Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics
Rui P. P. Neves, Pedro Alexandrino Fernandes, Maria J. Ramos
Abstract
conformation was also observed. Altogether, the combination of short distances for the acid-base reaction with the Glu233 and for the nucleophilic attack by the Asp197 nucleophile and the availability of water within hydrogen bonding distance of the glycosidic oxygen provides a reliable criteria to identify reactive conformations of α-amylase complexes.
Topics & Concepts
ChemistryMolecular dynamicsStereochemistryNucleophileActive siteSubstrate (aquarium)Hydrogen bondSN2 reactionCrystallographyComputational chemistryMoleculeCatalysisOrganic chemistryOceanographyGeologyEnzyme Production and CharacterizationEnzyme Structure and FunctionEnzyme Catalysis and Immobilization