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.