Protein folding pathways from replica exchange simulations and a kinetic network model

Proc Natl Acad Sci U S A. 2005 May 10;102(19):6801-6. doi: 10.1073/pnas.0408970102. Epub 2005 Mar 30.

Abstract

We present an approach to the study of protein folding that uses the combined power of replica exchange simulations and a network model for the kinetics. We carry out replica exchange simulations to generate a large ( approximately 10(6)) set of states with an all-atom effective potential function and construct a kinetic model for folding, using an ansatz that allows kinetic transitions between states based on structural similarity. We use this network to perform random walks in the state space and examine the overall network structure. Results are presented for the C-terminal peptide from the B1 domain of protein G. The kinetics is two-state after small temperature perturbations. However, the coil-to-hairpin folding is dominated by pathways that visit metastable helical conformations. We propose possible mechanisms for the alpha-helix/beta-hairpin interconversion.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Biophysics / methods*
  • Computer Simulation
  • Hydrogen Bonding
  • Kinetics
  • Models, Chemical
  • Models, Molecular
  • Molecular Structure
  • Monte Carlo Method
  • Peptides / chemistry
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Temperature
  • Thermodynamics
  • Time Factors

Substances

  • Peptides