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 β-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 Cα root-mean-square-deviations of less than 0.5 Å. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment.