title: The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.
abstract: We describe molecular dynamics simulations resulting in the folding the Fip35 Hpin1 WW domain. The simulations were run on a distributed set of graphics processors, which are capable of providing up to two orders of magnitude faster computation than conventional processors. Using the Folding@home distributed computing system, we generated thousands of independent trajectories in an implicit solvent model, totaling over 2.73 ms of simulations. A small number of these trajectories folded; the folding proceeded along several distinct routes and the system folded into two distinct three-stranded beta-sheet conformations, showing that the folding mechanism of this system is distinctly heterogeneous.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Ensign
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D001499:Bayes Theorem; D003198:Computer Simulation; D021621:Imaging, Three-Dimensional; D007700:Kinetics; D016013:Likelihood Functions; D008958:Models, Molecular; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012997:Solvents; D014783:Viscosity
chemical_list: D012997:Solvents