College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China.
Bioorg Med Chem Lett. 2012 Jan 15;22(2):837-43. doi: 10.1016/j.bmcl.2011.12.053. Epub 2011 Dec 16.
The hydrolysis of cellobiose by β-glucodisases is an important step of cellulose biodegradation. However, the interactive mechanism between cellobiose and β-glucosidases is still unclear until now. Thus, in this study, we explored the binding modes between cellobiose and three β-glucosidases from glycoside hydrolase family 1 by means of molecular docking. The three β-glucosidases were named as TmGH1 (from bacterium Thermotoga), SsGH1 (from archaea Sulfolobus solfataricus) and TrGH1 (from fungus Trichoderma reesei) respectively, according to the monophyletic groups they belong to. Molecular dockings were performed between cellobiose and the three β-glucosidases, resulting in three optimum docking complexes, that is TmGH1-cellobiose, SsGH1-cellobiose and TrGh1-cellobiose complexes. Our docking results indicated that there were non-bonded interactions between cellobiose and the three β-glucosidases. The binding affinities of the three complexes were -13.6669kJ/mol, -13.2973kJ/mol and -18.6492kJ/mol, respectively. Then the detailed interactions were investigated, which revealed the key amino acid residues interacted with cellobiose by hydrogen bonds (H-bonds) or hydrophobic interactions. It was observed that most of the key residues involved in the non-bonded interactions were equivalent and conserved for the three complexes, and these residues were a glutamine, a histidine, a tyrosine, a phenylalanine, three glutamics, and four tryptophans. This information is of great importance for designing β-glucosidase with higher cellobiose-hydrolyzing efficiency.
β-葡萄糖苷酶对纤维二糖的水解是纤维素生物降解的重要步骤。然而，到目前为止，纤维二糖与β-葡萄糖苷酶之间的相互作用机制仍不清楚。因此，在本研究中，我们通过分子对接探索了纤维二糖与糖苷水解酶家族 1 中的三种β-葡萄糖苷酶（分别来自细菌 Thermotoga 的 TmGH1、来自古菌 Sulfolobus solfataricus 的 SsGH1 和来自真菌 Trichoderma reesei 的 TrGH1）之间的结合模式。分子对接是在纤维二糖和三种β-葡萄糖苷酶之间进行的，得到了三个最佳的对接复合物，即 TmGH1-纤维二糖、SsGH1-纤维二糖和 TrGh1-纤维二糖复合物。我们的对接结果表明，纤维二糖与三种β-葡萄糖苷酶之间存在非键相互作用。三个复合物的结合亲和力分别为-13.6669kJ/mol、-13.2973kJ/mol 和-18.6492kJ/mol。然后我们对详细的相互作用进行了研究，结果表明，三个复合物中的关键氨基酸残基通过氢键（H-bonds）或疏水相互作用与纤维二糖相互作用。观察到，参与非键相互作用的大多数关键残基在三个复合物中是等效且保守的，这些残基是一个谷氨酰胺、一个组氨酸、一个酪氨酸、一个苯丙氨酸、三个谷氨酸和四个色氨酸。这些信息对于设计具有更高纤维二糖水解效率的β-葡萄糖苷酶具有重要意义。
