MOLECULAR MODELING AND DOCKING STUDIES OF COLD ACTIVE LIPASE FROM Pseudomonas fluorescens

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.