Recognition templates for predicting adenylate-binding sites in proteins. |
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Authors: | S Zhao G M Morris A J Olson D S Goodsell |
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Institution: | Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. |
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Abstract: | Recognition templates encapsulate the structural and energetic features for the specific recognition of a given ligand by a protein active site. These templates identify the major interactions used for specific recognition and may be used to find specific binding sites in proteins of unknown function. We present a grid-based method for deriving recognition templates for adenylate groups from a set of diverse nucleotide-binding proteins. The templates reveal the basis of specific binding of adenylate, including tight shape complementarity, specific hydrogen bonds, and underscoring the importance of a key steric contact for excluding guanylate from adenylate-specific sites. We demonstrate the utility of recognition templates in identifying specific adenylate-binding sites in a diverse set of dinucleotide-binding proteins. |
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