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Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin
http://hdl.handle.net/2237/00029130
http://hdl.handle.net/2237/00029130004417f6-be76-4b89-9fe9-577f6b30dcc1
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
1_4935964 (6.5 MB)
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| Item type | 学術雑誌論文 / Journal Article(1) | |||||
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| 公開日 | 2018-12-21 | |||||
| タイトル | ||||||
| タイトル | Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin | |||||
| 言語 | en | |||||
| 著者 |
Urano, Ryo
× Urano, Ryo× Okamoto, Yuko |
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| アクセス権 | ||||||
| アクセス権 | open access | |||||
| アクセス権URI | http://purl.org/coar/access_right/c_abf2 | |||||
| 権利 | ||||||
| 言語 | en | |||||
| 権利情報 | Copyright 2015 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.143, n.23, 2015, p.235101) and may be found at (http://dx.doi.org/10.1063/1.4935964). | |||||
| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | 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. | |||||
| 言語 | en | |||||
| 出版者 | ||||||
| 出版者 | AIP Publishing | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプresource | http://purl.org/coar/resource_type/c_6501 | |||||
| タイプ | journal article | |||||
| 出版タイプ | ||||||
| 出版タイプ | VoR | |||||
| 出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||
| DOI | ||||||
| 関連タイプ | isVersionOf | |||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | https://doi.org/10.1063/1.4935964 | |||||
| ISSN（print） | ||||||
| 収録物識別子タイプ | PISSN | |||||
| 収録物識別子 | 0021-9606 | |||||
| 書誌情報 |
en : The Journal of Chemical Physics 巻 143, 号 23, p. 235101, 発行日 2015-12-21 |
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| 著者版フラグ | ||||||
| 値 | publisher | |||||
