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 Angstroms. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment.
Satoh
Daisuke
D
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan.
Shimizu
Kentaro
K
Nakamura
Shugo
S
Terada
Tohru
T
D016000:Cluster Analysis; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D017510:Protein Folding
D009842:Oligopeptides; C506175:chignolin