Biological function molecular pathways and druggability of DNMT2/TRDMT1

5-methylcytosine (m5C) is among the most common epigenetic modification in DNA and RNA molecules, and plays an important role in the animal development and disease pathogenesis. Interestingly, unlike other m5C DNA methyltransferases (DNMTs), DNMT2/TRDMT1 has the double-substrate specificity and adopts a DNMT-similar catalytic mechanism to methylate RNA. Moreover, it is widely involved in a variety of physiological regulatory processes, such as the gene expression, precise protein synthesis, immune response, and disease occurrence. Thus, comprehending the epigenetic mechanism and function of DNMT2/TRDMT1 will probably provide new strategies to treat some refractory diseases. Here, we discuss recent studies on the spatiotemporal expression pattern and post-translational modifications of DNMT2/TRDMT1, and summarize the research advances in substrate characteristics, catalytic recognition mechanism, DNMT2/TRDMT1-related genes or proteins, pharmacological application, and inhibitor development. This review will shed light on the pharmacological design by targeting DNMT2/TRDMT1 to treat parasitic, viral and oncologic diseases.

Exploration of novel trehalases from cold-adapted Variovorax sp. PAMC28711: Functional characterization

The cold-adapted bacterium Variovorax sp. PAMC28711 possesses two distinct glycoside hydrolase (GH) families of trehalase, GH15 and GH37. While numerous studies have explored bacterial trehalase, the presence of two different trehalase genes within a single strain has not been reported until now. Interestingly, despite both GH37 and GH15 trehalases serving the same purpose of degrading trehalose, but do not share the sequence similarity. The substrate specificity assay confirmed that Vtre37 and Vtre15 displayed hydrolytic activity on α, α-trehalose. The key catalytic sites were identified as D280 and E469 in Vtre37 and E389 and E554 in Vtre15 through site-directed mutation and confirmed these two enzymes belong to trehalase. In addition, Vtre37 exhibited a relatively high level of enzyme activity of 1306.33 (±53.091) μmolmg-1, whereas Vtre15 showed enzyme activity of 408.39 (±12.503) μmolmg-1. Moreover, Vtre37 performed admirably showing resistance to ethanol (10 %), with high stable at acidic pH range. Furthermore, both prediction and experimental results indicate that validoxylamine A showed a potent inhibitory activity against Vtre37 trehalase with a Ki value of 16.85 nM. Therefore, we postulate that Vtre37 could be utilized as an ethanol enhancer and designed for screening inhibitors related to the trehalose degradation pathway. Additionally, we believe that characterizing these bacterial trehalase contributes to a better understanding of trehalose metabolism and its biological importance in bacteria.

Essential amino acid residues and catalytic mechanism of trans-epoxysuccinate hydrolase for production of meso-tartaric acid

OBJECTIVES

This study aimed to discuss the essential amino acid residues and catalytic mechanism of trans-epoxysuccinate hydrolase from Pseudomonas koreensis for the production of meso-tartaric acid.

RESULTS

The optimum conditions of the enzyme were 45 °C and pH 9.0, respectively. It was strongly inhibited by Zn2+, Mn2+ and SDS. Michaelis-Menten enzyme kinetics analysis gave a Km value of 3.50 mM and a kcat of 99.75 s-1, with an exceptional EE value exceeding 99.9%. Multiple sequence alignment and homology modeling revealed that the enzyme belonged to MhpC superfamily and possessed a typical α/β hydrolase folding structure. Site-directed mutagenesis indicated H34, D104, R105, R108, D128, Y147, H149, W150, Y211, and H272 were important catalytic residues. The 18O-labeling study suggested the enzyme acted via two-step catalytic mechanism.

CONCLUSIONS

The structure and catalytic mechanism of trans-epoxysuccinate hydrolase were first reported. Ten residues were critical for its catalysis and a two-step mechanism by an Asp-His-Asp catalytic triad was proposed.

Classification and functional origins of stereocomplementary alcohol dehydrogenases for asymmetric synthesis of chiral secondary alcohols: A review

Alcohol dehydrogenases (ADHs) mediated biocatalytic asymmetric reduction of ketones have been widely applied in the synthesis of optically active secondary alcohols with highly reactive hydroxyl groups ligated to the stereogenic carbon and divided into (R)- and (S)-configurations. Stereocomplementary ADHs could be applied in the synthesis of both enantiomers and are increasingly accepted as the "first of choice" in green chemistry due to the high atomic economy, low environmental factor, 100 % theoretical yield, and high environmentally friendliness. Due to the equal importance of complementary alcohols, development of stereocomplementary ADHs draws increasing attention. This review is committed to summarize recent advance in discovery of naturally evolved and tailor-made stereocomplementary ADHs, unveil the molecular mechanism of stereoselective catalysis in views of classification and functional basis, and provide guidance for further engineering the stereoselectivity of ADHs for the industrial biosynthesis of chiral secondary alcohol of industrial relevance.

Modulator-assisted solvent-free synthesis of amorphous zirconium terephthalate catalyst for efficient oxidative desulfurization

Oxidative desulfurization (ODS) emerges as a critical player in enhancing efficient fuel desulfurization and promoting sustainable clean energy. Metal-organic frameworks (MOFs) show great potential as ODS catalysts because of their exceptional porosity and versatility. This study explores the use of amorphous metal-organic frameworks (aMOFs), which combine MOFs' structural advantages with unique properties of amorphous materials, to enhance catalytic efficiency in ODS. Traditional methods for synthesizing MOFs rely on solvent-thermal or solvent-free methods, each with limitations in environmental impact or scalability. To address this, we introduce a novel strategy utilizing a small quantity of benzoic acid (BA) modifier to facilitate the solvent-free, one-pot, mechanical synthesis of amorphous zirconium terephthalate (GU-2BA-3h). The resulting GU-2BA-3h demonstrates exceptional ODS performance, efficiently removing 1000 ppm of dibenzothiophene (DBT) in just 6 min at 60 °C. Amorphous GU-2BA-3h features an expanded external surface area, increased acidic sites, and exceptional stability, resulting in a high turnover frequency (19.6 h-1) and outstanding catalytic activity (53.2 mmol g-1 h-1), establishing it as a highly efficient ODS catalyst. This remarkable performance arises from the formation of dangling carboxyl groups and active metal sites due to the competitive coordination of benzoic acid with the linker. Experimental evidence confirms that these carboxyl groups and exposed Zr-OH sites interact with oxidants, generating hydroxyl radicals that effectively eliminate sulfur-containing compounds. Furthermore, the methodology exhibits universality in constructing amorphous Zr-based MOFs, and provides an eco-friendly, cost-effective route for efficient ODS catalyst production.

Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semi-biotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

Structural and biochemical characterization of active sites mutant in human inorganic pyrophosphatase

Inorganic pyrophosphatases (PPases) are enzymes that catalyze the conversion of inorganic pyrophosphate (PPi) into phosphate (Pi). Human inorganic pyrophosphatase 1 (Hu-PPase) exhibits high expression levels in a variety of tumors and plays roles in cell proliferation, apoptosis, invasion and metastasis, making it a promising prognostic biomarker and a target for cancer therapy. Despite its widespread presence, the catalytic mechanism of Hu-PPase in humans remains inadequately understood. The signature motif amino acid sequence (DXDPXD) within the active sites of PPases is preserved across different species. In this research, an enzymatic activity assay revealed that mutations led to a notable reduction in enzymatic function, although the impact of the four amino acids on the activity of the pocket varied. To investigate the influence of these residues on the substrate binding and enzymatic function of PPase, the crystal structure of the Hu-PPase-ED quadruple mutant (D116A/D118A/P119A/D121A) was determined at 1.69 Å resolution. The resulting structure maintained a barrel-like shape similar to that of the wild-type, albeit lacking Mg2+ ions. Molecular docking analysis demonstrated a decreased ability of Hu-PPase-ED to bind to PPi. Further, molecular dynamics simulation analysis indicated that the mutation rendered the loop of Mg2+ ion-binding residues less stable. Therefore, the effect on enzyme activity did not result from a change in the gross protein structure but rather from a mutation that abolished the Mg2+-coordinating groups, thereby eliminating Mg2+ binding and leading to the loss of enzyme activity.

Enhanced hydrodechlorination of 4-chlorophenol through carboxymethylcellulose-modified Pd/Fe nanosuspension synthesized by one-step methods

Palladized iron (Pd/Fe) represents one of the most common modification strategies for nanoscale zero-valent iron (nZVI). Most studies prepared Pd/Fe by reducing iron salts and depositing Pd species on the surface of pre-synthesized nZVI, which can be called the two-step method. In this study, we proposed a one-step method to obtain Pd/Fe by the concurrent formation of Fe0 and Pd0 and investigated the effects of these two methods on 4-chlorophenol (4-CP) removal, with carboxymethylcellulose (CMC) coated as a surface modifier. Results indicated that the one-step method, not only streamlined the synthesis process, but also Pd/Fe-CMCone-step, synthesized by it, exhibited a higher 4-CP removal rate (97.9%) compared to the two-step method material Pd/Fe-CMCtwo-step (82.4%). Electrochemical analyses revealed that the enhanced activity of Pd/Fe-CMCone-step was attributed to its higher electron transfer efficiency and more available reactive species, active adsorbed hydrogen species (Hads*). Detection of intermediate products demonstrated that, under the influence of Pd/Fe-CMCone-step, the main route of 4-CP was through hydrodechlorination (HDC) to form phenol and H* was the main active specie, supported by EPR tests, quenching experiments and product analysis. Additionally, the effects of initial 4-CP concentration, initial pH, O2 concentration, anions such as Cl-, SO42-, HCO3-, and humic acid (HA) were also investigated. In conclusion, the results of this study suggest that Pd/Fe-CMCone-step, synthesized through the one-step method, is a convenient and efficient nZVI-modifying material suitable for the HDC of chlorinated organic compounds.

Research and application progress of microbial β-mannanases: a mini-review

Mannan is a predominant constituent of cork hemicellulose and is widely distributed in various plant tissues. β-Mannanase is the principal mannan-degrading enzyme, which breaks down the β-1,4-linked mannosidic bonds in mannans in an endo-acting manner. Microorganisms are a valuable source of β-mannanase, which exhibits catalytic activity in a wide range of pH and temperature, making it highly versatile and applicable in pharmaceuticals, feed, paper pulping, biorefinery, and other industries. Here, the origin, classification, enzymatic properties, molecular modification, immobilization, and practical applications of microbial β-mannanases are reviewed, the future research directions for microbial β-mannanases are also outlined.

Highly efficient catalytic Fenton-Like reactions of bimetallic Fe/Cu chelated on radiation functionalized nonwoven fabric for pollutant control

A remarkably efficient and affordable Fe/Cu bimetallic catalyst featuring a substantial light energy utilization and compatibility with a sizable substrate was developed for Fenton-like reactions aimed at pollutant control. Specifically, a novel strategy was employed to synthesize high-density metal sites (Fe:Cu ≈ 3:1) robustly embedded on polyethylene/polyethylene terephthalate nonwoven fabric (PE/PET NWF) via radiation-induced graft polymerization (RIGP) and subsequent chemical modification, labeled as Fe/Cu-PPAO. Its high effectiveness was demonstrated by degrading 50 mg/L of tetracycline hydrochloride within 30 min in the presence of H2O2 under simulate sunlight irradiation. It was investigated that amidoxime groups regulated the optical gaps and HOMO-LUMO gaps of metal ions to enable the absorption of a broader spectrum light while the Cu2+ facilitated the transfer of electrons between the bimetal ions to achieve an improved reaction path. Furthermore, X-ray absorption fine structure (XAFS) and density functional theory (DFT) calculations further revealed its special complex state and delicate electronic structure between bimetal ions and amidoxime groups. Our study offers a new strategy to synthesize high-density bimetallic sites catalyst for environmental remediation and pushes forward insight into understanding the catalytic mechanism of bimetallic Fenton-like catalysts.

Poly (3, 4-propylenedioxythiophene)/Hollow carbon sphere composites supported Pt NPs to facilitate methanol oxidation reactions

Direct methanol fuel cells (DMFCs) are thought of as portable, sustainable, and non-polluting energy devices. The exploration of efficient and affordable catalysts for the methanol oxidation reaction (MOR) is significant for the industrial application of DMFCs. In this study, nitrogen-doped hollow carbon spheres (HCS) derived from polydopamine were proposed for the catalyst support for platinum nanoparticles (Pt NPs) for serving as the anode catalyst for DMFCs, and a composite support material was fabricated by in-situ oxidation of 3,4-ethylenedioxythiophene (ProDOT) with HCS to get core-shell structured poly(3,4-propylenedioxythiophene) (PProDOT)-embellished hollow carbon spheres (HCS) (PProDOT/HCS) for further improving the catalytic activity for supported catalyst. The results indicated that the platinum (Pt) on the surface of HCS was well dispersed, and the Pt became smaller and more evenly distributed with the introduction of PProDOT. Simultaneously, the Schottky junction formed between PProDOT and Pt NPs contributes to enhanced charge transfer and catalytic activity of the catalyst. Notably, the core-shell structure of the ternary catalyst, its excellent charge transfer capability, and the interaction between platinum and the support contribute to its high electrocatalytic activity. Electrochemical tests demonstrated that the PProDOT/HCS/Pt catalyst exhibited a mass activity of 1169.6 mA mg-1Pt for methanol oxidation in acidic electrolytes, surpassing the activity of the HCS/Pt catalyst (472.4 mA mg-1Pt) and commercial Pt/C (281.0 mA mg-1Pt).

A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study

Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme-glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.

CoP/Co heterojunction on porous g-C3N4 nanosheets as a highly efficient catalyst for hydrogen generation

Designing non-precious catalysts to synergistically achieve a facilitated exposure of abundant active sites is highly desired but remains a significant challenge. Herein, a hetero-structured catalyst CoP-Co supported on porous g-C3N4 nanosheets (CoP-Co/CN-I) was prepared by pyrolysis and P-inducing strategy. The optimal catalyst achieves a turnover frequency (TOF) of 26 min-1 at room temperature and the apparent activation energy (Ea) is 35.5 kJ·mol-1. The catalytic activity is ranked top among the non-precious metal phosphides or the other supports. Meanwhile, the catalytic activity has no significant decrease even after 5 cycles. The CoP/Co interfaces provide richly exposed active sites, optimize hydrogen/water absorption free energy via electronic coupling, and thus improve the catalytic activity. The experimental results reveal that the CoP/Co heterojunction improves the catalytic activity due to the construction of dual-active sites. This research facilitates the innovative construction of non-noble metal catalysts to meet industrial demand for heterogeneous catalysis.

Dipole Coupling Accelerated H2 O Dissociation by Magnesium-Based Intermetallic Catalysts

The water (H2 O) dissociation is critical for various H2 O-associated reactions, including water gas shift, hydrogen evolution reaction and hydrolysis corrosion. While the d-band center concept offers a catalyst design guideline for H2 O activation, it cannot be applied to intermetallic or main group elements-based systems because Coulomb interaction was not considered. Herein, using hydrolysis corrosion of Mg as an example, we illustrate the critical role of the dipole of the intermetallic catalysts for H2 O dissociation. The H2 O dissociation kinetics can be enhanced using Mgx Mey (Me=Co, Ni, Cu, Si and Al) as catalysts, and the hydrogen generation rate of Mg2 Ni-loaded Mg reached 80 times as high as Ni-loaded Mg. The adsorbed H2 O molecules strongly couple with the Mg-Me dipole of Mgx Mey , lowering the H2 O dissociation barrier. The dipole-based H2 O dissociation mechanism is applicable to non-transition metal-based systems, such as Mg2 Si and Mg17 Al12 , offering a flexible catalyst design strategy for controllable H2 O dissociation.

Quantum chemical study on the catalytic debromination mechanism of brominated epoxy resins

The study employed Density Functional Theory (DFT) to investigate the catalytic debromination mechanism of brominated epoxy resins (BERs) by iron (Fe) and copper (Cu) catalysts. By introducing electric field (EF), intramolecular electron transfer and polarization effects on BERs debromination were explored and experimentally validated. Results indicated that the bond dissociation energy (BDE) of the C-Br bond was 312.27 kJ/mol without catalysis, while with Fe, Cu, and EF, it was 114.47 kJ/mol, 94.85 kJ/mol, and 292.59 kJ/mol, respectively, enhancing reactivity. EF parallel to the C-Br bond and oriented toward the C atom, altered electrostatic potential and dipole moment around C-Br bond, leading to 68.60% and 50.19% increment in electronic contribution difference and molecule polarity, respectively, thereby reducing the C-Br BDE. Fe and Cu facilitated electron transfers with BERs, inducing reactions between their negative electrostatic potentials and Br's positive potential, changing electron sharing, resulting in 19.87% and 12.11% increase in polarity, respectively, and further BDE reduction. Structural modifications by the EF and catalysts also intensified van der Waals forces with bromine atoms and decreased spatial hindrance, collectively making C-Br bond breakage easier. Experiments revealed the EF enhanced BERs' debromination efficiency but hindered Fe/Cu's catalysis at lower temperatures.

Structural and functional insights into the self-sufficient flavin-dependent halogenase

Flavin-dependent halogenases (FDHs) have tremendous applications in synthetic chemistry. A single-component FDH, AetF, exhibits both halogenase and reductase activities in a continuous polypeptide chain. AetF exhibits broad substrate promiscuity and catalyzes the two-step bromination of l-tryptophan (l-Trp) to produce 5-bromotryptophan (5-Br-Trp) and 5,7-dibromo-l-tryptophan (5,7-di-Br-Trp). To elucidate the mechanism of action of AetF, we solved its crystal structure in complex with FAD, FAD/NADP+, FAD/l-Trp, and FAD/5-Br-Trp at resolutions of 1.92-2.23 Å. The obtained crystal structures depict the unprecedented topology of single-component FDH. Structural analysis revealed that the substrate flexibility and dibromination capability of AetF could be attributed to its spacious substrate-binding pocket. In addition, highly-regulated interaction networks between the substrate-recognizing residues and 5-Br-Trp are crucial for the dibromination activity of AetF. Several Ala variants underwent monobromination with >98 % C5-regioselectivity toward l-Trp. These results reveal the catalytic mechanism of single-component FDH for the first time and contribute to efficient FDH protein engineering for biocatalytic halogenation.

Vitamin C-regulated CoAl- layered double hydroxide with oxygen vacancies to efficiently activate peroxydisulfate for sulfamethoxazole removal triggered via reactive oxygen and high-valent cobalt species

In this study, a vitamin C-regulated CoAl-layered double hydroxide with abundant oxygen vacancies was synthesized via a simple hydrothermal process. The resulting CoAl-layered double hydroxide was employed to activate peroxydisulfate for removal of sulfamethoxazole. The effect of the experimental parameters such as pH, catalyst dose and peroxydisulfate concentration on sulfamethoxazole removal was investigated. The current system exhibited excellent catalytic performance for sulfamethoxazole removal in a broad pH range (i.e., pH 3.0-11.0). Under the optimized condition, 94.2% of sulfamethoxazole was degraded within 15 min, accompanied by a 67.6% reduction in chemical oxygen demand. The effective sulfamethoxazole degradation could be attributed to four pathways. Firstly, the ≡ Co2+ in catalyst reacted with peroxydisulfate to generate reactive species, including SO4•-, •OH, O2•- and 1O2, which could degrade sulfamethoxazole. Secondly, the oxygen vacancies could modulate intrinsic electrons, resulted in the surface activation of catalyst and accelerated charge transfer, which was favorable for the degradation of sulfamethoxazole. Thirdly, the presence of vitamin C not only promoted the formation of oxygen vacancies but also expanded the interlayer spacing of layered double hydroxide. A large interlayer spacing facilitated the diffusion of peroxydisulfate and pollutants in the interlayer and improved the utilization efficiency of the active site. Lastly, the high-valent cobalt species exhibited excellent oxidation ability and enhanced the catalyst performance through continuously being employed as an electron acceptor. This study provided a valuable insight for the design and application of Co-based catalysts in peroxydisulfate-based advanced oxidation processes.

Chemical catalytic upgrading of polyethylene terephthalate plastic waste into value-added materials, fuels and chemicals

The substantial production of polyethylene terephthalate (PET) products, coupled with high abandonment rates, results in significant environmental pollution and resource wastage. This has prompted global attention to the development of rational strategies for PET waste treatment. In the context of renewability and sustainability, catalytic chemical technology provides an effective means to recycle and upcycle PET waste into valuable resources. In this review, we initially provide an overview of strategies employed in the thermocatalytic process to recycle PET waste into valuable carbon materials, fuels and typical refined chemicals. The effect of catalysts on the quality and quantity of specific products is highlighted. Next, we introduce the development of renewable-energy-driven electrocatalytic and photocatalytic systems for sustainable PET waste upcycling, focusing on rational catalysts, innovative catalytic system design, and corresponding underlying catalytic mechanisms. Moreover, we discuss advantages and disadvantages of three chemical catalytic strategies. Finally, existing limitations and outlook toward controllable selectivity and yield enhancement of value-added products and PET upvaluing technology for scale-up applications are proposed. This review aims to inspire the exploration of waste-to-treasure technologies for renewable-energy-driven waste management toward a circular economy.

Catalytic pyrolysis of liquor-industry waste: Product and mechanism analysis

The effects of three catalysts, namely Ni/γ-Al2O3, Fe/γ-Al2O3, and Mg/γ-Al2O3, on the three-phase products of liquor-industry waste pyrolysis were investigated in this study. Results indicated that the catalytic performance of Ni/γ-Al2O3 outperformed those of Fe/γ-Al2O3 and Mg/γ-Al2O3 significantly. The application of Ni/γ-Al2O3 facilitated the reformation of pyrolysis volatiles, leading to increased yields of H2 (174.1 mL/g), CH4 (80.7 mL/g), and CO (88.2 mL/g) by 980.00 %, 133.24 %, and 83.37 %, respectively. compared to catalyst-free conditions. The Ni/γ-Al2O3 also increased the low-level calorific value of biogas by 109.3 % compared to that under non-catalyst conditions. Moreover, Ni/γ-Al2O3 enhanced the relative concentrations of hydrocarbons in tar by 23.15 % while reducing the relative concentrations of O-species by 15.73 % compared to catalyst-free conditions through induced deoxygenation, decarboxylation, decarbonylation reactions as well as efficient steam reforming processes for tar and syngas upgrading purposes. Thus, incorporating Ni/γ-Al2O3 into the pyrolysis process represents a renewable approach for waste-to-energy conversion.

A comprehensive review on enzymatic biodegradation of polyethylene terephthalate

Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.

Advances in research on microbial conjugated linoleic acid bioconversion

Conjugated linoleic acid (CLA) is a functional food ingredient with prebiotic properties that provides health benefits for various human pathologies and disorders. However, limited natural CLA sources in animals and plants have led microorganisms like Lactobacillus and Bifidobacterium to emerge as new CLA sources. Microbial conversion of linoleic acid to CLA is mediated by linoleic acid isomerase and multicomponent enzymatic systems, with CLA production efficiency dependent on microbial species and strains. Additionally, complex factors like LA concentration, growth status, culture substrates, precursor type, prebiotic additives, and co-cultured microbe identity strongly influence CLA production and isomer composition. This review summarizes advances in the past decade regarding microbial CLA production, including bacteria and fungi. We highlight CLA production and potential regulatory mechanisms and discuss using microorganisms to enhance CLA content and nutritional value of fermented products. We also identify primary microbial CLA production bottlenecks and provide strategies to address these challenges and enhance production through functional gene and enzyme mining and downstream processing. This review aims to provide a reference for microbial CLA production and broaden the understanding of the potential probiotic role of microbial CLA producers.

Enhanced removal of phenolic compounds by ferrate(VI): Unveiling the Bi(III)-Bi(V) valence cycle with in situ formed bismuth hydroxide as catalyst

The use of 2-hydroxybenzophenone (2-HBP) in personal care products is of great concern due to its potential negative effects on the ecosystem and public health. This paper presents the degradation of 2-HBP by bismuth(III) (Bi3+)-ferrate(VI) (FeVIO42-, Fe(VI)) (Bi3+-Fe(VI) system). Experimental studies at different pH and dosages of Bi3+ and Fe(VI) showed that the Bi3+-Fe(VI) system increased the degradation rate and removal efficiency of 2-HBP compared to Fe(VI) alone. The in situ formed flake-like white flocculent precipitate of Bi(OH)3 showed catalytic performance through the Bi(III)-Bi(V)-Bi(III) valence cycle which was demonstrated through spectroscopic measurements. The hydrogen transfer-mediated reactions between Fe(VI) and Bi(OH)3 as well as subsequent formation of Bi(V) were supported by performing density functional theoretical (DFT) calculations. Seventeen identified transformation products of 2-HBP by Fe(VI) with and without Bi3+ revealed hydroxylation, bond breaking, carboxylation, and polymerization reaction pathways. Significantly, Bi3+ facilitated the polymerization reaction and the dioxygen transfer-mediated hydroxylation reaction pathways. The ions (anions and cations) and humic acids (HA) present in the Bi3+-Fe(VI) system had minimal influence on the removal efficiency of 2-HBP. Reusability tests and use of real water samples as well as toxicity assessments of transformation products unveiled the practical application aspect of the Bi3+-Fe(VI) system. Finally, the results showed that the system exhibits good removal efficiency for all 12 phenolic compounds, indicating theuniversality. The Bi3+-Fe(VI) system may be an easy-to-implement cost-effective method for the catalytic degradation of benzophenones by Fe(VI).

Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects

Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.

Enzymatic properties of a non-classical aldoxime dehydratase capable of producing alkyl and arylalkyl nitriles

Nitriles are of significant interest in the flavor and fragrance industries with potential application in cosmetics due to their higher stability than analogous aldehydes. However, the traditional methods to prepare nitriles need toxic reagents and hash conditions. This work aimed to develop a chemoenzymatic strategy to synthesize nitriles from natural aldehydes with aldoxime as the intermediate. A non-classical aldoxime dehydratase (Oxd) was discovered from the fungus Aspergillus ibericus (OxdAsp) to catalyze the dehydration of aldoximes to corresponding nitriles under mild conditions. The amino acid sequence of OxdAsp exhibits an approximately 20% identity with bacterial Oxds. OxdAsp contains a heme prosthetic group bound with the axial H287 in the catalytic pocket. The structure models of OxdAsp with substrates suggest that its catalytic triad is Y138-R141-E192, which is different from the classically bacterial Oxds of His-Arg-Ser/Thr. The catalytic mechanism of OxdAsp was proposed based on the mutagenesis of key residues. The hydroxyl group of the substrate is fixed by E192 to increase its basicity. Y138 acts as a general acid-based catalyst, and its phenolic proton is polarized by the adjacent R141. The protonated Y138 would donate a proton to the hydroxyl group of the substrate and eliminate a water molecule from aldoxime to produce nitrile. The recombinant OxdAsp can efficiently dehydrate citronellal oxime and cinnamaldoxime to citronellyl nitrile and cinnamonitrile in aqueous media, which are applied as fragrance ingredients in the food and cosmetic fields. KEY POINTS: • A novel aldoxime dehydratase from the Aspergillus genus was first characterized as a heme-binding protein. • The catalytic mechanism was predicted based on the molecular interactions of the catalytic pocket with the substrate. • A chemoenzymatic strategy was developed to synthesize nitriles from natural aldehydes with aldoxime as the intermediate.

Amorphous-crystalline heterostructures enable energy-level matching of cobalt sulfide/nickel iron layered double hydroxide for efficient oxygen evolution reaction

Interface engineering of heterostructures has emerged as a promising approach to enhance the catalytic activity of nonprecious electrocatalysts. Herein, a novel amorphous cobalt sulfide-crystalline nickel iron layered double hydroxide (a-CoS@NiFe-LDH) hybrid material is presented for application as an electrocatalyst for oxygen evolution reaction (OER). Benefitting from the well-matched energy level structures, the a-CoS@NiFe-LDH catalyst delivers a low overpotential of 221 ± 14 mV at an OER current density of 20 mA cm-2 and a small Tafel slope of 83.1 mV dec-1, showing good OER properties. First-principle computations reveal that the electronic interaction between amorphous cobalt sulfide (a-CoS) and crystalline nickel iron layered double hydroxide (NiFe-LDH) components within a-CoS@NiFe-LDH promotes the adsorbate evolution mechanism and reduces the adsorption energies for oxygen intermediates, thereby enhancing the activity and stability for OER. This work opens up a new avenue to enhance the OER catalytic efficiency via the construction of amorphous-crystalline heterostructures.

Deep Insight of Design, Mechanism, and Cancer Theranostic Strategy of Nanozymes

Since the discovery of enzyme-like activity of Fe3O4 nanoparticles in 2007, nanozymes are becoming the promising substitutes for natural enzymes due to their advantages of high catalytic activity, low cost, mild reaction conditions, good stability, and suitable for large-scale production. Recently, with the cross fusion of nanomedicine and nanocatalysis, nanozyme-based theranostic strategies attract great attention, since the enzymatic reactions can be triggered in the tumor microenvironment to achieve good curative effect with substrate specificity and low side effects. Thus, various nanozymes have been developed and used for tumor therapy. In this review, more than 270 research articles are discussed systematically to present progress in the past five years. First, the discovery and development of nanozymes are summarized. Second, classification and catalytic mechanism of nanozymes are discussed. Third, activity prediction and rational design of nanozymes are focused by highlighting the methods of density functional theory, machine learning, biomimetic and chemical design. Then, synergistic theranostic strategy of nanozymes are introduced. Finally, current challenges and future prospects of nanozymes used for tumor theranostic are outlined, including selectivity, biosafety, repeatability and stability, in-depth catalytic mechanism, predicting and evaluating activities.

Biochemical and structural characterization of a glucan synthase GFGLS2 from edible fungus Grifola frondosa to synthesize β-1, 3-glucan

BACKGROUND

Grifola frondosa is a Basidiomycete fungus belonging to the family of Grifolaceae and the order of Polyporales. β-Glucans are the main polymers in G. frondosa, playing a crucial role in the physiology and representing the healthy benefits for humans. The membrane-integrated β-1, 3-glucan synthase (GLS) is responsible for glucan synthesis, cell wall assembly, differentiation and growth of the edible fungi. However, the structural/catalytic characteristics and mechanisms of β-1, 3-glucan synthases in G. frondosa are still unknown due to their extremely complex structures with multi-transmembranes and large molecular masses.

RESULTS

Herein, a β-1, 3-glucan synthase (GFGLS2) was purified and identified from the cultured mycelia with a specific activity of 60.01 pmol min-1 μg-1 for the first time. The GFGLS2 showed a strict specificity to UDP-glucose with a Vmax value of 1.29 ± 0.04 µM min-1 at pH 7.0 and synthesized β-1, 3-glucan with a maximum degree of polymerization (DP) of 62. Sequence Similarity Network (SSN) analysis revealed that GFGLS2 has a close relationship with others in Ganoderma sinense, Trametes coccinea, Polyporus brumalis, and Trametes pubescens. With the assistance of 3D structure modelling by AlphaFold 2, molecular docking and molecular dynamics simulations, the central hydrophilic domain (Class III) in GFGLS2 was the main active sites through binding the substrate UDP-glucose to 11 amino acid residues via hydrogen bonds, π-stacking and salt bridges.

CONCLUSIONS

The biochemical, 3D structural characterization and potential catalytic mechanism of a membrane-bound β-1, 3-glucan synthase GFGLS2 from cultured mycelia of G. frondosa were well investigated and would provide a reasonable full picture of β-1, 3-glucan synthesis in fungi.

Electron coupling effect-triggered monatomic copper laccase-mimicking nanozyme for the degradation and detection of guaiacol produced by Alicyclobacillus acidoterrestris

The generation of guaiacol by Alicyclobacillus acidoterrestris (A. acidoterrestris) in fruit juices negatively affects public health and causes severe environmental pollution. Therefore, the sensitive detection and efficient degradation of guaiacol in real samples are crucial. Here, we develop an electrochemical sensor utilizing a copper single-atom nanozyme (CuN4-G) to detect and degrade guaiacol at the picomolar level. Density functional theory (DFT) calculations verify that the bonding electron coupling effect in the CuN4-G facilitates rapid electron transfer, enhances electrical conductivity, and provides abundant active sites, thereby leading to exceptional catalytic performance. Moreover, CuN4-G demonstrates a Km value similar to that of natural laccase but a higher Vmax, highlighting its potential as a highly efficient biocatalyst. The CuN4-G-based electrochemical sensor achieves a detection from 5 to 50,000 pM for guaiacol, with a 1.2 pM (S/N = 3) detection limit. Additionally, CuN4-G-modified electrodes display high selectivity and excellent stability. CuN4-G nanozyme can keep its activity in conditions of pH (3-9), temperature (30-90 °C), ionic strength (0-400 mM), and organic solvent (0-50% (v/v)), overcoming the deficiencies of natural enzymes. Furthermore, our electrochemical sensor can not only accurately detect guaiacol, but also degrade it in actual fruit juice samples infected by A. acidoterrestris, demonstrating its potential applications in food and environmental monitoring.

Electrochemical reduction and protonation of a biomimetic diiron azadithiolate hexacarbonyl complex: Mechanistic insights

The electrochemical reduction and protonation of [Fe2(adtH)(CO)6] (1, adtH = SCH2N(H)CH2S) and [Fe2(pdt)(CO)6] (2, pdt = SCH2CH2CH2S) in the presence of moderately strong acid in acetonitrile was investigated by cyclic voltammetry (CV), focusing on the catalysis of hydrogen evolution reaction (HER) by a {2e-,2H+} pathway. The turnover frequencies at zero overpotential (TOF0) of the N-protonated product 1(H)+ and 2 for the HER were estimated from simulations of the catalytic CV responses at low acid concentration using a simple ECEC mechanism (two electrochemical and chemical steps). This approach confirmed that 1(H)+ is clearly a better catalyst than 2, pointing to a possible role of the protonable and biologically relevant adtH ligand in the enhancement of the catalytic performances. Density functional theory (DFT) calculations further suggested that, owing to a strong structural rearrangement in the course of the catalytic cycle, the HER catalysis by 1(H)+ only involves the iron center adjacent to the amine group in adtH and not the two iron centers as in 2. Since terminal hydride species (FeFe-H) are known to more easily undergo protonolyse to H2 than their bridging hydride isomers (Fe-H-Fe), this may explain here the enhanced activity of 1(H)+ over 2 for the HER.

Cryo-EM structure and rational engineering of a superefficient ochratoxin A-detoxifying amidohydrolase

Ochratoxin A (OTA) is among the most prevalent mycotoxins detected in agroproducts, posing serious threats to human and livestock health. Using enzymes to conduct OTA detoxification is an appealing potential strategy. The recently identified amidohydrolase from Stenotrophomonas acidaminiphila, termed ADH3, is the most efficient OTA-detoxifying enzyme reported thus far and can hydrolyze OTA to nontoxic ochratoxin α (OTα) and L-β-phenylalanine (Phe). To elucidate the catalytic mechanism of ADH3, we solved the single-particle cryo-electron microscopy (cryo-EM) structures of apo-form, Phe- and OTA-bound ADH3 to an overall resolution of 2.5-2.7 Å. The role of OTA-binding residues was investigated by structural, mutagenesis and biochemical analyses. We also rationally engineered ADH3 and obtained variant S88E, whose catalytic activity was elevated by 3.7-fold. Structural analysis of variant S88E indicates that the E88 side chain provides additional hydrogen bond interactions to the OTα moiety. Furthermore, the OTA-hydrolytic activity of variant S88E expressed in Pichia pastoris is comparable to that of Escherichia coli-expressed enzyme, revealing the feasibility of employing the industrial yeast strain to produce ADH3 and its variants for further applications. These results unveil a wealth of information about the catalytic mechanism of ADH3-mediated OTA degradation and provide a blueprint for rational engineering of high-efficiency OTA-detoxifying machineries.

Insights into oxidation of pentachlorophenol (PCP) by low-dose ferrate(VI) catalyzed with α-Fe2O3 nanoparticles

In this study, the catalytic performance of α-Fe₂O₃ nanoparticles (nα-Fe₂O₃) in the low-dose ferrate (Fe(VI)) system was systematically studied through the degradation of pentachlorophenol (PCP). Based on the established quadratic functions between nα-Fe₂O₃ amount and observed pseudo first-order rate constant (k_obs), two linear correlation equations were offered to predict the optimum catalyst dosage and the maximum k_obs at an applied Fe(VI) amount. Moreover, characterization and cycling experiments showed that nα-Fe₂O₃ has good stability and recyclability. According to the results of reactive species identification and quenching experiment and galvanic oxidation process, the catalytic mechanism was proposed that Fe(III) on the surface of nα-Fe₂O₃ may react with Fe(VI) to enhance the generation of highly reactive Fe(IV)/Fe(V) species, which rapidly extracted a single electron from PCP molecule for its further reaction. Besides, two possible PCP degradation pathways, i.e., single oxygen transfer mediated hydroxylation and single electron transfer initiated polymerization were proposed. The formation of coupling products that are prone to precipition and separation was largely improved. This study proved that nα-Fe₂O₃ can effectively catalyze PCP removal at low-dose Fe(VI), which provides some support for the application of Fe(VI) oxidation technology in water treatment in the context of low-carbon emissions.

g-C3N4/MoO3 composite with optimized crystal face: A synergistic adsorption-catalysis for boosting cathode performance of lithium-sulfur batteries

The commercial application of lithium-sulfur batteries (LSBs) has been seriously hindered by the shuttle effect of lithium polysulfides (LiPSs) and their slow redox kinetics. In this work, g-C₃N₄/MoO₃ composed of graphite carbon nitride (g-C₃N₄) nanoflake and MoO₃ nanosheet is designed and applied to modify the separator. The polar MoO₃ can form chemical bond with LiPSs, effectively slowing down the dissolution of LiPSs. And based on the principle of "Goldilocks", LiPSs will be oxidized by MoO₃ to thiosulfate, which will promote the rapid conversion from long-chain LiPSs to Li₂S. Moreover, g-C₃N₄ can promote the electron transportation, and its high specific surface area can facilitate the deposition and decomposition of Li₂S. What's more, the g-C₃N₄ promotes the preferential orientation on the MoO₃(021) and MoO₃(040) crystal planes, which optimizes the adsorption capacity of g-C₃N₄/MoO₃ for LiPSs. As a result, the LSBs with g-C₃N₄/MoO₃ modified separator with a synergistic adsorption-catalysis, can achieve an initial capacity of 542 mAh g^-1 at 4C with capacity decay rate of 0.0053% per cycle for 700 cycles. This work achieves the synergy of adsorption and catalysis of LiPSs through the combination of two materials, providing a material design strategy for advanced LSBs.

H2O2 activation and contaminants removal in heterogeneous Fenton-like systems

Emerging contaminants can be removed effectively in heterogeneous Fenton-like systems. Currently, catalyst activity and contaminant removal mechanisms have been studied extensively in Fenton-like systems. However, a systematic summary was lacking. This review summarized: 1) The effects of various heterogeneous catalysts on emerging contaminants degradation by activating H₂O₂; 2) The role of active sites in different catalysts during the activation of H₂O₂ and their contribution to the generation of active species; 3) The modulation of degradation pathways of emerging contaminants. This paper will help scholars to advance the controlled construction of active sites in heterogeneous Fenton-like systems. Suitable heterogeneous Fenton catalysts can be selected in practical water treatment processes.

Properties and biotechnological applications of microbial deacetylase

Deacetylases, a class of enzymes that can catalyze the hydrolysis of acetylated substrates to remove the acetyl group, used in producing various products with high qualities, are one of the most influential industrial enzymes. These enzymes are highly specific, non-toxic, sustainable, and eco-friendly biocatalysts. Deacetylases and deacetylated compounds have been widely applicated in pharmaceuticals, medicine, food, and the environment. This review synthetically summarizes deacetylases' sources, characterizations, classifications, and applications. Moreover, the typical structural characteristics of deacetylases from different microbial sources are summarized. We also reviewed the deacetylase-catalyzed reactions for producing various deacetylated compounds, such as chitosan-oligosaccharide (COS), mycothiol, 7-aminocephalosporanic acid (7-ACA), glucosamines, amino acids, and polyamines. It is aimed to expound on the advantages and challenges of deacetylases in industrial applications. Moreover, it also serves perspectives on obtaining promising and innovative biocatalysts for enzymatic deacetylation. KEYPOINTS: • The fundamental properties of microbial deacetylases of various microorganisms are presented. • The biochemical characterizations, structures, and catalyzation mechanisms of microbial deacetylases are summarized. • The applications of microbial deacetylases in food, pharmaceutical, medicine, and the environment were discussed.

Folic Acid-Derived Low-dimensional carbons for efficient oxidative dehydrogenation of ethylbenzene

The oxidative dehydrogenation (ODH) of alkane is one of the most attractive routes in alkane production because of its favourable thermodynamic characteristic. Nitrogen-doped nanocarbons have demonstrated great potential in this reaction due to its cost-effective, high catalytic activity and stability. However, the influence of nitrogen on the catalytic properties of carbon materials is poorly understood due to the complexities of surface oxygen and nitrogen functional groups. Here we derive the performance descriptor that account for the nitrogen-dependent carbocatalysis in ODH reaction. To achieve this, we designed a set of nitrogen-doped nanocarbon materials with tunable nitrogen species by hydrothermal carbonization (HTC) treatment of the biomass folic acid (FA), which are applied in ODH of ethylbenzene. Among them, FA-180-1000 catalyst can achieve high ethylbenzene conversion (up to ∼62 %) and styrene selectivity (∼87 %), outperforming other HTC carbon-based catalysts. Structural characterizations and kinetic analyses revealed that nitrogen doping strongly interferes the charge polarization of CO site via electron transfer between CO, and nitrogen (mainly pyridine nitrogen and graphitic nitrogen) thus enhancing the reactivity of CO. Furthermore, the induction period during reaction process can be shortened by applying of sulfuric acid-assisted HTC method for constructing nitrogen-doped carbon catalyst with low crystallinity. The present work provides new insights into the contribution of nitrogen doping to the ODH reaction of carbon nanocatalysts, as well as guidance for the rational design of carbon catalysts for the conversion of hydrocarbons to high-value chemicals.

Characterization of RNase J

RNase J is involved in RNA maturation as well as degradation of RNA to the level of mononucleotides. This enzyme plays a vital role in maintaining intracellular RNA levels and governs different steps of the cellular metabolism in bacteria. RNase J is the first ribonuclease that was shown to have both endonuclease and 5'-3' exonuclease activity. RNase J enzymes can be identified by their characteristic sequence features and domain architecture. The quaternary structure of RNase J plays a role in regulating enzyme activity. The structure of RNase J has been characterized from several homologs. These reveal extensive overall structural similarity alongside a distinct active site topology that coordinates a metal cofactor. The metal cofactor is essential for catalytic activity. The catalytic activity of RNase J is influenced by oligomerization, the choice and stoichiometry of metal cofactors, and the 5' phosphorylation state of the RNA substrate. Here we describe the sequence and structural features of RNase J alongside phylogenetic analysis and reported functional roles in diverse organisms. We also provide a detailed purification strategy to obtain an RNase J enzyme sample with or without a metal cofactor. Different methods to identify the nature of the bound metal cofactor, the binding affinity and stoichiometry are presented. Finally, we describe enzyme assays to characterize RNase J using radioactive and fluorescence-based strategies with diverse RNA substrates.

Recent advances in polygalacturonase: Industrial applications and challenges

This review focuses on the applications of polygalacturonase (PG), one of the most commercially produced enzymes on the biocatalyst market, in the food, beverage, feed, textile, and paper industries. Most PGs are acidic mesophilic enzymes, as shown by a summary of their biochemical properties. However, the acidic PGs discovered to date are insufficiently effective for industrial applications. The sequence and structural characteristics of thermophilic PGs are analyzed based on the results of extensive discussions regarding the catalytic mechanism and structural characteristics of PGs with shared right-handed parallel β-helical structures. In addition, the molecular modification methods for obtaining thermostable PGs are systematically presented. Notably, the demand for alkaline heat-resistant PGs has increased significantly concurrent with the biomanufacturing industry development. Therefore, this review also provides a theoretical guideline for mining heat-resistant PG gene resources and modifying PG thermostability.

Recent advances of metal-organic framework-based and derivative materials in the heterogeneous catalytic removal of volatile organic compounds

Since the environmental hazards of volatile organic compounds (VOCs) are well known, heterogeneous catalysis has become one of the most popular methods to treat VOCs due to its environmental friendliness and simplicity of operation. Although a large number of reports have reviewed the application of catalytic oxidation for the degradation of VOCs, relatively few reports are based on this direction of metal organic frameworks (MOFs) and MOF derivatives. Herein, this paper reviews the recent applications of heterogeneous catalytic technologies in the degradation of VOCs, including photocatalysis, thermal catalysis and other catalytic approaches. The applications of MOFs and their derivatives in VOCs degradation, such as the progress of MOF-derived metal oxides in the treatment of toluene, were highlighted. The mechanisms of VOCs degradation by different catalytic approaches were systematically presented. Finally, we presented the views and directions of VOCs treatment technology development. We hope that this reaction type-oriented review will provide important insights into MOFs and MOF-derived materials for VOCs pollution control.

One-pot synthesis of ultrafine trimetallic PtPdCu alloy nanoparticles decorated on carbon nanotubes for bifunctional catalysis of ethanol oxidation and oxygen reduction

Bifunctional catalysts for ethanol oxidation reaction (EOR) and oxygen reduction reaction (ORR) with high noble-metal utilization are highly beneficial to direct ethanol fuel cells (DEFCs). This study developed a ternary bifunctional catalyst composed of ultrafine PtPdCu alloy nanoparticles and carbon nanotubes (CNTs) support through a facile surfactant-free solvothermal route. The carboxyl terminal groups on CNTs ensure the confined growth of PtPdCu alloys (∼5 nm) and suppress Ostwald ripening of metallic active sites during electrochemical cycling. Consequently, PtPdCu/CNTs exhibits high mass activity (1.95 A mg^-1) and specific activity (4.08 mA cm^-2) toward EOR, which are 7.8 and 8.9 times higher, respectively, than those of commercial Pt/C. Furthermore, PtPdCu/CNTs displays superior stability toward EOR compared with its bimetallic counterparts (PtPd/CNTs and PtCu/CNTs). In addition, PtPdCu/CNTs exhibits the highest half-wave potential of 0.888 V among all electrocatalysts, indicating high ORR activity. Density functional theory calculations reveal that Pd and Cu mediate the electronic structure of Pt, leading to enhanced catalytic activity of PtPdCu/CNTs. The excellent catalytic property of PtPdCu/CNTs can also be attributed to the bifunctional effects of Pd/Cu and the interaction between metal and the carbon support. The proposed material is a contribution to the family of efficient ternary-alloy electrocatalysts for fuel cells.

Structural and functional characterization of RNA dependent RNA polymerase of Macrobrachium rosenbergii nodavirus (MnRdRp)

Macrobrachium rosenbergii is a highly valued farmed freshwater species and its production has been affected globally by white tail disease caused by M. rosenbergii nodavirus (MrNV). MrNV is a single stranded positive sense RNA virus encoding RNA-dependent RNA polymerase (RdRp) for genome replication. Due to its essentiality for pathogenesis, it is an important drug target. The domain prediction of the complete sequence revealed the presence of two enzymatic regions namely methyl transferase and RdRp separated by transmembrane region. The predicted three-dimensional (3D) structure of MnRdRp using AlphaFold 2 shows that the structure is composed of three major sub-domains common for other polymerases namely fingers, palm and thumb. Structural similarity search revealed its similarity with other flaviviridea members especially with BVDV RdRp (BvdvRdRp). The structure of fingers and palm sub-domains is more conserved than the thumb sub-domain. A small α-helix named 'priming helix' having conserve Tyr was identified at position 829-833 with a potential role in de novo initiation. Analysis of electrostatic potential revealed that nucleotide and template channels are electropositive. Metal binding residues were identified as Asp599, Asp704 and Asp705. The α and β phosphates of incoming nucleotide interact with two Mn2+, Arg455 and Arg537. For recognition of 2'-OH of incoming rNTP, Asp604, Ser661 and Asn670 were identified which can form H-bond network with 2'-OH group. Docking study revealed that Dasabuvir can potentially inhibit MnRdRp. The study concluded that the overall structure and function of MnRdRp are similar to Flaviviridae polymerases and their inhibitors can work against this enzyme.Communicated by Ramaswamy H. Sarma.

Bioremediation potential of laccase for catalysis of glyphosate, isoproturon, lignin, and parathion: Molecular docking, dynamics, and simulation

The present study aimed to investigate the catalytic degradation produced by laccase in the detoxification of glyphosate, isoproturon, lignin polymer, and parathion. We explored laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion using molecular docking (MD) and molecular dynamics simulation (MDS) approaches. The results suggest that laccase interacts well with glyphosate, lignin polymer, isoproturon, and parathion during biodegradation. We calculated the root mean square deviations (RMSD) of laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion as 0.24 ± 0.02, 0.59 ± 0.32, 0.43 ± 0.07, and 0.43 ± 0.06 nm, respectively. In an aqueous solution, the stability of laccase with glyphosate, lignin polymer, isoproturon, and parathion is mediated through the formation of hydrophobic interactions, hydrogen bonds, and van der Waals interactions. The presence of xenobiotic toxic compounds in the active site changed the conformation of laccase. MDS of the laccase-substrate complexes confirmed their stability during catalytic degradation. Laccase assay results confirmed that the degradation of syringol, dihydroconiferyl alcohol, guaiacol, parathion, isoproturon, and glyphosate were 100%, 99.31%, 95.69%, 60.96%, 54.51%, and 48.34% within 2 h, respectively. Taken together, we describe a novel method to understand the molecular-level biodegradation of xenobiotic compounds through laccase and its potential application in contaminant removal.

Insights into the biosynthesis of septacidin l-heptosamine moiety unveils a VOC family sugar epimerase

l-Heptopyranoses are important components of bacterial polysaccharides and biological active secondary metabolites like septacidin (SEP), which represents a group of nucleoside antibiotics with antitumor, antifungal, and pain-relief activities. However, little is known about the formation mechanisms of those l-heptose moieties. In this study, we deciphered the biosynthetic pathway of the l,l-gluco-heptosamine moiety in SEPs by functional characterizing four genes and proposed that SepI initiates the process by oxidizing the 4'-hydroxyl of l-glycero-α-d-manno-heptose moiety of SEP-328 (2) to a keto group. Subsequently, SepJ (C5 epimerase) and SepA (C3 epimerase) shape the 4'-keto-l-heptopyranose moiety by sequential epimerization reactions. At the last step, an aminotransferase SepG installs the 4'-amino group of the l,l-gluco-heptosamine moiety to generate SEP-327 (3). An interesting phenomenon is that the SEP intermediates with 4'-keto-l-heptopyranose moieties exist as special bicyclic sugars with hemiacetal-hemiketal structures. Notably, l-pyranose is usually converted from d-pyranose by bifunctional C3/C5 epimerase. SepA is an unprecedented monofunctional l-pyranose C3 epimerase. Further in silico and experimental studies revealed that it represents an overlooked metal dependent-sugar epimerase family bearing vicinal oxygen chelate (VOC) architecture.

Resource utilization of high-concentration SO2 for sulfur production over La-Ce-Ox composite oxide catalyst

Sulfur dioxide is one of the main causes of air pollution such as acid rain and photochemical smog, and its pollution control and resource utilization have become important research directions. La₂O₃ was incorporated into CeO₂ to enhance the surface basicity of La-Ce-O_x catalyst and increase the concentration of chemisorbed oxygen, thereby promoting the improvement of catalytic performance of SO₂ reduction by CO. Results have showed that the incorporation of La₂O₃ would not only increase the concentration of chemisorbed oxygen and hydroxyl on the catalyst surface, but also increase the basicity of the catalyst, thereby facilitating the adsorption of SO₂ on the catalyst surface. The 12%La-Ce-O_x was the optimal catalyst, and its SO₂ conversion at 350-400 ℃ reached close to 100%, and the sulfur yield at this temperature range was higher than 93%. Finally, according to the in situ infrared diffuse reflectance spectrum, it was found that the main reaction intermediates of 12%La-Ce-O_x in the catalytic reduction of SO₂ were weakly adsorbed sulfate, SO₃^2-, non-coordinating CO₃^2-, monodentate carbonate, and CO, so the catalytic reaction followed the L-H and E-R mechanisms simultaneously.

Efficient synergistic catalysis of chlorinated aromatic hydrocarbons and NOx over novel low-temperature catalysts: Nano-TiO2 modification and interaction mechanism

For efficient and synergistic elimination of chlorinated aromatic hydrocarbons (e.g., dioxins and chlorobenzenes) and NO_x at low temperatures, a novel VO_x-CeO_x-WO_x/TiO₂ catalyst was systemically studied, involving the nano-TiO₂ modification and the interaction mechanism between 1,2-dichlorobenzen (1,2-DCB) catalytic oxidation (DCBCO) and NH₃-SCR. The VO_x-CeO_x-WO_x/TiO₂ performed excellent oxygen storage/release capacity (OSRC) and desirable 1,2-DCB conversion efficiency (95.1-97.4%) at 160-200 ℃ via M‒K and L‒H mechanism. The nano-TiO₂ modification slightly impaired the 1,2-DCB oxidation to 93.6-96.2% owing to the reduced surface area and Brønsted acidity, while it distinctly enhanced NO conversion and lowered the T₅₀ (from 162 to 112 ℃) and T₉₀ (from 232 to 205 ℃) by improving catalyst reducibility. Based on further synergistic catalysis evaluation and in-situ DRIFT analysis, NO enhanced the 1,2-DCB conversion and complete oxidation capacity of VO_x-CeO_x-WO_x/TiO₂ by promoting active oxygen (O₂^-, O^-, O^2-) generation and improving 1,2-DCB chemosorption and subsequent oxidation. In detail, the produced HCl and H₂O improved the catalyst acidity and promoted the formation of HONO and HNO₃. Moreover, their generation not only facilitated the chemisorption of NH₃ but also participated in the NH₃-SCR via L‒H mechanism. The ensuing problem was the competitive chemisorption among 1,2-DCB, NH₃, and their subsequent intermediates. As a result, NH₃ had distinct advantages in competing for acid sites and active oxygen species, especially at the higher temperature, resulting in the improved NO conversion with elevated reaction temperature but the reduced 1,2-DCB conversion. The results provided essential basics for developing new catalysts to synergistically control the emission of chloroaromatic organics and NO_x at low temperature.

Low quantity of Pt loaded onto CeCoOx nanoboxes: Surface-rich reactive oxygen species for catalytic oxidation of toluene

An optimized oxygen activity of catalysts can facilitate oxidation of volatile organic compounds. This work shows the first construction of Ce-Co oxide thin-walled nanoboxes. Bulk-phase lattice oxygen is activated by metal-metal interactions. The subsequent uniform dispersion of low loaded Pt nanoparticles further enhances the surface-adsorbed oxygen content, and creates an oxygen-rich reaction interface. Competitive adsorption of water vapor was also inhibited, and complete catalytic oxidation of toluene was achieved at low temperature (T₉₀ =140 °C). A diffuse reflectance infrared Fourier-transform spectroscopy probe was used to investigate the adsorption-catalytic process and the possible synergistic catalytic mechanism (Langmuir-Hinshelwood and Mars-van Krevelen). This work provides a strategy for improving the catalyt Crystal structure ic oxidation performance of nanocatalysts for volatile organic compounds by increasing the catalytic oxygen activity.

Conformational transitions induced by NADH binding promote reduction half-reaction in 2-hydroxybiphenyl-3-monooxygenase catalytic cycle

2-Hydroxybiphenyl-3-monoxygenase from Pseudomonas azelaica is an effective catalyst of the regiospecific conversions of various aromatic compounds. A comprehensive understanding of the complete catalytic cycle, including the as yet unclear details of NADH binding, NADH/FAD interaction as well as related conformational changes could facilitate the rational design of improved enzyme variants for practical applications. Induced fit formation of a specific pocket for the nicotinamide ring at NADH binding has been revealed using advanced molecular simulation methods including metadynamics and QM/MM modeling. The resulting triple stacking interaction of the nicotinamide as well as isoalloxazine rings and evolutionarily correlated amino acid residues of the active site greatly contributes to the stabilization of the charge-transfer complex and determines the Pro-S stereospecificity of the hydride transfer and the low energy barrier 11 kcal/mol. Then the resulting FADH^- anion undergoes the consequent conformational transition of the FAD isoalloxazine ring from the open out to the closed in position which is followed by the binding of an oxygen molecule what is crucial for the next step of substrate oxidation and the completion of the catalytic cycle.

Fe-N-C single-atom nanozyme for ultrasensitive, on-site and multiplex detection of mycotoxins using lateral flow immunoassay

Sensitive, on-site and multiple detection of mycotoxins is a vital early-warning tool to minimize food losses and protect human health and the environment. Although paper-based lateral flow immunoassay (LFIA) has been extensively applied in mycotoxins monitoring, low-cost, portable, ultrasensitive and quantitative detection is still a formidable challenge. Herein, a series of Fe-N-C single-atom nanozymes (SAzymes) were synthesized and systematic characterized. The optimal Fe-N-C SAzyme with highly efficient catalytic performance was successfully used as both label and catalyst in lateral flow immunoassays for mycotoxin detection. By taking advantage of the catalytic amplified system, the qualitative and quantitative detection can be easily and flexibly done via observing the test lines by naked eyes or a smartphone, with the limit of detections (LODs) of 2.8 and 13.9 pg mL^-1 for AFB₁ and FB₁, which were respectively over 700- and 71,000-fold lower than the maximum limit set by the European Union. Besides, underlying catalytic mechanisms and the active sites of the Fe-N-C SAzyme are also investigated by DFT simulation. This work not only provides a promising detection strategy for the application of advanced SAzymes but also offers experimental and theoretical guidelines to understand the active centers of Fe-N-C SAzymes and the catalytic process.

Insights into the catalytic and regulatory mechanisms of dihydroflavonol 4-reductase, a key enzyme of anthocyanin synthesis in Zanthoxylum bungeanum

Accumulation of anthocyanins largely determines the fruit color, and dihydroflavonol 4-reductase (DFR) is a key enzyme involved in the formation of anthocyanins. However, the catalytic and regulatory mechanisms of DFR are unclear. In this study, the gene encoding DFR from Zanthoxylum bungeanum Maxim. was cloned and ZbDFR was analyzed in detail. The ZbDFR accepted dihydrokaempferol, dihydroquercetin and dihydromyricetin as substrates. Flavonols such as myricetin, quercetin and kaempferol significantly inhibited the activity of ZbDFR, while quercitrin and isoquercitrin slightly increased the activity. Quercetin was a competitive inhibitor at low concentrations, and it had a combined effect of competitive and noncompetitive inhibition at high concentrations, which was consistent with ZbDFR having two inhibitor binding sites. In addition, the content of different types of flavonoids in Z. bungeanum peel at green, semi-red and red stage was analyzed, and the in vivo results could be explained by the regulation of ZbDFR activity in vitro. Site-directed mutagenesis combined with enzyme activity experiments showed that Ser128, Tyr163, Phe164 and Lys167 are the key catalytic amino acid residues. The Ser128, Tyr163 and Lys167 were crucial for the hydrogen transfer reaction, and mutation of these amino acids resulted in the loss of all or most of the activity. Phe164 was found to be important for the regulation of ZbDFR by flavonols. Accordingly, ZbDFR is a node at which flavonoids regulate the synthesis of anthocyanins and proanthocyanins.

Catalytic isomerization of glucose to fructose over organic ligands: a DFT study

CONTEXT

Isomerization processes between glucose and fructose catalyzed by four different organic ligands are investigated with quantum chemistry methods in this study. These organic ligands are the carboxylic pendant group, sulfonic pendant group, amino pendant group, and 1H-imidazole ligand. After guessing and verifying a variety of elementary reactions, transition states and energy barriers that are relevant to the optimum pathways have been confirmed. The effective barriers under the catalysis of the carboxylic pendant group, sulfonic pendant group, amino pendant group, and 1H-imidazole ligand are 97.5 kJ mol^-1, 134.7 kJ mol^-1, 146.7 kJ mol^-1, and 167.7 kJ mol^-1, respectively. Then, based on the conclusions of the non-solvation model, the effective barriers in solvents are briefly investigated. The implicit model predicts that solvents bring little improvement or setback to catalyzed reaction models. The explicit model shows that the proton transfer with the participant of water molecules can improve the catalytic performance of Lewis bases in these reactions. The detailed reaction mechanism combing and reliable reaction templates provided in this work will be useful for catalysis designs for glucose transformation to fructose.

METHODS

This work used the computational level of ωB97M-D3BJ/def2-SVP and the software package of ORCA 4.2. For solvent effects, energies of the gas phase were corrected by the combination of C-PCM and SMD.

Point mutation of V252 in neomycin C epimerase enlarges substrate-binding pocket and improves neomycin B accumulation in Streptomyces fradiae

Neomycin, an aminoglycoside antibiotic with broad-spectrum antibacterial resistance, is widely used in pharmaceutical and agricultural fields. However, separation and purification of neomycin B as an active substance from Streptomyces fradiae are complicated. Although NeoN can catalyze conversion of neomycin C to neomycin B, the underlying catalytic mechanism is still unclear. In this study, the genomic information of high-yielding mutant S. fradiae SF-2 was elucidated using whole-genome sequencing. Subsequently, the mechanism of NeoN in catalyzing conversion of neomycin C to neomycin B was resolved based on NeoN-SAM-neomycin C ternary complex. Mutant NeoNV252A showed improved NeoN activity, and the recombinant strain SF-2-NeoNV252A accumulated 16,766.6 U/mL neomycin B, with a decrease in neomycin C ratio from 16.1% to 6.28%, when compared with the parental strain SF-2. In summary, this study analyzed the catalytic mechanism of NeoN, providing significant reference for rational design of NeoN to improve neomycin B production and weaken the proportion of neomycin C.