Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases

Geronimo, Inacrist; Ntarima, Patricia; Piens, Kathleen; Gudmundsson, Mikael; Hansson, Henrik; Sandgren, Mats; Payne, Christina M.

doi:10.1074/jbc.ra118.007027

Cited by 8 publications

(5 citation statements)

References 60 publications

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“…Future studies of rational design of more glucose-tolerant GH3s can take the enhancing of the hydrophobicity at the flat region immediately outside the catalytic cleft and promote a higher water exclusion effect compared to the cleft itself. This could be of interest due to the higher usual catalytic activity of this class of enzymes [29,30]. Another possibility could be the shortening of the external loops, once their approximation contributes to bringing the −1 subsite residues on the imprisonment position around glucose (Figure S4).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…More specifically, by using hydrolytic enzymes as βglycosidases, food industries can improve the organoleptic properties of their products (juice, wine) or enrich them with nutritional aglycones (o-diphenols, coumarins, flavonoids, isoflavones), which mostly demonstrate enhanced bioactivities and aroma (Fernández-Pacheco et al, 2021;Monteiro et al, 2019); Several aglycone derivatives are of high pharmaceutical interest too (Cheng and Zhang, 2017;Ma et al, 2020). BGLs can also catalyze transglycosylation reactions (Ahmed et al, 2017;Xia et al, 2022); Especially immobilized β-glucosidases are ideal candidates for targeted enzymatic glycosylation of natural compounds due to the decreased enzyme inhibition by the substrates (Geronimo et al, 2019). To date, diverse BGLs have been explored to produce valuable compounds benefiting from the inclusion of DESs as co-solvents (Cheng and Zhang, 2017;Uhoraningoga et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Effect of deep eutectic solvents on the biocatalytic properties of β-glucosidase@ZnOFe nano-biocatalyst

Fotiadou

Bellou²,

Spyrou³

et al. 2022

Sustainable Chemistry and Pharmacy

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“…Molecular dynamics free energy simulation is a powerful approach to evaluate favorable substrate-binding modes at enzyme active sites and to infer substrate selectivity, , but this has not been applied in GH70. We used the crystal structure of LrN1 GtfB to perform molecular dynamics (MD) simulations with maltose and maltoheptaose (G7).…”

Section: Resultsmentioning

confidence: 99%

Insights into the Structure–Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme

Dong,

Bai,

Wang

et al. 2024

J. Agric. Food Chem.

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α-Glucanotransferases of the CAZy family GH70 convert starch-derived donors to industrially important α-glucans.Here, we describe characteristics of a novel GtfB-type 4,6-α-glucanotransferase of high enzyme activity (60.8 U mg −1 ) from Limosilactobacillus reuteri N1 (LrN1 GtfB), which produces surprisingly large quantities of soluble protein in heterologous expression (173 mg pure protein per L of culture) and synthesizes the reuteran-like α-glucan with (α1 → 6) linkages in linear chains and branch points. Protein structural analysis of LrN1 GtfB revealed the potential crucial residues at subsites −2∼+2, particularly H265, Y214, and R302, in the active center as well as previously unidentified surface binding sites. Furthermore, molecular dynamic simulations have provided unprecedented insights into linkage specificity hallmarks of the enzyme. Therefore, LrN1 GtfB represents a potent enzymatic tool for starch conversion, and this study promotes our knowledge on the structure−function relationship of GH70 GtfB α-glucanotransferases, which might facilitate the production of tailored α-glucans by enzyme engineering in future.

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Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases

Abstract: The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1-S5 and Tables S1-S13.

Cited by 8 publications

References 60 publications

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

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

Effect of deep eutectic solvents on the biocatalytic properties of β-glucosidase@ZnOFe nano-biocatalyst

Insights into the Structure–Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme

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