Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.

ABSTRACT: A recent report of (3)J(HNHα) scalar coupling constants for hundreds of two-residue peptides has provided an important opportunity to test simulation force fields for proteins. Here, we compare the abilities of three derivatives of the Amber ff99SB force field to reproduce these data. We report molecular dynamics (MD) simulations of 256 two-residue peptides and show that the recently developed residue-specific force field (RSFF2) produces a dramatic improvement in the agreement with experimental (3)J(HNHα) coupling constants. We further show that RSFF2 also appears to produce a modest improvement in reproducing the (3)J(HNHα) coupling constants of five model proteins. Perhaps surprisingly, an analysis of neighboring residue effects (NREs) on the (3)J(HNHα) coupling constants of the two-res

SUBMITTER: Li S 

PROVIDER: S-EPMC4657862 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature