The effect of ionic liquid on the structure of active site pocket and catalytic activity of a β-glucosidase from Halothermothrix orenii

Abstract

Abstract Understanding the inhibition of cellulase activity in the presence of ionic liquids (IL) is extremely important towards engineering IL tolerant enzymes for biomass saccharification and subsequent biofuel production. Here we report the all-atom molecular dynamics simulations of a highly active and thermostable GH1 β-glucosidase (EC 3.2.1.21) B8CYA8 from Halothermothrix orenii in the presence of the IL, 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]). In the presence of IL, we observed a lack of destabilization of the overall protein structure but instead a localized increase in fluctuations of active site pocket residues corresponding to the loop region, gatekeeper region, aglycone binding site, and glycone binding site. The role of specific residues was confirmed by the Principal Component Analysis (PCA) and Chemical Shift Perturbation (CSP) analyses. Since the enzymatic saccharification requires the proper arrangement of catalytic side chains, residue fluctuation within the active site tunnel affects the reaction rate. Indeed, while B8CYA8 exhibits very high IL tolerance, high concentrations of IL inhibit the enzyme, our analyses show that in high concentrations of IL, the IL accumulates at the active site pocket entrance and near the active site catalytic residues to restrict substrate accessibility to the catalytic site and decreases enzyme activity. Unlike the reaction product glucose, the IL does not change the overall tunnel diameter to constrict substrate access. To understand how IL viscosity may affect enzyme behavior, we determined the self-diffusion constant and show that the presence of IL has a significant effect on substrate access to the catalytic site due to the low diffusivity of the substrate in IL. These results highlight the role played by the residues in active site pocket and the IL properties and may guide in the design of better protein and IL pairs for efficient catalysis.