Document Type

Article

Publication Version

Published Version

Publication Date

2010

Journal or Book Title

Journal of Chemical Physics

Volume

133

Issue

9

First Page

095101-1

Last Page

095101-11

DOI

10.1063/1.3474624

Abstract

In this paper, we used a coarse-grained model at the residue level to calculate the binding free energies of three protein-protein complexes. General formulations to calculate the electrostatic binding free energy and the van der Waals free energy are presented by solving linearized Poisson-Boltzmann equations using the boundary element method in combination with the fast multipole method. The residue level model with the fast multipole method allows us to efficiently investigate how the mutations on the active site of the protein-protein interface affect the changes in binding affinities of protein complexes. Good correlations between the calculated results and the experimental ones indicate that our model can capture the dominant contributions to the protein-protein interactions. At the same time, additional effects on protein binding due to atomic details are also discussed in the context of the limitations of such a coarse-grained model.

Comments

The following article is from Journal of Chemical Physics 133 (2010): 095101 and may be found at doi: 10.1063/1.3474624.

Rights

Copyright 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Copyright Owner

American Institute of Physics

Language

en

File Format

application/pdf

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