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

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 ß-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 ß-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 ß-glucosidase and xylanase, respectively. The binding affinity of ß-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 ß-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (ΔGbind) of ß-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 ß-glucosidase and xylanase of T. asperellum UC1.Communicated by Ramaswamy H. Sarma.

Substrate docking and molecular dynamic simulation for prediction of fungal enzymes from Trichoderma species-assisted extraction of nanocellulose from oil palm leaves.

Fungi of the Trichoderma species are valued industrial enzymes in support of the 'zero-waste' technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic (MD) simulation was used to predict the order of which the multilayers of cellulosic polymers, i.e. lignin, hemicellulose and cellulose in oil palm leaves (OPL) are degraded by fungal enzymes, endocellulase and exocellulase. The study aimed to establish the catalytic tendencies of the enzymes to optimally degrade the cellulosic components of OPL for high yield production of NC. Energy minimized endocellulase and exocellulase models revealed satisfactory scores of PROCHECK (90.0% and 91.2%), Verify3D (97.23% and 98.85%) and ERRAT (95.24% and 91.00%) assessments. Active site prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase and exocellulase were Ser116-His205-Glu249 and Ser382-Arg124-Asp385, respectively. Binding energy of endocellulase docked with hemicellulose (-6.0 kcal mol-1) was the most favourable followed by lignin (-5.6 kcal mol-1) and cellulose (-4.4 kcal mol-1). Exocellulase, contrarily, bonded favorably with lignin (-8.7 kcal mol-1), closely followed by cellulose (-8.5 kcal mol-1) and hemicellulose (-8.4 kcal mol-1). MDs simulations showed that interactions of complexes, endocellulase-hemicellulose and the exocellulase-cellulose being the most stable. Thus, the findings of the study successfully identified the specific actions of sugar-acting enzymes for NC production. Communicated by Ramaswamy H. Sarma.