β-葡萄糖苷酶在第二代生物燃料(2G-biofuel)生产中起着关键作用。对于此应用程序,由于生物反应器上的变性条件,热稳定酶是必需的。随机氨基酸取代已经产生了新的热稳定的β-葡萄糖苷酶,但没有清楚了解它们的分子机制。这里,我们通过不同的分子动力学模拟方法与不同的力场和提交的结果进行各种计算分析,多粘芽孢杆菌GH1β-葡萄糖苷酶通过两点突变E96K(TR1)和M416I(TR2)热稳定的分子基础。不同温度下的平衡分子动力学模拟(EMD),主成分分析(PCA),虚拟对接,元动力学(MetaDy),加速分子动力学(aMD),泊松-玻尔兹曼表面分析,网格不均匀溶剂化理论和菌落方法对构象熵的估计可以收敛到这样的想法,即两种取代所携带的稳定取决于三种经典机制的不同贡献:(i)静电表面稳定;(ii)从溶剂中有效分离疏水核,在溶剂化帽具有能量优势;(iii)移动活性位点环比蛋白质核心的蛋白质动力学分布更高,具有功能和熵的优势。机制i和ii占TR1的主导地位,而在TR2中,机制iii占主导地位。循环A完整性和循环A,C,D,E动力学在这种机制中起着至关重要的作用。热稳定突变体和野生型蛋白与氨基酸共进化网络和来自文献的热稳定热点之间观察到的动态和拓扑变化的比较允许推断这里恢复的机制可以与通过沿着整个家族GH1的不同取代获得的热稳定性有关。我们希望这里讨论的结果和见解可以有助于未来合理的方法来优化β-葡萄糖苷酶的工程,用于工业的2G-生物燃料生产,生物技术,和科学。
β-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β-glucosidase by two-point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co-evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β-glucosidases for 2G-biofuel production for industry, biotechnology, and science.