- Article -
| In Silico Biology 8, 0036 (2008); ©2008, Bioinformation Systems e.V. |
Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6
Natarajan Vidya, Bagavathkumar Vadivukkarasi*, Gopalakrishnan Manivannan and Krishnan Anbarasu
Department of Bioinformatics, HelixInfoSystems, 132A, II Floor,
Sterling Towers, IV Cross Street, Sterling Road,Chennai-600034, India
* Corresponding author
Email: vadivu1@gmail.com
Edited by H. Michael; received June 16, 2008; revised and accepted August 22, 2008; published October 11, 2008
Abstract
Identification of novel drug targets in silico in Vibrio vulnificus is important as it is one of the emerging pathogenic microorganisms. Glutamate racemase, an important constituent of bacterial cell wall is chosen for structure prediction using homology modeling. With the aid of tools and softwares like MODELLER and Swiss-PdbViewer, the 3D structure is predicted and the final model is refined by energy minimization. The quality of the refined model is assessed using PROCHECK. The interaction between the predicted structure of glutamate racemase and its potential inhibitors namely L-serine O-sulfate, (2R,4R)-2-amino-4-(2-benzo[b]thienyl)methyl pentanedioic acid, aziridino glutamate, exiguaquinol, γ-2 naphthylmethyl-D-glutamate and D-glutamine is analysed in silico by Autodock. The results indicate that certain residues like Asp13, Tyr45, Gly46, Asn78, Thr79, Cys185, His187 are highly conserved across the active site stretches of different bacterial species and may possibly assume precedence over the other residues for inhibitory action. This study provides an insight into the structure of glutamate racemase in V. vulnificus and also gives an idea about potential sites responsible for inhibitory action that could further be substantiated by experimental investigations.
Keywords: glutamate racemase, Vibrio vulnificus, modeller, docking