All‐atom fast protein folding simulations: The villin headpiece

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Abstract
We provide a fast folding simulation using an all-atom solute, implicit solvent method that eliminates the need for treating solvent degrees of freedom. The folding simulations for the 36-residue villin headpiece exhibit close correspondence with the landmark all-atom explicit solvent molecular dynamics simulations by Duan and Kollman (Duan & Kollman, Science 1998;282:740–744; Duan, Wang, & Kollman, Proc Natl Acad Sci USA 1998;95:9897–9902). Our implicit solvent approach uses only an entry-level single CPU PC with comparable throughput (∼4 nsec/day) to the DK supercomputer simulation. The native state is shown to be stable. Our 200-nsec folding trajectory agrees with the DK simulation in displaying a burst phase, a rapid initial shrinkage, a highly native-like binding site structure, and more. Proteins 2002;49:439–445.