Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach

• Published in: Journal of molecular graphics & modelling Vol. 85; pp. 190 - 197
• Main Authors: Thiruvengadam, Kothai, Baskaran, Sarath Kumar, Pennathur, Gautam
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2018
• Subjects: GROMACS; Lid; Lipid lipase interaction; Molecular dynamics simulation; Pseudomonas aeruginosa lipase; Lipid lipase interaction; Molecular dynamics simulation; GROMACS; Lid; Pseudomonas aeruginosa lipase
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2018.09.005

Lipases are biocatalysts which exhibit optimal activity at the aqueous-lipid interface. Molecular Dynamics (MD) Simulation studies on lipases have revealed the structural changes occurring in the enzyme, at the loop-helix-loop, often designated as the “lid”, which is responsible for its interfacial activation. In recent years, MD simulation of lipases at molecular level have been studied in detail, whereas very few studies are carried over on its interaction with lipid molecules. Hence, in the current study we have investigated molecular interaction of bacterial lipase (Pseudomonas aeruginosa lipase, PAL) with a lipid molecule (tristearoyl glycerol, TGL). This provides an insight into the interfacial activation of the enzyme. The lipid molecule was placed near the lids of the enzyme and MD simulations were performed for 100 ns to understand the nature and site of the interaction. The results clearly indicate that, the presence of a lipid molecule near the lids affects the motion of the enzyme through changes in conformation. Lipid molecule near the lids reduces the movements of both lids, and the TGL molecule was observed moving towards the active site. The movement of the lids, surface accessibility and the domain movements of PAL are discussed and the results provide valuable insight in to the role played by the two lids in the interfacial activation of PAL with TGL. [Display omitted] •Interfacial activation of Pseudomonas aeruginosa lipase (PAL) was investigated for 100 ns.•Lid2 in PAL showed more fluctuations and triggered the movement of lid1.•Lid2 and lid1 movements leading to the interfacial activation of PAL in the presence and absence of a lipid molecule tristearoyl glycerol (TGL).