Molecular Modeling and Docking Studies of Cold Active Lipase from Pseudomonas fluorescens.
Loading...
Date
2015-01
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Molecular Modeling is essential tool in the drug design process describes the generation, manipulation
or representation of 3D structures of the molecules and associated physico-chemical properties while docking predicts
the preferred orientation of one molecule to a second when bound to each other to form a stable complex. A cold active
lipase producing potential psychrophilic bacteria (GN) was isolated and identified by 16S rRNA molecular studies as
Pseudomonas vancouverensis. Lipase gene from closely related species P. fluorescens was investigated for their
functional role and in silico characterization using molecular modeling and docking studies. A 3D structure of lipase
gene was generated with SWISS-MODEL and Discovery Studio 3.0. The stereochemistry of the constructed model of
cold active lipase was subjected to energy minimization and the stereo-chemical quality of the predicted structure was
assessed. The superimposition of the template (PDBID: 2Z8X) with predicted structure showed that weighted root
mean square deviation of Cα trace between the template and the final refined model was 0.2 Å with a significant Zscore
of 8.2 and sequence identity was 80.5%. Three ligands P-Nitrophenol, Acetate ion and Diethyl phosphonate were
taken for docking calculation with generated structure. They were interacting on the functional motifs of predicted
model. It has been observed that Leu26, Tyr29, Asn31, Asp33, Pro315 and Thr316 residues were involved in hydrogen
bonding interactions with selected ligands. So these interacted residues can be used as prominent active binding sites
and which was common to the predicted active site. Based on above investigations it has been found that P.
vancouverensis lipase protein can play a similar role in lipid metabolic process and triglyceride lipase functional
activity as reported for P. fluorescens lipase protein.
Description
Keywords
SWISS-MODEL, Discovery Studio, Docking, Cold active lipase, Psychrophile, Pseudomonas, 16S rRNA
Citation
Gupta G N, Singh V K, Prakash V. Molecular Modeling and Docking Studies of Cold Active Lipase from Pseudomonas fluorescens. International Journal of Applied Biology and Pharmaceutical Technology. 2015 Jan-Mar; 6(1): 59-67.