Prediction of transition metal-binding sites from apo protein structures

@article{Babor:2007, abstract = {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.}, author = {Babor, M. and Gerzon, S. and Raveh, B. and Sobolev, V. and Edelman, M. }, citeulike-article-id = {1538114}, journal = {Proteins}, keywords = {bioinformatics, metalloregulation, software, structure\_prediction}, posted-at = {2007-08-06 14:33:01}, priority = {0}, title = {Prediction of transition metal-binding sites from apo protein structures}, url = {http://dx.doi.org/10.1002/prot.21587}, year = {in press} }

TY - JOUR ID - Babor:2007 L3 - citeulike-article-id:1538114 N2 - 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. JF - Proteins TI - Prediction of transition metal-binding sites from apo protein structures KW - bioinformatics KW - metalloregulation KW - software KW - structure_prediction AU - Babor, M AU - Gerzon, S AU - Raveh, B AU - Sobolev, V AU - Edelman, M PY - in press/// UR - http://dx.doi.org/10.1002/prot.21587 ER -