Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment

摘要

While several experimental techniques now exist for characterizing protein unfolded states, allatomnsimulation of unfolded states has been challenging due to the long time scales and conformationalnsampling required. We address this problem by using a combination of accelerated calculations on graphicsnprocessor units and distributed computing to simulate tens of thousands of molecular dynamics trajectoriesneach up to ∼10 μs (for a total aggregate simulation time of 127 ms). We used this approach in conjunctionnwith Trp-Cys contact quenching experiments to characterize the unfolded structure and dynamics of proteinnL. We employed a polymer theory method to make quantitative comparisons between high-temperaturensimulated and chemically denatured experimental ensembles and find that reaction-limited quenching ratesncalculated from simulation agree remarkably well with experiment. In both experiment and simulation, wenfind that unfolded-state intramolecular diffusion rates are very slow compared to highly denatured chainsnand that a single-residue mutation can significantly alter unfolded-state dynamics and structure. This worknsuggests a view of the unfolded state in which surprisingly low diffusion rates could limit folding and opensnthe door for all-atom molecular simulation to be a useful predictive tool for characterizing protein unfoldednstates along with experiments that directly measure intramolecular diffusion.