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Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study
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 | |
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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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 | |||||
著者 |
Mori, Takaharu
× Mori, Takaharu× Okamoto, Yuko |
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権利 | ||||||
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. | |||||
内容記述タイプ | Abstract | |||||
出版者 | ||||||
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 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 0021-9606 | |||||
書誌情報 |
THE JOURNAL OF CHEMICAL PHYSICS 巻 131, 号 16, p. 165103-165103, 発行日 2009-10 |
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フォーマット | ||||||
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 |