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Understanding the Xylooligosaccharides Utilization Mechanism of Lactobacillus brevis and Bifidobacterium adolescentis: Proteins Involved and Their Conformational Stabilities for Effectual Binding.
- Source :
-
Molecular biotechnology [Mol Biotechnol] 2022 Jan; Vol. 64 (1), pp. 75-89. Date of Electronic Publication: 2021 Sep 20. - Publication Year :
- 2022
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Abstract
- Xylooligosaccharides having various degrees of polymerization such as xylobiose, xylotriose, and xylotetraose positively affect human health by interacting with gut proteins. The present study aimed to identify proteins present in gut microflora, such as xylosidase, xylulokinase, etc., with the help of retrieved whole-genome annotations and find out the mechanistic interactions of those with the above substrates. The 3D structures of proteins, namely Endo-1,4-beta-xylanase B (XynB) from Lactobacillus brevis and beta-D-xylosidase (Xyl3) from Bifidobacterium adolescentis, were computationally predicted and validated with the help of various bioinformatics tools. Molecular docking studies identified the effectual binding of these proteins to the xylooligosaccharides, and the stabilities of the best-docked complexes were analyzed by molecular dynamic simulation. The present study demonstrated that XynB and Xyl3 showed better effectual binding toward Xylobiose with the binding energies of - 5.96 kcal/mol and - 4.2 kcal/mol, respectively. The interactions were stabilized by several hydrogen bonding having desolvation energy (- 6.59 and - 7.91). The conformational stabilities of the docked complexes were observed in the four selected complexes of XynB-xylotriose, XynB-xylotetraose, Xyl3-xylobiose, and Xyn3-xylotriose by MD simulations. This study showed that the interactions of these four complexes are stable, which means they have complex metabolic activities among each other. Extending these studies of understanding, the interaction between specific probiotics enzymes and their ligands can explore the detailed design of synbiotics in the future.<br /> (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
- Subjects :
- Bacterial Proteins chemistry
Bacterial Proteins genetics
Bifidobacterium adolescentis genetics
Computational Biology
Disaccharides chemistry
Disaccharides metabolism
Endo-1,4-beta Xylanases chemistry
Endo-1,4-beta Xylanases genetics
Genome, Bacterial genetics
Glucuronates chemistry
Humans
Levilactobacillus brevis genetics
Molecular Docking Simulation
Molecular Dynamics Simulation
Oligosaccharides chemistry
Probiotics metabolism
Trisaccharides chemistry
Trisaccharides metabolism
Xylosidases chemistry
Xylosidases genetics
Bifidobacterium adolescentis metabolism
Glucuronates metabolism
Levilactobacillus brevis metabolism
Oligosaccharides metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1559-0305
- Volume :
- 64
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Molecular biotechnology
- Publication Type :
- Academic Journal
- Accession number :
- 34542815
- Full Text :
- https://doi.org/10.1007/s12033-021-00392-x