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Open AccessArticle

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

1
Laboratory of Molecular and Bioinformatics Modeling, Department of Exact and Biological Sciences (DECEB), Universidade Federal de São João Del-Rei, Campus Sete Lagoas, Sete Lagoas 35701-970, Brazil
2
Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
3
Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
4
Institute of General, Inorganic and Theoretical Chemistry (IGITC), Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens-Universität-Innsbruck, Innrain 82, 6020 Innsbruck, Austria
5
Institute of Technological Sciences, Universidade Federal de Itajubá, Campus Itabira, Itabira 35903-087, Brazil
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Molecules 2019, 24(18), 3215; https://doi.org/10.3390/molecules24183215
Received: 29 July 2019 / Revised: 15 August 2019 / Accepted: 23 August 2019 / Published: 4 September 2019
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. View Full-Text
Keywords: β-Glucosidases; GH1; GH3; glucose tolerance; slingshot mechanism; allosteric channel; molecular dynamics simulation; free energy landscape; Poisson–Boltzmann surface area; grid inhomogeneous solvation theory β-Glucosidases; GH1; GH3; glucose tolerance; slingshot mechanism; allosteric channel; molecular dynamics simulation; free energy landscape; Poisson–Boltzmann surface area; grid inhomogeneous solvation theory
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Costa, L.S.C.; Mariano, D.C.B.; Rocha, R.E.O.; Kraml, J.; Silveira, C.H.; Liedl, K.R.; de Melo-Minardi, R.C.; Lima, L.H.F. Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases. Molecules 2019, 24, 3215.

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    Doi: 10.5281/zenodo.3368753
    Link: https://zenodo.org/record/3368753#.XVSd6pNKgyk
    Description: # VIDEO_FILES (ZENODO) ************************************************** Video S1: MD of the glucose exit in a glucose-tolerant GH1 β-Glucosidase Video S2: Interactions among glucose, D228, K257, and N312 in a glucose-tolerant GH1 β-glucosidase --- # PDF FILE ********************************************************************** Fig. S1. The two starting poses for glucose along the GH1 simulations and comparison with different crystallographic structures.   Fig. S2. Structural alignment of representative poses of HiBG in complex with glucose (GH1-Glucose).   Fig. S3. Structural alignment of representative conformations of HiBG in complex with cellobiose (GH1-Cellobiose).   Fig. S4. Structural alignment of representative conformations of AaBG in complex with glucose (GH3-Glucose).   Fig. S5. Structural alignment of representative conformations of AaBG in complex with cellobiose (GH3-Cellobiose).   Fig. S6. Statistics for the ligand-protein contacts and structure of the substrate channel in GH1-cellobiose complex. Fig. S7. Statistics for the ligand-protein contacts and structure for the substrate channel in GH1-Glucose complex.   Fig. S8. Statistics for the ligand-protein contacts estimated along the MD sets for the GH3-Cellobiose complex.   Fig. S9Statistics for the ligand-protein contacts estimated along the MD sets for the GH3-Glucose complex.   Fig. S10. Comparison of the principal components for the protein and ligand in the different systems.   Fig. S11. Results of APBS and GIST for HiBG and AaBG. (A-C) GH1; and (D-F) GH3. Fig. S12. RMSD against the first frame of each trajectory shows convergence for all systems.   Fig. S13. Conformations recovered by the FEL profiles of the glucose positioning in GH1 and GH3, colored by the APBS and GIST data. --- Table S1. Percentage of hydrogen bonds between residues of HiBG (GH1) with glucose (G) and cellobiose (C). Table S2. Percentage of water-mediated hydrogen bonds between residues of HiBG (GH1) with glucose (G) and cellobiose (C). Table S3. Percentage of hydrophobic contacts between residues of HiBG (GH1) with glucose (G) and cellobiose (C).   Table S4. Percentage of hydrogen bonds between residues of AaBG (GH3) with glucose (G) and cellobiose (C). Table S5. Percentage of water-mediated hydrogen bonds between residues of AaBG (GH3) with glucose (G) and cellobiose (C).   Table S6. Percentage of hydrophobic contacts between residues of AaBG (GH3) with glucose (G) and cellobiose (C).
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