Docking Study of β-glucosidase B (BglB) from P. Polymyxca with Cellobiose and Cellotetrose

Mazlan, Nur Shima Fadhilah; Khairudin, Nurul Bahiyah Ahmad

doi:10.12720/jomb.3.2.78-83

Cited by 3 publications

(2 citation statements)

References 9 publications

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“…Earlier, Haq and colleagues [4] using different docking models showed that BglA of T. petrophila contained two or three conserved Glu residues (Glu 166, 351, and 405) in close contact to the substrate to catalyze the reaction. In our studies, Glu166 and Glu405 were in hydrophobic contact with cellobiose and may have a role in recognition of inhibitors, as reported earlier by Mazlan and Khairudin [7]. Moreover, Trp122, Glu166, Gly224, Tyr294, Tyr295, Trp324, Phe414, and Glu405 ( Fig.…”

Section: Discussionsupporting

confidence: 87%

Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach

Rajoka

Idrees²,

Ashfaq³

et al. 2015

Journal of Microbiology and Biotechnology

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Thermostable enzymes derived from Thermotoga maritima have attracted worldwide interest for their potential industrial applications. Structural analysis and docking studies were preformed on T. maritima β-glucosidase enzyme with cellobiose and pNP-linked substrates. The 3D structure of the thermostable β-glucosidase was downloaded from the Protein Data Bank database. Substrates were downloaded from the PubCehm database and were minimized using MOE software. Docking of BglA and substrates was carried out using MOE software. After analyzing docked enzyme/substrate complexes, it was found that Glu residues were mainly involved in the reaction, and other important residues such as Asn, Ser, Tyr, Trp, and His were involved in hydrogen bonding with pNP-linked substrates. By determining the substrate recognition pattern, a more suitable β-glucosidase enzyme could be developed, enhancing its industrial potential.

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Section: Discussionsupporting

confidence: 87%

Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach

Rajoka

Idrees²,

Ashfaq³

et al. 2015

Journal of Microbiology and Biotechnology

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“…The cellobiose structure was obtained from the ZINC database (http://zinc.docking.org). 61 For each system, we used grid sizes of 60 × 98 × 56 (X, Y, Z), centered at the geometric center occupied by the catalytic triad. This considerable grid size was selected to contain all residues suggested in the literature relevant to substrate interactions and obtain a sufficient margin for the structural changes in the different protein constructions at different temperatures 7,62 .…”

Section: Methodsmentioning

confidence: 99%

Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β‐glucosidase probed by multiple MD and computational approaches

et al. 2022

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β‐glucosidases play a pivotal role in second‐generation biofuel (2G‐biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β‐glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β‐glucosidase by two‐point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson‐Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co‐evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β‐glucosidases for 2G‐biofuel production for industry, biotechnology, and science.

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A molecular dynamics study of Beta-Glucosidase B upon small substrate binding

Mazlan

Khairudin

2015

Journal of Biomolecular Structure and Dynamics

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Paenibacillus polymyxa β-glucosidase B (BglB), belongs to a GH family 1, is a monomeric enzyme that acts as an exo-β-glucosidase hydrolysing cellobiose and cellodextrins of higher degree of polymerization using retaining mechanism. A molecular dynamics (MD) simulation was performed at 300 K under periodic boundary condition for 5 ns using the complexes structure obtained from previous docking study, namely BglB-Beta-d-glucose and BglB-Cellobiose. From the root-mean-square deviation analysis, both enzyme complexes were reported to deviate from the initial structure in the early part of the simulation but it was stable afterwards. The root-mean-square fluctuation analysis revealed that the most flexible regions comprised of the residues from 26 to 29, 43 to 53, 272 to 276, 306 to 325 and 364 to 367. The radius of gyration analysis had shown the structure of BglB without substrate became more compact towards the end of the simulation compare to other two complexes. The residues His122 and Trp410 were observed to form stable hydrogen bond with occupancy higher than 10%. In conclusion, the behaviour of BglB enzyme towards the substrate binding was successfully explored via MD simulation approaches.

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Docking Study of β-glucosidase B (BglB) from P. Polymyxca with Cellobiose and Cellotetrose

Cited by 3 publications

References 9 publications

Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach

Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach

Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β‐glucosidase probed by multiple MD and computational approaches

A molecular dynamics study of Beta-Glucosidase B upon small substrate binding

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