Probing the Effect of Glucose on the Activity and Stability of β-Glucosidase: An All-Atom Molecular Dynamics Simulation Investigation

Konar, Sukanya; Sinha, Sushant K.; Datta, Supratim; Ghorai, Pradip Kr.

doi:10.1021/acsomega.9b00509

Cited by 30 publications

(23 citation statements)

References 45 publications

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“…To estimate the consequences for ligand accessibility, we have analyzed the average active site width as the mean distance between the Cα atoms of the active site loops ( R Av ) ( Figure 4(B,C) ). This measure has already proved to be well correlated with ligand accessibility/resistance in previous studies (Konar et al., 2019 ; Lima et al., 2020 ). First, we have measured the R av statistics for conformations with the potential of mean force (PMF) at the 20% more favorable values from our MetaDy analyses (i.e.…”

Section: Resultsmentioning

confidence: 66%

A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers

Rocha

Chaves

Fischer

et al. 2021

Journal of Biomolecular Structure and Dynamics

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The main-protease (M pro ) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (M CoV2 pro ) with 12 mutations compared to SARS-CoV (M CoV1 pro ). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of M CoV2 pro , as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the M CoV2 pro monomer compared to M CoV1 pro . A higher hydration propensity for the M CoV2 pro S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for M CoV2 pro are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti M CoV2 pro ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs. Communicated by Ramaswamy H. Sarma

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Section: Resultsmentioning

confidence: 66%

A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers

Rocha

Chaves

Fischer

et al. 2021

Journal of Biomolecular Structure and Dynamics

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“…A comparison with PDB structure 3F5K and 2O9P indicates the presence of the +2 subsite in B8CYA8 which can potentially assist in the non-productive binding of the substrate. Recently we showed that in the presence of low substrate concentrations (1 mM p NPGlc), B8CYA8 is inhibited at all concentrations of glucose [48]. We also reported by MD simulations of B8CYA8 in the presence of glucose that at the gatekeeper region, the number of glucose molecules increases significantly with glucose concentration than inside the pocket [48].…”

Section: Discussionmentioning

confidence: 96%

“…Recently we showed that in the presence of low substrate concentrations (1 mM p NPGlc), B8CYA8 is inhibited at all concentrations of glucose [48]. We also reported by MD simulations of B8CYA8 in the presence of glucose that at the gatekeeper region, the number of glucose molecules increases significantly with glucose concentration than inside the pocket [48]. Our results reported here do not preclude the possibility of substrate binding non-productively to the +1 to +2 subsite or the possibility of glucose binding at this subsite to relieve the non-productive binding of the substrate and increase enzyme activity.…”

Section: Discussionmentioning

confidence: 99%

Elucidating the regulation of glucose tolerance through the interaction between the reaction product and active site pocket residues of a β-glucosidase from Halothermothrix orenii

Sinha

Das

Konar

et al. 2019

Preprint

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2 β-glucosidase catalyzes the hydrolysis of β-1,4 linkage between two glucose molecules in cello-3 oligosaccharides and is prone to inhibition by the reaction product glucose. Relieving the glucose inhibition 4 of β-glucosidase is a significant challenge. Towards the goal of understanding how glucose interacts with 5 β-glucosidase, we expressed in Escherichia coli, the Hore_15280 gene encoding a β-glucosidase in 6 Halothermothrix orenii. Our results show that the enzyme is glucose tolerant, and its activity stimulated in 7 the presence of up to 0.5 M glucose. NMR analyses show the unexpected interactions between glucose and 8 the β-glucosidase at lower concentrations of glucose that however does not lead to enzyme inhibition. We 9 identified non-conserved residues at the aglycone-binding and the gatekeeper site and show that increased 10 hydrophobicity at the pocket entrance and a reduction in steric hindrances are critical towards enhanced 11 substrate accessibility and significant improvement in activity. Analysis of structures and in combination 12 with molecular dynamics simulations show that glucose increases the accessibility of the substrate by 13 enhancing the structural flexibility of the active site pocket and may explain the stimulation in specific 14 activity up to 0.5 M glucose. Such novel regulation of β-glucosidase activity by its reaction product may 15 offer novel ways of engineering glucose tolerance.

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“…Overall, minimal topological modifications represent a promising strategy for suggesting mutations, especially in the beta-glucosidase loop regions that surround the active site. The topology and dynamics of these loops can allow or restrict movements involved in glucose entrance and exit (i.e., glucose tolerance) 30,32,36,43 or also can affect the thermostability [41][42][43] . These are both examples of industrially desirable characteristics for these and other proteins.…”

Section: Implications For Protein Engineeringmentioning

confidence: 99%

VTR: an algorithm for identifying analogous contacts on protein structures and their complexes

Pimentel

Mariano

Cantão

et al. 2020

Preprint

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Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macromolecular structures such as proteins. Here we show VTR, a new method for the detection of analogous contacts in protein pairs. VTR performs structural alignment between proteins and detects interactions that occur in similar regions. To evaluate our tool, we proposed three case studies: (i) we compared a vertebrate myoglobin and a truncated invertebrate hemoglobin; (ii) analyzed interactions between the spike protein RBD of SARS-CoV-2 and the cell receptor ACE2; and (iii) compared a glucose-tolerant and a non-tolerant β-glucosidase enzyme used for biofuel production. The case studies demonstrate the potential of VTR for the understanding of functional similarities between distantly sequence-related proteins, as well as the exploration of important drug targets and rational design of enzymes for industrial applications. We envision VTR as a promising tool for understanding differences and similarities between homologous proteins with similar 3D structures but different sequences. VTR is available at http://bioinfo.dcc.ufmg.br/vtr.

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Probing the Effect of Glucose on the Activity and Stability of β-Glucosidase: An All-Atom Molecular Dynamics Simulation Investigation

Cited by 30 publications

References 45 publications

A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers

A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers

Elucidating the regulation of glucose tolerance through the interaction between the reaction product and active site pocket residues of a β-glucosidase from Halothermothrix orenii

VTR: an algorithm for identifying analogous contacts on protein structures and their complexes

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