Taylor J S, Teo B, Wilson D B, Brady J W
Department of Food Science, Cornell University, Ithica, NY 14853, USA.
Protein Eng. 1995 Nov;8(11):1145-52. doi: 10.1093/protein/8.11.1145.
Molecular mechanics calculations have been used to place a cellotetraose substrate into the active site of the crystallographically determined structure of endocellulase E2 from Thermomonospora fusca. In the lowest energy model structure, the second residue of the substrate oligosaccharide is tilted away from the planar ribbon geometry of cellulose as it is in the X-ray structure of the E2cd-cellobiose co-crystal. This tilt is the result of the topology of the binding site, and results in several strong carbohydrate-protein hydrogen bonds. The tilting produces a twisting of the glycosidic linkage of the cleavage site between residues two and three. In the predicted enzyme-substrate complex both of the Asp residues believed to function in general acid and base roles in the previously proposed model for the mechanism are distant from the bond being cleaved. Molecular dynamics simulations of the complex were conducted, and while the putative catalytic Asp residues remained distant from the cleavage site, the proton of Tyr73 briefly came within van der Waals contact of the linkage oxygen.
分子力学计算已被用于将纤维四糖底物放置到来自嗜热栖热放线菌的内切纤维素酶E2晶体结构测定的活性位点中。在能量最低的模型结构中，底物寡糖的第二个残基如在E2cd-纤维二糖共晶体的X射线结构中那样，倾斜远离纤维素的平面带状结构。这种倾斜是结合位点拓扑结构的结果，并导致几个强的碳水化合物-蛋白质氢键。这种倾斜导致残基2和3之间裂解位点的糖苷键发生扭曲。在预测的酶-底物复合物中，在先前提出的机制模型中被认为起一般酸和碱作用的两个天冬氨酸残基都远离被裂解的键。对该复合物进行了分子动力学模拟，虽然假定的催化天冬氨酸残基仍远离裂解位点，但Tyr73的质子短暂地进入了连接氧的范德华接触范围内。
