The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential

In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded beta-sheet WW domain. Replica exchange Monte Carlo simulations starting from random coils find native-like (C alpha RMSD of 2.68 angstrom) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two beta-hairpins, the folding mechanism of each individual beta-hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous P-fold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Phi values. Our analysis shows that the turn structure between first and second beta strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. Proteins 2011; 79:1704-1714. (C) 2011 Wiley-Liss, Inc.