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Online Journal of Bioinformatics ©
Volume 13(2):260-273, 2012
Homology and molecular docking of Pseudomonas aeruginosa RND MexY efflux pump
DBT-Bioinformatics Center, Department of Zoology, Sri Venkateswara University, Tirupati
Bhaskar BV, Munichandrababu T, Bhuvaneswar C, Rajendra W., Homology and molecular docking of Pseudomonas aeruginosa RND MexY efflux pump, Onl J Bioinform., 13(2):260-273, 2012. Pseudomonas aeruginosa has 10 multidrug efflux pumps which play a crucial role in development of resistance to several antibiotics. MexXY an overexpressed efflux pump, confers resistance to quinolones, macrolides, tetracyclines, lincomycin, chloramphenicol, penicillin and aminoglycosides. The 3D structure of MexY transmembrane protein was modeled with Modeller 9v7 and refined with PROCHECK, WHATCHEK, Verify3D, ERRAT and energy minimization. Secondary structure elements, transmembrane helices and binding pockets of the MexY efflux pump are shown. Molecular docking revealed residues which affect the extrusion of penicillin, chloramphenicol, lincomycin, tetracycline and aminoglycoside. Virtual screening of PuchChem compounds against MexY efflux pump showed that CID 11143966, CID 24199712, CID 9209489, and CID 433940 had the highest binding energies viz., -11.0, 10.9, 10.6, 10.4 kcal/mol respectively.
Keywords: MexY Efflux Pump, Sequence analysis, Homology modeling, Docking.