Identifying the protein folding nucleus using molecular dynamics

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

Research output: Contribution to journalArticlepeer-review

130 Scopus citations


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. Amino acid residues participating in those contacts may serve as 'accelerator pedals' used by molecular evolution to control protein folding rate. (C) 2000 Academic Press.

Original languageEnglish (US)
Pages (from-to)1183-1188
Number of pages6
JournalJournal of Molecular Biology
Issue number5
StatePublished - Mar 10 2000

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


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