Elucidating the molecular mechanism of ultrasound-enhanced lipase-catalyzed biodiesel synthesis: a computational study

Kumar, Karan; Patro, Pallavi; Raut, Unnati; Yadav, Varsha; Barbora, Lepakshi; Moholkar, Vijayanand S.

doi:10.1007/s13399-023-04742-4

Cited by 8 publications

(3 citation statements)

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“…The model system for molecular simulations comprised glucoamylase (GLCM) enzyme with alpha-1,4-maltotriose (or amylotriose), the major constituent of food waste, as the substrate. The catalytic mechanism of the GLCM enzyme was investigated using molecular docking protocols reported in our previous study [12,16]. The 3-D coordinates of GLCM from Aspergillus niger complexed with tris and glycerol were imported from the Protein Data Bank (PDB) [17].…”

Section: Selection Of Glucoamylase Structure For Molecular Dockingmentioning

confidence: 99%

“…Thus, intensifying the kinetics of hydrolysis by glucoamylase is crucial to the large-scale implementation of food waste-based processes for value-added products. Sonication (or ultrasound irradiation) is known to enhance the kinetics of enzymatic processes [10][11][12]. Ultrasound and its secondary effect of cavitation (which essentially is nucleation, growth, and transient collapse of gas or vapor microbubbles) generate intense microturbulence in the liquid medium.…”

Section: Introductionmentioning

confidence: 99%

“…Sonication (or ultrasound irradiation) is known to enhance the kinetics of enzymatic processes [10–12]. Ultrasound and its secondary effect of cavitation (which essentially is nucleation, growth, and transient collapse of gas or vapor microbubbles) generate intense micro-turbulence in the liquid medium.…”

Section: Introductionmentioning

confidence: 99%

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Ultrasound-Assisted Hydrolysis of Food Waste using Glucoamylase: Statistical Optimization and Mechanistic Analysis with Molecular Simulations

Anand,

Kumar,

Khaire

et al. 2023

Preprint

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Food waste represents a promising and cost-effective resource for synthesizing value-added products through a fermentative pathway. Preceding fermentation, the hydrolysis of food waste into monomeric sugars is a crucial step. This study presents a comprehensive investigation of food waste hydrolysis, encompassing experimental and computational approaches, using glucoamylase (GLCM) enzyme. Initial optimization of hydrolysis parameters was conducted through the Box–Behnken design of experiments, resulting in a total reducing sugar yield (TRS) of 263.4 mg/g biomass under optimized conditions within 42 hours. Sonication of hydrolysis mixture at 35 kHz at 20% duty cycle, yielded a 4× reduction in hydrolysis time with 22% enhancement in TRS yield (320 mg/g biomass). Analysis of GLCM’s secondary structure revealed sonication-induced changes through FTIR spectra deconvolution in both control and test experiments. Sonication led to a reduction in α-helix content and an increase in random coil content. Molecular dynamics simulations, including molecular docking, unveiled the majority of amino acid residues associated with the GLCM binding pocket in the α-helix and random coil regions. Consequently, sonication widened the binding pockets, facilitating easier transport of substrate and product. This effect translated into improved reaction kinetics in food waste hydrolysis.Research HighlightsStatistical optimization of food waste hydrolysis: TRS yield = 263.4 mg/g in 42 h4x reduction of hydrolysis time, 22% rise in TRS yield with 35 kHz sonicationSonication reduced α-helix content & increased random coil content of glucoamylaseMolecular docking simulation to deduce mechanism of ultrasound-assisted hydrolysisMD simulations reveal widening of binding pockets and enhancing catalytic efficiency

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Section: Selection Of Glucoamylase Structure For Molecular Dockingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%