Residue-specific α-helix propensities from molecular simulation.

ABSTRACT: Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w and Amber ff99SB(∗). Encouragingly, we find that the overall helix propensity of many residues is captured well by both energy functions, with Amber ff99SB(∗) being more accurate. Nonetheless, there are some residues that deviate considerably from experiment, which can be attributed to two aspects of the energy function: i), variations of the charge model used to determine the atomic partial charges, with residues whose backbone charges differ most from alanine tending to hav

SUBMITTER: Best RB 

PROVIDER: S-EPMC3309278 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature