Identifying the protein folding nucleus using molecular dynamics

Molecular dynamics simulations of folding in an off-lattice protein model r eveal a nucleation scenario, in which a few well-defined contacts are forme d with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model prot ein into its folded conformation. Amino acid residues participating in thos e contacts may serve as "accelerator pedals" used by molecular evolution to control protein folding rate. (C) 2000 Academic Press.