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

D. L. Ensign and V. S. Pande. Biophysical Journal 96 L53-55 (2009)

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.