Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.
The computational sampling of rare, large-scale, conformational transitions in proteins is a well appreciated challenge-for which a number of potentially efficient path-sampling methodologies have been proposed. Here, we study a large-scale transition in a united-residue model of calmodulin using the "weighted ensemble" (WE) approach of Huber and Kim. Because of the model's relative simplicity, we are able to compare our results with brute-force simulations. The comparison indicates that the WE approach quantitatively reproduces the brute-force results, as assessed by considering (i) the reaction rate, (ii) the distribution of event durations, and (iii) structural distributions describing the heterogeneity of the paths. Importantly, the WE method is readily applied to more chemically accurate models, and by studying a series of lower temperatures, our results suggest that the WE method can increase efficiency by orders of magnitude in more challenging systems.
Zhang
Bin W
BW
Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Jasnow
David
D
Zuckerman
Daniel M
DM
D002147:Calmodulin / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation
D002147:Calmodulin