A simple shape characteristic of protein-protein recognition.
BACKGROUND
Observation of co-crystallized protein-protein complexes and low-resolution protein-protein docking studies suggest the existence of a binding-related anisotropic shape characteristic of protein-protein complexes.


RESULTS
Our study systematically assessed the global shape of proteins in a non-redundant database of co-crystallized protein-protein complexes by measuring the distance of the surface residues to the protein's center of mass. The results show that on average the binding site residues are closer to the center of mass than the non-binding surface residues. Thus, the study directly detects an important and simple binding-related characteristic of protein shapes. The results provide an insight into one of the fundamental properties of protein structure and association.
Nicola
George
G
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Vakser
Ilya A
IA
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods
D011506:Proteins