Molecular modeling, docking and dynamic studies of fungal DyPs to determine substrate specificity for an efficient lignin biodegradation towards bioethanol production. (June 2022)

• Record Type: Journal Article
• Authors: Rath, Subhashree; Paul, Manish; Thatoi, Hrudayanath
• Is Part Of: Bioresource technology reports. Volume 18(2022)
• Publication Date: 2022-06
• Subjects: Dye decolorizing peroxidase -- Phylogenetic analysis -- Docking -- Substrate-Inhibitor specificity -- Molecular Dynamics simulation -- Bioethanol; DyP Dye Decolorizing Peroxidase -- ABTS 2, 2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid -- VA veratryl alcohol -- DMP 2, 6 dimethoxyphenol -- MsDyP DyPs from Mycentinis scorodonius -- MeDyP DyPs from Mycena epipterygia -- AA Acetic acid -- HMF Hydroxymethylfurfural -- LA Levulinic acid; Biomass energy -- Periodicals; Biotransformation (Metabolism) -- Periodicals; Agricultural wastes -- Periodicals; Factory and trade waste -- Periodicals; Organic wastes -- Periodicals; Waste products as fuel -- Periodicals; Waste products as fuel; Organic wastes; Factory and trade waste; Biotransformation (Metabolism); Biomass energy; Agricultural wastes; Periodicals; Electronic journals; 662.88
• DOI: 10.1016/j.biteb.2022.101036
• Languages: English
• ISSNs: 2589-014X

Abstract

Abstract: Dye-decolourizing peroxidase (DyP) is a heme-containing peroxidase well-known for its ligninolytic activity having great potential in the field of biotechnology towards efficient lignin degradation and valorisation. In the present investigation, an in silico modeling and docking of fungal DyPs from Mycena epipterygia, Exidia glandulosa, and Mycentinis scorodonius with substrates ABTS, VA, catechol, DMP, guaiacol, and inhibitors (AA, furan, LA, HMF) was performed to determine the active site residues, substrate and inhibitor specificity during enzymatic catalysis. The fungus M. epipterygia and ABTS complex showed maximum molecular interaction and binding affinity of −7.20 Kcal/mol from all fungal DyPs-substrate and inhibitor complexes. Further, Molecular Dynamics simulation studies showed that the VA and LA bound DyPs from M. scorodonius is moderately stable in comparison to other DyPs-substrate/inhibitor complexes. Thus, DyPs from two fungal strains can effectively catalyse important reactions involved in lignin degradation using ABTS and VA and can be explored towards bioethanol production. Graphical abstract: Unlabelled Image Highlights: The fungal DyP efficiently degrades lignin compounds towards bioethanol production. M. scorodonius DyP has a characteristic loop assist in stable substrate interaction. In silico docking study identified M. epipterygia DyP-ABTS as most stable complex. For retaining larger substrates Met227, His365, Ile233, Gln440 showed higher RMSF. Smaller substrate like VA showed better accessibility in active site of DyPs.