Molecular docking simulation on the interactions of laccase from Trametes versicolor with nonylphenol and octylphenol isomers

Efficient catalytic removal of phenolic pollutants by laccase from Coriolopsis gallica: Binding interaction and polymerization mechanism

Laccase is a green catalyst that can efficiently catalyze phenolic pollutants, and its catalytic efficiency is closely related to the interaction between enzyme and substrates. To investigate the binding effects between enzyme and phenolic pollutants, phenol, p-chlorophenol, and bisphenol A were used as substrates in this study. We focused on the removal and catalytic mechanism of these pollutants in water using yellow laccase derived from Coriolopsis gallica. The enzymatic catalytic products were characterized using Ultraviolet-Visible Absorption Spectroscopy (UV-Vis), Fourier Transform Infrared Spectroscopy (FTIR), and High-Resolution Mass Spectrometry (HRMS), and the catalytic mechanism of laccase on phenolic pollutants was further explored by molecular docking. Based on the structural characterization and molecular docking results, the possible polymerization pathways of these phenolic compounds were speculated. Laccase catalyzed phenol to produce phenolic hydroxyl radicals, their para-radicals, and ortho-radicals, which polymerized to form oligomers linked by benzene‑oxygen-benzene and benzene-benzene. P-chlorophenol produced phenolic hydroxyl radicals and their ortho-radicals, polymerizing to form oligomers connected by benzene‑oxygen-benzene or benzene-benzene. The CC bond of the isopropyl group of bisphenol A broke to formed an intermediate product, which was further polymerized to formed a benzene‑oxygen-benzene linked oligomer.

Isolation of the Antifungal Compound Alliodorin from the Heartwood of Cordia elaeagnoides A. DC. and the In Silico Analysis of the Laccase

Cordia elaeagnoides A. DC. is an endemic species of Mexico valued for its timber. Renowned for its durability, resistance, and versatile applications in medicine, this tree holds significant commercial importance. Tetrahydrofuran (THF) extract from the heartwood of C. elaeagnoides was studied. Through chromatographic column purification, the compound 8-(2,5-Dihydroxyphenyl)-2,6-dimethylocta-2,6-dienal, also known as alliodorin, was successfully isolated. Identification of alliodorin was confirmed through comprehensive analysis utilizing NMR, IR, and mass spectrometry techniques. Inhibition tests were conducted using both the THF extract and alliodorin against the rotting fungus Trametes versicolor (L.) Lloyd, employing the agar well diffusion assay. Remarkably, alliodorin exhibited 100% inhibition with a median lethal concentration of 0.079 mg/mL and a total lethal concentration of 0.127 mg/mL, in comparison to the commercial fungicide benomyl, which requires a concentration of 1 mg/mL. In silico analysis through molecular docking on the laccase enzyme was proposed in order to explain the inhibitory activity against the fungus T. versicolor, as this enzyme is one of the main sources of nutrients and development for the fungus. Based on these findings, we deduced that alliodorin holds promise as a potent antifungal agent, potentially applicable in a wide array of technological and environmentally friendly initiatives.

Visible light-driven oxidation of non-native substrate by laccase attached on Ru-based metal-organic frameworks

Light-induced electron transfer can broaden the substrate range of metalloenzyme. However, the efficiency of photo-enzyme coupling is limited by the poor combination of photosensitizer or photocatalyst with enzyme. Herein, we prepared the nano-photocatalyst MIL-125-NH2@Ru(bpy) by in site embedding ruthenium pyridine-diimine complex [Ru(bpy)3]2+ into metal organic frameworks MIL-125-NH2 and associated it with multicopper oxidase (MCO) laccase. Compared to [Ru(bpy)3]2+, the coupling efficiency of MIL-125-NH2@Ru(bpy)3 for enzymatic oxygen reduction increased by 35.7%. A series of characterizations confirmed that the amino group of laccase formed chemical bonds with the surface defects or hydrophobic groups of MIL-125-NH2@Ru(bpy)3. Consequently, the tight binding accelerated the quenching process and electron transfer between laccase and the immobilized ruthenium pyridine-diimine complex. This work would open an avenue for the synthesis of MOFs photocatalyst towards photo-enzyme coupling.

In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets

An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Laccase Engineering: Redox Potential Is Not the Only Activity-Determining Feature in the Metalloproteins

Laccase, one of the metalloproteins, belongs to the multicopper oxidase family. It oxidizes a wide range of substrates and generates water as a sole by-product. The engineering of laccase is important to broaden their industrial and environmental applications. The general assumption is that the low redox potential of laccases is the principal obstacle, as evidenced by their low activity towards certain substrates. Therefore, the primary goal of engineering laccases is to improve their oxidation capability, thereby increasing their redox potential. Even though some of the determinants of laccase are known, it is still not entirely clear how to enhance its redox potential. However, the laccase active site has additional characteristics that regulate the enzymes' activity and specificity. These include the electrostatic and hydrophobic environment of the substrate binding pocket, the steric effect at the substrate binding site, and the orientation of the binding substrate with respect to the T1 site of the laccase. In this review, these features of the substrate binding site will be discussed to highlight their importance as a target for future laccase engineering.

Recent Theoretical Insights into the Oxidative Degradation of Biopolymers and Plastics by Metalloenzymes

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.

Endocrine Disrupting Compounds (Nonylphenol and Bisphenol A)-Sources, Harmfulness and Laccase-Assisted Degradation in the Aquatic Environment

Environmental pollution with organic substances has become one of the world's major problems. Although pollutants occur in the environment at concentrations ranging from nanograms to micrograms per liter, they can have a detrimental effect on species inhabiting aquatic environments. Endocrine disrupting compounds (EDCs) are a particularly dangerous group because they have estrogenic activity. Among EDCs, the alkylphenols commonly used in households deserve attention, from where they go to sewage treatment plants, and then to water reservoirs. New methods of wastewater treatment and removal of high concentrations of xenoestrogens from the aquatic environment are still being searched for. One promising approach is bioremediation, which uses living organisms such as fungi, bacteria, and plants to produce enzymes capable of breaking down organic pollutants. These enzymes include laccase, produced by white rot fungi. The ability of laccase to directly oxidize phenols and other aromatic compounds has become the focus of attention of researchers from around the world. Recent studies show the enormous potential of laccase application in processes such as detoxification and biodegradation of pollutants in natural and industrial wastes.

A Pre-clinical Trial Study: Anti-human Colon Cancer Effect of Thalassiolin B in vitro with Enzymes Inhibition Effects and Molecular Docking Studies

In this study, it is recorded the inhibition effect of Thalassiolin B on aldose reductase, alpha-glucosidase and alpha-amylase enzymes. In the next step, the molecular docking method was used to compare the biological activities of the Thalassiolin B molecule against enzymes formed from the assembly of proteins. In these calculations, the enzymes used are Aldose reductase, Alpha-Amylase, and Alpha-Glucosidase, respectively. After the docking method, ADME/T analysis of Thalassiolin B molecule was performed to be used as a drug in the pharmaceutical industry. In the MTT assay, the anti-human colon cancer properties of Thalassiolin B against EB, LS1034, and SW480 cell lines were investigated. The cell viability of Thalassiolin B was very low against human colon cancer cell lines without any cytotoxicity on the human normal (HUVEC) cell line. The IC₅₀ of the Thalassiolin B against EB, LS1034, and SW480 were 483, 252, and 236 µg/mL, respectively. Thereby, the best cytotoxicity results and anti-human colon cancer potentials of our Thalassiolin B were observed in the case of the SW480 cell line. Maybe the anti-human colon cancer properties of Thalassiolin B are related to their antioxidant effects.

Oxidoreductases as a versatile biocatalytic tool to tackle pollutants for clean environment – a review

With the growing population and rapid industrial development of the world, various pollutants — explicitly known as emerging pollutants (EPs) and including micro and nanoplastics, pharmaceuticals, hazardous dyes, steroid estrogen, and organic pollutants — continue to enter into the environment and water sources. These EPs cause a variety of side effects and diseases, such as cancer, neurotoxic and mutagenic effects, stomach cramps, intestinal disorders, loss of peripheral vision, deteriorated movement coordination, and weakened muscles, even in low concentrations. The presence of EPs in the environment/water sources affects humans and animals and disturbs ecological integrity. Therefore, removing these EPs from the environment with a smart, greener, and environmentally competent technology has become a meaningful goal. Most of the EPs are stable in the media, and their removal is a considerable scientific challenge. Different treatment methods, like adsorption and degradation processes, have been used to eliminate these pollutants. Enzyme‐mediated approaches hold immense prospects in environmental cleanup and have been keenly explored recently. Many efforts have been made to apply biocatalytic‐based materials, like laccases and peroxidases, as unique tools alongside a powerful oxidation approach for the degradation and treatment of EPs. These enzymes' unique properties in terms of excellent selectivity and exclusive catalytic features make them robust candidates for biocatalytic treatment. This work spotlights the biocatalytic properties and application of oxidoreductases to remove EPs. The challenges, conclusive remarks, and standpoints for robust biocatalysts are also given. © 2021 Society of Chemical Industry (SCI).

Biodegradation of anionic polyacrylamide mediated by laccase and amidase: docking, virtual mutation based on affinity and DFT study

The aim of this work was to document the elucidation of a mechanism as a reference.

Reversal of Endothelial Extracellular Vesicle-Induced Smooth Muscle Phenotype Transition by Hypercholesterolemia Stimulation: Role of NLRP3 Inflammasome Activation

Recent studies reported that vascular endothelial cells (ECs) secrete NLR family pyrin domain-containing 3 (NLRP3) inflammasome products such as interleukin-1β (IL-1β) via extracellular vesicles (EVs) under various pathological conditions. EVs represent one of the critical mechanisms mediating the cell-to-cell communication between ECs and vascular smooth muscle cells (VSMCs). However, whether or not the inflammasome-dependent EVs directly participate in the regulation of VSMC function remains unknown. In the present study, we found that in cultured carotid ECs, atherogenic stimulation by oxysterol 7-ketocholesterol (7-Ket) induced NLRP3 inflammasome formation and activation, reduced lysosome-multivesicular bodies (MVBs) fusion, and increased secretion of EVs that contain inflammasome product IL-1β. These EC-derived IL-1β-containing EVs promoted synthetic phenotype transition of co-cultured VSMCs, whereas EVs from unstimulated ECs have the opposite effects. Moreover, acid ceramidase (AC) deficiency or lysosome inhibition further exaggerated the 7-Ket-induced release of IL-1β-containing EVs in ECs. Using a Western diet (WD)-induced hypercholesterolemia mouse model, we found that endothelial-specific AC gene knockout mice (Asah1fl/fl/ECCre) exhibited augmented WD-induced EV secretion with IL-1β and more significantly decreased the interaction of MVBs with lysosomes in the carotid arterial wall compared to their wild-type littermates (WT/WT). The endothelial AC deficiency in Asah1fl/fl/ECCre mice also resulted in enhanced VSMC phenotype transition and accelerated neointima formation. Together, these results suggest that NLRP3 inflammasome-dependent IL-1β production during hypercholesterolemia promotes VSMC phenotype transition to synthetic status via EV machinery, which is controlled by lysosomal AC activity. Our findings provide novel mechanistic insights into understanding the pathogenic role of endothelial NLRP3 inflammasome in vascular injury through EV-mediated EC-to-VSMC regulation.

Correlation between initial biodegradability determined by docking studies and structure of alkylbenzene sulfonates: A new tool for intelligent design of environmentally friendly anionic surfactants

Gray water constitutes an important fraction of total wastewater. Some of the most problematic compounds in gray water are the anionic surfactants used as an ingredient for domestic and industrial soaps and detergents. The alkylbenzene sulfonates used in commercially available formula are highly complex mixtures of linear (LAS) and branched (BAS) molecules. LAS are classified generally as biodegradable, although their widespread use generates accumulation in the environment. Docking tools, widely used in recent years in the bioremediation field, allow molecular modeling of the ligand-enzyme interaction, which is key to understanding and evaluating the possibility of biodegradation. In this work, molecular details that allow us to establish a biodegradation pattern for some alkylbenzene sulfonates were elucidated. Two hydrogen bonds, key for the anchorage of surfactants to the monooxygenase active site involved in the initial biodegradation, were found. These bonds determine the way surfactants locate in the hydrophobic pocket of the enzyme affecting the biodegradation rate in a structurally dependent manner. For C10 to C12 linear isomers, the degradation rate increased together with the length of the hydrocarbon chain. For C13 and C14 isomers, steric difficulties to accommodate the surfactant molecule in the catalytic site were observed. For branched chain isomers, little or no biodegradation was found. In addition, biodegradation was lower in mixtures than for the pure isomers. These results will allow an intelligent design of this family of anionic surfactants to attenuate their contaminating effects in waters and soils. This study constitutes, to the best of our knowledge, a novel contribution towards the design of environmentally friendly surfactants with higher probabilities of being biodegraded to complete mineralization.

Laccases and peroxidases: The smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants

Various organic pollutants so-called emerging pollutants (EPs), including active residues from pharmaceuticals, pesticides, surfactants, hormones, and personal care products, are increasingly being detected in numerous environmental matrices including water. The persistence of these EPs can cause adverse ecological and human health effects even at very small concentrations in the range of micrograms per liter or lower, hence called micropollutants (MPs). The existence of EPs/MPs tends to be challenging to mitigate from the environment effectively. Unfortunately, most of them are not removed during the present-day treatment plants. So far, a range of treatment processes and degradation methods have been introduced and deployed against various EPs and/or MPs, such as ultrafiltration, nanofiltration, advanced oxidation processes (AOPs) and enzyme-based treatments coupled with membrane filtrations. To further strengthen the treatment processes and to overcome the EPs/MPs effective removal dilemma, numerous studies have revealed the applicability and notable biocatalytic potentialities of laccases and peroxidases to degrade different classes of organic pollutants. Exquisite selectivity and unique catalytic properties make these enzymes powerful biocatalytic candidates for bio-transforming an array of toxic contaminants to harmless entities. This review focuses on the use of laccases and peroxidases, such as soybean peroxidase (SBP), horseradish peroxidase (HRP), lignin peroxidase (LiP), manganese peroxidase (MnP), and chloroperoxidase (CPO) as a greener oxidation route towards efficient and effective removal or degradation of EPs/MPs.

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.

Downregulation of Lysosomal Acid Ceramidase Mediates HMGB1-Induced Migration and Proliferation of Mouse Coronary Arterial Myocytes

High-mobility group box 1 protein (HMGB1) has been reported to trigger lysosome destabilization causing a wide of inflammatory diseases. The present study tested whether a lysosomal enzyme, acid ceramidase (AC), plays a critical role in HMGB1-induced alteration in ceramide metabolism and whether such HMGB1-AC interaction is associated with abnormal migration and proliferation of vascular smooth muscle cells (SMCs). We first observed that the expression of AC in the medial layer of mouse coronary arterial wall and colocalization of AC with a lysosome marker Lamp-1. In primary cultured coronary arterial myocytes (CAMs), AC expression and colocalization with Lamp-1 were significantly up-regulated by AC inducer, genistein, but down-regulated by AC inhibitor, N-oleoylethanolamine (NOE). HMGB1 dose-dependently decreased the colocalization of AC with Lamp-1 and reduced mRNA and protein expressions of AC in CAMs, but reversed by genistein. Consistently, HMGB1 significantly induced increases in the levels of long-chain ceramides in CAMs, which were not further enhanced by NOE but blocked by genistein. More importantly, HMGB1 promoted migration and proliferation of CAMs, which were not further increased by NOE but reduced by genistein. Lastly, CAMs isolated from smooth muscle-specific AC knockout mice (AC gene Asah1) exhibited increased ceramide levels and enhanced the migration and proliferation, which resembles the effects of HMGB1 on wild-type CAMs. Together, these results suggest that HMGB1 promotes SMC migration and proliferation via inhibition of AC expression and ceramide accumulation.

Endothelial acid ceramidase in exosome-mediated release of NLRP3 inflammasome products during hyperglycemia: Evidence from endothelium-specific deletion of Asah1 gene

Exosomes have been demonstrated to be one of the mechanisms mediating the release of intracellular signaling molecules to conduct cell-to-cell communication. However, it remains unknown whether and how exosomes mediate the release of NOD-like receptor pyrin domain 3 (NLRP3) inflammasome products such as interleukin-1 beta (IL-1β) from endothelial cells. The present study hypothesized that lysosomal acid ceramidase (AC) determines the fate of multivesicular bodies (MVBs) to control the exosome-mediated release of NLRP3 inflammasome products during hyperglycemia. Using a streptozotocin (STZ)-induced diabetes mouse model, we found that endothelium-specific AC gene knockout mice (Asah1fl/fl/ECcre) significantly enhanced the formation and activation of NLRP3 inflammasomes in coronary arterial ECs (CECs). These mice also had increased thickening of the coronary arterial wall and reduced expression of tight junction protein compared to wild-type (WT/WT) littermates. We also observed the expression of exosome markers such as CD63 and alkaline phosphatase (ALP) was augmented in STZ-treated Asah1fl/fl/ECcre mice compared to WT/WT mice, which was accompanied by an increased IL-1β release of exosomes. In the primary cultures of CECs, we demonstrated that AC deficiency markedly enhanced the formation and activation of NLRP3 inflammasomes, but significantly down-regulated tight junction proteins when these cells were exposed to high levels of glucose. The CECs from Asah1fl/fl/ECcre mice had decreased MVB-lysosome interaction and increased IL-1β-containing exosome release in response to high glucose stimulation. Together, these results suggest that AC importantly controls exosome-mediated release of NLRP3 inflammasome products in CECs, which is enhanced by AC deficiency leading to aggravated arterial inflammatory response during hyperglycemia.

Study on transformation and degradation of bisphenol A by Trametes versicolor laccase and simulation of molecular docking

As a typical class of environmental endocrine disruptors, bisphenol A poses a potential threat to the sustainable survival and reproduction of living beings and human beings. In this study, the interaction between Trametes versicolor laccase and bisphenol A (BPA) was studied by molecular docking simulation, and the catalytic degradation of BPA was verified by experiments. The conditions for the laccase production of T. versicolor were optimized by orthogonal design, and the degradation of BPA was studied using its crude enzyme solution. The optimum degradation conditions were obtained by response surface methodology (RSM). Ultimately, the transformation products after 3 and 6 h of reaction were detected by gas chromatography-mass spectrometry. Docking results demonstrated that the reaction between laccase and BPA was spontaneous, and the degradation rate in 24 h reached 88.76%. RSM results showed that the highest BPA degradation rate of 97.68% was reached after 1 h reaction at 44.6 °C, 5 mg/L initial BPA concentration, and pH 5.20. The intermediate products of BPA catalyzed by laccase included ethylbenzene, p-xylene, and cyclohexanone 1-methyl-4-isopropenyl-2-cyclohexenol. This finding reveals that BPA degradation by the crude laccase from T. versicolor starts from the C atoms between two benzene rings that connect BPA. Compared with expensive pure enzyme, the crude laccase solution prepared by T. versicolor showed greater efficiency in BPA degradation. This work provides theoretical references and experimental methods for the biological processing of harmful pollutants.

Acidogenic bacteria assisted biodegradation of nonylphenol in waste activated sludge during anaerobic fermentation for short-chain fatty acids production

Nonylphenol (NP) biodegradation under anaerobic conditions is difficult. Here, enhancement of anaerobic NP biodegradation mainly by regulating the role of acidogenic bacteria during anaerobic fermentation of waste activated sludge (WAS) for short-chain fatty acids production is reported. The maximum degradation efficiency of NP (69.4%) was achieved under conditions of pH 10.0 and 10 mg/L Brij 35 within 8 d, which was nearly 3-fold of that in the control (24.6%). Mechanism exploration revealed that the bioavailability of NP and specific NP-degrading bacteria and their functional genes were advantageous to NP biodegradation with alkaline pH and surfactant. More importantly, acidogenic bacteria, the dominant functional bacteria in WAS fermentation systems, were demonstrated to be involved in NP anaerobic biodegradation by providing intermediate organic substrates, as well as through their intrinsic NP-degrading abilities. Possible pathways of NP biodegradation assisted by acidogenic bacteria during anaerobic fermentation were also proposed based on the detected metabolites.

Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies

Some surfactants can enhance the removal of phenol by laccase (Lac) in various industrial effluents. Their behavior and function in the biodegradation of phenolic wastewater have been experimentally reported by many researchers, but the underlying molecular mechanism is still unclear. Therefore, the interaction mechanisms of phenol with Lac from Trametes versicolor were investigated in the presence or absence of Triton X-100 (TX100) or rhamnolipid (RL) by molecular docking and molecular dynamics (MD) simulations. The results indicate that phenol contacts with an active site of Lac by hydrogen bonds (HBs) and van der Waals (vdW) interactions in aqueous solution for maintaining its stability. The presence of TX100 or RL results in the significant changes of enzymatic conformations. Meanwhile, the hydrophobic parts of surfactants contact with the outside surface of Lac. These changes lead to the decrease of binding energy between phenol and Lac. The migration behavior of water molecules within hydration shell is also inevitably affected. Therefore, the amphipathic TX100 or RL may influence the phenol degradation ability of Lac by modulating their interactions and water environment. This study offers molecular level of understanding on the function of surfactants in biosystem.