An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants.

Published

Journal Article

Here we introduce an electrostatic model that treats the complexity of electrostatic interactions in a heterogeneous protein environment by using multiple parameters that take into account variations in protein geometry, local structure, and the type of interacting residues. The optimal values for these parameters were obtained by fitting the model to a large dataset of 260 experimentally determined pK(a) values distributed over 41 proteins. We obtain fits between the calculated and observed values that are significantly better than the null model. The model performs well on the groups that exhibit large pK(a) shifts from solution values in response to the protein environment and compares favorably with other, successful continuum models. The empirically determined values of the parameters correlate well with experimentally observed contributions of hydrogen bonds and ion pairs as well as theoretically predicted magnitudes of charge-charge and charge-polar interactions. The magnitudes of the dielectric constants assigned to different regions of the protein rank according to the strength of the relaxation effects expected for the core, boundary, and surface. The electrostatic interactions in this model are pairwise decomposable and can be calculated rapidly. This model is therefore well suited for the large computations required for simulating protein properties and especially for prediction of mutations for protein design.

Full Text

Duke Authors

Cited Authors

  • Wisz, MS; Hellinga, HW

Published Date

  • May 15, 2003

Published In

Volume / Issue

  • 51 / 3

Start / End Page

  • 360 - 377

PubMed ID

  • 12696048

Pubmed Central ID

  • 12696048

Electronic International Standard Serial Number (EISSN)

  • 1097-0134

Digital Object Identifier (DOI)

  • 10.1002/prot.10332

Language

  • eng

Conference Location

  • United States