Title: Microsecond Explicit Solvent Molecular Dynamics Simulations of Protein Folding
Abstract: Explicit solvent molecular dynamics (MD) simulations of protein folding offer information on the protein folding process with tremendous temporal and spatial resolution. Long timescale protein folding trajectories can aid in interpretation of experimentally observed protein folding kinetics, and in the design of new fast-folding mutants. At the same time, protein folding simulations offer a demanding test for MD force fields to assess their accuracy in describing long-timescale conformational transitions in proteins. Until recently, however, little overlap existed between the timescales accessible to simulations and the time required for small proteins to fold. Recent experimental advances have lead to the discovery and characterization of a variety of proteins which fold on the 1-10 microsecond timescale; at the same time, increased computational power has made multiple microsecond timescales accessible for explicit solvent MD simulations. We performed multiple-microsecond folding simulations of two well-characterized fast-folding proteins, namely the villin headpiece subdomain and Pin1 WW domain. The villin headpiece folds to a native state after ∼6 microseconds of molecular dynamics simulation. Furthermore, a common folding mechanism is observed in multiple simulations from different starting conditions, where all secondary structure elements form over 1-2 microseconds after an initial hydrophobic collapse, but the native structure is only obtained after a complete dissociation and rearrangement of the secondary structure elements relative to each other. In the case of the WW domain, the protein misfolds in all simulated folding attempts. Conformational free energy calculations indicate that the WW domain's native state, a three-stranded beta sheet, is significantly higher (∼ 9 kcal/mol) in free energy for the force field (CHARMM22/CMAP) used than several misfolded helical structures obtained from folding simulations. Our results agree with several other recent studies in suggesting a bias toward helical secondary structure in modern MD force fields.