Identifying the protein folding nucleus using molecular dynamics
Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley, Eugene I. Shakhnovich
Abstract
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation.
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