Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

ABSTRACT: Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A

SUBMITTER: Best RB 

PROVIDER: S-EPMC3115786 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature