Paper Citing NAMD - Abstract
Li, Jinghua; Du, Likai; Wang, Lushan
Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15261-15268, NOV 25 2010
Cellulase Cel7A from Trichoderma reesei is one of the most abundant and effective cellulases. Structural studies have established that Cel7A is a retaining glycosidase and it can processively hydrolyze cellobiose units from the reducing end of a cellulose chain. Here, to elucidate the mechanism of enzymatic catalysis of cellulase Cel7A, we carried out a multisized level theoretical study by performing MD, QM, and QM/MM calculations. At the accurate level of theory, we showed the mechanism details of the catalytic cycle, which involves the configuration inversion of the anomeric center twice: the first results in the glycosidic bond cleavage and the formation of covalent glycosyl-enzyme intermediate, and the second restores the anomeric carbon to its original configuration. Calculated results have provided detailed structural and energetic information about these two processes, both of which proceed according to a S(N)2-type-like mechanism via loose transition state structures. It is clearly indicated that the glycosidic bond hydrolysis involves the formation of a covalent glycosyl-enzyme intermediate, which has been identified as the minimum on the potential energy surface. At the catalytic active region, hydrogen bond interactions exist throughout the whole process of the catalytic cycle, which are of special importance for stabilizing the glycosyl-enzyme intermediate. The present results provide a clear paradigm of the mechanisms of general glycosidases, which hydrolyze the glycosidic bonds with net retention of the anomeric configuration.
