Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production

Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of D-xylulose 5-phosphate (XU5P) and D-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicoti...

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Main Author:	Razali, Siti Aisyah
Format:	Thesis
Language:	English
Published:	2018
Subjects:	Q Science (General)
Online Access:	http://eprints.utm.my/id/eprint/81420/1/SitiAisyahRazaliPFS2018.pdf
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spelling	my-utm-ep.814202019-08-23T04:07:16Z Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production 2018 Razali, Siti Aisyah Q Science (General) Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of D-xylulose 5-phosphate (XU5P) and D-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Although these enzymes have been shown to produce xylitol, however there is a limited understanding of the mechanism of the catalytic events of these reactions and the detailed mechanism has yet to be elucidated. Understanding of the catalytic activity of these enzymes would provide novel information for protein engineering to improve xylitol production. The main goal of this work is to analyse the conformational changes of XPDH-bound ligands such as Zn2^ NADH, XU5P, and RU5P to elucidate the key amino acids involved in the substrate binding. In silico modelling, comparative molecular dynamic simulations, interaction analysis and conformational study were carried out on three XPDH enzymes of the Medium-chain dehydrogenase (MDR) family; XPDH from Lactobacillus rhamnosus (LrXPDH) and Clostridium difficile (CdXPDH, Cd1XPDH) in order to elucidate the atomistic details of conformational transition, especially on the open and closed state of XPDH. The critical residues involved in substrate binding and conformational changes were mutated using in silico site-directed mutagenesis. The result showed that residues Cys37, His58, Glu59, and Glu142 form an active site pocket within the catalytic domain. In the coenzyme domain, NADH is shown to bind to highly conserved glycine-rich motif; GXGXXG (residues 166-171). The results also revealed that XPDH consists of a dual mechanism that can catalyse hydride transfer to dissimilar substrates (XU5P and RU5P), which His58 and Ser39 would act as the proton donor for reduction of XU5P and RU5P respectively. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues (W48, I259, and W285). The study also identified the effect of S39A and W285A mutations on substrate binding and conformational changes. The study successfully elucidated the mechanistic aspect of catalysis mechanism and dynamical event of XPDH enzymes at molecular level. The results from this study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry. 2018 Thesis http://eprints.utm.my/id/eprint/81420/ http://eprints.utm.my/id/eprint/81420/1/SitiAisyahRazaliPFS2018.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:125032 phd doctoral Universiti Teknologi Malaysia Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	Q Science (General)
spellingShingle	Q Science (General) Razali, Siti Aisyah Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
description	Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of D-xylulose 5-phosphate (XU5P) and D-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Although these enzymes have been shown to produce xylitol, however there is a limited understanding of the mechanism of the catalytic events of these reactions and the detailed mechanism has yet to be elucidated. Understanding of the catalytic activity of these enzymes would provide novel information for protein engineering to improve xylitol production. The main goal of this work is to analyse the conformational changes of XPDH-bound ligands such as Zn2^ NADH, XU5P, and RU5P to elucidate the key amino acids involved in the substrate binding. In silico modelling, comparative molecular dynamic simulations, interaction analysis and conformational study were carried out on three XPDH enzymes of the Medium-chain dehydrogenase (MDR) family; XPDH from Lactobacillus rhamnosus (LrXPDH) and Clostridium difficile (CdXPDH, Cd1XPDH) in order to elucidate the atomistic details of conformational transition, especially on the open and closed state of XPDH. The critical residues involved in substrate binding and conformational changes were mutated using in silico site-directed mutagenesis. The result showed that residues Cys37, His58, Glu59, and Glu142 form an active site pocket within the catalytic domain. In the coenzyme domain, NADH is shown to bind to highly conserved glycine-rich motif; GXGXXG (residues 166-171). The results also revealed that XPDH consists of a dual mechanism that can catalyse hydride transfer to dissimilar substrates (XU5P and RU5P), which His58 and Ser39 would act as the proton donor for reduction of XU5P and RU5P respectively. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues (W48, I259, and W285). The study also identified the effect of S39A and W285A mutations on substrate binding and conformational changes. The study successfully elucidated the mechanistic aspect of catalysis mechanism and dynamical event of XPDH enzymes at molecular level. The results from this study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Razali, Siti Aisyah
author_facet	Razali, Siti Aisyah
author_sort	Razali, Siti Aisyah
title	Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
title_short	Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
title_full	Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
title_fullStr	Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
title_full_unstemmed	Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
title_sort	computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production
granting_institution	Universiti Teknologi Malaysia
granting_department	Science
publishDate	2018
url	http://eprints.utm.my/id/eprint/81420/1/SitiAisyahRazaliPFS2018.pdf
_version_	1747818327383736320

Computational analysis on protein-ligand interaction of xylitol-phosphate dehydrogenase enzymes for xylitol production

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