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Prediction of transition metal‐binding sites from apo protein structures
Author(s) -
Babor Mariana,
Gerzon Sergey,
Raveh Barak,
Sobolev Vladimir,
Edelman Marvin
Publication year - 2008
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.21587
Subject(s) - structural genomics , chemistry , metal , metal ions in aqueous solution , protein structure , function (biology) , binding site , protein data bank , protein function , crystallography , biochemistry , biology , gene , genetics , organic chemistry
Metal ions are crucial for protein function. They participate in enzyme catalysis, play regulatory roles, and help maintain protein structure. Current tools for predicting metal–protein interactions are based on proteins crystallized with their metal ions present (holo forms). However, a majority of resolved structures are free of metal ions (apo forms). Moreover, metal binding is a dynamic process, often involving conformational rearrangement of the binding pocket. Thus, effective predictions need to be based on the structure of the apo state. Here, we report an approach that identifies transition metal‐binding sites in apo forms with a resulting selectivity >95%. Applying the approach to apo forms in the Protein Data Bank and structural genomics initiative identifies a large number of previously unknown, putative metal‐binding sites, and their amino acid residues, in some cases providing a first clue to the function of the protein. Proteins 2008. © 2007 Wiley‐Liss, Inc.