Homology Modeling, Molecular Dynamic Simulations and Docking Studies of a New Cold Active Extracellular Lipase, EnL A from Emericella nidulans NFCCI 3643

Abstract

A cold active lipase producing mesophilic fungus was isolated from Palm Oil Mill Effluent (POME) dump sites and identified by 28S rRNA molecular identification studies as Emericella nidulans NFCCI 3643. The BLAST P search with the sequence of the purified cold active lipase obtained by MALDI-TOF/MS analysis revealed that the protein is a hypothetical protein from Emericella nidulans with a gi number 67522685. Search of Lipase Engineering Database (LED) for this protein sequence revealed that this protein belongs to Candida antarctica lipase A like super family and to Aspergillus lipase like homologous family of class Y lipases. In the present study, a 3D structure of EnL A (Emericella nidulans lipase A) was built using homology modeling, the model was further optimized by molecular dynamic simulations and the optimized model was then docked with natural substrates. Secondary structure analysis of EnL A showed 37.11% of its content to be alpha helix making it stable for three dimensional structure modeling. Homology model of EnL A was constructed using the X-ray structure of Candida antarctica Lip A (3 guu.1.A) as a template with which EnL A showed 32.77% sequence identity. The stereo chemical quality and side chain environment of the model was validated by Ramachandran plot, ERRAT and Verify 3D. Natural substrates like tributyrin and trioctanoin were docked in to the optimized 3D model to further investigate the ligand-enzyme interactions.