Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation.

ABSTRACT: Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the α-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures-corrections that capture many-body effects missing from an energy surface fitted to gas phase calculations on dipeptides. The experimental temperature de

SUBMITTER: Best RB 

PROVIDER: S-EPMC3433603 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature