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  1. B100 理学部/理学研究科
  2. B100a 雑誌掲載論文
  3. 学術雑誌

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/2237/00029125
9cae231c-344e-488a-9cf9-ff9a78946ddf
名前 / ファイル ライセンス アクション
1_1712942.pdf 1_1712942 (687.0 kB)
Item type 学術雑誌論文 / Journal Article(1)
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

WEKO 88215

en Kokubo, Hironori

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Okamoto, Yuko

× Okamoto, Yuko

WEKO 88216

en Okamoto, Yuko

Search repository
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 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
内容記述タイプ Abstract
出版者
言語 en
出版者 AIP Publishing
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/10.1063/1.1712942
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
著者版フラグ
値 publisher
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