Identifying the protein folding nucleus using molecular dynamics

Nikolay V. Dokholyan; Sergey V. Buldyrev; H. Eugene Stanley; Eugene I. Shakhnovich

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Identifying the protein folding nucleus using molecular dynamics

Nikolay V. Dokholyan·Sergey V. Buldyrev·H. Eugene Stanley·Eugene I. Shakhnovich

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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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Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley, Eugene I. Shakhnovich. 1998-12-17. Identifying the protein folding nucleus using molecular dynamics. https://arxiv.org/abs/cond-mat/9812284

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