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タイトル: Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent.
著者: Kodama, Ryota
Roth, Roland
Harano, Yuichi
Kinoshita, Masahiro  kyouindb  KAKEN_id
著者名の別形: 木下, 正弘
キーワード: integral equations
molecular biophysics
proteins
solvation
solvent effects
thermodynamic properties
発行日: 28-Jul-2011
出版者: American Institute of Physics
誌名: The Journal of chemical physics
巻: 135
号: 4
論文番号: 045103
抄録: The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1, [ellipsis (horizontal)], m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.
著作権等: © 2011 American Institute of Physics.
URI: http://hdl.handle.net/2433/145962
DOI(出版社版): 10.1063/1.3617247
PubMed ID: 21806161
出現コレクション:学術雑誌掲載論文等

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