Analysis of Helix-Helix Interactions of Bacteriorhodopsin by Replica-Exchange Simulations

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• 作者：Hironori Kokubo ; Yuko Okamoto
• 刊名：Biophysical Journal
• 出版年：2009
• 出版时间：4 February 2009
• 年：2009
• 卷：96
• 期：3
• 页码：765-776
• 全文大小：1940 K

文摘

We performed long-time replica-exchange Monte Carlo simulations of bacteriorhodopsin transmembrane helices, which made it possible that wide conformational space was sampled. Using only the helix-helix interactions and starting from random initial configurations, we obtained the nativelike helix arrangement successfully and predicted a part of the configurations (three helices out of seven) precisely. By the principal component analysis we classified low-energy structures into some clusters of similar structures, and we showed that the above nativelike three-helix configuration is reproduced properly in most clusters and that not only the van der Waals interactions but also the electrostatic interactions contributed to the stabilization of the native structures.