Bioinformatics analyses of lignin peroxidases from the smoky bracket fungi Bjerkandera adusta for endocrine disrupting chemical bioremediation.

Abstract

Lignin peroxidases (LiP; EC 1.11.1.14) are important oxidative enzymes involved in lignin biodegradation, a key constituent of plant cell walls. Despite their environmental and industrial potential, fungal LiPs are difficult to express and purify. Bjerkandera adusta is a white-rot fungus that secretes LiPs, the three-dimensional structure of which remains unknown. In this study, two LiPs from B. adusta were subjected to various bioinformatics tools to determine their physio-chemical, structural, and functional properties. Their 3D structure was modeled and molecular dynamic simulations were performed to assess their binding to endocrine disrupting chemicals (EDCs). Moreover, molecular docking analysis revealed that among the model lignin compounds, the dimer guaiacyl 4-O-5 guaiacyl exhibited the lowest binding energy with the EDC ligands, estrone (E1) and bisphenol A showing the strongest binding affinity for LiP 588479560 and LiP 444058, respectively. Molecular dynamics simulations further confirmed the stability of these complexes, with bisphenol A exhibiting particularly high stability as indicated by its low RMSD (≤2 Å) and favorable RoG values, reflecting a strong fit within the enzyme's active site. Additionally, the binding free energy calculations showed the substrate dimer had the most favorable binding energy, driven primarily by Van der Waals and lipophilic interactions, suggesting its intrinsic compatibility with B. adusta LiPs. This in silico characterization advances the understanding of LiP structure-function relationships and bioremediation potential. B. adusta LiPs demonstrate promising capacity to target persistent EDCs, offering solutions for environmental pollution mitigation.