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Distance and exposure dependent effective dielectric function
Author(s) -
Mallik Buddhadeb,
Masunov Artem,
Lazaridis Themis
Publication year - 2002
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.10104
Subject(s) - dielectric , electrostatics , chemistry , function (biology) , range (aeronautics) , globular protein , molecular dynamics , charge (physics) , standard deviation , statistical physics , molecular physics , thermodynamics , physics , computational chemistry , materials science , mathematics , quantum mechanics , crystallography , statistics , evolutionary biology , composite material , biology
In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D eff ) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D eff versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the “exposure”). The D eff values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D eff from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance‐dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior. © 2002 Wiley Periodicals, Inc. J Comput Chem 11: 1090–1099, 2002