Effect of temperature variation on the structure of gene-translated thermostable lipase by molecular dynamic simulation

Abstract

Molecular modeling has increasingly been used to investigate the structural dynamics, properties, and thermodynamics of biological systems. This study aims to evaluate the structural dynamics of gene-translated lipase structure from PLS 80, a novel bacterium previously isolated from undersea fumaroles, subjected to various temperatures. Prediction using SWISS-MODEL showed PLS 80 lipase had the highest homology (97,7%) with lipase 2DSN. The pair of PLS 80 lipase – 2DSN had the highest Global Model Quality Estimation (GMQE) and Qualitative Model Energy Analysis (QMEAN) values of 0.99 and 0.7, respectively. The lipase 2DSN was then used as the template. The temperature variation simulation was conducted using Assisted Model Building with Energy Refinement (AMBER) software at 300, 350, and 400 K for 50 ns. The parameters used for evaluation were Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), the gyration radii (Rg), total energy, number of hydrogen bonds, and Solvent Accessible Surface Area (SASA). Although produced by a thermophile, the molecular dynamic simulation showed that the lipase had the lowest RMSD, Rg, and total energy when at 300 K. Higher temperatures increased the Rg and reduced the number of hydrogen bonds in the molecule. The RMSF values indicated that some residues were conformationally less rigid than other residues in the structure. The difference in RMSF values of some residues was significant when the temperature was increased, but not necessarily those with high RMSF values. The SASA values increased slightly when the temperature was alleviated by 100 K. However, the polar SASA value at 350 K was the lowest than the other temperatures. Visual evaluation of the lipase structure indicated that the b-sheet only shifted slightly at various temperatures. However, conformational changes were observed in the a-helix and turn/loop. At 350 K, the lipase had an additional b-sheet, while some turn/loop structures frayed to coil structures. These structural differences may explain the optimum lipase activity at around thermophilic temperature.