Lu Chenlin, Peng Xue, Lu Diannan, Liu Zheng
Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China.
ACS Omega. 2020 Apr 23;5(17):9806-9812. doi: 10.1021/acsomega.9b04432. eCollection 2020 May 5.
Profiling substrate diffusion pathways with kinetic information, which accounts for the dynamic nature of enzyme-substrate interaction, can enable molecular reengineering of enzymes and process optimization of enzymatic catalysis. lipase B (CALB) is extensively used for producing various chemicals because of its rich catalytic mechanisms, broad substrate spectrum, thermal stability, and tolerance to organic solvents. In this study, an all-atom molecular dynamics (MD) combined with Markov-state models (MSMs) implemented in pyEMMA was proposed to simulate diffusion pathways of 4-nitrophenyl ester (4NPE), a commonly used substrate, from the surface into the active site of CALB. Six important metastable conformations of CALB were identified in the diffusion process, including a closed state. An induced-fit mechanism incorporating multiple pathways with molecular information was proposed, which might find unprecedented applications for the rational design of lipase for green catalysis.
利用动力学信息剖析底物扩散途径，这考虑到了酶 - 底物相互作用的动态性质，能够实现酶的分子改造和酶催化过程的优化。脂肪酶B（CALB）因其丰富的催化机制、广泛的底物谱、热稳定性和对有机溶剂的耐受性，被广泛用于生产各种化学品。在本研究中，提出了一种结合全原子分子动力学（MD）和在pyEMMA中实现的马尔可夫状态模型（MSM），以模拟常用底物4 - 硝基苯酯（4NPE）从表面扩散到CALB活性位点的途径。在扩散过程中确定了CALB的六个重要亚稳构象，包括一个封闭状态。提出了一种包含多条具有分子信息途径的诱导契合机制，这可能为绿色催化脂肪酶的合理设计找到前所未有的应用。
