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

Molecules

Johannes Kraml¹  KlausRoman Liedl¹  CarlosHenrique da Silveira²  DiegoCésar Batista Mariano³  RaquelCardoso de Melo-Minardi³  RafaelEduardo Oliveira Rocha³  LeonardoHenrique Franca de Lima⁴  LeonSulfierry Corrêa Costa⁴ 

[1] Institute of General, Inorganic and Theoretical Chemistry (IGITC), Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens-Universität-Innsbruck, Innrain 82, 6020 Innsbruck, Austria;Institute of Technological Sciences, Universidade Federal de Itajubá, Campus Itabira, Itabira 35903-087, Brazil;Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;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;

关键词: β-Glucosidases;    GH1;    GH3;    glucose tolerance;    slingshot mechanism;    allosteric channel;    molecular dynamics simulation;    free energy landscape;    Poisson–Boltzmann surface area;    grid inhomogeneous solvation theory;   

DOI  :  10.3390/molecules24183215

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown