Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides.

ABSTRACT: Reliability of force fields is an essential aspect of protein-folding simulation. In this work, we introduced a newly developed on-the-fly charge-updating scheme called the polarized structure-specific backbone charge (PSBC) model. The PSBC model was designed with the purpose of building the polarizability of backbone hydrogen bonds into the force field by updating the partial charges of backbone hydrogen-bond donor and acceptor atoms during folding simulation. This implementation was intended to mimic the heterogeneity of the protein surrounding during folding. Multiple single-trajectory molecular dynamics simulations were performed to fold a polyalanine peptide, namely ER (Ac-A(EAAAR)₃A-NH₂), using both polarizable (PSBC) and nonpolarizable (Amber03) force fields. T

SUBMITTER: Zhang D 

PROVIDER: S-EPMC6895711 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature