Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations.
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.
Kokubo
Hironori
H
University of Houston.
Okamoto
Yuko
Y
D001436:Bacteriorhodopsins / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013696:Temperature
D001436:Bacteriorhodopsins