An accurate description of the rate of formation of alpha helices and beta hairpins is important for obtaining the correct rate and mechanism of protein folding in molecular simulations. We use all-atom molecular simulations to study the kinetics of secondary structure formation. For a model alpha helical peptide, we determine a temperature-dependent master equation from replica exchange simulations. This allows us to determine rates for elementary processes in helix formation (nucleation and elongation), and to simulate temperature-jump experiments. As a model beta hairpin we use the C-terminal hairpin of protein GB1. By analyzing folding transition paths, we determine that the mechanism is compatible with what had been experimentally proposed. Timescales for folding and unfolding are within an order of magnitude of experiment at 300 K, however we find a strong dependence of folding rates on initial conditions, which we explain using a coarse-grained master equation for the dynamics.

Elementary time scales for protein folding: Simulation vs. experiment

243rd National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.