Identifying the Protein Folding Nucleus Using Molecular Dynamics

J Mol Biol. 2000 Mar 10;296(5):1183-8. doi: 10.1006/jmbi.1999.3534.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Computer Simulation*
  • Evolution, Molecular
  • Kinetics
  • Models, Molecular*
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding*
  • Protein Renaturation
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Temperature
  • Thermodynamics


  • Proteins