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

Bahaman A. H., Wahab R. A., Hamid A. A. A., Abd Halim K. B., Kaya Y.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, cilt.39, sa.7, ss.2628-2641, 2021 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 39 Sayı: 7
  • Basım Tarihi: 2021
  • Doi Numarası: 10.1080/07391102.2020.1751713
  • Dergi Adı: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE
  • Sayfa Sayıları: ss.2628-2641
  • Anahtar Kelimeler: Trichoderma, molecular docking, MM-PBSA, nanocellulose, molecular dynamics simulation, IN-SILICO, TRITICUM-AESTIVUM, DRUG DESIGN, MM-PBSA, PROTEIN, FEATURES, MMPBSA, ENZYME
  • Ondokuz Mayıs Üniversitesi Adresli: Evet

Özet

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 beta-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 beta-glucosidase- and xylanase from Trichoderma asperellum UC1 in complex with each substrate. Molecular docking of the enzyme-substrate complex showed residues Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160 being the likely catalytic residues of beta-glucosidase and xylanase, respectively. The binding affinity of beta-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 beta-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (Delta G(bind)) of beta-glucosidase and xylanase in complex with cellulose (-207.23 +/- 47.13 kJ/mol) and hemicellulose (-131.48 +/- 24.57 kJ/mol) were observed, respectively. The findings thus successfully identified the cellulose component selectivity of the polymer-acting beta-glucosidase and xylanase of T. asperellum UC1. Communicated by Ramaswamy H. Sarma