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.
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21 December 2015
Research Article|
December 15 2015
Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin
Ryo Urano;
Ryo Urano
a)
1Department of Physics, Graduate School of Science,
Nagoya University
, Nagoya, Aichi 464-8602, Japan
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Yuko Okamoto
Yuko Okamoto
b)
1Department of Physics, Graduate School of Science,
Nagoya University
, Nagoya, Aichi 464-8602, Japan
2Center for Computational Science, Graduate School of Engineering,
Nagoya University
, Nagoya, Aichi 464-8603, Japan
3Structural Biology Research Center, Graduate School of Science,
Nagoya University
, Nagoya, Aichi 464-8602, Japan
4Information Technology Center,
Nagoya University
, Nagoya, Aichi 464-8601, Japan
5
JST-CREST
, Nagoya, Aichi 464-8602, Japan
Search for other works by this author on:
Ryo Urano
1,a)
Yuko Okamoto
1,2,3,4,5,b)
1Department of Physics, Graduate School of Science,
Nagoya University
, Nagoya, Aichi 464-8602, Japan
2Center for Computational Science, Graduate School of Engineering,
Nagoya University
, Nagoya, Aichi 464-8603, Japan
3Structural Biology Research Center, Graduate School of Science,
Nagoya University
, Nagoya, Aichi 464-8602, Japan
4Information Technology Center,
Nagoya University
, Nagoya, Aichi 464-8601, Japan
5
JST-CREST
, Nagoya, Aichi 464-8602, Japan
a)
Current address: Chemistry Department, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.
b)
Author to whom correspondence should be addressed. Electronic mail: [email protected]. R. Urano and Y. Okamoto contributed equally to this work.
J. Chem. Phys. 143, 235101 (2015)
Article history
Received:
August 11 2015
Accepted:
October 28 2015
Citation
Ryo Urano, Yuko Okamoto; Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin. J. Chem. Phys. 21 December 2015; 143 (23): 235101. https://doi.org/10.1063/1.4935964
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