Combined MD and QM/MM Calculations Reveal Allostery‐Driven Promiscuity in Dipeptide Epimerases of Enolase Family

Abstract

The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…A combination of ChemShell QM/MM simulations and serial crystallography, which provides a ''movie'' of the reduction process in a protein crystal, yield complementary information on the system, resulting in a full description of the reaction mechanism. 107 The flexibility of QM/MM approaches to describe a wide range of metal cofactors is demonstrated by recent ChemShell applications on magnesium-dependent taxadiene synthase 108 and ala-glu-epimerase, 109 xyloside a-1,3-xylosyltransferase (where magnesium was modelled in place of manganese), 110 nickel-containing quercetinases, 111,112 tungsten-dependent benzoyl-coenzyme A reductase 113 and zinc-dependent leukotriene A 4 hydrolase, 114 matrix metalloproteinase-1 115 and matrix metalloproteinase-9. 116 Zhao et al used ChemShell to find the most favourable pathway for catalysis of N-N bond formation by a family of zinc-binding cupin proteins.…”