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Tytuł:
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Deciphering effectual binding potential of xylo-substrates towards xylose isomerase and xylokinase through molecular docking and molecular dynamic simulation.
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Autorzy:
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Skariyachan S; Department of Microbiology, St. Pius X College Rajapuram, Kasaragod, India.
Khangwal I; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India.
Niranjan V; Department of Biotechnology, R.V. College of Engineering, Bangalore , Karnatka, India.
Kango N; Enzyme Technology and Molecular Catalysis Laboratory, Department of Microbiology, Dr. Hari Singh Gour Vishwavidyalaya (A Central University), Sagar, India.
Shukla P; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India.
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Źródło:
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Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2021 Jul; Vol. 39 (11), pp. 3948-3957. Date of Electronic Publication: 2020 Jun 08.
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Typ publikacji:
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Journal Article
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Język:
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English
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Imprint Name(s):
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Publication: June 2012- : Oxon, UK : Taylor & Francis
Original Publication: Guilderland, NY : Adenine Press, [c1983-
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MeSH Terms:
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Aldose-Ketose Isomerases*
Molecular Dynamics Simulation*
Molecular Docking Simulation
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Contributed Indexing:
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Keywords: Molecular docking; Xylobiose; Xylotriose; molecular dynamic simulation
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Substance Nomenclature:
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EC 5.3.1.- (Aldose-Ketose Isomerases)
EC 5.3.1.5 (xylose isomerase)
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Entry Date(s):
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Date Created: 20200609 Date Completed: 20210811 Latest Revision: 20210811
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Update Code:
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20240104
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DOI:
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10.1080/07391102.2020.1772882
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PMID:
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32508225
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Xylooligosaccharides (XOS) such as xylobiose and xylotriose are prebiotics with important functions and relevance and the study of interaction mechanism between these substrate and their respective enzymes has scope and applications. Thus, the present study aimed to decipher the interaction mechanisms of xylose isomerase (XylA) and xylokinase (XylB) towards their xylo-substrates namely xylobiose and xylotriose by computational modeling and molecular dynamic simulation studies. The three-dimensional structures of XylA and XylB, not available in their native forms, were predicted, energy minimized and validated by various computational biology tools and software. The binding mechanisms of xylobiose and xylotriose towards XylA and XylB were modeled by molecular docking and the stability of the docked complexes was confirmed by molecular dynamic (MD) simulation. The current study suggested that the theoretical models of XylA and XylB possessed good stereo-chemical validity, structural stabilities and minimum energy conformers. The molecular docking studied showed that xylotriose showed better binding interactions to XylA than xylobiose and xylobiose showed better binding interaction to XylB than xylotriose with ideal root mean square deviation (RMS), minimum binding energy (kcal/mol), hydrogen bonding and weak interactions. The MD simulation confirmed the stabilities of the docked complexes predicted by docking studies. The study suggested that interactions between the probiotics and prebiotics and provides the novel insights in exploring synbiotics as functional foods towards their futuristic applications. [Formula: see text]HighlightsThis study deciphers the interactions of xylosubstrates to XylA and XylB.The XylA and XylB possessed ideal structural stability and stereochemistryXylotriose and Xylobiose showed significant interactionsThe interactions of Xylotriose-XylA and Xylobiose-XylB were found stable in MD studies.Communicated by Ramaswamy H. Sarma.
