Development of unified statistical potentials describing protein-protein interactions.
A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer database is constructed. The protein complexes in this dataset are checked by a literature search to confirm that they form multimers, and the pairwise amino acid preference to interact across a protein-protein interface is analyzed and pair potentials constructed. The performance of the residue-based potentials is evaluated by using four jackknife tests and by assessing the potentials' ability to select true protein-protein interfaces from false ones. Compared to potentials developed for monomeric protein structure prediction, the interdomain potential performs much better at distinguishing protein-protein interactions. The potential developed from homodimer interfaces is almost the same as that developed from heterodimer interfaces with a correlation coefficient of 0.92. The residue-based potential is well suited for genomic scale protein interaction prediction and analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR. However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys.
Lu
Hui
H
Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
Lu
Long
L
Skolnick
Jeffrey
J
D000465:Algorithms; D001665:Binding Sites; D030562:Databases, Protein; D019281:Dimerization; D046911:Macromolecular Substances; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D046911:Macromolecular Substances; D008565:Membrane Proteins; D011506:Proteins