Molecular modelling, docking, and MD simulation of bacterial lipase: Binding interaction investigation against...

Bacterial lipase has thermostability and solvent stability making it suitable for development as a biodiesel catalyst. Biodiesel industry relies on triglycerides as the main substrate. Therefore, to find the best bacterial lipase activity towards triglycerides substrate, efficient screening activity methods can be used throughout the silico study. Bacterial lipases used in this investigation are Pseudomonas aeruginosa lipase, Burkholderia cepacia lipase, Serratia marcescens lipase, and Bacillus pumilus lipase. UniProtKB was used to retrieve these four bacterial lipases, which were then modeled in three dimensions using homology methods using Alphafold2. Those four bacterial lipase were docking against triglycerides substrates, such as glyceryl tridecanoate, glyceryl trilaurate, glyceryl trimyristate, glyceryl tripalmitate, glyceryl tristearate, glyceryl trioleate, and glyceryl trilinoleate. Autodock Vina was utilized to conduct a docking investigation. According to the docking studies, all bacterial lipase had the highest affinity for glyceryl tristearate. To study the stability of binding interaction between bacterial lipase and triglycerides, we run a molecular dynamics simulation based on AMBER. Based on RMSD, RMSF, catalytical distance measurements, and Rgyration analysis data, it was determined that Burkholderia cepacia lipase-glyceryl trioleate and Serratia marcescens lipase-glyceryl trioleate are the most stable interactions. In the future, the insights obtained in this study can be referenced to choose the best candidates for bacterial lipase towards triglycerides substrates and develop engineered lipases to enhance biocatalysis performance.