Title
Calculations of the binding affinities of protein-protein complexes with the fast multipole method
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.
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
Copyright Date
2010
Language
en
File Format
application/pdf
Recommended Citation
Kim, Bongkeun; Song, Jiming; and Song, Xueyu, "Calculations of the binding affinities of protein-protein complexes with the fast multipole method" (2010). Electrical and Computer Engineering Publications. 68.
https://lib.dr.iastate.edu/ece_pubs/68
Comments
The following article is from Journal of Chemical Physics 133 (2010): 095101 and may be found at doi: 10.1063/1.3474624.