title: Potential of mean force for protein-protein interaction studies.
abstract: Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations.
authors.affiliation: Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Jiang
authors.forename: Ying
authors.initials: Y
authors.lastname: Gao
authors.forename: Fenglou
authors.initials: F
authors.lastname: Mao
authors.forename: Zhijie
authors.initials: Z
authors.lastname: Liu
authors.forename: Luhua
authors.initials: L
authors.lastname: Lai
mesh_terms: D030562:Databases, Protein; D006860:Hydrogen Bonding; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins