Roman G Efremov

Summary

Country: Russia

Publications

  1. ncbi request reprint Monte Carlo simulations of voltage-driven translocation of a signal sequence
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    FEBS Lett 526:97-100. 2002
  2. ncbi request reprint Peptides and proteins in membranes: what can we learn via computer simulations?
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Curr Med Chem 11:2421-42. 2004
  3. pmc Snake cytotoxins bind to membranes via interactions with phosphatidylserine head groups of lipids
    Anastasia G Konshina
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 6:e19064. 2011
  4. ncbi request reprint Human chemokine receptors CCR5, CCR3 and CCR2B share common polarity motif in the first extracellular loop with other human G-protein coupled receptors implications for HIV-1 coreceptor function
    R Efremov
    M M Shemyakin, Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Eur J Biochem 263:746-56. 1999
  5. pmc Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: location of the ATP-binding site, domain dynamics and potential effects of the major disease mutations
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Biochem J 382:293-305. 2004
  6. ncbi request reprint Molecular lipophilicity in protein modeling and drug design
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Curr Med Chem 14:393-415. 2007
  7. pmc Interaction of cardiotoxins with membranes: a molecular modeling study
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow V 437, 117997 GSP, Russia
    Biophys J 83:144-53. 2002
  8. ncbi request reprint Association of transmembrane helices: what determines assembling of a dimer?
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, V 437, 117997 GSP, Moscow, Russia
    J Comput Aided Mol Des 20:27-45. 2006
  9. ncbi request reprint The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    J Biomol Struct Dyn 25:195-205. 2007
  10. ncbi request reprint Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, V 437, 117871 GSP, Moscow, Russia
    FEBS Lett 462:205-10. 1999

Collaborators

Detail Information

Publications60

  1. ncbi request reprint Monte Carlo simulations of voltage-driven translocation of a signal sequence
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    FEBS Lett 526:97-100. 2002
    ..From these results it is concluded that the membrane potential stabilizes the transmembrane orientation of a signal sequence, explaining the membrane potential dependence of preprotein translocation...
  2. ncbi request reprint Peptides and proteins in membranes: what can we learn via computer simulations?
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Curr Med Chem 11:2421-42. 2004
    ..The approximations and shortcomings of the models, along with their perspectives in design of new membrane active drugs, are discussed...
  3. pmc Snake cytotoxins bind to membranes via interactions with phosphatidylserine head groups of lipids
    Anastasia G Konshina
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 6:e19064. 2011
    ..This feature together with the diverse binding affinities of the sites to a wide variety of anionic targets on the membrane surface appears to be functionally meaningful and may adjust CT action against different types of cells...
  4. ncbi request reprint Human chemokine receptors CCR5, CCR3 and CCR2B share common polarity motif in the first extracellular loop with other human G-protein coupled receptors implications for HIV-1 coreceptor function
    R Efremov
    M M Shemyakin, Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Eur J Biochem 263:746-56. 1999
    ..The potential biological significance of the identified structural motif shared by the human CCR5, CCR3, CCR2B and other GPCRs is discussed...
  5. pmc Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: location of the ATP-binding site, domain dynamics and potential effects of the major disease mutations
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Biochem J 382:293-305. 2004
    ..This may be achieved after relative domain motions of the 'closure' type observed in molecular dynamics simulations. The results provide a framework for analysis of disease mutations and for future mutagenesis studies...
  6. ncbi request reprint Molecular lipophilicity in protein modeling and drug design
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Curr Med Chem 14:393-415. 2007
    ....
  7. pmc Interaction of cardiotoxins with membranes: a molecular modeling study
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow V 437, 117997 GSP, Russia
    Biophys J 83:144-53. 2002
    ..Accomplished with our previous simulations of membrane alpha-helices, the computational method may be used to study partitioning of proteins with diverse folds into lipid bilayers...
  8. ncbi request reprint Association of transmembrane helices: what determines assembling of a dimer?
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, V 437, 117997 GSP, Moscow, Russia
    J Comput Aided Mol Des 20:27-45. 2006
    ..The computational approach permits efficient prediction of TM helical oligomers based solely on the sequences of interacting peptides...
  9. ncbi request reprint The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    J Biomol Struct Dyn 25:195-205. 2007
    ..The modeling results agree well with experimental data and provide a strategy to delineate fusogenic regions in amino acid sequences of viral proteins...
  10. ncbi request reprint Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, V 437, 117871 GSP, Moscow, Russia
    FEBS Lett 462:205-10. 1999
    ..The conclusion was reached that these factors are among the most important for the specific destabilization of a bilayer, which is followed by membrane fusion...
  11. pmc A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117871 GSP, Russia
    Biophys J 76:2460-71. 1999
    ....
  12. pmc A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117871 GSP, Russia
    Biophys J 76:2448-59. 1999
    ..Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed...
  13. ncbi request reprint Molecular modeling of HIV-1 coreceptor CCR5 and exploring of conformational space of its extracellular domain in molecular dynamics simulation
    R G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP, Moscow
    J Biomol Struct Dyn 16:77-90. 1998
    ..Perspectives of rational alteration of virus-binding activity of CCR5 are discussed...
  14. doi request reprint Adaptation of a membrane-active peptide to heterogeneous environment. I. Structural plasticity of the peptide
    Anton A Polyansky
    Russian Academy of Sciences, Moscow, 117997, Russia
    J Phys Chem B 113:1107-19. 2009
    ..The latter effect is much more pronounced in anionic bilayers and might be related to the initial stage of peptide-induced destabilization of lipid bilayers...
  15. pmc Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1
    Eduard V Bocharov
    Division of Structural Biology, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow 117997, Russia
    J Biol Chem 283:29385-95. 2008
    ..This makes the EphA1 receptor unique among the Eph family, implying its possible physiological role as an "extracellular pH sensor," and can have relevant physiological implications...
  16. pmc Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases
    Eduard V Bocharov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
    Biophys J 98:881-9. 2010
    ..A possible role of membrane lipid rafts in relation to Eph transmembrane domain oligomerization and Eph signal transduction was also discussed...
  17. doi request reprint Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state
    Eduard V Bocharov
    Division of Structural Biology, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ulitsa Miklukho Maklaya 16 10, Moscow 117997, Russia
    J Biol Chem 283:6950-6. 2008
    ..ErbB2 transmembrane segments associate in a right-handed alpha-helical bundle through the N-terminal tandem GG4-like motif Thr652-X3-Ser656-X3-Gly660, providing an explanation for the pathogenic power of some oncogenic mutations...
  18. pmc Specific membrane binding of neurotoxin II can facilitate its delivery to acetylcholine receptor
    Dmitry M Lesovoy
    Division of Structural Biology, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
    Biophys J 97:2089-97. 2009
    ....
  19. ncbi request reprint Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions
    Timothy V Pyrkov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    Proteins 66:388-98. 2007
    ....
  20. pmc Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins
    Peter V Dubovskii
    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16 10 Miklukho Maklaya str, V 437, Moscow 117997, Russia
    Biochem J 387:807-15. 2005
    ..These results clearly demonstrate that the P-type cytotoxins interact with membranes stronger than those of the S-type, although the mode of the membrane insertion is similar for both the types...
  21. doi request reprint Adaptation of a membrane-active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface
    Anton A Polyansky
    Russian Academy of Sciences, Moscow, 117997, Russia
    J Phys Chem B 113:1120-6. 2009
    ....
  22. doi request reprint Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity
    Peter V Dubovskii
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, 16 10 Miklukho Maklaya str, Moscow 117997, Russia
    Biochemistry 47:3525-33. 2008
    ..The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane...
  23. ncbi request reprint Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study
    Yana A Vereshaga
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow V 437, 117997 GSP, Russia
    Proteins 69:309-25. 2007
    ..This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions...
  24. ncbi request reprint Effect of lipid composition on the "membrane response" induced by a fusion peptide
    Pavel E Volynsky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
    Biochemistry 44:14626-37. 2005
    ..Implications of the observed effects to molecular events on initial stages of membrane destabilization induced by fusion peptides are discussed...
  25. ncbi request reprint PREDDIMER: a web server for prediction of transmembrane helical dimers
    Anton A Polyansky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Max F Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, Vienna AT 1030, Austria and Moscow Institute of Physics and Technology State University, Dolgoprudny, Moscow Region 141700, Russia
    Bioinformatics 30:889-90. 2014
    ....
  26. doi request reprint Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact
    Darya V Pyrkova
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow, 117997, Russia
    J Biomol Struct Dyn 31:87-95. 2013
    ..Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell...
  27. pmc Modular organization of α-toxins from scorpion venom mirrors domain structure of their targets, sodium channels
    Anton O Chugunov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
    J Biol Chem 288:19014-27. 2013
    ..In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Na(v)s...
  28. ncbi request reprint Recent advances in computational modeling of α-helical membrane-active peptides
    Anton A Polyansky
    M M Shemyakin and Yu A OvchinnikovInstitute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Curr Protein Pept Sci 13:644-57. 2012
    ..Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities...
  29. doi request reprint Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit
    Valeriy G Ostapchenko
    Laboratory of Protein Bioengineering, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
    J Biomol Struct Dyn 30:62-73. 2012
    ..Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles...
  30. doi request reprint PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
    Timothy V Pyrkov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    Bioinformatics 25:1201-2. 2009
    ..g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP)...
  31. ncbi request reprint Docking of ATP to Ca-ATPase: considering protein domain motions
    Timothy V Pyrkov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    J Chem Inf Model 47:1171-81. 2007
    ..The performance of this ligand-specific scoring function was considerably better than that of a standard scoring function used in the docking algorithm...
  32. ncbi request reprint Computer simulations of membrane-lytic peptides: perspectives in drug design
    Anton A Polyansky
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 16 10 Miklukho Maklaya str, Moscow, 117997, Russia
    J Bioinform Comput Biol 5:611-26. 2007
    ..Results of MD simulations of Ltc2a in model membranes were used to develop a number of its analogs with predefined activity...
  33. pmc Structure elucidation of dimeric transmembrane domains of bitopic proteins
    Eduard V Bocharov
    Division of Structural Biology, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
    Cell Adh Migr 4:284-98. 2010
    ..These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism...
  34. doi request reprint Structural, dynamic, and functional aspects of helix association in membranes: a computational view
    Anton A Polyansky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Adv Protein Chem Struct Biol 83:129-61. 2011
    ..Limitations and shortcomings of the methods, along with their perspectives in design of new membrane active agents, are discussed...
  35. ncbi request reprint Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger
    Eduard V Bocharov
    Laboratory of Structural Biology, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow 117997, Russia
    J Biol Chem 282:16256-66. 2007
    ..A possible biological implication of the findings in relation to triggering necrosis-like cell death by BNip3 is discussed...
  36. ncbi request reprint Method to assess packing quality of transmembrane alpha-helices in proteins. 2. Validation by "correct vs misleading" test
    Anton O Chugunov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho Maklaya 16 10, GSP Moscow 117997, Russia
    J Chem Inf Model 47:1163-70. 2007
    ..We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs...
  37. ncbi request reprint Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations
    Nikolay A Krylov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow 117997, Russia
    ACS Nano 7:9428-42. 2013
    ..The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed. ..
  38. ncbi request reprint Method to assess packing quality of transmembrane alpha-helices in proteins. 1. Parametrization using structural data
    Anton O Chugunov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho Maklaya 16 10, GSP Moscow 117997, Russia
    J Chem Inf Model 47:1150-62. 2007
    ..We assume that the developed "membrane score" method will be helpful in optimizing computer models of TM domains of MPs, especially G-protein coupled receptors...
  39. ncbi request reprint Development of the force field parameters for phosphoimidazole and phosphohistidine
    Yuri A Kosinsky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    J Comput Chem 25:1313-21. 2004
    ..Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent...
  40. doi request reprint N-terminal amphipathic helix as a trigger of hemolytic activity in antimicrobial peptides: a case study in latarcins
    Anton A Polyansky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russsian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    FEBS Lett 583:2425-8. 2009
    ..A proof of concept is gained through engineering specific mutations that resulted in elimination of the hemolytic activity of AMPs (latarcins) while leaving the beneficial antimicrobial effect intact...
  41. ncbi request reprint Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations
    Anton A Polyansky
    Department of Bioengineering, Biological Faculty, M V Lomonosov Moscow State University, Moscow 119992, Russia
    J Phys Chem B 109:15052-9. 2005
    ..This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers...
  42. doi request reprint Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor
    V N Novoseletsky
    MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, Moscow V 437, Russia
    SAR QSAR Environ Res 21:37-55. 2010
    ..8) with experimental data...
  43. doi request reprint Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane alpha-helical dimers: ephrin receptor A1
    P E Volynsky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Ul, Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    Phys Biol 7:16014. 2010
    ..The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins...
  44. pmc Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating
    Z O Shenkarev
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
    Biophys J 82:762-71. 2002
    ..The results are discussed in a context of voltage-driven peptaibol insertion into membrane...
  45. ncbi request reprint [Interaction of cardiotoxin A5 with a membrane: role of conformational heterogeneity and hydrophilic properties]
    A G Konshina
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho Maklaya 16 10, GSP Moscow, 117997 Russia
    Bioorg Khim 29:577-88. 2003
    ..The English version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol. 29, no. 6; see also http://www.maik.ru...
  46. doi request reprint Ligand-specific scoring functions: improved ranking of docking solutions
    T V Pyrkov
    MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    SAR QSAR Environ Res 19:91-9. 2008
    ..The proposed method was then tested on the results of docking obtained for an additional 70 complexes. In both cases the success rate was 5-8% better compared to the standard functions implemented in popular docking software...
  47. ncbi request reprint Differences in binding sites of two melatonin receptors help to explain their selectivity to some melatonin analogs: a molecular modeling study
    Anton O Chugunov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho Maklaya 16 10, GSP Moscow, 117997, Russia
    J Biomol Struct Dyn 24:91-107. 2006
    ..The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed...
  48. doi request reprint Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3
    Pavel E Volynsky
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
    J Am Chem Soc 135:8105-8. 2013
    ..Results of our simulations provide novel atomistic prospective of the role of G380 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor. ..
  49. ncbi request reprint Structure and dynamics of cardiotoxins
    Anastasia G Konshina
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16 10 Miklukho Maklaya str, 117997 GSP, Moscow V 437, Russia
    Curr Protein Pept Sci 13:570-84. 2012
    ..The present review summarizes experimental and computational data on the spatial organization of CTs and their dynamics in various environments (aqueous solution, membranous milieus)...
  50. pmc A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1
    Leonid V Aseev
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
    J Bacteriol 195:95-104. 2013
    ..Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation...
  51. ncbi request reprint Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method
    Anna D Koromyslova
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
    J Chem Inf Model 54:1189-99. 2014
    ..We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins...
  52. doi request reprint The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution
    Alexander A Lashkov
    A V Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Prospect, 119333 Moscow, Russia
    Acta Crystallogr D Biol Crystallogr 66:51-60. 2010
    ..The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI...
  53. doi request reprint Linker and/or transmembrane regions of influenza A/Group-1, A/Group-2, and type B virus hemagglutinins are packed differently within trimers
    Larisa V Kordyukova
    Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
    Biochim Biophys Acta 1808:1843-54. 2011
    ....
  54. ncbi request reprint A new method to characterize hydrophobic organization of proteins: application to rational protein engineering of barnase
    A P Golovanov
    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
    J Biomol Struct Dyn 15:673-87. 1998
    ..The other of predicted mutations were not studied experimentally yet. Several new mutations of barnase and barstar are also proposed to enhance the hydrophobic interactions on their binding interface...
  55. ncbi request reprint A novel method for packing quality assessment of transmembrane alpha-helical domains in proteins
    A O Chugunov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Biochemistry (Mosc) 72:293-300. 2007
    ..The developed "membrane scoring function" will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors...
  56. ncbi request reprint 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
    Clinton T Morgan
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239 3098, USA
    J Biol Chem 279:36363-71. 2004
    ..Together, the results directly demonstrate the phenotypic diversity of WD mutations within the N-domain and indicate that the nucleotide-binding properties of the P(1)-ATPases are distinct from those of the P(2)-ATPases...
  57. pmc A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect
    Ziedulla Kh Abdullaev
    Laboratory of Spectral Analysis, M M Shemyakin and Y A Ovchinnikov Institute of Bioorganic Chemistry, Moscow 177871, Russia
    Biochem J 362:749-54. 2002
    ....
  58. ncbi request reprint The role of the invariant His-1069 in folding and function of the Wilson's disease protein, the human copper-transporting ATPase ATP7B
    Ruslan Tsivkovskii
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, USA
    J Biol Chem 278:13302-8. 2003
    ..We conclude that His-1069 is responsible for proper orientation of ATP in the catalytic site of WNDP prior to ATP hydrolysis...
  59. ncbi request reprint Human copper-transporting ATPase ATP7B (the Wilson's disease protein): biochemical properties and regulation
    Svetlana Lutsenko
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97201, USA
    J Bioenerg Biomembr 34:351-62. 2002
    ..In addition, we speculate on how copper binding may regulate the activity and intracellular distribution of WNDP, and what role the human copper chaperone Atox1 may play in these processes...
  60. ncbi request reprint Spatial structure and activity mechanism of a novel spider antimicrobial peptide
    Peter V Dubovskii
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, 16 10 Miklukho Maklaya str, Moscow, 117997 Russia
    Biochemistry 45:10759-67. 2006
    ..The approach we suggested may be useful in studying not only other latarcins but also a wider class of membrane-active peptides...