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

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• 作者：Daisuke Satoh ; Kentaro Shimizu ; Shugo Nakamura and Tohru Terada
• 关键词：Folding simulation ; Molecular dynamics ; Multicanonical ; Generalized Born model ; Chignolin ; β ; -Hairpin
• 刊名：FEBS Letters
• 出版年：2006
• 出版时间：12 June 2006
• 年：2006
• 卷：580
• 期：14
• 页码：3422-3426
• 全文大小：544 K

文摘

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