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

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 angstrom. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.