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OJBTM
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
ABSTRACT
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.
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