Theoretical modeling of the O-intermediate structure of bacteriorhodopsin

Hiroshi C. Watanabe, Takakazu Ishikura, Takahisa Yamato

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Bacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light-activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O-intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light-adapted state to the O-intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O-intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution.

Original languageEnglish
Pages (from-to)53-61
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Issue number1
Publication statusPublished - 2009 Apr 1
Externally publishedYes


  • Acid blue form
  • Constrained relaxation with a free energy perturbation potential
  • Molecular dynamics simulation
  • Photocycle
  • Proton transfer
  • Purple membrane

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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