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Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations
http://hdl.handle.net/2237/20621
http://hdl.handle.net/2237/206213dd4bdb3-513a-4e2b-9be5-6995df1c3c2c
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
ItohSasaiJCP2011.pdf (3.0 MB)
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| アイテムタイプ | 学術雑誌論文 / Journal Article(1) | |||||
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| 公開日 | 2014-10-30 | |||||
| タイトル | ||||||
| タイトル | Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations | |||||
| 言語 | en | |||||
| 著者 |
Itoh, Kazuhito
× Itoh, Kazuhito× Sasai, Masaki |
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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 | ||||||
| 権利情報 | © 2011 American Institute of Physics | |||||
| 言語 | en | |||||
| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-basedmodel of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energysurfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca^2+ binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca^2+ before its binding. Here, the pre-existing fluctuations to accept the second and third Ca^2+ ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the β4–α4 loop, which explains the pre-existing Y–T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition. | |||||
| 言語 | en | |||||
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| 出版者 | AIP | |||||
| 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 | AM | |||||
| 出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||
| DOI | ||||||
| 関連タイプ | isVersionOf | |||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | https://doi.org/10.1063/1.3565025 | |||||
| ISSN | ||||||
| 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 134, 号 12, p. 125102-125102, 発行日 2011-03 |
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| 著者版フラグ | ||||||
| 値 | author | |||||
| URI | ||||||
| 識別子 | http://dx.doi.org/10.1063/1.3565025 | |||||
| 識別子タイプ | DOI | |||||
| URI | ||||||
| 識別子 | http://hdl.handle.net/2237/20621 | |||||
| 識別子タイプ | HDL | |||||
