分子动力学模拟研究壳寡糖与脂肪酶相互作用机制

A Molecular Dynamics Simulation Study on the Mechanism Underlying the Interaction between Chitooligosaccharides and Lipase

壳聚糖及其衍生物在酶固定化领域有着广泛的应用。了解酶与壳聚糖衍生物在分子水平上的相互作用机制,对相关生物催化剂的设计和应用具有重要意义。本研究采用分子动力学模拟方法研究南极假丝酵母脂肪酶B(CaLB)与壳寡糖(OCTS)的相互作用,并对脂肪酶与催化底物进行分子对接研究脂肪酶催化活性中心和底物结合构象和结合亲和力。结果表明,脂肪酶与OCTS之间的静电和L-J相互作用在自组装过程的初始阶段起着重要的作用。模拟过程结束后,CaLB-OCTS组装体共包含14个OCTS分子和1个CaLB分子。CaLB与OCTS之间存在静电相互作用和氢键相互作用,在模拟过程中,L-J势能和库仑势能分别降低了约1480 kJ/mol和2324.0 kJ/mol,两者间的平均氢键数从0增加到约17,CaLB与OCTS的可及面积均因为相互作用而降低了20 nm2。二级结构表明,与游离酶对照相比,CaLB-OCTS的β折叠含量从9.78%增加至12.62%,无规卷曲loop从49.21%下降至46.50%,CaLB-OCTS的β折叠的含量更高,而无规卷曲含量更低。此外,CaLB-OCTS保留了其原有的蛋白骨架结构以及活性位点口袋的构象。

Chitosan and its derivatives have a wide range of applications in the field of enzyme immobilization.Understanding the mechanism of the interaction between enzymes and chitosan derivatives at the molecular level is of great significance to the design and application of related biocatalysts.In this study,molecular dynamics simulation was used to investigate the interaction of Candida Antarctica Lipase B(CaLB)and oligo-chitosan(OCTS),and molecular docking of lipase and catalytic substrate was conducted to study the binding conformation and affinity for the catalytically active centre of CaLB and substrate.The results showed that both electrostatic and L-J interactions between CaLB and OCTS play important roles in the initial stage of the self-assembly process.After the simulation process,the CaLB-OCTS assembly contained 14 OCTS molecules and 1 CaLB molecule.The electrostatic interaction and hydrogen bond interaction existed between CaLB and OCTS.During the simulation,the L-J potential energy and Coulomb potential energy decreased by about 1480 KJ/mol and 2324.0 KJ/mol,respectively,with the average number of hydrogen bonds between CaLB and OCTS increasing from 0 to about 17,and the accessible area of both CaLB and OCTS reducing by 20 nm2 due to the interactions.The analysis of secondary structure showed that compared to the free enzyme,the beta-sheet content of CaLB-OCTS increased from 9.78% to 12.62%,and the content of random coil loop decreased from 49.21% to 46.50%.Moreover,the CaLB-OCTS retained its original protein skeleton structure and the conformation of the active site pocket.