title: Calculations of the binding affinities of protein-protein complexes with the fast multipole method.
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.
authors.affiliation: Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Bongkeun
authors.initials: B
authors.lastname: Kim
authors.forename: Jiming
authors.initials: J
authors.lastname: Song
authors.forename: Xueyu
authors.initials: X
authors.lastname: Song
mesh_terms: D000818:Animals; D007611:Aprotinin / Q000378:metabolism; D001407:Bacillus / Q000201:enzymology; D001426:Bacterial Proteins / Q000378:metabolism; D002417:Cattle; D008954:Models, Biological; D010059:Ovomucin / Q000378:metabolism; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000191:economics / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism; D012697:Serine Endopeptidases / Q000378:metabolism; D013305:Streptomyces griseus / Q000201:enzymology; D013816:Thermodynamics; D014357:Trypsin / Q000378:metabolism; D014421:Turkey
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D010059:Ovomucin; C057438:barstar protein, Bacillus amyloliquefaciens; D007611:Aprotinin; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D012697:Serine Endopeptidases; D014357:Trypsin; C024984:streptogrisin B