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Author(s): Natércia F.Braz
Pedro A. Fernandes
Maria J. Ramos
Title: QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions
Issue Date: 2010
Abstract: Carbohydrates perform a wide range of crucial functions in biological systems andare of great interest for the food and pharmaceutical industries. -Galactosidase from Escherichiacoli catalyzes both the hydrolytic breaking of the very stable glycosidic bond of lactose and aseries of transglycosylation reactions. These reactions are crucial for the development of newcarbohydrate molecules, as well as the optimization of their syntheses. In this work we haveused computational methods to study the catalytic mechanism of hydrolysis and a set of distincttransglycosylation reactions of a retaining galactosidase, with atomic detail, with lactose as thenatural substrate. The ONIOM method (BB1K:AMBER//B3LYP:AMBER calculations) wasemployed to address such a large enzymatic system. Such a methodology can efficiently accountfor the stereochemistry of the reactive residues, as well as the long-range enzyme-substrateinteractions. The possible importance of the magnesium ion in the catalytic reaction wasinvestigated, and it was found that, indeed, the magnesium ion catalyzes the transformation,lowering the activation barrier by 14.9 kcal/mol. The calculations indicate that the formation of(1-3) glycosidic linkages is thermodynamically very unfavorable. In contrast, the formation of(1-6) glycosidic bonds is the most favored, in complete agreement with the enantioselectivityobserved experimentally. The data also clearly show the importance of the enzyme scaffoldbeyond the first-shell amino acids in the stabilization of the transition states. It is fundamentalto include the enzyme explicitly in computational studies.
Subject: Engenharia química
Chemical engineering
Scientific areas: Ciências da engenharia e tecnologias::Engenharia química
Engineering and technology::Chemical engineering
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:FCUP - Artigo em Revista Científica Internacional

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