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Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution
Author(s) -
Haberthür Urs,
Majeux Nicolas,
Werner Philipp,
Caflisch Amedeo
Publication year - 2003
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10317
Subject(s) - solvation , macromolecule , dielectric , aqueous solution , measure (data warehouse) , function (biology) , poisson distribution , chemistry , computational chemistry , statistical physics , poisson's equation , simple (philosophy) , chemical physics , molecular physics , physics , molecule , quantum mechanics , mathematics , computer science , organic chemistry , biochemistry , statistics , philosophy , epistemology , database , evolutionary biology , biology
We propose an analytical approach to calculate the effective dielectric function of proteins in aqueous solution. The screening effect if quantified by a measure of enclosure which is based on the distribution of solute atomic volumes around a pair of charges in a macromolecule. For protein conformations that vary significantly in size and shape, a comparison with finite difference Poisson calculations shows that pair interaction energies, their sums and solvation energies are well reproduced. The approach rivals the speed of simple distance dependent dielectric functions and the accuracy of the generalized Born model. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1936–1949, 2003