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

• Main Authors: Bahaman, Aina Hazimah, Abdul Wahab, Roswanira, Abdul Hamid, Azzmer Azzar, Abd Halim, Khairul Bariyyah, Kaya, Yilmaz
• Format: Article
• Language: English; English
• Published: Taylor Francis 2020
• Subjects: QD Chemistry; S Agriculture (General)
• Online Access: http://irep.iium.edu.my/84066/1/84066_Molecular%20docking%20and%20molecular%20dynamics_in%20press.pdf; http://irep.iium.edu.my/84066/13/84066_Molecular%20docking%20and%20molecular%20dynamics_Scopus.pdf; http://irep.iium.edu.my/84066/; https://www-tandfonline-com.ezproxy.um.edu.my/doi/full/10.1080/07391102.2020.1751713

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.