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Prediction of membrane protein structures by replica-exchange Monte Carlo simulations : Case of two helices
http://hdl.handle.net/2237/00029125
http://hdl.handle.net/2237/000291259cae231c-344e-488a-9cf9-ff9a78946ddf
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
1_1712942 (687.0 kB)
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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 | Prediction of membrane protein structures by replica-exchange Monte Carlo simulations : Case of two helices | |||||
| 言語 | en | |||||
| 著者 |
Kokubo, Hironori
× Kokubo, Hironori× 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 2004 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.120, n.22, 2004, p.10837-10847) and may be found at (http://dx.doi.org/10.1063/1.1712942). | |||||
| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | We test our prediction method of membrane protein structures with glycophorin A transmembrane dimer and analyze the predicted structures in detail. Our method consists of two parts. In the first part, we obtain the amino-acid sequences of the transmembrane helix regions from one of existing WWW servers and use them as an input for the second part of our method. In the second part, we perform a replica-exchange Monte Carlo simulation of these transmembrane helices with some constraints that indirectly represent surrounding lipid and water effects and identify the predicted structure as the global-minimum-energy state. The structure obtained in the case for the dielectric constant ε=1.0 is very close to that from the nuclear magnetic resonance experiments, while that for ε=4.0 is more packed than the native one. Our results imply that the helix–helix interaction is the main driving force for the native structure formation and that the stability of the native structure is determined by the balance of the electrostatic term, van der Waals term, and torsion term, and the contribution of electrostatic energy is indeed important for correct predictions. The inclusion of atomistic details of side chains is essential for estimating this balance accurately because helices are tightly packed. | |||||
| 言語 | en | |||||
| 出版者 | ||||||
| 出版者 | AIP Publishing | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
| 資源タイプ | 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/10.1063/1.1712942 | |||||
| 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 120, 号 22, p. 10837-10847, 発行日 2004-06-08 |
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| 著者版フラグ | ||||||
| 値 | publisher | |||||
