Molecular Insight into Glucose-Induced Conformational Change to Investigate Uncompetitive Inhibition of GH1 β-Glucosidase

beta-glucosidase-catalyzed cellobiose conversion to glucose is the principal rate-limiting step in the deconstruction of lignocellulosic biomass to biofuel production as most beta-glucosidases are feedback inhibited by glucose. Thus, deciphering the mechanism of glucose inhibition has been a prime focus for years. In this study, atomistic molecular dynamics simulations were performed to understand the effect of low (0.1 M) and high (0.8 M) glucose concentrations on the structure and dynamics of GH1 beta-glucosidase (H0HC94) from Agrobacterium tumefaciens 5A. A protein structure network was constructed on each protein snapshot from the simulation, suggesting a glucose-induced conformational change of the enzyme in the high glucose concentration. Additionally, the conformational changes were characterized in terms of cliques and communities. The increasing number of cliques rigidified the residue fluctuations around the enzyme's tunnel in the high glucose concentration and hindered the glucose interaction at the active site. It was also supported by the low radial distribution of glucose and no glucose-enzyme hydrogen bonds at the active site tunnel. Moreover, the essential dynamic motions for catalysis were lost by the elevated number of glucose-enzyme interactions in the high glucose concentration. Furthermore, six secondary binding sites were predicted, which could induce uncompetitive inhibition of H0HC94. Overall, we propose a molecular basis of the H0HC94 inhibition, which will further help to design glucose-tolerant beta-glucosidases for sustainable lignocellulosic biofuel production.

Automated summary

This study used molecular dynamics simulations to investigate the impact of low and high glucose concentrations on the structure and dynamics of GH1 beta-glucosidase. It found that high glucose concentrations induced conformational changes in the enzyme and hindered essential dynamic motions for catalysis, providing insights into the molecular basis of H0HC94 inhibition.