Abstract
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 language | English |
|---|---|
| Pages (from-to) | 53-61 |
| Number of pages | 9 |
| Journal | Proteins: Structure, Function and Bioinformatics |
| Volume | 75 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - 2009 Apr 1 |
| Externally published | Yes |
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Keywords
- 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
Cite this
Theoretical modeling of the O-intermediate structure of bacteriorhodopsin. / Watanabe, Hiroshi; Ishikura, Takakazu; Yamato, Takahisa.
In: Proteins: Structure, Function and Bioinformatics, Vol. 75, No. 1, 01.04.2009, p. 53-61.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Theoretical modeling of the O-intermediate structure of bacteriorhodopsin
AU - Watanabe, Hiroshi
AU - Ishikura, Takakazu
AU - Yamato, Takahisa
PY - 2009/4/1
Y1 - 2009/4/1
N2 - 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.
AB - 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.
KW - Acid blue form
KW - Constrained relaxation with a free energy perturbation potential
KW - Molecular dynamics simulation
KW - Photocycle
KW - Proton transfer
KW - Purple membrane
UR - http://www.scopus.com/inward/record.url?scp=65249113392&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=65249113392&partnerID=8YFLogxK
U2 - 10.1002/prot.22221
DO - 10.1002/prot.22221
M3 - Article
C2 - 18767148
AN - SCOPUS:65249113392
VL - 75
SP - 53
EP - 61
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
SN - 0887-3585
IS - 1
ER -