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Dissecting protein–protein recognition sites
Author(s) -
Chakrabarti Pinak,
Janin Joël
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10085
Subject(s) - interface (matter) , surface (topology) , crystallography , amino acid , protein structure , cluster analysis , pairwise comparison , molecular recognition , chemistry , surface protein , biological system , geometry , chemical physics , computer science , biology , molecule , mathematics , artificial intelligence , biochemistry , gibbs isotherm , organic chemistry , virology
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 Å 2 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. Proteins 2002;47:334–343. © 2002 Wiley‐Liss, Inc.