Bioinformatics Advance Access originally published online on February 10, 2006
Bioinformatics 2006 22(10):1183-1189; doi:10.1093/bioinformatics/btl040
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Generation of 3D templates of active sites of proteins with rigid prosthetic groups
Faculty of Computing, Information Systems & Mathematics, Kingston University Kingston-upon-Thames, Surrey KT1 2EE, UK
Motivation: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful.
Results: In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 Å or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses.
Availability: Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html
Contact: j.nebel{at}kingston.ac.uk
Received on November 10, 2005; revised on January 15, 2006; accepted on February 3, 2006
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