Berezovsky group

Computational biophysics is currently at an exciting stage when rapid growth of genomic data is coupled with achievements in comprehensive coverage of individual protein structures, single-molecule experiments, and analysis of complex structures. Advances in experimental techniques have led to the integration of structural information gathered at different levels of the biological hierarchy into a common framework. At the same time, one frequently encounters molecular phenomena and interactions between molecular entities that are still poorly described by existing theoretical models. Our research will be focused on the development of new physical models and computational approaches to investigating protein stability and adaptation, protein-protein interactions, and evolution of protein function.

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Representative publications:

• Berezovsky, I.N., Zeldovich, K.B. & Shakhnovich, E.I. 2007. Positive and negative design in stability and thermal adaptation of natural proteins.
  PLoS Comp. Biol. 3, e52. PDF
• Berezovsky, I.N. & Shakhnovich, E.I. 2005. Physics and evolution of thermophilic adaptation. PNAS USA 102, 12742-12747. PDF
• Berezovsky, I.N. 2003. Discrete structure of van der Waals domains in globular proteins. Protein Engineering 16, 161-167. PDF
• Trifonov, E.N. & Berezovsky, I.N. 2003. Evolutionary aspects of protein structure and folding. Curr. Opin. Struct. Biol. 13, 110-114.PDF
• Berezovsky, I.N. & Trifonov, E.N. 2001. Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol. 307, 1419-1426. PDF
• Berezovsky, I.N., Grosberg, A.Y. & Trifonov, E.N. 2000. Closed loops of nearly standard size: common basic element of protein structure. FEBS Letters 466, 283-286. PDF
• Berezovsky, I.N., Esipova, N.G., Tumanyan, V.G. & Namiot, V.A. 2000. A
  new approach for the calculation of the energy of van der Waals interactions
  in macromolecules of globular proteins. JBSD 17, 799-809. PDF