Nanotech 2002 Vol. 2
Nanotech 2002 Vol. 2
Technical Proceedings of the 2002 International Conference on Computational Nanoscience and Nanotechnology

Extended-Scale Atomistics Chapter 8

Kinetic Monte Carol Simulations of Protein Folding and Unfolding

Authors: D.E. Makarov and H. Metiu

Affilation: U.C. Santa Barbara, United States

Pages: 169 - 172

Keywords: protein folding, AFM, titin

We report here kinetic Monte Carlo (KMC) studies of two problems: (1) Unfolding of the protein titin under mechanical tension and (2) The formation of native contacts in the process of folding of small, single domain proteins. Both cases involve long time scales and cannot be directly addressed by molecular dynamics methods. In order to overcome this time scale problem we use a kinetic Monte Carlo method, in which elementary processes (such as the formation of a single native contact or dissociation of a hydrogen bond) are viewed as first order processes whose rates are calculated from a crude microscopic model. Our simulations explain the observed behavior in unfolding of titin when pulled by a force and the correlation between the folding rate of single domain protein and the number of contacts in the folded state.

ISBN: 0-9708275-6-3
Pages: 504