From laws of inference to protein folding dynamics

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Aug;82(2 Pt 1):021914. doi: 10.1103/PhysRevE.82.021914. Epub 2010 Aug 18.

Abstract

Protein folding dynamics is one of major issues constantly investigated in the study of protein functions. The molecular dynamic (MD) simulation with the replica exchange method (REM) is a common theoretical approach considered. Yet a trade-off in applying the REM is that the dynamics toward the native configuration in the simulations seems lost. In this work, we show that given REM-MD simulation results, protein folding dynamics can be directly derived from laws of inference. The applicability of the resulting approach, the entropic folding dynamics, is illustrated by investigating a well-studied Trp-cage peptide. Our results are qualitatively comparable with those from other studies. The current studies suggest that the incorporation of laws of inference and physics brings in a comprehensive perspective on exploring the protein folding dynamics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Protein Folding
  • Proteins / chemistry*
  • Proteins / ultrastructure*

Substances

  • Proteins