Folding-unfolding transition in the mini-protein villin headpiece (HP35): An equilibrium study using the Wang-Landau algorithm

摘要

A computational study, using the Wang-Landau algorithm, is carried out for the 35 residue mini-protein villin headpiece (HP35) to investigate some equilibrium aspects of its folding-unfolding transition in water. The force field used is ECEPP/3 and a solvent-accessible surface area method is used to describe the interaction with water. The density of states and the conditional probabilities of some physically interesting geometrical descriptors of the molecule at various energies are calculated by analyzing the high-statistics data generated by the simulations. All canonical ensemble averages are subsequently calculated by using these data. The computed quantities include specific heat, radius of gyration, number of native contacts, number of helical residues and the potential of mean force for three pairs of geometric descriptors. High precision and a systematic check on the convergence of the computation are the two key points of our methodology. (C) 2016 Elsevier B.V. All rights reserved.