We applied a newly proposed prediction method for
membrane protein structures to
bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a
retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for
retinal and a structure with this empty space filled with a helix. Previous experiments of
bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a
retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of
Protein Data Bank's data, the amount of
bends was more similar for helices away from the
retinal than for those close to the
retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices,
lipids, and
retinal.