In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes

Increasing interest towards the enzyme industry has led to studies exploring possible applications of new enzymes for improving different manufacturing processes. This study focuses on capitalizing the oil palm biomass rich in lignocellulosic residues such as lignin, cellulose, and hemicellulose, wh...

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Main Author:	Bahaman, Aina Hazimah
Format:	Thesis
Language:	English
Published:	2020
Subjects:	QD Chemistry
Online Access:	http://eprints.utm.my/id/eprint/102064/1/AinaHazimahBahamanMFS2020.pdf.pdf
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spelling	my-utm-ep.1020642023-07-31T07:40:40Z In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes 2020 Bahaman, Aina Hazimah QD Chemistry Increasing interest towards the enzyme industry has led to studies exploring possible applications of new enzymes for improving different manufacturing processes. This study focuses on capitalizing the oil palm biomass rich in lignocellulosic residues such as lignin, cellulose, and hemicellulose, which have an array of biotechnological applications. Literature has shown that oil palm frond leaves (OPFL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by Trichoderma species. The study aimed to comprehend this aspect by in silico approach of molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM- PBSA) analysis to identify the catalytic mechanism and selectivity of fungal enzymes endocellulase, exocellulase, β-glucosidase, and xylanase degrading the polymeric structures of OPFL. The study also seeks to identify the most stable enzymes to catalyse the optimal degradation of OPFL to yield maximal production of NC. It is an alternative greener avenue by a biotechnological approach to enzymatically extract NC from OPFL in order to circumvent the environmentally unfriendly use of corrosive acids and bases to extract NC. Energy minimized fungal enzyme models revealed satisfactory scores of PROCHECK, Verify3D and ERRAT according to the requirement of the validation which are >90%, >80% and >50%, respectively. Catalytic residue prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase, exocellulase, β-glucosidase and xylanase were Ser116-His205-Glu249, Ser382-Arg124-Asp385, Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160, respectively. The binding affinity of endocellulase for the substrates are as follows: hemicellulose (−6.0 kcal mol-1) > lignin (−5.6 kcal mol-1) > cellulose (−4.4 kcal mol-1), while exocellulase showed its preference on lignin (−8.7 kcal mol-1) > cellulose (−8.5 kcal mol-1) > hemicellulose (−8.4 kcal mol-1). The binding affinity of β- glucosidase for the substrates are as follows: cellulose (−8.1 kcal mol-1) > lignin (−7.9 kcal mol-1) > hemicellulose (−7.8 kcal mol-1), whereas xylanase showed a corresponding preference for hemicellulose (−6.7 kcal mol-1) > cellulose (−5.8 kcal mol-1) > lignin (−5.7 kcal mol-1). Selectivity of the enzymes was reiterated by MD simulations where interactions between endocellulase-hemicellulose, exocellulase-lignin, β-glucosidase-cellulose and xylanase- hemicellulose were the strongest. Notably low free-binding energy (ΓGbind) of endocellulase- hemicellulose (−141.50 +/− 74.59 kJ/mol), exocellulase-lignin (−149.73 +/− 39.00 kJ/mol), β-glucosidase-cellulose (−207.23 +/− 47.13 kJ/mol) and xylanase-hemicellulose (−131.48 +/− 24.57 kJ/mol) were observed. The findings thus successfully identified the specific actions of sugar-acting enzymes for NC production and cellulose component selectivity of the polymer- acting endocellulase, exocellulase, β-glucosidase and xylanase of T. asperellum UC1. 2020 Thesis http://eprints.utm.my/id/eprint/102064/ http://eprints.utm.my/id/eprint/102064/1/AinaHazimahBahamanMFS2020.pdf.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146320 masters Universiti Teknologi Malaysia Faculty of Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	QD Chemistry
spellingShingle	QD Chemistry Bahaman, Aina Hazimah In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
description	Increasing interest towards the enzyme industry has led to studies exploring possible applications of new enzymes for improving different manufacturing processes. This study focuses on capitalizing the oil palm biomass rich in lignocellulosic residues such as lignin, cellulose, and hemicellulose, which have an array of biotechnological applications. Literature has shown that oil palm frond leaves (OPFL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by Trichoderma species. The study aimed to comprehend this aspect by in silico approach of molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM- PBSA) analysis to identify the catalytic mechanism and selectivity of fungal enzymes endocellulase, exocellulase, β-glucosidase, and xylanase degrading the polymeric structures of OPFL. The study also seeks to identify the most stable enzymes to catalyse the optimal degradation of OPFL to yield maximal production of NC. It is an alternative greener avenue by a biotechnological approach to enzymatically extract NC from OPFL in order to circumvent the environmentally unfriendly use of corrosive acids and bases to extract NC. Energy minimized fungal enzyme models revealed satisfactory scores of PROCHECK, Verify3D and ERRAT according to the requirement of the validation which are >90%, >80% and >50%, respectively. Catalytic residue prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase, exocellulase, β-glucosidase and xylanase were Ser116-His205-Glu249, Ser382-Arg124-Asp385, Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160, respectively. The binding affinity of endocellulase for the substrates are as follows: hemicellulose (−6.0 kcal mol-1) > lignin (−5.6 kcal mol-1) > cellulose (−4.4 kcal mol-1), while exocellulase showed its preference on lignin (−8.7 kcal mol-1) > cellulose (−8.5 kcal mol-1) > hemicellulose (−8.4 kcal mol-1). The binding affinity of β- glucosidase for the substrates are as follows: cellulose (−8.1 kcal mol-1) > lignin (−7.9 kcal mol-1) > hemicellulose (−7.8 kcal mol-1), whereas xylanase showed a corresponding preference for hemicellulose (−6.7 kcal mol-1) > cellulose (−5.8 kcal mol-1) > lignin (−5.7 kcal mol-1). Selectivity of the enzymes was reiterated by MD simulations where interactions between endocellulase-hemicellulose, exocellulase-lignin, β-glucosidase-cellulose and xylanase- hemicellulose were the strongest. Notably low free-binding energy (ΓGbind) of endocellulase- hemicellulose (−141.50 +/− 74.59 kJ/mol), exocellulase-lignin (−149.73 +/− 39.00 kJ/mol), β-glucosidase-cellulose (−207.23 +/− 47.13 kJ/mol) and xylanase-hemicellulose (−131.48 +/− 24.57 kJ/mol) were observed. The findings thus successfully identified the specific actions of sugar-acting enzymes for NC production and cellulose component selectivity of the polymer- acting endocellulase, exocellulase, β-glucosidase and xylanase of T. asperellum UC1.
format	Thesis
qualification_level	Master's degree
author	Bahaman, Aina Hazimah
author_facet	Bahaman, Aina Hazimah
author_sort	Bahaman, Aina Hazimah
title	In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
title_short	In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
title_full	In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
title_fullStr	In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
title_full_unstemmed	In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes
title_sort	in silico analysis on degradation order of cellulosic components in oil palm leaves by trichoderma asperellum uc1 enzymes
granting_institution	Universiti Teknologi Malaysia
granting_department	Faculty of Science
publishDate	2020
url	http://eprints.utm.my/id/eprint/102064/1/AinaHazimahBahamanMFS2020.pdf.pdf
_version_	1776100837166153728

In silico analysis on degradation order of cellulosic components in oil palm leaves by Trichoderma asperellum UC1 enzymes

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