title: Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.
abstract: Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but transitions between protein conformational states sometimes take place on time scales that are infeasible or very expensive to reach by direct simulation. Enhanced sampling methods, the aim of which is to increase the sampling efficiency of MD simulations, have thus been extensively employed. The effectiveness of such methods when applied to complex biological systems like proteins, however, has been difficult to establish because even enhanced sampling simulations of such systems do not typically reach time scales at which convergence is extensive enough to reliably quantify sampling efficiency. Here, we obtain sufficiently converged simulations of three proteins to evaluate the performance of simulated tempering, a member of a widely used class of enhanced sampling methods that use elevated temperature to accelerate sampling. Simulated tempering simulations with individual lengths of up to 100 μs were compared to (previously published) conventional MD simulations with individual lengths of up to 1 ms. With two proteins, BPTI and ubiquitin, we evaluated the efficiency of sampling of conformational states near the native state, and for the third, the villin headpiece, we examined the rate of folding and unfolding. Our comparisons demonstrate that simulated tempering can consistently achieve a substantial sampling speedup of an order of magnitude or more relative to conventional MD.
authors: D. E. Shaw Research , New York, New York 10036, United States.
authors: Albert C
authors: AC
authors: Pan
authors: D. E. Shaw Research , New York, New York 10036, United States.
authors: Thomas M
authors: TM
authors: Weinreich
authors: D. E. Shaw Research , New York, New York 10036, United States.
authors: Stefano
authors: S
authors: Piana
authors: D. E. Shaw Research , New York, New York 10036, United States.|Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York 10032, United States.
authors: David E
authors: DE
authors: Shaw
mesh_terms: D007611:Aprotinin / Q000737:chemistry*; D008840:Microfilament Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: D008840:Microfilament Proteins; D025801:Ubiquitin; C026615:villin; D007611:Aprotinin