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.

Indoxyl Acetate as a Substrate for Analysis of Lipase Activity

“…As can be seen from the results, a small amount of energy was released suggesting that lipase has low affinity to IA. Compared with the energy released during cleavage of natural substrates like tripalmitin or tributyrin, the affinity of lipase to IA seems to be low; however, it still can be used as lipase substrate with additional benefit of coloring when it is used for screening of lipase activity of microbial cultures on agar plate [43, 44]. On the other hand, the affinity to substrates varies between types of lipase and used substrate as can be learned from the literature [30, 31].…”

Determinación de secuencia y modelaje por homología de la lipasa de Marinobacter sp. LB

“…El programa ERRAT (Colovos & Yeates 1993) asignó un "Factor de calidad general" de 95.60% que indica un buen modelo estructural debido a que el programa recomienda valores superiores a 95%. A pesar de esto, se han validado estructuras con 84.67% (Lanka et al, 2015). Por otro lado, el programa Verify 3D muestra que el 78.52% de los aminoácidos presenta un "Puntaje promedio 3D-1D" mayor a +0.2.…”

“…LB degrada más tributirina que trioleina, refuerzan lo antes mencionado. Adicionalmente, describen que las lipasas interaccionan con bajas energías de acoplamiento con trioctanoina, tributirina y trioleina (Messaoudi et al 2011, Lanka et al 2015.…”