Setting the stage for electron transfer: Molecular basis of ABTS-binding to four laccases from Trametes versicolor at variable pH and protein oxidation state

Characterization of laccases from Trametes hirsuta in the context of bioremediation of wastewater treatment plant effluent

The bioremediation of pharmaceutical compounds contained in wastewater, in an ecological and sustainable way, is possible via the oxidative action of fungal laccases. The discovery of new fungal laccases with unique physico-chemical characteristics pushes researchers to identify suitable laccases for specific applications. The aim of this study is to purify and characterize laccase isoenzymes produced from the Trametes hirsuta IBB450 strain for the bioremediation of pharmaceutical compounds. Two main laccases mixtures were observed and purified in the extracts and were called Yn and Yg. Peptide fingerprinting analysis suggested that Yn was constituted mainly of laccase Q02497 and Yg of laccase A0A6M5CX58, respectively. Robustness tests, based on tolerance and stability, showed that both laccases were affected in a relatively similar way by salts (KCl, NaCl), organic solvents (ACN, MeOH), denaturing compounds (urea, trypsin, copper) and were virtually unaffected and stable in wastewater. Determination of kinetic constants (Michaelis (KM), catalytic constant (kcat) and kinetic efficiency (K=kcat/KM)) for the transformation of synthetic hormone 17α-ethynylestradiol and the anti-inflammatory agent diclofenac indicates a lower KM and kcat for laccase Yn but relative similar K constant compared to Yg. Synergistic effects were observed for the transformation of diclofenac, unlike 17α-ethynylestradiol. Transformation studies of 17α-ethynylestradiol at different temperatures (4 and 21 °C) indicate a transformation rate reduction of approximately 75-80% at 4 °C against 25% for diclofenac in less than an hour. Finally, the classification of laccases Yg and Yn into one of eight groups (group A-H) suggests that laccase Yg belongs to group A (constitutive laccase) and laccase Yn belongs to group B (inducible laccase).

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.

Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller?

Laccases stand out in the industrial context due to their versatile biotechnological applications. Although these enzymes are frequently investigated, currently, Pleurotus ostreatus laccase structural model is unknown. Therefore, this research aims to predict and validate a P. ostreatus laccase theoretical model by means of comparative homology. The laccase target's primary structure (AOM73725.1) was obtained from the NCBI database, the model was predicted from homologous structures obtained from the PDB (PDB-ID: 5A7E, 2HRG, 4JHU, 1GYC) using the Swiss-Model and Modeller, and was refined in GalaxyRefine. The models were validated using PROCHECK, VERIFY 3D, ERRAT, PROVE and QMEAN Z-score servers. Moreover, molecular docking between the laccase model (Lacc4MN) and ABTS was performed on AutoDock Vina. The models that were generated by the Modeller showed superior stereochemical and structural characteristics to those predicted by the Swiss Model. The refinement made it difficult to stabilize the copper atoms which are typical of laccases. The Lacc4MN model showed the interactions between the amino acids in the active site of the laccase and the copper atoms, thereby hinting the stabilization of the metal through electrostatic interactions with histidine and cysteine. The molecular docking between Lacc4MN and ABTS showed negative free energy and the formation of two hydrogen bonds involving the amino acids ASP 208 and GLY 268, and a Pi-sulfur bond between residue HIS 458 and ABTS, which demonstrates the typical catalytic functionality of laccases. Furthermore, the theoretical model Lacc4MN presented stereochemical and structural characteristics that allow its use in silico tests.Communicated by Ramaswamy H. Sarma.

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.

Preparation of Fe3O4@Fe(0) immobilized enzyme to enhance the efficient degradation of methoxychlor

The presence of methoxychlor (MXC) in soil and wastewater is considered a nonnegligible environmental threat. Herein, Fe₃O₄@Fe(0) was obtained by NaBH₄ reduction of Fe₃O₄ nanoparticles and served as a carrier for laccase to construct catalyst. The catalyst was evaluated for the degradation of MXC in treated wastewater and soil with 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) being used as cocatalyst. The removal rate of MXC in wastewater and soil was found to be 89% and 88% in optimum conditions, and the influences of initial MXC concentration, pH, and temperature on the degradation rate were evaluated. The metabolites including 2-methylpentane, 3-methylpentane, and n-pentane of MXC were identified, and possible degradation mechanisms were proposed. Overall, this work successfully demonstrates not only the ability to degrade MXC in different circumstances but also provides a new idea for environmental remediation in the future.

Functional Coating from Amyloid Superwetting Films

Tailoring the hydrophilicity of solid surfaces with a strong affinity to water has been extensively explored in the last 20 years, but studies have been limited to the single function of wettability. Here, the multifunctional properties of tailored surface films are extended from exhibiting superwettability to facilitating biological activities. It is shown that amyloid fibrils can be universally coated onto various substrates, such as fabrics (non-woven organic masks), metal meshes, polyethersulfone (PES), glass, and more, endowing the resulting surfaces with excellent performance in oil/water mixture and emulsion separation, antifouling, and antifogging. Moreover, the biocompatible crosslinked amyloid fibril coatings can serve as a platform for biocatalytic activities by immobilizing enzymes, as shown in the 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) oxidation and Reactive Black 5 (RB5) degradation by laccase from Trametes versicolor. The study provides a universal approach to modifying surface morphology and chemical properties via fibrous protein templates, opening the way to unexplored bio-based applications and functionalities.

Identification of Antioxidant Peptides Derived from Tilapia (Oreochromis niloticus) Skin and Their Mechanism of Action by Molecular Docking

Antioxidants, which can activate the body’s antioxidant defence system and reduce oxidative stress damage, are important for maintaining free radical homeostasis between oxidative damage and antioxidant defence. Six antioxidant peptides (P1–P6) were isolated and identified from the enzymatic hydrolysate of tilapia skin by ultrafiltration, reversed-phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography–tandem mass spectrometry (LC–MS/MS). Moreover, the scavenging mechanism of the identified peptides against DPPH (2,2-Diphenyl-1-picrylhydrazyl) and ABTS (2-azido-bis (3-ethylbenzothiazoline-6-sulfonic acid) was studied by molecular docking. It was found that Pro, Ala and Tyr were the characteristic amino acids for scavenging free radicals, and hydrogen bonding and hydrophobic interactions were the main interactions between the free radicals and antioxidant peptides. Among them, the peptide KAPDPGPGPM exhibited the highest DPPH free radical scavenging activity (IC₅₀ = 2.56 ± 0.15 mg/mL), in which the hydrogen bond between the free radical DDPH and Thr-6 was identified as the main interaction, and the hydrophobic interactions between the free radical DDPH and Ala, Gly and Pro were also identified. The peptide GGYDEY presented the highest scavenging activity against ABTS (IC₅₀ = 9.14 ± 0.08 mg/mL). The key structures for the interaction of this peptide with the free radical ABTS were identified as Gly-1 and Glu-5 (hydrogen bond sites), and the amino acids Tyr and Asp provided hydrophobic interactions. Furthermore, it was determined that the screened peptides are suitable for applications as antioxidants in the food industry, exhibit good water solubility and stability, are likely nonallergenic and are nontoxic. In summary, the results of this study provide a theoretical structural basis for examining the mechanism of action of antioxidant peptides and the application of enzymatic hydrolysates from tilapia skin.

Toward Characterizing the Genetic Basis of Trace Organic Contaminant Biotransformation in Activated Sludge: The Role of Multicopper Oxidases as a Case Study

Activated sludge treatment leverages the ability of microbes to uptake and (co)-metabolize chemicals and has shown promise in eliminating trace organic contaminants (TrOCs) during wastewater treatment. However, targeted interventions to optimize the process are limited as the fundamental drivers of the observed reactions remain elusive. In this work, we present a comprehensive workflow for the identification and characterization of key enzymes involved in TrOCs biotransformation pathways in complex microbial communities. To demonstrate the applicability of the workflow, we investigated the role of the enzymatic group of multicopper oxidases (MCOs) as one putatively relevant driver of TrOCs biotransformation. To this end, we analyzed activated sludge metatranscriptomic data and selected, synthesized, and heterologously expressed three phylogenetically distinct MCO-encoding genes expressed in communities with different TrOCs oxidation potentials. Following the purification of the encoded enzymes, we screened their activities against different substrates. We saw that MCOs exhibit significant activities against selected TrOCs in the presence of the mediator compound 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid and, in some cases, also in the presence of the wastewater contaminant 4'-hydroxy-benzotriazole. In the first case, we identified oxidation products previously reported from activated sludge communities and concluded that in the presence of appropriate mediators, bacterial MCOs could contribute to the biological removal of TrOCs. Similar investigations of other key enzyme systems may significantly advance our understanding of TrOCs biodegradation and assist the rational design of biology-based water treatment strategies in the future.

Molecular docking studies and in vitro degradation of four aflatoxins (AFB1 , AFB2 , AFG1 , and AFG2 ) by a recombinant laccase from Saccharomyces cerevisiae

Here, molecular docking simulation was used to predict and compare interactions between a recombinant Trametes sp. C30 laccase from Saccharomyces cerevisiae and four aflatoxins (AFB₁ , AFB₂ , AFG₁ , and AFG₂ ) as well as their degradation at a molecular level. The computational result of docking simulation indicates that each of the aflatoxins tested can interact with laccase with a binding ability of AFB₁ >AFG₂ >AFG₁ >AFB₂ . Simultaneously, it also demonstrated that aflatoxin B₁ ， B₂ ， G₁ ， G₂ may interact near the T1 copper center of the enzyme through H-bonds and hydrophobic interactions with amino acid residues His481 and Asn288; His481； Asn288, and Asp230; His481 and Asn288. Biological degradation test was performed in vitro in the presence of a recombinant laccase. Degradation increased as incubation time increased from 12 to 60 hr and the maximum degradation obtained for AFB₁ , AFB₂ , AFG₁ , and AFG₂ was 90.33%, 74.23%, 85.24%, and 87.58%, respectively. Maximum degradation of aflatoxins was determined with a total activity 3 U laccase at 30 °C in 0.1 M phosphate buffer, pH 5.7 after 48-hr incubation. The experimental results are consistent with that of docking calculation on the biological degradation test of four aflatoxins by laccase. PRACTICAL APPLICATION: In this study, the degradation efficiencies of laccase for B and G series of aflatoxins were determined by computer simulation and verified by performing in vitro experiments. It can provide reference for rapid screening of aflatoxin degradation-related enzymes.

Correlation between the T1 copper reduction potential and catalytic activity of a small laccase

Laccases are multicopper enzymes that catalyze oxidation of electron-rich substrates coupled to reduction of molecular oxygen to water. Since the Type 1 copper (T1 Cu) is the site where electrons are withdrawn from the substrate, it is assumed that the reduction potential of this copper correlates with enzyme activity. Herein, we studied the correlation of the T1 Cu reduction potential and the enzymatic activity of the small two-domain laccase Ssl1 from Streptomyces sviceus. For a systematic approach, we aimed to minimize any effects other than the reduction potential difference. To this end, we constructed a series of Ssl1 mutants with reduction potentials varying from <290 to 560 mV. Along with the hydrophobicity of the axial ligand of the T1 Cu also structural changes in the substrate binding site and additional hydrogen bonding increased the reduction potential. Enzyme activity experiments demonstrated that the T1 Cu reduction potential has a different effect on oxidation of different substrates. Whereas there was no obvious correlation between the T1 Cu reduction potential and kinetic parameters for the oxidation of syringaldazine (with a reduction potential of 390 mV), a good correlation was observed between the T1 Cu reduction potential and the conversion of substituted phenols with reduction potentials between 660 and 820 mV. This correlation was pronounced for the Ssl1 variants with reduction potentials above 470 mV, which demonstrated increased activities also during the oxidation of two dyes, alizarin red S and indigo carmine.

Contribution of substrate reorganization energies of electron transfer to laccase activity

Laccase substrate reorganization energies computed by DFT show that electronic structure changes of these substrates contribute to enzymatic proficiency.

A structural-chemical explanation of fungal laccase activity

Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatly facilitate the rational design of new laccases for technological purposes. We report a study of three datasets of experimental K_m values and activities for Trametes versicolor and Cerrena unicolor laccase, using a range of protein modeling techniques. We identify diverse binding modes of the various substrates and confirm an important role of Asp-206 and His-458 (T. versicolor laccase numbering) in guiding substrate recognition. Importantly, we demonstrate that experimental K_m values correlate with binding affinities computed by MMGBSA. This confirms the common assumption that the protein-substrate affinity is a major contributor to observed K_m. From quantitative structure-activity relations (QSAR) we identify physicochemical properties that correlate with observed K_m and activities. In particular, the ionization potential, shape, and binding affinity of the substrate largely determine the enzyme’s K_m for the particular substrate. Our results suggest that K_m is not just a binding constant but also contains features of the enzymatic activity. In addition, we identify QSAR models with only a few descriptors showing that phenolic substrates employ optimal hydrophobic packing to reach the T1 site, but then require additional electronic properties to engage in the subsequent electron transfer. Our results advance our ability to model laccase activity and lend promise to future rational optimization of laccases toward phenolic substrates.

Molecular dynamics derived life times of active substrate binding poses explainKMof laccase mutants

Molecular dynamics derived life times of reactive poses and MMGBSA substrate affinities explain trends in experimentalK_Mfor laccases.

Evolving stability and pH-dependent activity of the high redox potential Botrytis aclada laccase for enzymatic fuel cells

Fungal high redox potential laccases are proposed as cathodic biocatalysts in implantable enzymatic fuel cells to generate high cell voltages. Their application is limited mainly through their acidic pH optimum and chloride inhibition. This work investigates evolutionary and engineering strategies to increase the pH optimum of a chloride-tolerant, high redox potential laccase from the ascomycete Botrytis aclada. The laccase was subjected to two rounds of directed evolution and the clones screened for increased stability and activity at pH 6.5. Beneficial mutation sites were investigated by semi-rational and combinatorial mutagenesis. Fourteen variants were characterised in detail to evaluate changes of the kinetic constants. Mutations increasing thermostability were distributed over the entire structure. Among them, T383I showed a 2.6-fold increased half-life by preventing the loss of the T2 copper through unfolding of a loop. Mutations affecting the pH-dependence cluster around the T1 copper and categorise in three types of altered pH profiles: pH-type I changes the monotonic decreasing pH profile into a bell-shaped profile, pH-type II describes increased specific activity below pH 6.5, and pH-type III increased specific activity above pH 6.5. Specific activities of the best variants were up to 5-fold higher (13 U mg⁻¹) than BaL WT at pH 7.5.

Degradation of Aflatoxins by Means of Laccases from Trametes versicolor: An In Silico Insight

Mycotoxins are secondary metabolites of fungi that contaminate food and feed, and are involved in a series of foodborne illnesses and disorders in humans and animals. The mitigation of mycotoxin content via enzymatic degradation is a strategy to ensure safer food and feed, and to address the forthcoming issues in view of the global trade and sustainability. Nevertheless, the search for active enzymes is still challenging and time-consuming. The in silico analysis may strongly support the research by providing the evidence-based hierarchization of enzymes for a rational design of more effective experimental trials. The present work dealt with the degradation of aflatoxin B₁ and M₁ by laccase enzymes from Trametes versicolor. The enzymes–substrate interaction for various enzyme isoforms was investigated through 3D molecular modeling techniques. Structural differences among the isoforms have been pinpointed, which may cause different patterns of interaction between aflatoxin B₁ and M₁. The possible formation of different products of degradation can be argued accordingly. Moreover, the laccase gamma isoform was identified as the most suitable for protein engineering aimed at ameliorating the substrate specificity. Overall, 3D modeling proved to be an effective analytical tool to assess the enzyme–substrate interaction and provided a solid foothold for supporting the search of degrading enzyme at the early stage.

The Trametes hirsuta 072 laccase multigene family: Genes identification and transcriptional analysis under copper ions induction

Laccases, blue copper-containing oxidases, ≿ an play an important role in a variety of natural processes. The majority of fungal laccases are encoded by multigene families that express closely related proteins with distinct functions. Currently, only the properties of major gene products of the fungal laccase families have been described. Our study is focused on identification and characterization of laccase genes, which are transcribed in basidiomycete Trametes hirsuta 072, an efficient lignin degrader, in a liquid medium, both without and with induction of laccase transcription by copper ions. We carried out production of cDNA libraries from total fungal RNA, followed by suppression subtractive hybridization and mirror orientation selection procedures, and then used Next Generation Sequencing to identify low abundance and differentially expressed laccase transcripts. This approach resulted in description of five laccase genes of the fungal family, which, according to the phylogenetic analysis, belong to distinct clusters within the Trametes genus. Further analysis established similarity of physical, chemical, and catalytic properties between laccases inside each cluster. Structural modeling suggested importance of the sequence differences in the clusters for laccase substrate specificity and catalytic efficiency. The implications of the laccase variations for the fungal physiology are discussed.

Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy

Understanding the molecular determinants of enzyme performance is of primary importance for the rational design of ad hoc mutants. A novel approach, which combines efficient conformational sampling and quick reactivity scoring, is used here to shed light on how substrate oxidation was improved during the directed evolution experiment of a fungal laccase (from Pycnoporus cinnabarinus), an industrially relevant class of oxidoreductases. It is found that the enhanced activity of the evolved enzyme is mainly the result of substrate arrangement in the active site, with no important change in the redox potential of the T1 copper. Mutations at the active site shift the binding mode into a more buried substrate position and provide a more favorable electrostatic environment for substrate oxidation. As a consequence, engineering the binding event seems to be a viable way to in silico evolution of oxidoreductases.

Laccase engineering by rational and evolutionary design

Laccases are considered as green catalysts of great biotechnological potential. This has attracted a great interest in designing laccases a la carte with enhanced stabilities or activities tailored to specific conditions for different fields of application. Over 20 years, numerous efforts have been taken to engineer these multicopper oxidases and to understand their reaction mechanisms by site-directed mutagenesis, and more recently, using computational calculations and directed evolution tools. In this work, we review the most relevant contributions made in the field of laccase engineering, from the comprehensive study of their structure–function relationships to the tailoring of outstanding biocatalysts.