Enzymatic analysis, structural study and molecular docking of laccase and catalase from B. subtilis SK1 after textile dye exposure

Functional and structural characterization of a thermostable flavin reductase from Geobacillus mahadii Geo-05

Flavin reductases play a vital role in catalyzing the reduction of flavin through NADH or NADPH oxidation. The gene encoding flavin reductase from the thermophilic bacterium Geobacillus mahadii Geo-05 (GMHpaC) was cloned, overexpressed in Escherichia coli BL21 (DE3) pLysS, and purified to homogeneity. The purified recombinant GMHpaC (Class II) contains chromogenic cofactors, evidenced by maximal absorbance peaks at 370 nm and 460 nm. GMHpaC stands out as the most thermostable and pH-tolerant flavin reductase reported to date, retaining up to 95 % catalytic activity after incubation at 70 °C for 30 min and maintaining over 80 % activity within a pH range of 2-12 for 30 min. Furthermore, GMHpaC's catalytic activity increases by 52 % with FMN as a co-factor compared to FAD and riboflavin. GMHpaC, coupled with 4-hydroxyphenylacetate-3-monooxygenase (GMHpaB) from G. mahadii Geo-05, enhances the hydroxylation of 4-hydroxyphenylacetate (HPA) by 85 %. The modeled structure of GMHpaC reveals relatively conserved flavin and NADH binding sites. Modeling and docking studies shed light on structural features and amino acid substitutions that determine GMHpaC's co-factor specificity. The remarkable thermostability, high catalytic activity, and general stability exhibited by GMHpaC position it as a promising enzyme candidate for various industrial applications.

Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics

Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL-1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL-1 for rGILCC 1 and 5291.665 ± 45.83 UL-1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10-2 mM for rGILCC 1 and 3.72 × 10-2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10-2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1-ABTS and POXA 1B-ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model-ABTS interactions (GILCC 1-ABTS and POXA 1B-ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme-substrate interactions, offering potential applications in environmental substrate treatments.

Investigating Bio-Inspired Degradation of Toxic Dyes Using Potential Multi-Enzyme Producing Extremophiles

Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied on a large scale because of the extremely harsh conditions in effluents polluted with multiple dyes, such as alkaline pH, high salinity/heavy metals/dye concentration, high temperature, and oxidative stress. Therefore, extremophilic microorganisms offer enormous opportunities for practical biodegradation processes as they are naturally adapted to multi-stress conditions due to the special structure of their cell wall, capsule, S-layer proteins, extracellular polymer substances (EPS), and siderophores structural and functional properties such as poly-enzymes produced. This review provides scientific information for a broader understanding of general dyes, their toxicity, and their harmful effects. The advantages and disadvantages of physicochemical methods are also highlighted and compared to those of microbial strategies. New techniques and methodologies used in recent studies are briefly summarized and discussed. In particular, this study addresses the key adaptation mechanisms, whole-cell, enzymatic degradation, and non-enzymatic pathways in aerobic, anaerobic, and combination conditions of extremophiles in dye degradation and decolorization. Furthermore, they have special metabolic pathways and protein frameworks that contribute significantly to the complete mineralization and decolorization of the dye when all functions are turned on. The high potential efficiency of microbial degradation by unculturable and multi-enzyme-producing extremophiles remains a question that needs to be answered in practical research.

Encapsulated laccase in bimetallic Cu/Zn ZIFs as stable and reusable biocatalyst for decolorization of dye wastewater

Laccase have received extensive attention in pollutant degradation, but its practical viability is largely affected by the poor stability, easy inactivation and difficulty in recycling for the present. Enzyme immobilization offers enhanced enzyme stability and constructs a synergistic system for the efficient adsorption and degradation of pollutants. In this study, bimetallic Cu/Zn ZIFs were synthesized by co-precipitation method as the protective carrier for laccase. Lac@Cu-ZIF-90 exhibited a good protective effect on laccase and showed a high operational stability in various interfering environments. Free laccase was completely inactivated at pH 7.0 but Lac@Cu-ZIF-90 could maintain 50.0 % activity. Benefiting from the encapsulation of laccase and porous structure of Cu-ZIF-90, the Lac@Cu-ZIF-90 exhibited decolorization efficiency for dye wastewater. More importantly, the Lac@Cu-ZIF-90 could be recovered from the dye solution and re-used to adsorb and degrade the synthetic dye for multiple times, its removal rate for reactive deep green was only decreased about 10.8 % after five cycles. This work reveals that the Cu-ZIF-90 provides a favorable environment for laccase and as a protective layer to relieve the conformation change, which provides an efficient strategy to decolorize dye wastewater. Therefore, Cu-ZIF-90 promises applications as enzymes encapsulation has great potential in water remediation.

Experimental-theoretical study of laccase as a detoxifier of aflatoxins

We investigate laccase-mediated detoxification of aflatoxins, fungal carcinogenic food contaminants. Our experimental comparison between two aflatoxins with similar structures (AFB₁ and AFG₂) shows significant differences in laccase-mediated detoxification. A multi-scale modeling approach (Docking, Molecular Dynamics, and Density Functional Theory) identifies the highly substrate-specific changes required to improve laccase detoxifying performance. We employ a large-scale density functional theory-based approach, involving more than 7000 atoms, to identify the amino acid residues that determine the affinity of laccase for aflatoxins. From this study we conclude: (1) AFB₁ is more challenging to degrade, to the point of complete degradation stalling; (2) AFG₂ is easier to degrade by laccase due to its lack of side products and favorable binding dynamics; and (3) ample opportunities to optimize laccase for aflatoxin degradation exist, especially via mutations leading to π-π stacking. This study identifies a way to optimize laccase for aflatoxin bioremediation and, more generally, contributes to the research efforts aimed at rational enzyme optimization.

Artificial intelligence modeling and molecular docking to analyze the laccase delignification process of rice straw by Comamonas testosteroni FJ17

The laccase enzymatic characteristics and delignification processes of rice straw by Comamonas testosteroni FJ17 were investigated. Artificial intelligence modeling and molecular docking revealed the specific functional properties involved in the interaction between laccase and lignin compounds with a maximum laccase activity of 2016.7 U L^-1 at 24 h. Scanning electron microscopy and X-ray diffractometer analysis confirmed that laccase caused fractures and holes on the surface of rice straw, where crystallinity decrease from 45.3 to 39.9%, and lignin content decreased from 19.0 to 10.3%. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analysis showed that the main delignification process for laccase was via β-o-4 and α-aryl ether cleavage, which generated several small molecular products. The laccase gene was cloned and bioinformatics analysis presented 317 amino acids with a predicted molecular weight of 33.13 kDa. Finally, laccase protein was found to have low binding energies with all lignin compounds tested, and lignin compounds were oxidized by laccase through hydrogen-bonding interactions with the amino acid residues.

Construction of supramolecular laccase enzymes and understanding of catalytic dye degradation using multispectral and molecular docking approaches

A non-covalent supramolecular enzyme system which was successfully constructed by non-covalent interaction of enzyme with substrates analogs can effectively recognize and degrade 13 kinds of dyes.

Application of docking and active site analysis for enzyme linked biodegradation of textile dyes

Growth of textile industries led to production of enormous dye varieties. These textile dyes are largely used, chemically stable and easy to synthesize. But they are recalcitrant and persist as less biodegradable pollutants when discharged into waterbodies. Potential use of enzyme-linked bioremediation of textile dyes will control their toxicity in waterbodies. Bioinformatics and Molecular docking tool provides an insight into remediation mechanism by predicting susceptibility of dye degradation using oxidoreductive enzymes. In this study, six dyes, Reactive Red F3B, Remazol Red RGB, Joyfix Red RB, Joyfix Yellow MR, Remazol Blue RGB and Turquoise CL-5B of azo, anthraquinone and phthalocyanine molecular class were identified as potential targets for degradation by laccase and azoreductase of Aeromonas hydrophila in addition to Lysinibacillus sphaericus through in silico docking tool BioSolveIT-FlexX. Azoreductase breaks azo bonds by ping-pong mechanism whereas laccase decolorizes dyes by free radical mechanism which is not specific in nature. Results were analyzed based on parameters like stability, catalytic action and selectivity for enzyme-dye interactions. Amino acids of enzymes interacted with several dyes substantiating variations in active site for enzyme-ligand binding affinity. This suggests the role of enzymes in decolorizing an extensive variety of textile dyes, thereby, aiding in understanding the enzyme mechanisms in Bioremediation.