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題名 Universal geometrical factor of protein conformations as a consequence of energy Minimization
作者 馬文忠
Wu,Ming-Chya ; Li,Mai Suan ; Ma,Wen-Jong ; Maksim Kouza; Hu,Chin-Kun
貢獻者 應物所
日期 2011.12
上傳時間 29-Sep-2014 15:07:50 (UTC+8)
摘要 The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A<r>)) of the van der Waals volume V to the surface area A and average atomic radius <r> of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.
關聯 Europhysics Letter,96,68005
資料類型 article
DOI http://dx.doi.org/10.1209/0295-5075/96/68005
dc.contributor 應物所en_US
dc.creator (作者) 馬文忠zh_TW
dc.creator (作者) Wu,Ming-Chya ; Li,Mai Suan ; Ma,Wen-Jong ; Maksim Kouza; Hu,Chin-Kunen_US
dc.date (日期) 2011.12en_US
dc.date.accessioned 29-Sep-2014 15:07:50 (UTC+8)-
dc.date.available 29-Sep-2014 15:07:50 (UTC+8)-
dc.date.issued (上傳時間) 29-Sep-2014 15:07:50 (UTC+8)-
dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/70182-
dc.description.abstract (摘要) The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A<r>)) of the van der Waals volume V to the surface area A and average atomic radius <r> of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.en_US
dc.format.extent 911513 bytes-
dc.format.mimetype application/pdf-
dc.language.iso en_US-
dc.relation (關聯) Europhysics Letter,96,68005en_US
dc.title (題名) Universal geometrical factor of protein conformations as a consequence of energy Minimizationen_US
dc.type (資料類型) articleen
dc.identifier.doi (DOI) 10.1209/0295-5075/96/68005en_US
dc.doi.uri (DOI) http://dx.doi.org/10.1209/0295-5075/96/68005en_US