Density of states simulations of proteins

Abstract

A modified version of a recently introduced algorithm that calculates density of states by performing a random walk in energy space has been proposed and implemented to study protein folding in a continuum. A united atom representation and the CHARMM19 [B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983)] force field are employed for these simulations. This method permits estimation of the density of states of a protein via a random walk in the energy space, thereby allowing the system to escape from local free-energy minima with relative ease. Unlike the earlier formulation that showed slow convergence for continuum simulations, this methodology is designed to achieve better sampling and faster convergence. The modified method is used to examine folding transitions of two peptides: deca-alanine and Met-enkephalin. Protein folding both with and without an implicit solvent (solvent accessible surface area model) has been studied to validate the usefulness of the proposed algorithm.