), 9428–9442.
Pyrkova D.V., Tarasova N.K., Krylov N.A., Nolde D.E., Pentkovsky V.M., Efremov R.G. Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact. (2013). J. Biomol. Struct. & Dyn. 31(1), 87–95.
Aseev L.V., Chugunov A.O., Efremov R.G., Boni I.V. A single missence mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers thermo-sensitive phenotype that can be suppressed by ribosomal protein S1. (2013). J. Bacteriology 195(1), 95–104.
Blanchevoye C., Floquet N., Scandolera A., Baud S., Maurice P., Bocquet O., Blaise S., Ghoneim C., Cantarelli B., Delacoux F., Dauchez M., Efremov R.G., Martiny L., Duca L., Debelle L. Interaction between the elastin peptide VGVAPG and human elastin binding protein. (2013). J. Biol. Chem. 288(2), 1317–1328.

2012

Ostapchenko V.G., Gasparian M.E., Kosinsky Yu.A., Efremov R.G., Dolgikh D.A., Kirpichnikov M.P. Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit. (2012). J. Biomol. Struct. & Dyn. 30(1), 62–73.
Polyansky A.A., Volynsky P.E., Efremov R.G. Multistate organization of transmembrane helical protein dimers governed by the host membrane. (2012). J. Amer. Chem. Soc. 134(35), 14390–14400.
Charlier L., Topin J., Ronin C., Kim S.-K., Goddard III W.A., Efremov R., Golebiowski J. How broadly tuned Olfactory Receptors equally recognize their agonists. Human OR1G1 as a test case. (2012). Cell Mol. Life Sci. 69(24), 4205–4213.
Konshina A.G., Dubovskii P.V., Efremov R.G. Structure and Dynamics of Cardiotoxins. (2012). Curr. Prot. Peptide Science 13(6), 570–584.
Polyansky A.A., Chugunov A.O., Vassilevski1 A.A., Grishin E.V., Efremov R.G. Recent Advances in Computational Modeling of α-Helical Membrane-Active Peptides. (2012). Curr. Prot. Peptide Science 13(7), 644–657.
Semenova A.A., Chugunov A.O., Dubovskii P.V., Chupin V.V., Volynsky P.E., Boldyrev I.A. The role of chain rigidity in lipid self-association: comparative study of dihexanoyl- and disorbyl-phosphatidylcholines. (2012). Chem. Phys.Lipids 165, 382–386.
Polyansky A.A., Zagrovic B. Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation. (2012). J. Phys. Chem. Lett. 3, 973–976.
Чугунов А.О., Нольде Д.Е., Пыркова Д.В., Полянский А.А., Пентковский В.М., Ефремов Р.Г. На пути к новым антибиотикам. (2012). Суперкомпьютеры 12, 34–36.
Чугунов А.О., Полянский А.А., Ефремов Р.Г. (2013). Физическая водобоязнь. Природа (2013) 1, 24–34.

2011

Пыркова Д.В., Тарасова Н.К., Крылов Н.А., Нольде Д.Е., Ефремов Р.Г. Латеральная кластеризация липидов в гидратированных бислоях из диолеоилфосфатидилхолина и дипальмитоилфосфатидилхолина. (2011). Биологические мембраны 28 (4), 298–306.
Pyrkova D.V., Tarasova N.K., Pyrkov T.V., Krylov N.A., Efremov R.G. (2011). Atomic-scale lateral heterogeneity and dynamics of two-component lipid bilayers composed of saturated and unsaturated phosphatidylcholines. Soft Matter 7, 2569–2579;
Polyansky A.A., Volynsky P.E., Efremov R.G. (2011). Structural, Dynamic, and Functional Aspects of Helix Association in Membranes: a Computational View. Adv. Prot. Chem. Struct. Biol. 83, 129–161;
Konshina A.G., Boldyrev I.A., Utkin Yu.N., Omel’kov А.V., Efremov R.G. (2011). Snake cytotoxins bind to membranes via interactions with phosphatidylserine head groups of lipids. PLoS ONE 6, e19064;
Kordyukova L.V., Serebryakova M.V., Polyansky A.A., Kropotkina E.A., Alexeevski A.V., Veit M., Efremov R.G., Filippova I.Y., Baratova L.A.(2011). Linker and/or transmembrane regions of influenza A/Group-1, A/Group-2 and type B virus hemagglutinins are packed differently within trimmers. Biochim. Biophys. Acta — Biomembranes 1808, 1843–1854;
Deyev I.E, Sohet F., Vassilenko K.P, Serova O.V, Popova N.V., Zozulya S.A., Burova E.B., Houillier P., Rzhevsky D.I., Berchatova A.A., Murashev A.N., Chugunov A.O., Efremov R.G., Nikol’sky N.N., Bertelli E., Eladari D., Petrenko A.G. (2011). Insulin receptor-related receptor as an extracellular alkali sensor. Cell Metabolism 13, 679–689;
Минеев К.С., Бочаров Э.В., Волынский П.Е., Гончарук М.В., Ткач Е.Н., Ермолюк Я.С., Шульга А.А., Чупин В.В., Масленников И.В., Ефремов Р.Г., Арсеньев А.С. (2011). Структура димера трансмембранного домена гликофорина А в окружении липидов и детергентов. (2011). Acta Naturae 3, 113–121;
Mineev K.S., Bocharov E.V., Volynsky P.E., Goncharuk M.V., Tkach E.N., Ermolyuk Ya.S., Shulga A.A., Chupin V.V., Maslennikov I.V.., Efremov R.G., Arseniev A.S. (2011). Dimeric structure of transmembrane domain of glycophorin A in lipidic and in detergent environments. Acta Naturae 3, 113–121;
Пыркова Д.В., Тарасова Н.К., Крылов Н.А., Нольде Д.Е., Ефремов Р.Г. (2011). Латеральная кластеризация липидов в гидратированных бислоях из диолеоилфосфатидилхолина и дипальмитоилфосфатидилхолина. Биологические мембраны 28 (4), 298–306.

2010

Bocharov E.V., Mayzel M.L., Volynsky P.E., Mineev K.S., Tkach E.N., Ermolyuk Ya.S., Schulga A.A., Efremov R.G., Arseniev A.S. (2010). Left-Handed Dimeric Structure of Transmembrane Domain of the Human Receptor Tyrosine Kinase EphA2 via a Heptad Repeat Motif. Biophys. J. 98, 881–889;
Lashkov A.A., Zhukhlistova N.E., Gabdoulkhakov A.H., Shtil A.A., Efremov R.G., Mikhailov A.M. (2010). The X-Ray Structure of Salmonella typhimurium Uridine Nucleoside Phosphorylase Complexed with 2,2’-Anhydrouridine, Phosphate and Potassium Ions at 1.86 Â Resolution. Acta Cryst. D 66 (Pt 1), 51–60;
Novoseletsky V.N., Pyrkov T.V., Efremov R.G. (2010). Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor. SAR QSAR Environ Res. 21, 37–55;
Volynsky P.E., Mineeva E.A., Goncharuk M.V., Ermolyuk Ya.S., Arseniev A.S., Efremov R.G. (2010). Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane α-helical dimers: ephrin receptor A1. (2010). Phys. Biol. 7, 1–15;
Пырков Т.В., Озеров И.В., Балицкая Е.Д., Ефремов Р.Г. (2010). Молекулярный докинг: роль невалентных взаимодействий в образовании комплексов белков с нуклеотидами и пептидами. Биоорганическаяхимия 36, 482–492;
Bocharov E.V., Volynsky P.E., Pavlov K.V., Efremov R.G., Arseniev A.S. (2010). Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adhesion & Migration 4, 284–298;
Kоншинa A.Г., Болдырев И.А., Омельков А.В., Уткин Ю.Н., Ефремов Р.Г. (2010). Анионные липиды как детерминанты связывания цитотоксинов из яда змей на поверхности клеточной мембраны. Acta Naturae 2, 93–101;
Polyansky A.A., Ramaswamy R., Volynsky P.E., Sbalzarini I.F., Marrink S.J., Efremov R.G. (2010). Antimicrobial peptides induce the growth of nascent phosphatidylglycerol domains in a model bacterial membrane. J. Phys. Chem. Lett. 1, 3108–3111;
Chugunov AO, Simms J, Poyner DR, Dehouck Y, Rooman M, Gilis D, Langer I. (2010). Evidence that interaction between conserved residues in transmembrane helices 2, 3, and 7 are crucial for human VPAC1 receptor activation. Mol. Pharmacol. 78, 394–401.

2009

Pyrkov T.V., Chugunov A.O., Krylov N.A., Nolde D.E., Efremov R.G. PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. (2009). Bioinformatics 25(9), 1201–1202;
Polyansky A.A., Vassilevski A.A., Volynsky P.E., Vorontsova O.V., Samsonova O.V., Egorova N.S., Krylov N.A., Feofanov A.V., Arseniev A.S., Grishin E.V., Efremov R.G. N-terminal amphipathic helix as a trigger of hemolytic activity in antimicrobial peptides: a case study in latarcins. (2009). FEBS Lett. 583(14), 2425–2428;
Пырков Т. В., Пыркова Д. В., Балицкая Е. Д., Ефремов Р. Г. Роль стэкинг-взаимодействий в комплексах белков с аденин- и гуанинсодержащими лигандами. (2009). Acta Naturae 1, 124–127.
Lesovoy D.M., Bocharov E.V., Lyukmanova E.N., Kosinsky Yu.A., Shulepko M.A., Dolgikh D.A., Kirpichnikov M.P., Efremov R.G., Arseniev A.S. Specific membrane binding of neurotoxin II can facilitate its delivery to acetylcholine receptor. (2009). Biophys. J. 97(7), 2089–2097;
Чугунов А. О., Ефремов Р. Г. Предсказание пространственной структуры белков: акцент на мембранных мишенях. (2009). Биоорг. хим. 35(6), 744–760;
Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. Adaptation of a membrane active peptide to heterogeneous environment. I. Structural plasticity of the peptide. (2009). J. Phys. Chem.B. 113, 1107–1119 (См. в пабмеде).
Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. Adaptation of a membrane active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface. (2009). J. Phys. Chem.B. 113, 1120–1126 (See @ medline).

2008

Farce A., Chugunov A.O., Logé C., Yous S., Vergoten G., Efremov R.G., Lesieur D., Chavatte P. Homology Modeling of MT₁ and MT₂ Receptors (2008). Eur. J. Med. Chem. 43, 1926–1944 (См. в пабмеде).
Pyrkov T.V., Priestle J., Jacoby E., Efremov R.G. Ligand-specific scoring functions: Improved ranking of docking solutions. (2008). SAR and QSAR in Environmental Research. 19, 91–99 (См. в пабмеде).
Bocharov E.V., Mineev K.S., Volynsky P.E., Ermolyuk Ya.S., Tkach E.N., Sobol A.G., Chupin V.V., Kirpichnikov M.P., Efremov R.G., Arseniev A.S. Spatial structure of dimeric transmembrane domain of growth factor receptor ErbB2. (2008). J. Biol. Chem. 283, 6950–6956 (См. в пабмеде).
Dubovskii P.V., Volynsky P.E., Polyansky A.A., Karpunin D.V., Chupin V.V., Efremov R.G., Arseniev A.S. 3D Structure/Hydrophobicity of Latarcins Specifies their Mode of Membrane Activity. (2008). Biochemistry 47, 3525–3533 (См. в пабмеде).
Bocharov E.V., Mayzel M.L., Volynsky P.E., Goncharuk M.V., Ermolyuk Ya.S., Schulga A.A., Artemenko E.O., Efremov R.G., Arseniev A.S. Spatial Structure and pH-Dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1. (2008). J. Biol. Chem. 283, 29385–29395 (См. в пабмеде).

2007

Efremov R.G., Volynsky P.E., Polyansky A.A., Nolde D.E., Arseniev A.S. Protein-membrane interactions: lessons from in silico studies. In: “Structure and Biophysics—New Technologies for current Challenges in Biology and Beyond”. Puglisi J.D. (Ed.), Springer 2007. pp. 19–39 (doi: 10.1007/978-1-4020-5900-1_3).
Bocharov E.V., Pustovalova Yu.E., Pavlov K.V., Volynsky P.E., Goncharuk M.V., Ermolyuk Ya.S., Karpunin D.V., Shulga A.A., Kirpichnikov M.P., Efremov R.G., Maslennikov I.V., Arseniev A.S. (2007). Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger. J. Biol. Chem. 282, 16256–16266 (См. в пабмеде);
Vereshaga Ya.A., Volynsky P.E., Pustovalova Ju.E., Nolde D.E., Arseniev A.S., Efremov R.G. (2007). Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins: Structure, Function, and Bioinformatics 69, 309–325 (См. в пабмеде).
Efremov R.G., Volynsky P.E., Nolde D.E., Vergoten G., Arseniev A.S. (2007). The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding. J. Biomol. Struct. & Dynamics 25, 195–206 (См. в пабмеде).
Chugunov, A.O., Novoseletsky, V.N., Nolde, D.E., Arseniev, A.S., Efremov, R.G. (2007). A method to assess packing quality of transmembrane α-helices in proteins. I. Parameterization using structural data. J. Chem. Inf. Model. 47, 1150–1162 (doi: 10.1021/ci600516x).
Chugunov, A.O., Novoseletsky, V.N., Nolde, D.E., Arseniev, A.S., Efremov, R.G. (2007). A method to assess packing quality of transmembrane α-helices in proteins. II. Validation by “correct vs. misleading” test. J. Chem. Inf. Model. 47, 1163–1170 (doi: 10.1021/ci600517c).
Pyrkov, T.V., Kosinsky, Yu.A, Arseniev, A.S., Priestle, J.P., Jacoby, E., Efremov, R.G. (2007). Docking of ATP to Ca-ATPase: Considering Protein Domain Motions. J. Chem. Inf. Model. 47, 1171–1181 (doi: 10.1021/ci700067f).
Pyrkov T.V., Efremov R.G. Fragment-Based Scoring Function to Re-rank Results of Docking ATP. (2007). Int. J. Mol. Sci. v. 8, 1083–1094 (doi: 10.3390/i8111083).
Чугунов А.О., Новоселецкий В.Н., Арсеньев А.С., Ефремов Р.Г. (2007). Интегральные мембранные белки: подход к созданию реалистичных моделей in silico. Серия. Критические технологии. Мембраны 33, 21–31 (в интернете).
Efremov R.G., Chugunov A.O., Pyrkov T.V., Priestle J.P., Arseniev A.S., Jacoby E. Molecular lipophilicity in protein modeling and drug design. (2007). Curr. Med. Chem. 14(4) 393–415 (См. в пабмеде).
Чугунов А.О., Новоселецкий В.Н., Арсеньев А.С., Ефремов Р.Г. Новый метод оценки качества упаковки трансмембранных α-спиральных доменов в белках. (2007). Биохимия Т. 72(3), 358–367 (DOI: 10.1134/S0006297907030066).
Polyansky A.A., Volynsky P.E., Efremov R.G. Computer simulations of membrane-lytic peptides: perspectives in drug design. (2007). J. Bioinform. & Comput. Biology 5, 611–626 (См. в пабмеде).
Pyrkov T.V., Kosinsky Yu.A., Arseniev A.S., Priestle J.P., Jacoby E., Efremov R.G. Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. (2007) Proteins: Structure, Function, and Bioinformatics 66(2), 388–398. См. в пабмеде.

2005—2006

Chugunov A.O., Chavatte P., Farce A., Efremov R.G. Differences in binding sites of two melatonin receptors help to explain their selectivity to some melatonin analogs: a molecular modeling study. (2006) J. Biomol. Struct. & Dynamics 24, 91-108. См. в пабмеде.
Косинский Ю.А., Пырков Т.В., Луценко С.В., Ефремов Р.Г. Предсказание структуры комплексов белок-лиганд: от компьютерной модели к биологической функции. (2006). Российский химический журнал Т. L, С. 36-44. See @ RChJ page.
Volynsky P.E., Bocharov E.V., Nolde D.E., Vereshaga Ya.A., Mayzel M.L., Mineev K.S., Mineeva E.A., Pustovalova Yu.E., Gagnidze I.A., Efremov R.G., Arseniev A.S. Solution of the spatial structure of dimeric transmembrane domains of proteins by heteronuclear NMR spectroscopy and molecular modeling. (2006) Biophysics (Russian). V. 51 Suppl. 1, S23–S27 (doi: 10.1134/S0006350906070050).
Dubovskii P.V., Volynsky P.E., Polyansky A.A., Chupin V.V., Efremov R.G., Arseniev A.S. Spatial structure and activity mechanism of a novel spider antimicrobial peptide. (2006). Biochemistry 45, 10759-10767. См. в пабмеде.
Efremov R.G., Vereshaga Y.A., Volynsky P.E., Nolde D.E., Arseniev A.S. Association of transmembrane helices: what determines assembling of a dimer? (2006) J. Comput. Aid. Mol. Design 20, 27-45. См. в пабмеде.
Dubovskii P.V., Lesovoy D.M., Dubinnyi M.A., Konshina A.G., Utkin Y.N., Efremov R.G., Arseniev A.S. Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins. (2005). Biochem. J. 387, Part 3, p. 807-815. См. в пабмеде.
Polyansky A.A., Volynsky P.E., Nolde D.E., Arseniev A.S., Efremov R.G. The Role of Lipid Charge in Organization of Water/Lipid Bilayer Interface: Insights via Computer Simulations. (2005). J. Phys. Chem. B, 109(31), p. 15052-15059. DOI:10.1021/jp0510185.
Vereshaga, Y.A., Volynsky P.E., Nolde D.E., Arseniev A.S., Efremov R.G. Helix interactions in membranes: lessons from unrestrained Monte Carlo simulations. (2005). J. Chem. Theory & Comput. 1(6), p. 1252-1264. DOI:10.1021/ct0501250.
Volynsky P.E., Polyansky A.A., Simakov N.A., Arseniev A.S., Efremov R.G. Effect of lipid composition on the «membrane response» induced by a fusion peptide. (2005). Biochemistry 44(44), p. 14626–14637. См. в пабмеде
Chugunov A., Chavatte P., Efremov R. Molecular modeling of human MT₁ and MT₂ melatonin receptors. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, p. 259-270. DOI: 10.1007/0-387-29455-4_26
Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. Computer simulations of anionic unsaturated lipid bilayer — a suitable model to study membrane interactions with a cell-penetrating peptide. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, p. 235-246. DOI: 10.1007/0-387-29455-4_24

2003—2004

Tsivkovskii R., Efremov R.G., Lutsenko S. The Role of Invariant His1069 in Folding and Function of the Wilson"s disease Protein, the Human Copper-transporting ATPase ATP7B. J. Biol. Chem. (2003). 278, 13302-8.
Konshina A.G., Volynsky P.E., Arseniev A.S., Efremov R.G. Interaction of Cardiotoxin A5 with Membrane: Role of Conformational Heterogeneity and Hydrophobic Properties. (2003). Russian J. Bioorg. Chem. 29(6), 523-533. DOI:10.1023/B:RUBI.0000008892.75272.ab.
Dioubankova N.N., Malakhov A.D., Stetsenko D.A., Gait M.J., Volynsky P.E., Efremov R.G., Korshun V.A. Pyrenemethyl ara-Uridine-2’-carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex. (2003) ChemBioChem 4:841-847. См. в пабмеде.
Polyansky A.A., Kosinsky Yu.A., Efremov R.G. Correlation of Local Changes in the Temperature-Dependent Conformational Flexibility of Thioredoxins with Their Thermostability. (2004). Russian J. Bioorg. Chem. 30(5), 421-430. DOI:10.1023/B:RUBI.0000043784.51859.41.
Efremov R.G., Nolde D.E., Konshina A.G., Syrtcev N.P., Arseniev A.S. Peptides and proteins in membranes: what can we learn via computer simulations? (2004) Curr. Med. Chem., 11(18), 2421-2442. См. в пабмеде.
Kosinsky Yu.A., Volynsky P.E., Lagant P., Vergoten G., Suzuki E., Arseniev A.S., Efremov R.G. Development of the Force Field Parameters for Phosphoimidazole and Phosphohistidine. (2004) J. Comput. Chem., 25(11), 1313-1321. См. в пабмеде.
Efremov, R. G., Kosinsky Yu.A., Nolde D.E., Tsivkovskii, R., Arseniev A.S., Lutsenko, S. Molecular Modeling of the Nucleotide-Binding Domain of the Wilson’s Disease Protein: Location of the ATP-binding Site, Domain Dynamics, and Potential Effects of the Major Disease Mutations. (2004) Biochem. J. 382, Part I, 293-305. DOI:10.1042/BJ20040326.
Morgan C.T., Tsivkovskii R., Kosinsky Yu.A., Efremov R.G., Lutsenko S. The Distinct Functional Properties of the Nucleotide-binding Domain of ATP7B, the Human Copper-transporting ATPase. Analysis of the Wilson disease mutations E1064A, H1069Q, R1151H, and C1104F. (2004) J. Biol. Chem. 279(35), 36363-36371. См. в пабмеде.
Efremov R.G., Nolde D.E., Volynsky P.E., Vereshaga Y.A., Simakov N.A., Polyansky A.A. Molecular modeling of membrane peptides and proteins. (2004). Fundametal and Clinical Pharmacology, 18, p. 594. DOI:10.1111/j.1472-8206.2004.00288.x.

2000—2002

Efremov R.G., Nolde D.E., Volynsky P.E., Arseniev A.S. Modeling of peptides in implicit membrane-mimetic media. Molecular Simulation (2000). 24, 275-291.
Kosinsky Yu.A., Dubovskii P.V., Nolde D.E., Arseniev A.S., Efremov R.G. Fusion peptide interaction with lipid bilayer: modeling with Monte Carlo simulation and continuum electrostatics calculation. Molecular Simulation (2000). 24, 341-349.
Nolde, D.E., P.E. Volynsky, A.S. Arseniev, and R.G. Efremov. Modeling of peptides and proteins in a membrane environment: I. A solvation model mimicking a lipid bilayer. Russian J. Bioorg. Chem. (2000) 26, 115-124. See @ medline.
Volynskii P.E., Nolde D.E., Arseniev A.S., Efremov R.G. Modeling of peptides and proteins in a membrane environment. II. Structural and energetic aspects of Glycophorin A in a lipid bilayer. Russian J. Bioorg. Chem. (2000) 26, 163-172. See @ medline.
Efremov R.G., Volynsky P.E., Nolde D.E., Arseniev A.S. Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimic media. Theor. Chem. Acc. (2001a). 106, 48-54. See @ Springer Link.
Efremov R.G., Volynsky P.E., Dauchez M.A.M., Nolde D.E., Arseniev A.S., Alix A.J.P. Assessment of conformation and energetics of the N-terminal part of elafin via computer simulations. Theor. Chem. Acc. (2001b). 106, 55-61. See @ Springer Link.
Efremov R.G., Volynsky P.E., Nolde D.E., Dubovskii P.V., Arseniev A.S. Interaction of cardiotoxins with membranes: a molecular modeling study. Biophys. J. (2002a). 83, 144-153. See @ medline.
Efremov R.G., Volynsky P.E., Nolde D.E., van Dalen A., de Kruijff B., Arseniev A.S. Monte Carlo simulations of voltage-driven translocation of a signal sequence. FEBS Lett. (2002b). 526, 97-100. See @ medline.
Shenkarev Z.O., Balashova T.A., Efremov R.G., Yakimenko Z.A., Ovchinnikova T.V., Raap J., Arseniev A.S. Spatial structure of Zervamicin IIB bound to DPC micelles. Implications for voltage-gating. Biophys. J. (2002). 82, 762-771. См. в пабмеде.
Abdullaev Z.Kh., Bodrova M.E., Chernyak B.V., Dolgikh D.A., Kluck R.M., Pereverzev M.O., Arseniev A.S., Efremov R.G., Kirpichnikov M.P., Mokhova E.N., Newmeyer D.D., Roder H., Skulachev V.P. A cytochrome c mutant of high electron transfer and antioxidant activities which is completely devoid apoptogenic effect. Biochem. J. (2002). 362, 749-754. См. в пабмеде.
Lutsenko S., Efremov R.G., Tsivkovskii R., Walker J.M. Human copper-transporting ATPase ATP7B (the Wilson’s disease protein): Biochemical properties and regulation. J. Bioenerg. Biomemb. (2002). 34 (5), 351-362. .

1990-е

Efremov R.G., Gulyaev D.I., Vergoten G., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. I. Hydrophobic properties of transmembrane segments of Na,K-ATPase. J. Protein Chemistry. (1992a). 11, 665-675. See @ medline.
Efremov R.G., Gulyaev D.I., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na,K-ATPase. J. Protein Chemistry. (1992b). 11, 699-708.
Modyanov N.N., Vladimirova N.M., Gulyaev D.I., Efremov R.G. Architecture of the Sodium Pump: vectorial labeling and computer modeling. Ann. New York Acad. Sci. (1992). 671, 134-146.
Efremov R.G., Alix A.J.P. Environmental characteristics of residues in proteins. J. Biomol. Struct. & Dynamics. (1993), 11, 483-507. See @ medline.
Efremov R.G., Gulyaev D.I., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. III. Modeling of intramembrane moiety of Na,K-ATPase. J. Protein Chemistry. (1993). 12, 143-152.
Efremov R.G., Vergoten G. The hydrophobic nature of membrane-spanning a-helices as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis. J. Physical Chemistry. (1995). 99, 10658-10666.
Golovanov A.P., Efremov R.G., Jaravine V.A., Vergoten G., Arseniev A.S. Amino acid residue: is it structural or functional? FEBS Lett. (1995), 375, 162-166. See @ medline.
Efremov R.G., Golovanov A.P., Vergoten G., Alix A.J.P., Tsetlin V.I., Arseniev A.S. Detailed assessment of spatial hydrophobic and electrostatic properties of 2D NMR-derived models of neurotoxin II. J. Biomol. Struct. & Dynamics. (1995), 12, 971-991.
Efremov R.G., Vergoten G. Hydrophobic organization of membrane helix bundle in bacteriorhodopsin. J. Protein Chemistry. (1996a). 15, 1, 63-76. See @ medline.
Efremov R.G., Vergoten G. Recognition of transmembrane a-helical segments with environmental profiles. Protein Engineering. (1996b). 9, 253-263. See @ Protein Engineering.
Nolde D.E., Arseniev A.S., Vergoten G., Efremov R.G. Atomic solvation parameters for protein in a membrane environment. Application to transmembrane a-helices. J. Biomol. Struct. & Dynamics. (1997). 15, p. 1-18. See @ medline.
Golovanov A.P., Efremov R.G., Jaravine V.A., Vergoten G., Kirpichnikov M.P., Arseniev A.S. A new method to characterize hydrophobic organization of proteins: Application to rational protein engineering of barnase. J. Biomol. Struct. & Dynamics. (1998). 15, 673-687. See @ medline.
Efremov R.G., Legret F., Vergoten G., Capron A., Bahr G.M., Arseniev A.S. Molecular modeling of HIV-1 coreceptor CCR5 and exploring of conformational space of its extracellular domain in molecular dynamics simulation. J. Biomol. Struct. & Dynamics. (1998). 16, 77-90.
Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. Peptides in membranes: assessment of the effects of environment via simulations with implicit solvation model. Theor. Chem. Acc. (1999a). 101, 170-174. See @ Springer Link.
Efremov R.G., Vergoten G., Arseniev A.S. A new "hydrophobic template" method detects segments forming transmembrane alpha-helical bundles in ion channels. Theor. Chem. Acc. (1999b). 101, 73-76. See @ Springer Link.
Efremov, R.G., Nolde, D.E., Vergoten G., Arseniev, A.S. A solvent model for simulations of peptides in bilayers. I. Testing on model systems. Biophys. J. (1999c). 76, 2448-2459. See @ Biophysical Journal.
Efremov, R.G., Nolde, D.E., Vergoten G., Arseniev, A.S. A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices. Biophys. J. (1999d). 76, 2460-2471. See @ Biophysical Journal.
Efremov R.G., Truong M.-J., Darcissac E.C.A., Zeng J., Grau O., Vergoten G., Debard C., Capron A., Bahr G.M. Human chemokine receptors CCR5, CCR3, and CCR2B share common polarity motif in the first extracellular loop with other human GPCRs: implications for HIV-1 coreceptor function. Eur. J. Biochem. (1999e). 263, 746-756. See @ EJB.
Efremov R.G., Nolde D.E., Volynsky P.E., Chernyavsky A.A., Dubovsky P.V., Arseniev A.S. Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin. FEBS Lett. (1999f). 462, 205-210. See @ Elsevier.
Golovanov A.P., Volynsky P.E., Ermakova S.B., Arseniev A.S. (1999). Protein Eng. 12, 31-40. См. в пабмеде.

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