Identifying the protein folding nucleus using molecular dynamics

(2) Department of Chemistry; Boston; Boston University; Cambridge); Eugene I. Shakhnovich(2) ((1) Center for Polymer Studies; Harvard University; H. Eugene Stanley (1); Nikolay V. Dokholyan (1); Physics Department; Sergey V. Buldyrev (1)

arxiv: cond-mat/9812284 · v2 · submitted 1998-12-16 · ❄️ cond-mat.stat-mech · q-bio

Identifying the protein folding nucleus using molecular dynamics

Nikolay V. Dokholyan (1) , Sergey V. Buldyrev (1) , H. Eugene Stanley (1) , Eugene I. Shakhnovich(2) ((1) Center for Polymer Studies , Physics Department , Boston University , Boston , (2) Department of Chemistry

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Harvard University Cambridge)

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classification ❄️ cond-mat.stat-mech q-bio

keywords foldingproteindynamicsmodelmolecularappearanceconformationconformations

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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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Identifying the protein folding nucleus using molecular dynamics

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