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The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations

2009; Elsevier BV; Volume: 96; Issue: 8 Linguagem: Inglês

10.1016/j.bpj.2009.01.024

1542-0086

Daniel L. Ensign, Vijay S. Pande,

Enzyme Structure and Function

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.