a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China.
b National Engineering Laboratory for AIDS Vaccine, School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China.
J Biomol Struct Dyn. 2019 Mar;37(5):1360-1374. doi: 10.1080/07391102.2018.1450164. Epub 2018 Mar 24.
Glycoside hydrolase cellulase family 6 from Trichoderma reesei (TrCel6A) is an important cellobiohydrolase to hydrolyze cellooligosaccharide into cellobiose. The knowledge of enzymatic mechanisms is critical for improving the conversion efficiency of cellulose into ethanol or other chemicals. However, the process of product expulsion, a key component of enzymatic depolymerization, from TrCel6A has not yet been described in detail. Here, conventional molecular dynamics and steered molecular dynamics (SMD) were applied to study product expulsion from TrCel6A. Tyr103 may be a crucial residue in product expulsion given that it exhibits two different posthydrolytic conformations. In one conformation, Tyr103 rotates to open the -3 subsite. However, Tyr103 does not rotate in the other conformation. Three different routes for product expulsion were proposed on the basis of the two different conformations. The total energy barriers of the three routes were calculated through SMD simulations. The total energy barrier of product expulsion through Route 1, in which Tyr103 does not rotate, was 22.2 kcal·mol. The total energy barriers of product expulsion through Routes 2 and 3, in which Tyr103 rotates to open the -3 subsite, were 10.3 and 14.4 kcal·mol, respectively. Therefore, Routes 2 and 3 have lower energy barriers than Route 1, and Route 2 is the thermodynamically optimal route for product expulsion. Consequently, the rotation of Tyr103 may be crucial for product release from TrCel6A. Results of this work have potential applications in cellulase engineering.
里氏木霉（Trichoderma reesei）的糖苷水解酶纤维素酶家族 6（TrCel6A）是一种重要的纤维二糖水解酶，可将纤维寡糖水解成纤维二糖。了解酶的作用机制对于提高纤维素转化为乙醇或其他化学品的效率至关重要。然而，TrCel6A 中产物释放的过程（酶解的关键组成部分）尚未详细描述。本研究应用传统分子动力学和导向分子动力学（SMD）研究了 TrCel6A 中产物的释放。由于 Tyr103 在后水解构象中表现出两种不同的构象，因此 Tyr103 可能是产物释放的关键残基。在一种构象中，Tyr103 旋转以打开-3 亚位点。然而，在另一种构象中，Tyr103 不旋转。基于这两种不同的构象，提出了三种不同的产物释放途径。通过 SMD 模拟计算了这三种途径的总能量障碍。在 Tyr103 不旋转的途径 1 中，产物释放的总能量障碍为 22.2 kcal·mol。在 Tyr103 旋转以打开-3 亚位点的途径 2 和 3 中，产物释放的总能量障碍分别为 10.3 和 14.4 kcal·mol。因此，途径 2 和 3 的能量障碍低于途径 1，途径 2 是产物释放的热力学最优途径。因此，Tyr103 的旋转可能对 TrCel6A 中产物的释放至关重要。这项工作的结果在纤维素酶工程中有潜在的应用。
