Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation

Bahaman, Aina Hazimah and Abdul Wahab, Roswanira and Abdul Hamid, Azzmer Azzar and Abd Halim, Khairul Bariyyah and Kaya, Yilmaz (2020) Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation. Journal of Molecular Structure and Dynamics. pp. 1-14. ISSN 0739-1102 E-ISSN 1538-0254

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Abstract

Literature has shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of b-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The study aimed to comprehend this aspect by an in silico approach of molecular docking, molecular dynamics (MD) simulation and Molecular-mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, to compare interactions between the b-glucosi dase- and xylanase from Trichoderma asperellum UC1 in complex with each substrate. Molecular dock ing of the enzyme-substrate complex showed residues Glu165-Asp226-Glu423 and Arg155-Glu210- Ser160 being the likely catalytic residues of b-glucosidase and xylanase, respectively. The binding affin ity of b-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 both enzymes was reiterated by MD simulations where interactions between b-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (DGbind) of b-glucosi dase and xylanase in complex with cellulose ( 207.23 þ/ 47.13 kJ/mol) and hemicellulose ( 131.48 þ/ 24.57 kJ/mol) were observed, respectively. The findings thus successfully identified the cellulose component selectivity of the polymer-acting b-glucosidase and xylanase of T. asperellum UC1.

Item Type:	Article (Journal)
Additional Information:	7228/84066
Uncontrolled Keywords:	Trichoderma; molecular docking; MM-PBSA; nanocellulose; molecular dynamics simulation.
Subjects:	Q Science > QD Chemistry S Agriculture > S Agriculture (General)
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science Kulliyyah of Science > Department of Biotechnology
Depositing User:	Dr Khairul Bariyyah Abd Halim
Date Deposited:	03 Nov 2020 11:26
Last Modified:	09 Jun 2021 14:36
URI:	http://irep.iium.edu.my/id/eprint/84066

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