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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

Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics

http://hdl.handle.net/2237/25575
http://hdl.handle.net/2237/25575
20e5b812-21df-4988-b8fb-762d5a2d8f73
名前 / ファイル ライセンス アクション
25802_3_merged_1475679896.pdf 25802_3_merged_1475679896.pdf ファイル公開:2017/11/01 (10.2 MB)
Item type 学術雑誌論文 / Journal Article(1)
公開日 2017-02-15
タイトル
タイトル Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics
言語 en
著者 Yamada, Tatsuya

× Yamada, Tatsuya

WEKO 69314

en Yamada, Tatsuya

Search repository
Yamato, Takahisa

× Yamato, Takahisa

WEKO 69315

en Yamato, Takahisa

Search repository
Mitaku, Shigeki

× Mitaku, Shigeki

WEKO 69316

en Mitaku, Shigeki

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 © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
抄録
内容記述 Developments in atomic force microscopy have opened up a new path toward single-molecular phenomena; in particular, during the process of pulling a membrane protein out of a lipid bilayer. However, the characteristic features of the force-distance (F-D) curve of a bacteriorhodopsin in purple membrane, for instance, have not yet been fully elucidated in terms of physicochemical principles. To address the issue, we performed a computer simulation of bacteriorhodopsin with, to our knowledge, a novel coarse-grained (C-G) model. Peptide planes are represented as rigid spheres, while the surrounding environment consisting of water solvents and lipid bilayers is represented as an implicit continuum. Force-field parameters were determined on the basis of auxiliary simulations and experimental values of transfer free energy of each amino acid from water to membrane. According to Popot’s two-stage model, we separated molecular interactions involving membrane proteins into two parts: I) affinity of each amino acid to the membrane and intrahelical hydrogen bonding between main chain peptide bonds; and II) interhelix interactions. Then, only part I was incorporated into the C-G model because we assumed that the part plays a dominant role in the forced unfolding process. As a result, the C-G simulation has successfully reproduced the key features, including peak positions, of the experimental F-D curves in the literature, indicating that the peak positions are essentially determined by the residue-lipid and intrahelix interactions. Furthermore, we investigated the relationships between the energy barrier formation on the forced unfolding pathways and the force peaks of the F-D curves.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 Elsevier
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/10.1016/j.bpj.2016.09.051
ISSN
収録物識別子タイプ PISSN
収録物識別子 0006-3495
書誌情報 en : Biophysical Journal

巻 111, 号 10, p. 2086-2098, 発行日 2016-11
著者版フラグ
値 author
URI
識別子 http://dx.doi.org/10.1016/j.bpj.2016.09.051
識別子タイプ DOI
URI
識別子 http://hdl.handle.net/2237/25575
識別子タイプ HDL
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