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Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates

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Abstract

Glycosidases constitute a vast family of enzymes that catalyze the breaking and formation of glycosidic bonds. The synthesized oligosaccharides, being crucial to life, are involved in many biochemical processes, particularly in the pharmaceutical and food industries. The proposed catalytic mechanism of retaining glycoside hydrolases (glycosidases) occurs via a double displacement mechanism involving a covalent glycosyl enzyme intermediate. During the transglycosylation reactions, the control of the stereoselectivity for the formation of the new bond remains a complicated problem in the chemical synthesis of oligosaccharides. In this paper, docking and molecular dynamics methods were used to study the second step of the mechanism of transglycosylation in retaining glycosidases from six microorganisms with known stereoselectivity. Using the natural substrates as donor and acceptor molecules, we were able to corroborate and provide structural information about the active site, the trapped monosaccharide acceptor and the bound intermediates during the step that precedes transglycosylation, as well as identify and understand the commonly displayed stereoselectivity by these glycosidases in nature. The information obtained with this procedure helps to recognize, explain and predict the stereoselectivity of the sugars studied. These kind of procedures can be used to improve the efficiency of large-scale industrial synthesis of a specific sugar.

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Acknowledgments

The authors would like to thank the Portuguese Science and Technology Foundation (FCT-MCTES) for financial support (scholarship SFRH/BD/31359/2006).

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Authors and Affiliations

  1. REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007, Porto, Portugal

    Natércia F. Brás, Pedro A. Fernandes & Maria J. Ramos

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  1. Natércia F. Brás
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  2. Pedro A. Fernandes
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  3. Maria J. Ramos
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Correspondence to Maria J. Ramos.

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Brás, N.F., Fernandes, P.A. & Ramos, M.J. Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates. Theor Chem Account 122, 283–296 (2009). https://doi.org/10.1007/s00214-009-0507-2

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