A study of ab initio folding of chignolins using replica-exchange molecular dynamics simulations

Abstract

More and more studies have confirmed the importance of polarization effects in hydrogen bonding interactions in protein folding simulations. In this paper, a recently developed charge update scheme termed polarized structure-specific backbone charge (PSBC) model was applied to the folding of 10-residue chignolin. A comparison between simulations performed using PSBC and a nonpolarizable (AMBER99SB) force field demonstrably showed the importance of the electrostatic polarization effect in the folding of the short β-hairpin peptide by a series of analyses such as DSSP, free-energy landscape, hydrogen bond occupancy, and melting curve. The PSBC model was further validated by folding two other chignolin variants.