Folding time predictions from all-atom replica exchange simulations

J Mol Biol. 2007 Sep 21;372(3):756-63. doi: 10.1016/j.jmb.2007.07.010. Epub 2007 Jul 17.

Abstract

We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models.

Publication types

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

MeSH terms

  • Computer Simulation*
  • Diffusion
  • GTP-Binding Proteins / chemistry
  • GTP-Binding Proteins / metabolism
  • Hydrogen Bonding
  • Protein Folding*
  • Protein Structure, Secondary
  • Temperature
  • Time Factors

Substances

  • GTP-Binding Proteins