All-atom fast protein folding simulations: the villin headpiece.
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 ( approximately 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.
Shen
Min-yi
MY
James Franck Institute and Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
Freed
Karl F
KF
D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D002645:Chickens; D003198:Computer Simulation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008840:Microfilament Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D012984:Software; D012997:Solvents; D055672:Static Electricity; D014867:Water / Q000737:chemistry / Q000378:metabolism
D002352:Carrier Proteins; D008840:Microfilament Proteins; D012997:Solvents; C026615:villin; D014867:Water