Biography Details
 
Dr. BEREZOVSKY Igor
Principal Investigator
 
Biography
 
Igor Berezovsky studied physics and biophysics in the Moscow Engineering Physics Institute (MSc, 1993) and obtained PhD in biophysics from the Moscow Institute of Physics and Technology (1997). Igor started his scientific career in the Engelhardt Institute of Molecular Biology (Moscow), where he conducted his MSc and PhD research, then worked as a research fellow (until 1998). He worked as a postdoctoral researcher at the Weizmann Institute of Science (1999-2002) and Harvard University (2003-2006). In 2007-2012 he was a senior scientist/group leader at the Bergen Center for Computational Science, University of Bergen (Norway), then visited the Weizmann Institute of Science in 2013. Igor joined Bioinformatics Institute in January 2014.
 
Selected Publications
 
  1. Berezovsky IN, Bastolla U.
    Editorial overview: Proteins: bridging theory and experiment.
    Curr Opin Struct Biol. 2017 Feb;42:viii-x. doi: 10.1016/j.sbi.2016.12.013. Epub 2017 Jan 10. No abstract available.


  2. Kurochkin IV, Guarnera E, Wong JH, Eisenhaber F, Berezovsky IN.
    Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides.
    Biochemistry. 2017 Jan 10;56(1):228-239. doi: 10.1021/acs.biochem.6b00783. Epub 2016 Dec 16.


  3. Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F.
    Protein function machinery: from basic structural units to modulation of activity.
    Curr Opin Struct Biol. 2017 Feb;42:67-74. doi: 10.1016/j.sbi.2016.10.021. Epub 2016 Nov 16. Review.


  4. Berezovsky IN, Guarnera E, Zheng Z.
    Basic units of protein structure, folding, and function.
    Prog Biophys Mol Biol. 2016 Sep 30. pii: S0079-6107(16)30086-4. doi: 10.1016/j.pbiomolbio.2016.09.009. [Epub ahead of print] Review.


  5. Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F.
    The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.
    Methods Mol Biol. 2016;1415:477-506. doi: 10.1007/978-1-4939-3572-7_25.


  6. Guarnera E, Berezovsky IN.
    Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.
    PLoS Comput Biol. 2016 Mar 3;12(3):e1004678. doi: 10.1371/journal.pcbi.1004678. eCollection 2016 Mar.


  7. Guarnera E, Berezovsky IN.
    Allosteric sites: remote control in regulation of protein activity.
    Curr Opin Struct Biol. 2016 Apr;37:1-8. doi: 10.1016/j.sbi.2015.10.004. Epub 2015 Nov 10. Review.


  8. Zheng Z, Goncearenco A, Berezovsky IN.
    Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions.
    Nucleic Acids Res. 2016 Jan 4;44(D1):D301-7. doi: 10.1093/nar/gkv1124. Epub 2015 Oct 26.


  9. Berezovsky IN, Zheng Z, Kurotani A, Tokmakov AA, Kurochkin IV.
    Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding.
    Protein Sci. 2015 Sep;24(9):1475-85. doi: 10.1002/pro.2735. Epub 2015 Jul 14.


  10. Goncearenco A, Berezovsky IN.
    Protein function from its emergence to diversity in contemporary proteins.
    Phys Biol. 2015 Jun 9;12(4):045002. doi: 10.1088/1478-3975/12/4/045002.


  11. Goncearenco A, Berezovsky IN.
    The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins.
    Biol Direct. 2014 Dec 12;9:29. doi: 10.1186/s13062-014-0029-2.


  12. Goncearenco A, Ma BG, Berezovsky IN.
    Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.
    Nucleic Acids Res. 2014 Mar;42(5):2879-92. doi: 10.1093/nar/gkt1336. Epub 2013 Dec 25.


  13. Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN.
    SPACER: Server for predicting allosteric communication and effects of regulation.
    Nucleic Acids Res. 2013 Jul;41(Web Server issue):W266-72. doi: 10.1093/nar/gkt460. Epub 2013 Jun 3.


  14. Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I.
    Unraveling hidden regulatory sites in structurally homologous metalloproteases.
    J Mol Biol. 2013 Jul 10;425(13):2330-46. doi: 10.1016/j.jmb.2013.04.009. Epub 2013 Apr 11.


  15. Berezovsky IN.
    Thermodynamics of allostery paves a way to allosteric drugs.
    Biochim Biophys Acta. 2013 May;1834(5):830-5. doi: 10.1016/j.bbapap.2013.01.024. Epub 2013 Feb 1. Review.


  16. Lasry I, Seo YA, Ityel H, Shalva N, Pode-Shakked B, Glaser F, Berman B, Berezovsky I, Goncearenco A, Klar A, Levy J, Anikster Y, Kelleher SL, Assaraf YG.
    A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency.
    J Biol Chem. 2012 Aug 24;287(35):29348-61. doi: 10.1074/jbc.M112.368159. Epub 2012 Jun 25.


  17. Goncearenco A, Berezovsky IN.
    Exploring the evolution of protein function in Archaea.
    BMC Evol Biol. 2012 May 30;12:75.


  18. Mitternacht S, Berezovsky IN.
    Coherent conformational degrees of freedom as a structural basis for allosteric communication.
    PLoS Comput Biol. 2011 Dec;7(12):e1002301. doi: 10.1371/journal.pcbi.1002301. Epub 2011 Dec 8.


  19. Mitternacht S, Berezovsky IN.
    Binding leverage as a molecular basis for allosteric regulation.
    PLoS Comput Biol. 2011 Sep;7(9):e1002148. doi: 10.1371/journal.pcbi.1002148. Epub 2011 Sep 15.


  20. Goncearenco A, Berezovsky IN.
    Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins.
    Bioinformatics. 2011 Sep 1;27(17):2368-75. doi: 10.1093/bioinformatics/btr396. Epub 2011 Jun 30.


  21. Berezovsky IN.
    The diversity of physical forces and mechanisms in intermolecular interactions.
    Phys Biol. 2011 Jun;8(3):035002. doi: 10.1088/1478-3975/8/3/035002. Epub 2011 May 13. Review.


  22. Mitternacht S, Berezovsky IN.
    A geometry-based generic predictor for catalytic and allosteric sites.
    Protein Eng Des Sel. 2011 Apr;24(4):405-9. doi: 10.1093/protein/gzq115. Epub 2010 Dec 15.


  23. Mitternacht S, Berezovsky IN.
    On the importance of amino acid sequence and spatial proximity of interacting residues for protein folding.
    J Biomol Struct Dyn. 2011 Feb;28(4):607-9; discussion 669-674. No abstract available.


  24. Ma BG, Berezovsky IN.
    The MBLOSUM: a server for deriving mutation targets and position-specific substitution rates.
    J Biomol Struct Dyn. 2010 Dec;28(3):415-9.


  25. Goncearenco A, Berezovsky IN.
    Prototypes of elementary functional loops unravel evolutionary connections between protein functions.
    Bioinformatics. 2010 Sep 15;26(18):i497-503. doi: 10.1093/bioinformatics/btq374.


  26. Ma BG, Goncearenco A, Berezovsky IN.
    Thermophilic adaptation of protein complexes inferred from proteomic homology modeling.
    Structure. 2010 Jul 14;18(7):819-28. doi: 10.1016/j.str.2010.04.004.


  27. Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN, Tawfik DS.
    Do viral proteins possess unique biophysical features?
    Trends Biochem Sci. 2009 Feb;34(2):53-9. doi: 10.1016/j.tibs.2008.10.009. Epub 2008 Dec 4.


  28. Berezovsky IN, Trifonov EN.
    Flowering buds of globular proteins: transpiring simplicity of protein organization.
    Comp Funct Genomics. 2002;3(6):525-34. doi: 10.1002/cfg.223.


  29. Koczyk G, Berezovsky IN.
    Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure.
    Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W239-45. doi: 10.1093/nar/gkn326. Epub 2008 May 23.


  30. Berezovsky IN, Zeldovich KB, Shakhnovich EI.
    Positive and negative design in stability and thermal adaptation of natural proteins.
    PLoS Comput Biol. 2007 Mar 23;3(3):e52. Epub 2007 Feb 1.


  31. Zeldovich KB, Berezovsky IN, Shakhnovich EI.
    Protein and DNA sequence determinants of thermophilic adaptation.
    PLoS Comput Biol. 2007 Jan 12;3(1):e5. Epub 2006 Nov 30.


  32. Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, Eisenhaber F.
    Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases.
    BMC Bioinformatics. 2006 Mar 21;7:164.


  33. Zeldovich KB, Berezovsky IN, Shakhnovich EI.
    Physical origins of protein superfamilies.
    J Mol Biol. 2006 Apr 7;357(4):1335-43. Epub 2006 Feb 6.


  34. Berezovsky IN, Chen WW, Choi PJ, Shakhnovich EI.
    Entropic stabilization of proteins and its proteomic consequences.
    PLoS Comput Biol. 2005 Sep;1(4):e47. Epub 2005 Sep 30.


  35. Berezovsky IN, Shakhnovich EI.
    Physics and evolution of thermophilic adaptation.
    Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12742-7. Epub 2005 Aug 24.


  36. Papandreou N, Berezovsky IN, Lopes A, Eliopoulos E, Chomilier J.
    Universal positions in globular proteins.
    Eur J Biochem. 2004 Dec;271(23-24):4762-8.


  37. Berezovsky IN, Kirzhner A, Kirzhner VM, Trifonov EN.
    Spelling protein structure.
    J Biomol Struct Dyn. 2003 Dec;21(3):327-39.


  38. Berezovsky IN, Kirzhner A, Kirzhner VM, Rosenfeld VR, Trifonov EN.
    Protein sequences yield a proteomic code.
    J Biomol Struct Dyn. 2003 Dec;21(3):317-25.


  39. Berezovsky IN.
    Discrete structure of van der Waals domains in globular proteins.
    Protein Eng. 2003 Mar;16(3):161-7.


  40. Berezovsky IN, Kirzhner VM, Kirzhner A, Rosenfeld VR, Trifonov EN.
    Closed loops: persistence of the protein chain returns.
    Protein Eng. 2002 Dec;15(12):955-7.


  41. Trifonov EN, Berezovsky IN.
    Evolutionary aspects of protein structure and folding.
    Curr Opin Struct Biol. 2003 Feb;13(1):110-4. Review.


  42. Berezovsky IN, Trifonov EN.
    Back to units of protein folding.
    J Biomol Struct Dyn. 2002 Dec;20(3):315-6.


  43. Trifonov E, Berezovsky I.
    Molecular evolution from abiotic scratch.
    FEBS Lett. 2002 Sep 11;527(1-3):1-4. Review.


  44. Berezovsky IN, Trifonov EN.
    Loop fold structure of proteins: resolution of Levinthas paradox.
    J Biomol Struct Dyn. 2002 Aug;20(1):5-6.


  45. Trifonov E, Berezovsky IN.
    [Proteomic code].
    Mol Biol (Mosk). 2002 Mar-Apr;36(2):315-9. Review. Russian.


  46. Berezovsky IN, Trifonov EN.
    Protein structure and folding: a new start.
    J Biomol Struct Dyn. 2001 Dec;19(3):397-403. Review.


  47. Berezovsky IN, Kirzhner VM, Kirzhner A, Trifonov EN.
    Protein folding: looping from hydrophobic nuclei.
    Proteins. 2001 Dec 1;45(4):346-50.


  48. Trifonov EN, Kirzhner A, Kirzhner VM, Berezovsky IN.
    Distinct stages of protein evolution as suggested by protein sequence analysis.
    J Mol Evol. 2001 Oct-Nov;53(4-5):394-401.


  49. Berezovsky IN, Trifonov EN.
    Loop fold nature of globular proteins.
    Protein Eng. 2001 Jun;14(6):403-7.


  50. Berezovsky IN, Trifonov EN.
    Van der Waals locks: loop-n-lock structure of globular proteins.
    J Mol Biol. 2001 Apr 13;307(5):1419-26.


  51. Berezovsky IN, Esipova NG, Tumanyan VG.
    Hierarchy of regions of amino acid sequence with respect to their role in the protein spatial structure.
    J Comput Biol. 2000 Feb-Apr;7(1-2):183-92.


  52. Berezovsky IN, Esipova NG, Tumanyan VG, Namiot VA.
    A new approach for the calculation of the energy of van der Waals interactions in macromolecules of globular proteins.
    J Biomol Struct Dyn. 2000 Apr;17(5):799-809.


  53. Berezovsky IN, Grosberg AY, Trifonov EN.
    Closed loops of nearly standard size: common basic element of protein structure.
    FEBS Lett. 2000 Jan 28;466(2-3):283-6.


  54. Berezovsky IN, Namiot VA, Tumanyan VG, Esipova NG.
    Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition.
    J Biomol Struct Dyn. 1999 Aug;17(1):133-55.


  55. Berezovsky IN, Kilosanidze GT, Tumanyan VG, Kisselev LL.
    Amino acid composition of protein termini are biased in different manners.
    Protein Eng. 1999 Jan;12(1):23-30.


  56. Berezovsky IN, Tumanyan VG, Esipova NG.
    Representation of amino acid sequences in terms of interaction energy in protein globules.
    FEBS Lett. 1997 Nov 24;418(1-2):43-6.


  57. Berezovsky IN, Kilosanidze GT, Tumanyan VG, Kisselev L.
    COOH-terminal decamers in proteins are non-random.
    FEBS Lett. 1997 Mar 10;404(2-3):140-2.


 

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