DOI: 10.1002/jcc.10104. Distance and exposure dependent effective dielectric function

Distance and exposure dependent effective dielectric function

10.1002/jcc.10104

Crossref journal-article

Wiley

Journal of Computational Chemistry (311)

Abstract

AbstractIn an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (Deff) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of Deff 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 Deff 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 Deff 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

Bibliography

Mallik, B., Masunov, A., & Lazaridis, T. (2002). Distance and exposure dependent effective dielectric function. Journal of Computational Chemistry, 23(11), 1090â1099. Portico.

Authors 3

Buddhadeb Mallik (first)
Artem Masunov (additional)
Themis Lazaridis (additional)

References 33 Referenced 49

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Dates

Type	When
Created	22 years, 10 months ago (Oct. 6, 2002, 8:29 a.m.)
Deposited	1 year, 10 months ago (Oct. 17, 2023, 8:39 a.m.)
Indexed	1 year, 5 months ago (March 25, 2024, 4:18 a.m.)
Issued	23 years, 2 months ago (June 10, 2002)
Published	23 years, 2 months ago (June 10, 2002)
Published Online	23 years, 2 months ago (June 10, 2002)
Published Print	23 years, 1 month ago (Aug. 1, 2002)

Funders 0

None

BibTeX

@article{Mallik_2002, title={Distance and exposure dependent effective dielectric function}, volume={23}, ISSN={1096-987X}, url={http://dx.doi.org/10.1002/jcc.10104}, DOI={10.1002/jcc.10104}, number={11}, journal={Journal of Computational Chemistry}, publisher={Wiley}, author={Mallik, Buddhadeb and Masunov, Artem and Lazaridis, Themis}, year={2002}, month=jun, pages={1090–1099} }

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