Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables

Phys Rev Lett. 2013 Mar 8;110(10):108106. doi: 10.1103/PhysRevLett.110.108106. Epub 2013 Mar 8.

Abstract

Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Models, Chemical*
  • Models, Molecular
  • Peptides / chemistry*
  • Protein Folding
  • Protein Structure, Secondary
  • Thermodynamics

Substances

  • Peptides
  • Trp-cage peptide