Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

Ryo Urano, Yuko Okamoto

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


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.

Original languageEnglish
Article number235101
JournalJournal of Chemical Physics
Issue number23
Publication statusPublished - Dec 21 2015
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry


Dive into the research topics of 'Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin'. Together they form a unique fingerprint.

Cite this