Folding free-energy landscape of a 10-residue mini-protein, chignolin

FEBS Lett. 2006 Jun 12;580(14):3422-6. doi: 10.1016/j.febslet.2006.05.015. Epub 2006 May 11.

Abstract

Chignolin is an artificial mini-protein composed of 10 residues (GYDPETGTWG) that has been shown to cooperatively fold into a beta-hairpin structure in water. We extensively explored the conformational space of chignolin using a 180-ns multicanonical molecular dynamics (MD) simulation and analyzed its folding free-energy landscape. In the MD trajectory, we found structures that satisfy 99% of the experimental restraints and are quite close to the experimentally determined structures with C(alpha) root-mean-square-deviations of less than 0.5 Angstroms. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cluster Analysis
  • Models, Molecular
  • Oligopeptides / chemistry*
  • Protein Folding*

Substances

  • Oligopeptides
  • chignolin