Dissecting protein-protein recognition sites |
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Authors: | Chakrabarti Pinak Janin Joël |
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Affiliation: | Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta, India. pinak@bic.boseinst.ernet.in |
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Abstract: | 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. |
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Keywords: | molecular recognition protein–protein interaction interfaces protein surface residue clusters amino acid composition |
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