Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.

ABSTRACT: While several experimental techniques now exist for characterizing protein unfolded states, all-atom simulation of unfolded states has been challenging due to the long time scales and conformational sampling required. We address this problem by using a combination of accelerated calculations on graphics processor units and distributed computing to simulate tens of thousands of molecular dynamics trajectories each up to approximately 10 mus (for a total aggregate simulation time of 127 ms). We used this approach in conjunction with Trp-Cys contact quenching experiments to characterize the unfolded structure and dynamics of protein L. We employed a polymer theory method to make quantitative comparisons between high-temperature simulated and chemically denatured experimental ensembles and fin

SUBMITTER: Voelz VA 

PROVIDER: S-EPMC2853762 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature