Department of Biotechnology, Anna University, Chennai, 600025, India.
J Mol Graph Model. 2018 Oct;85:190-197. doi: 10.1016/j.jmgm.2018.09.005. Epub 2018 Sep 8.
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.
脂肪酶是在水脂界面处表现出最佳活性的生物催化剂。对脂肪酶的分子动力学（MD）模拟研究揭示了酶中loop-helix-loop 结构的变化，通常称为“盖子”，这是其界面激活的原因。近年来，对脂肪酶在分子水平上的 MD 模拟进行了详细研究，而对其与脂质分子的相互作用的研究却很少。因此，在本研究中，我们研究了细菌脂肪酶（铜绿假单胞菌脂肪酶，PAL）与脂质分子（三硬脂酰基甘油，TGL）的分子相互作用。这提供了对酶的界面激活的深入了解。将脂质分子置于酶盖附近，并进行了 100ns 的 MD 模拟，以了解相互作用的性质和位置。结果清楚地表明，脂质分子在盖子附近的存在通过构象变化影响酶的运动。靠近盖子的脂质分子减少了两个盖子的运动，并且观察到 TGL 分子向活性位点移动。讨论了盖子的运动、表面可及性和 PAL 的结构域运动，结果提供了有关两个盖子在 PAL 与 TGL 的界面激活中所起作用的有价值的见解。
