Dissecting protein-protein recognition sites.
The recognition sites in 70 pairwise protein-protein complexes of known three-dimensional structure are dissected in a set of surface patches by clustering atoms at the interface. When the interface buries <2000 A2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single-patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex. A simple geometric model reproduces the number and distribution of atoms within a patch. The rim is similar in composition to the rest of the protein surface, but the core has a distinctive amino acid composition, which may help in identifying potential protein recognition sites on single proteins of known structures.
Chakrabarti
Pinak
P
Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta, India. pinak@bic.boseinst.ernet.in
Janin
Joël
J
D000596:Amino Acids / Q000032:analysis; D000818:Animals; D001665:Binding Sites; D046911:Macromolecular Substances; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D000596:Amino Acids; D046911:Macromolecular Substances; D011506:Proteins