Allostery in a coarse-grained model of protein dynamics

Phys Rev Lett. 2005 Nov 4;95(19):198103. doi: 10.1103/PhysRevLett.95.198103. Epub 2005 Nov 2.

Abstract

We propose a criterion for optimal parameter selection in coarse-grained models of proteins and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM disagrees with the bimodal distribution obtained from an all-atom model; however, the bimodal distribution is recovered by strengthening interactions between atoms that are backbone neighbors. We use the backbone-enhanced model to analyze allosteric mechanisms of trypsinogen and find relatively strong communication between the regulatory and active sites.

Publication types

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

MeSH terms

  • Algorithms
  • Animals
  • Carbon / chemistry
  • Cattle
  • Elasticity
  • Energy Transfer
  • Models, Molecular
  • Models, Statistical
  • Pressure
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / physiology*
  • Trypsinogen / chemistry

Substances

  • Proteins
  • Carbon
  • Trypsinogen