Normal Mode Analysis of Polytheonamide B(Cross-disciplinary physics and related areas of science and technology)
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概要
- 論文の詳細を見る
Polytheonamide B is a linear 48-residue peptide which forms a single , β-helix structure with alternating D and L-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ, Ψ), and correlation factors for the C^α atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.
- 社団法人日本物理学会の論文
- 2007-09-15
著者
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Shimizu Hirofumi
Division Of Molecular Physiology And Biophysics University Of Fukui Faculty Of Medical Sciences
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清水 啓史
福井大学医学部分子生理
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Mori Takaharu
Department Of Physics School Of Science Nagoya University
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Okamoto Yuko
Department Of Otolaryngology Head And Neck Surgery Graduate School Of Medicine Chiba University
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Iwamoto Masayuki
Univ. Fukui Fac. Med. Sri.
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Oiki Shigetoshi
Univ. Fukui Fac. Med. Sri.
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Oiki Shigetoshi
Department of Molecular Physiology and Biophysics, University of Fukui Faculty of Medical Sciences
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SHIMIZU Hirofumi
Department of Urology,Teikyo University School of Medicine
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Oiki Shigetoshi
Department Of Molecular And Cellular Physiology National Institute For Physiological Sciences
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Iwamoto Masayuki
Department of Molecular Physiology and Biophysics, University of Fukui Faculty of Medical Sciences
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KOKUBO Hironori
Department of Chemistry, University of Houston
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Iwamoto Masayuki
Department Of Mathematics Graduate School Of Science Kyoto University
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Shimizu Hirofumi
Department Of Electrical And Electronic Engineering College Of Engineering Nihon University
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Kokubo Hironori
Department Of Chemistry University Of Houston
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Okamoto Yuko
Department Of Internal Medicine National Cancer Center Hospital
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Okamoto Yuko
Department of Physics, School of Science, Nagoya University
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Iwamoto Masayuki
Department of Chemistry, Osaka Kyoiku University
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