title: Assessing the Accuracy of Two Enhanced Sampling Methods Using EGFR Kinase Transition Pathways: The Influence of Collective Variable Choice.
abstract: Structurally elucidating transition pathways between protein conformations gives deep mechanistic insight into protein behavior but is typically difficult. Unbiased molecular dynamics (MD) simulations provide one solution, but their computational expense is often prohibitive, motivating the development of enhanced sampling methods that accelerate conformational changes in a given direction, embodied in a collective variable. The accuracy of such methods is unclear for complex protein transitions, because obtaining unbiased MD data for comparison is difficult. Here, we use long-time scale, unbiased MD simulations of epidermal growth factor receptor kinase deactivation as a complex biological test case for two widely used methods-steered molecular dynamics (SMD) and the string method. We found that common collective variable choices, based on the root-mean-square deviation (RMSD) of the entire protein, prevented the methods from producing accurate paths, even in SMD simulations on the time scale of the unbiased transition. Using collective variables based on the RMSD of the region of the protein known to be important for the conformational change, however, enabled both methods to provide a more accurate description of the pathway in a fraction of the simulation time required to observe the unbiased transition.
authors.affiliation: D. E. Shaw Research, New York, New York 10036, United States.
authors.forename: Albert C
authors.initials: AC
authors.lastname: Pan
authors.affiliation: D. E. Shaw Research, New York, New York 10036, United States.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Weinreich
authors.affiliation: D. E. Shaw Research, New York, New York 10036, United States.
authors.forename: Yibing
authors.initials: Y
authors.lastname: Shan
authors.affiliation: D. E. Shaw Research, New York, New York 10036, United States.
authors.forename: Daniele P
authors.initials: DP
authors.lastname: Scarpazza
authors.affiliation: 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.forename: David E
authors.initials: DE
authors.lastname: Shaw