Understanding how natural enzymes work can be used in the development of novel, efficient and cost-effective synthetic enzymes. To accomplish this aim, we have studied the mechanism of action of glycerophosphodiesterase (GpdQ) enzyme, which displays an uncommon activity by hydrolyzing all three kinds of phosphoesters (mono, di, and tri). Interestingly, this substrate promiscuous enzyme has been proposed as a promising agent for the remediation of pesticides and the deactivation of nerve agents. In this work, we have exhausted various computational techniques in understanding the enzyme-substrate interactions, their mechanism of action and use this information to develop metal containing synthetic analogues. Primarily, four chemically diverse substrates i.e. NPP (phosphomonoester), BNPP, and GPE (phosphodiester), and paraoxon (phosphotriester) and their interaction with GpdQ was elucidated. Our molecular dynamics simulations showed that the chemical nature of the substrate influences its binding mode by changing the coordination flexibility of the enzyme’s active site. Additionally, QM and QMMM method were used to elaborate the reaction mechanism of this enzyme, which shows the energy barrier of phosphodiesters (~10 kcal/mol) is lower than phosphotriesters (12.7 kcal/mol) and phosphomonoesters (23.1 kcal/mol). Finally, have also studied the reaction mechanism of Zn(II), Fe(III), Cu(II) containing metallohydrolases of GpdQ analogs. Our results provide a deeper understanding of the complex mechanism of not only of GpdQ but of other related binuclear synthetic analogues of metallohydrolases as well and may form the basis for the engineering of optimized enzyme variants (mutants) for applications in bioremediation and other relevant processes in biotechnology.<br/>

Reaction mechanism of glycerophosphodiesterase (gpdq) and its synthetic analogues

2019 Spring National Meeting

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