Thermodynamically important contacts in folding of model proteins

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Mar;63(3 Pt 1):032901. doi: 10.1103/PhysRevE.63.032901. Epub 2001 Feb 23.

Abstract

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acids / chemistry*
  • Binding Sites
  • Computer Simulation
  • Entropy
  • Models, Molecular*
  • Models, Statistical
  • Motion
  • Protein Binding
  • Protein Conformation
  • Protein Folding*
  • Proteins / chemistry*
  • Structure-Activity Relationship
  • Thermodynamics

Substances

  • Amino Acids
  • Proteins