Universal geometrical factor of protein conformations as a consequence of energy minimization

Please use this identifier to cite or link to this item: http://ir.lib.ncu.edu.tw/handle/987654321/52992

Title:	Universal geometrical factor of protein conformations as a consequence of energy minimization
Authors:	Wu,MC;Li,MS;Ma,WJ;Kouza,M;Hu,CK
Contributors:	物理學系
Keywords:	ACCESSIBLE SURFACE-AREA;PACKING DENSITY;MOLECULAR AREA;FORCE QUENCH;MONTE-CARLO;VOLUMES;MACROMOLECULES;SIMULATIONS;PRINCIPLES;ALGORITHM
Date:	2011
Issue Date:	2012-06-11 10:53:15 (UTC+8)
Publisher:	國立中央大學
Abstract:	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 shows that the ratio for real and well-designed proteins is universal and equal to 0.491 +/- 0.005. 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. Copyright (C) EPLA, 2011
Relation:	EPL
Appears in Collections:	[Department of Physics] journal & Dissertation

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