Research Article
Prediction of transition metal-binding sites from apo protein structures
Mariana Babor,
Sergey Gerzon,
Barak Raveh,
Vladimir Sobolev,
Marvin Edelman,
Mariana Babor
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorSergey Gerzon
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorBarak Raveh
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorCorresponding Author
Vladimir Sobolev
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Plant Sciences Department, Weizmann Institute of Science, Rehovot 76100, Israel===Search for more papers by this authorCorresponding Author
Marvin Edelman
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Plant Sciences Department, Weizmann Institute of Science, Rehovot 76100, Israel===Search for more papers by this authorMariana Babor,
Sergey Gerzon,
Barak Raveh,
Vladimir Sobolev,
Marvin Edelman,
Mariana Babor
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorSergey Gerzon
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorBarak Raveh
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Search for more papers by this authorCorresponding Author
Vladimir Sobolev
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Plant Sciences Department, Weizmann Institute of Science, Rehovot 76100, Israel===Search for more papers by this authorCorresponding Author
Marvin Edelman
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
Plant Sciences Department, Weizmann Institute of Science, Rehovot 76100, Israel===Search for more papers by this authorAbstract
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.
Supporting Information
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