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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

Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study

http://hdl.handle.net/2237/14159
http://hdl.handle.net/2237/14159
0719f2b7-df4b-4ee1-ab9e-0eb5c2b03f1e
名前 / ファイル ライセンス アクション
THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf (375.9 kB)
Item type 学術雑誌論文 / Journal Article(1)
公開日 2010-09-16
タイトル
タイトル Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study
言語 en
著者 Mori, Takaharu

× Mori, Takaharu

WEKO 38770

en Mori, Takaharu

Search repository
Okamoto, Yuko

× Okamoto, Yuko

WEKO 38771

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 (2010) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
抄録
内容記述 Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β^6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β^4.4-helix as the lowest-potential-energy structure, and left-handed β^4.4-helix, right-handed and left-handed β^6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β^6.3-helix and β^4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β^6.3-helix is more stable than β^4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β^6.3-helix conformation.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 American Institute of Physics
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/10.1063/1.3247578
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 131, 号 16, p. 165103-165103, 発行日 2009-10
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application/pdf
著者版フラグ
値 publisher
URI
識別子 http://hdl.handle.net/2237/14159
識別子タイプ HDL
URI
識別子 http://dx.doi.org/10.1063/1.3247578
識別子タイプ DOI
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