Application of the polarized structure-specific backbone charge scheme on the folding of Beta3s

Abstract

In this paper, a successful folding simulation was carried out for a three-stranded β-sheet, namely Beta3s, with an accurate prediction of experimental NOE distances. The simulation shows clearly that the inclusion of polarization effects in the backbone hydrogen bonding interactions based on the polarized structure-specific backbone charge (PSBC) model during folding simulation can effectively stabilize the obtained three-stranded anti-parallel β-sheet, which was supported by a series analyses such as DSSP, hydrogen bond distance profile and free-energy landscapes.