Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding

Phys Rev Lett. 2009 Feb 27;102(8):088103. doi: 10.1103/PhysRevLett.102.088103. Epub 2009 Feb 27.

Abstract

The Gaussian network model is used to derive the correlations between energy and residue fluctuations in native proteins. Residues are identified that respond strongly to energy fluctuations and that display correlations with the remaining residues of the protein at the highest modes. We postulate that these residues are located at specific sites for drug binding. We test the validity of this postulate on a data set of 33 structurally distinct proteins in the unbound state. Detailed results are presented for drug binding to the HIV protease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • HIV Protease / chemistry
  • HIV Protease / metabolism
  • HIV-1 / enzymology
  • Models, Chemical*
  • Models, Molecular
  • Normal Distribution
  • Protein Binding
  • Proteins / chemistry*
  • Proteins / metabolism
  • Thermodynamics

Substances

  • Proteins
  • HIV Protease