Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases

• Published in: Molecules (Basel, Switzerland) Switzerland), 2019-09, Vol.24 (18), p.3215
• Main Authors: Costa, Leon Sulfierry Corrêa, Mariano, Diego César Batista, Rocha, Rafael Eduardo Oliveira, Kraml, Johannes, Silveira, Carlos Henrique da, Liedl, Klaus Roman, de Melo-Minardi, Raquel Cardoso, Lima, Leonardo Henrique Franca de
• Format: Article
• Language: English
• Subjects: allosteric channel; Allosteric properties; Amino Acids; beta-Glucosidase - chemistry; beta-Glucosidase - metabolism; Binding sites; Biodiesel fuels; Biofuels; Catalytic Domain; Cellobiase; Design optimization; Enzymes; Free energy; free energy landscape; GH1; GH3; Glucose; Glucose - chemistry; Glucose - metabolism; Glucose tolerance; Glucosidase; grid inhomogeneous solvation theory; Hydrophobicity; Kinetics; Ligands; Lignocellulose; Molecular Conformation; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; Mutation; Poisson–Boltzmann surface area; Principal components analysis; Product inhibition; Protein Binding; Proteins; Simulation; slingshot mechanism; Solvation; Structure-Activity Relationship; Substrate Specificity; Sugar; Water activity; β-Glucosidase; β-Glucosidases
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules24183215

β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson-Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests.