蛋白质设计研究组知识库

QM/MD simulations are performed to study mutational effects on the glycosylation step of the oligosaccharide hydrolysis catalyzed by Trichoderma reesei cellobiohydrolase I. The potential of mean force along the reaction pathway is determined by the umbrella sampling method. A detailed mechanism is developed to illustrate the decrease in activity of the mutants. Our calculations demonstrate that (1) the E212Q mutation increases the overall activation barrier by ~4.0 kcal/mol, while the D214N mutation causes ~0.4 kcal/mol increase of the barrier, and (2) there is only one transition state identified in the wild type (WT) and D214N mutant, while two transition states exist in the E212Q mutant for the glycosylation process. The results explain the experimental observation that the E212Q mutant loses most of its hydrolysis capability, while the D214N mutant only reduces it slightly compared to the WT. Further analysis suggests that the proton transfer from Glu(217) to O(4) and the glycosidic bond cleavage between subsites +1 and -1 are concerted, facilitating the subsequent nucleophilic attack of Glu(212) on C(1)' in subsite -1. Our QM/MD study illustrates the importance of the prearrangement of the active site and provides atomic details of the enzymatic catalytic mechanism.