Carbon-based nanozymes: design, catalytic mechanisms, and environmental applications.

Carbon-based nanozymes are synthetic nanomaterials that are predominantly constituted of carbon-based materials, which mimic the catalytic properties of natural enzymes, boasting features such as tunable catalytic activity, robust regenerative capacity, and exceptional stability. Due to the impressive enzymatic performance similar to various enzymes such as peroxidase, superoxide dismutase, and oxidase, they are widely used for detecting and degrading pollutants in the environment. This paper presents an exhaustive review of the fundamental design principles, catalytic mechanisms, and prospective applications of carbon-based nanozymes in the environmental field. These studies not only serve to augment the comprehension on the intricate operational mechanism inherent in these synthetic nanostructures, but also provide essential guidelines and illuminating perspectives for advancing their development and practical applications. Future studies that are imperative to delve into the untapped potential of carbon-based nanozymes within the environmental domain was needed to be explored to fully harness their ability to deliver broader and more impactful environmental preservation and management outcomes.

Ceria-Based Nanozymes in Point-of-Care Diagnosis: An Emerging Futuristic Approach for Biosensing.

In recent years, there has been a notable increase in interest surrounding nanozymes due to their ability to imitate the functions and address the limitations of natural enzymes. The scientific community has been greatly intrigued by the study of nanoceria, primarily because of their distinctive physicochemical characteristics, which include a variety of enzyme-like activities, affordability, exceptional stability, and the ability to easily modify their surfaces. Consequently, nanoceria have found extensive use in various biosensing applications. However, the impact of its redox activity on the enzymatic catalytic mechanism remains a subject of debate, as conflicting findings in the literature have presented both pro-oxidant and antioxidant effects. Herein, we creatively propose a seesaw model to clarify the regulatory mechanism on redox balance and survey possible mechanisms of multienzyme mimetic properties of nanoceria. In addition, this review aims to showcase the latest advancements in this field by systematically discussing over 180 research articles elucidating the significance of ceria-based nanozymes in enhancing, downsizing, and enhancing the efficacy of point-of-care (POC) diagnostics. These advancements align with the ASSURED criteria established by the World Health Organization (WHO). Furthermore, this review also examines potential constraints in order to offer readers a concise overview of the emerging role of nanoceria in the advancement of POC diagnostic systems for future biosensing applications.

Crystal Structure Determination of Nucleotide-sugar Binding Domain of Human UDP-glucuronosyltransferases 2B10.

BACKGROUND: UDP-glucuronosyltransferases (UGTs) play a crucial role in maintaining endobiotic homeostasis and metabolizing xenobiotic compounds, particularly clinical drugs. However, the detailed catalytic mechanism of UGTs has not been fully elucidated due to the limited availability of reliable protein structures. Determining the catalytic domain of human UGTs has proven to be a significant challenge, primarily due to the difficulty in purifying and crystallizing the full-length protein. OBJECTIVES: This study focused on the human UGT2B10 C-terminal cofactor binding domain, aiming to provide structural insights into the fundamental catalytic mechanisms. METHODS: In this study, the C-terminal sugar-donor binding domain of human UGT2B10 was purified and crystallized using the vapor-diffusion method. The resulting UGT2B10 CTD crystals displayed high-quality diffraction patterns, allowing for data collection at an impressive resolution of 1.53 Å using synchrotron radiation. Subsequently, the structure of the UGT2B10 CTD was determined using the molecule replacement method with a homologous structure. RESULTS: The crystals were monoclinic, belonging to the space C2 with unit-cell parameters a = 85.90 Å, b = 58.39 Å, c = 68.87 Å, α = γ = 90°, and ß = 98.138°. The Matthews coefficient VM was determined to be 2.24 Å3 Da-1 (solvent content 46.43%) with two molecules in the asymmetric unit. CONCLUSION: The crystal structure of UGT2B10 CTD was solved at a high resolution of 1.53 Å, revealing a conserved cofactor binding pocket. This is the first study determining the C-terminal cofactor binding domain of human UGT2B10, which plays a key role in additive drug metabolism.

A highly selective C-rhamnosyltransferase from Viola tricolor and insights into its mechanisms.

C-Glycosides are important natural products with various bioactivities. In plant biosynthetic pathways, the C-glycosylation step is usually catalyzed by C-glycosyltransferases (CGTs), and most of them prefer to accept uridine 5'-diphosphate glucose (UDP-Glc) as sugar donor. No CGTs favoring UDP-rhamnose (UDP-Rha) as sugar donor has been reported, thus far. Herein, we report the first selective C-rhamnosyltransferase VtCGTc from the medicinal plant Viola tricolor. VtCGTc could efficiently catalyze C-rhamnosylation of 2-hydroxynaringenin 3-C-glucoside, and exhibited high selectivity towards UDP-Rha. Mechanisms for the sugar donor selectivity of VtCGTc were investigated by molecular dynamics (MD) simulations and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) binding free energy calculations. Val144 played a vital role in recognizing UDP-Rha, and the V144T mutant could efficiently utilize UDP-Glc. This work provides a new and efficient approach to prepare flavonoid C-rhamnosides such as violanthin and iso-violanthin.

Carbon Dioxide Hydrogenation to Formate Catalyzed by a Neutral, Coordinatively Saturated Tris-Carbonyl Mn(I)-PNP Pincer-Type Complex.

CO2 catalytic hydrogenation to formate was achieved (TONmax =ca. 3800) in the presence of the neutral, halide-free, coordinatively saturated tris(carbonyl) manganese pincer-type complex [Mn(PNP)(CO)3 ], bearing a diarylamido pincer-type PNP ligand, using DBU as base and LiOTf as Lewis acid additive, under mild reaction conditions (60 bar, 80 °C). DFT calculations suggest that the precatalyst activation key step occurs by intermolecular, base assisted dihydrogen heterolytic splitting rather than by the expected ligand-assisted intramolecular MLC-type mechanism.

Gaining Deep Understanding of Electrochemical CO2 RR with In Situ/Operando Techniques.

Electrocatalysis for CO2 conversion has been extensively studied to mitigate the energy shortage and environmental issues, which are gaining ever-increasing attention. However, the complicated CO2 reduction process and the dynamic evolution occurring on electrocatalyst surface make it hard to understand the catalytic mechanism. The development of advanced in situ/operando techniques intelligently coupled with electrochemical cells sheds light on the related study via capturing surface atomic rearrangement, tracing chemical state change of catalysts, monitoring the behavior of intermediates and products, and depicting microenvironment near the electrode surface. In this review, fundamentals of the state-of-the-art in situ/operando techniques are clarified first. Case studies on the in situ/operando techniques performed to probe the CO2 reduction reaction processes are then discussed in detail. Finally, conclusions and outlook on this field are presented.

Modulation of radical and nonradical pathways via modified carbon nanotubes toward efficient oxidation of binary pollutants in water.

In order to minimize the knowledge gap between single and binary pollutants degradation by persulfate-based advanced oxidation processes (PS-AOPs), iron-loaded N-doped carbon nanotubes (Fe-NCNT) and its acid-washing sample (Fe-NCNT-W) were synthesized as peroxymonosulfate (PMS) activator for simultaneous oxidation of acid orange 7 (AO7) and electron-rich (phenol/ibuprofen) or electron-deficient pollutants (nitrobenzene/benzoic acid). Mechanistic studies revealed that both radical (HO•, SO4•-) and nonradical (electron-transfer, high-valent iron) pathways involved for organic oxidation in Fe-NCNT/PMS system, while electron-transfer pathway (ETP) and high-valent iron-oxo species accounted for pollutant degradation at the surface and inner space of Fe-NCNT-W, respectively. The oxidation performances in single or binary systems were systematically investigated. In comparison to benchmark radical-based (Fe2+/PMS), nonradical ETP (NCNT/PMS) and mixed (Fe-NCNT/PMS) systems, Fe-NCNT-W/PMS outperformed superior performance toward oxidation of binary pollutants with little inference from solution pH or background substances, which could also be fabricated into membrane reactor for actual dyeing sewage treatment. Such superiorities should be mainly ascribed to the particular selectivity and intensive treatment of nonradical pathways in Fe-NCNT-W/PMS system with nanoconfinement effect. This work affords novel insights into the treatment of combined pollution via PMS activation by engineered nanomaterials.

Molecular mechanisms of processive glycoside hydrolases underline catalytic pragmatism.

Processive and distributive catalysis defines the conversion continuum, thus underpinning the transformation of oligo- and polymeric substrates by enzymes. Distributive catalysis follows an association-transformation-dissociation pattern during the formation of enzyme-reactant complexes, whereas during processive catalysis, enzymes partner with substrates and complete multiple catalytic events before dissociation from an enzyme-substrate complex. Here, we focus on processive catalysis in glycoside hydrolases (GHs), which ensures efficient conversions of substrates with high precision, and has the advantage over distributive catalysis in efficiency. The work presented here examines a recent discovery of substrate-product-assisted processive catalysis in the GH3 family enzymes with enclosed pocket-shaped active sites. We detail how GH3 ß-d-glucan glucohydrolases exploit a transiently formed lateral pocket for product displacement and reactants sliding (or translocation motion) through the catalytic site without dissociation, including movements during nanoscale binding/unbinding and sliding. The phylogenetic tree of putative 550 Archaean, bacterial, fungal, Viridiplantae, and Metazoan GH3 entries resolved seven lineages that corresponded to major substrate specificity groups. This analysis indicates that two tryptophan residues in plant ß-d-glucan glucohydrolases that delineate the catalytic pocket, and infer broad specificity, high catalytic efficiency, and substrate-product-assisted processivity, have evolved through a complex evolutionary process, including horizontal transfer and neo-functionalisation. We conclude that the definition of thermodynamic and mechano-structural properties of processive enzymes is fundamentally important for theoretical and practical applications in bioengineering applicable in various biotechnologies.

Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology.

Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational framework, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.

Molecular Dynamics Simulations Reveal the Conformational Transition of GH33 Sialidases.

Sialidases are increasingly used in the production of sialyloligosaccharides, a significant component of human milk oligosaccharides. Elucidating the catalytic mechanism of sialidases is critical for the rational design of better biocatalysts, thereby facilitating the industrial production of sialyloligosaccharides. Through comparative all-atom molecular dynamics simulations, we investigated the structural dynamics of sialidases in Glycoside Hydrolase family 33 (GH33). Interestingly, several sialidases displayed significant conformational transition and formed a new cleft in the simulations. The new cleft was adjacent to the innate active site of the enzyme, which serves to accommodate the glycosyl acceptor. Furthermore, the residues involved in the specific interactions with the substrate were evolutionarily conserved in the whole GH33 family, highlighting their key roles in the catalysis of GH33 sialidases. Our results enriched the catalytic mechanism of GH33 sialidases, with potential implications in the rational design of sialidases.

Rhodium-Based Nanozymes: Recent Advances and Challenges.

Rhodium (Rh) is a non-toxic transition metal used as various nanomaterials with unique structures and properties. Rh-based nanozymes can mimic the activities of natural enzymes, overcome the limitation of the application scope of natural enzymes, and interact with various biological microenvironments to play a variety of functions. Rh-based nanozymes can be synthesized in various ways, and different modification and regulation methods can also enable users to control catalytic performance by adjusting enzyme active sites. The construction of Rh-based nanozymes has attracted great interest in the biomedical field and impacted the industry and other areas. This paper reviews the typical synthesis and modification strategies, unique properties, applications, challenges, and prospects of Rh-based nanozymes. Next, the unique features of Rh-based nanozymes are emphasized, including adjustable enzyme-like activity, stability, and biocompatibility. In addition, we discuss Rh-based nanozymes biosensors and detection, biomedical therapy, and industrial and other applications. Finally, the future challenges and prospects of Rh-based nanozymes are proposed.

Electrocatalysis Mechanism and Structure-Activity Relationship of Atomically Dispersed Metal-Nitrogen-Carbon Catalysts for Electrocatalytic Reactions.

Atomically dispersed metal-nitrogen-carbon catalysts (M-N-C) have been widely used in the field of energy conversion, which has already attracted a huge amount of attention. Due to their unsaturated d-band electronic structure of the center atoms, M-N-C catalysts can be applied in different electrocatalytic reactions by adjusting their own microscopic electronic structures to achieve the optimization of the structure-activity relationship. Consequently, it is of great significance for the revelation of electrocatalytic mechanism and structure-activity relationship of M-N-C catalysts. Thus, this review first introduces the relative research methods, including in situ/operando characterization techniques and theoretical calculation methods. Furthermore, clarifying the electrocatalytic mechanism and structure-activity relationship of M-N-C catalysts in different electrochemical energy conversion reactions is focused. Moreover, the future research directions are pointed out based on the discussion. This review will provide good guidance to systematically study the catalytic mechanism of single-atom catalysts and reasonably design the single-atom catalysts.

Structure-based rational design of hydroxysteroid dehydrogenases for improving and diversifying steroid synthesis.

A group of steroidogenic enzymes, hydroxysteroid dehydrogenases are involved in steroid metabolism which is very important in the cell: signaling, growth, reproduction, and energy homeostasis. The enzymes show an inherent function in the interconversion of ketosteroids and hydroxysteroids in a position- and stereospecific manner on the steroid nucleus and side-chains. However, the biocatalysis of steroids reaction is a vital and demanding, yet challenging, task to produce the desired enantiopure products with non-natural substrates or non-natural cofactors, and/or in non-physiological conditions. This has driven the use of protein design strategies to improve their inherent biosynthetic efficiency or activate their silent catalytic ability. In this review, the innate features and catalytic characteristics of enzymes based on sequence-structure-function relationships of steroidogenic enzymes are reviewed. Combining structure information and catalytic mechanisms, progress in protein redesign to stimulate potential function, for example, substrate specificity, cofactor dependence, and catalytic stability are discussed.

Supported Mn2O3-based catalysts for NO-SCO: an experimental study.

In this paper, the NO-SCO (the selective catalytic oxidation of NO) experiments of single-phase Mn2O3, supported Mn2O3/Al2O3, and the Ce-doped MnxCey/Al catalyst system were carried out. The physical and chemical properties of the catalysts were analyzed by XRD, BET, XPS, SEM, O2-TPD, and H2-TPR. The effects of loading and Ce doping on catalyst activity were studied. The results show that the Mn2O3 catalyst exhibited the best activity at 300 ℃, and the NO conversion rate of Mn2O3 was 78.2%. The relative content of Oα adsorbed on the surface of the Mnx/Al catalyst decreased obviously by loading Mn2O3 on γ-Al2O3, which led to the decrease in catalyst activity. And the temperature window moved to the high-temperature region. After doping Ce, the dispersion of Mn enhanced, and the relative content of oxygen Oα adsorbed on the surface increased. The low-temperature activity and fluidity of oxygen in catalysts were improved. Among them, the Mn0.2Ce0.08/Al catalyst obtained a high specific surface area, good pore structure, large oxygen storage capacity, and excellent surface oxygen species. The corresponding NO conversion rate reached 83.5% at 290 ℃. Then, the effects of operating parameters such as space velocity, NO concentration, and O2 content on the catalytic activity of Mn0.2Ce0.08/Al were discussed. The experimental results show that the NO conversion rate of Mn0.2Ce0.08/Al decreased with increasing NO concentration and space velocity. The O2 content had a positive effect on the catalytic activity of the catalyst. However, the NO conversion rate tended to be stable due to the saturation of oxygen adsorbed on the catalyst. Through cycling experiments, we found that Mn2O3, Mn0.2/Al, and Mn0.2Ce0.08/Al catalysts showed good oxidation stabilities for NO oxidation. The evaluation of the water and sulfur resistance of the catalyst shows that the toxicity of SO2 was reduced by the aqueous atmosphere to a certain extent. Through the structural optimization of the basic model and the calculation of the NO-SCO reaction path, the results show that the NO-SCO reaction on the Mn2O3 (110) face followed the ER mechanism more. For the Mn2O3/Al2O3 (110) surface, the LH-MvK hybrid mechanism can greatly reduce the desorption energy barrier of the reaction intermediates, which is more favorable for the NO-SCO reaction. The catalytic mechanisms of the MnxCey/Al catalysts require further in-depth research.

A highly selective C-rhamnosyltransferase from Viola tricolor and insights into its mechanisms

C-Glycosides are important natural products with various bioactivities. In plant biosynthetic pathways, the C-glycosylation step is usually catalyzed by C-glycosyltransferases (CGTs), and most of them prefer to accept uridine 5'-diphosphate glucose (UDP-Glc) as sugar donor. No CGTs favoring UDP-rhamnose (UDP-Rha) as sugar donor has been reported, thus far. Herein, we report the first selective C-rhamnosyltransferase VtCGTc from the medicinal plant Viola tricolor. VtCGTc could efficiently catalyze C-rhamnosylation of 2-hydroxynaringenin 3-C-glucoside, and exhibited high selectivity towards UDP-Rha. Mechanisms for the sugar donor selectivity of VtCGTc were investigated by molecular dynamics (MD) simulations and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) binding free energy calculations. Val144 played a vital role in recognizing UDP-Rha, and the V144T mutant could efficiently utilize UDP-Glc. This work provides a new and efficient approach to prepare flavonoid C-rhamnosides such as violanthin and iso-violanthin.

Catalase-Like Nanozymes: Classification, Catalytic Mechanisms, and Their Applications.

The field of nanozymes has developed rapidly over the past decade. Among various oxidoreductases mimics, catalase (CAT)-like nanozyme, acting as an essential part of the regulation of reactive oxygen species (ROS), has attracted extensive research interest in recent years. However, CAT-like nanozymes are not as well discussed as other nanozymes such as peroxidase (POD)-like nanozymes, etc. Compared with natural catalase or artificial CAT enzymes, CAT-like nanozymes have unique properties of low cost, size-dependent properties, high catalytic activity and stability, and easy surface modification, etc., which make them widely used in various fields, especially in tumor therapy and disease treatment. Consequently, there is a great requirement to make a systematic discussion on CAT-like nanozymes. In this review, some key aspects of CAT-like nanozymes are deeply summarized as: 1) Typical CAT-like nanozymes classified by different nanomaterials; 2) The catalytic mechanisms proposed by experimental and theoretical studies; 3) Extensive applications in regard to tumor therapy, cytoprotection and sensing. Therefore, it is prospected that this review will contribute to the further design of CAT-like nanozymes and optimize their applications with much higher efficiency than before.

Elucidation of radical- and oxygenate-driven paths in zeolite-catalysed conversion of methanol and methyl chloride to hydrocarbons.

Understanding hydrocarbon generation in the zeolite-catalysed conversions of methanol and methyl chloride requires advanced spectroscopic approaches to distinguish the complex mechanisms governing C-C bond formation, chain growth and the deposition of carbonaceous species. Here operando photoelectron photoion coincidence (PEPICO) spectroscopy enables the isomer-selective identification of pathways to hydrocarbons of up to C14 in size, providing direct experimental evidence of methyl radicals in both reactions and ketene in the methanol-to-hydrocarbons reaction. Both routes converge to C5 molecules that transform into aromatics. Operando PEPICO highlights distinctions in the prevalence of coke precursors, which is supported by electron paramagnetic resonance measurements, providing evidence of differences in the representative molecular structure, density and distribution of accumulated carbonaceous species. Radical-driven pathways in the methyl chloride-to-hydrocarbons reaction(s) accelerate the formation of extended aromatic systems, leading to fast deactivation. By contrast, the generation of alkylated species through oxygenate-driven pathways in the methanol-to-hydrocarbons reaction extends the catalyst lifetime. The findings demonstrate the potential of the presented methods to provide valuable mechanistic insights into complex reaction networks.

Atomically Dispersed Fe-N3 C Sites Induce Asymmetric Electron Structures to Afford Superior Oxygen Reduction Activity.

Introducing heteroatoms into atomically dispersed Fe-N4 sites with symmetric electron distribution can adjust the imperfect oxygenated adsorption-activation and promote oxygen reduction reaction (ORR) activity. However, the relevant design synthesis and deeply understanding the electrocatalytic mechanism of such an asymmetric structure by introducing Fe-C coordination remains challenging. Herein, the structural stability of Fe-Nx Cy (x = 0 ≈ 4, y = 4-x) is first theoretically predicted and indicates that the energy of Fe-N4 in the two most stable structures is greater than that of Fe-N3 C. Subsequently, Fe-N4 and Fe-N3 C configurations are controlled synthesized by adjusting pyrolytic temperature. The Fe-N3 C-based electrocatalyst displays a boosted ORR activity with a half-wave potential of 0.91 V and superior long-term stability, outperforming Fe-N4 , Pt/C, and state-of-the-art noble metal-free electrocatalysts. Density functional theory calculations unveil that Fe-N3 C is much more favorable for electron delocalization than Fe-N4 . Furthermore, the residual Zn atom derived from ZIF-8 would give its d-orbit electron to the Fe atom, so the synergy between Fe-N3 C and Zn-N4 makes an enhanced ORR activity.

The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study.

The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.

Emerging Single-Atom Catalysts/Nanozymes for Catalytic Biomedical Applications.

Single-atom catalysts (SACs) are a type of atomically dispersed nanozymes with the highest atom utilization, which employ low-coordinated single atoms as the catalytically active sites. SACs not only inherit the merits of traditional nanozymes, but also hold high catalytic activity and superb catalytic selectivity, which ensure their tremendous application potential in environmental remediation, energy storage and conversion, chemical industry, nanomedicine, etc. Nevertheless, undesired aggregation effect of single atoms during preactivation and reaction processes is significantly enhanced owing to the high surface free energy of single atoms. In this case, appropriate substrates are requisite to prevent the aggregation event through the powerful interactions between the single atoms and the substrates, thereby stabilizing the high catalytic activity of the catalysts. In this review, the synthetic methods and characterization approaches of SACs are first described. Then the application cases of SACs in nanomedicine are summarized. Finally, the current challenges and future opportunities of the SACs in nanomedicine are outlined. It is hoped that this review may have implications for furthering the development of new SACs with improved biophysicochemical properties and broadened biomedical applications.