Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

Abstract

All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the folded structure. The ongoing study of protein folding through computational methods thus requires both improvements in the performance of molecular dynamics programs to make longer timescales accessible, and testing of force fields in the context of folding simulations. We report a ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds, respectively. The protein simulated in explicit solvent exhibits several metastable states with incorrect topology and does not assume the native state during the present simulations.

FIGURE 1

Experimental relaxation kinetics of Fip35 with a time resolution of 280 ns at 352 K.

FIGURE 2

Percentage of native contacts formed (top), secondary structure content (middle), and exposed surface area of hydrophobic side chains (bottom) through the 10 μs folding trajectory. Values in the native structure are shown as dashed lines.

FIGURE 3

(a) Native state, molten globule formed after 500 ns, and most representative structures from clustering analysis. (b) Cluster occupied throughout the trajectory. The first 10 clusters are shown.