The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase

Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2

Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.

Inflammation-free electrochemical in vivo sensing of dopamine with atomic-level engineered antioxidative single-atom catalyst

Electrochemical methods with tissue-implantable microelectrodes provide an excellent platform for real-time monitoring the neurochemical dynamics in vivo due to their superior spatiotemporal resolution and high selectivity and sensitivity. Nevertheless, electrode implantation inevitably damages the brain tissue, upregulates reactive oxygen species level, and triggers neuroinflammatory response, resulting in unreliable quantification of neurochemical events. Herein, we report a multifunctional sensing platform for inflammation-free in vivo analysis with atomic-level engineered Fe single-atom catalyst that functions as both single-atom nanozyme with antioxidative activity and electrode material for dopamine oxidation. Through high-temperature pyrolysis and catalytic performance screening, we fabricate a series of Fe single-atom nanozymes with different coordination configurations and find that the Fe single-atom nanozyme with FeN4 exhibits the highest activity toward mimicking catalase and superoxide dismutase as well as eliminating hydroxyl radical, while also featuring high electrode reactivity toward dopamine oxidation. These dual functions endow the single-atom nanozyme-based sensor with anti-inflammatory capabilities, enabling accurate dopamine sensing in living male rat brain. This study provides an avenue for designing inflammation-free electrochemical sensing platforms with atomic-precision engineered single-atom catalysts.

Oxygen-bridged W-Pd atomic pairs enable H2O2 activation for sensitive immunoassays

Regulating the performance of peroxidase (POD)-like nanozymes is a prerequisite for achieving highly sensitive and accurate immunoassays. Inspired by natural enzyme catalysis, we design a highly active and selective nanozyme by loading atomically dispersed tungsten (W) sites on Pd metallene (W-O-Pdene) to construct an artificial three-dimensional (3D) catalytic center. The 3D asymmetric W-O-Pd atomic pairs can effectively stretch the O-O bonds in H2O2 and further promote the desorption of H2O to enhance POD-like activity. Moreover, the W-O-Pd sites with unique spatial structures demonstrate satisfactory specificity for H2O2 activation, effectively preventing the interference of dissolved oxygen. Accordingly, the highly active and specific W-O-Pdene nanozymes are utilized for sensitive and accurate prostate-specific antigen (PSA) immunoassay with a low detection limit of 1.92 pg mL-1, superior to commercial enzyme-linked immunosorbent assay.

Atomically Precise Regulation of the N-Heterocyclic Microenvironment in Triazine Covalent Organic Frameworks for Coenzyme Photocatalytic Regeneration

Artificial photosynthesis represents a sustainable strategy for accessing high-value chemicals; however, the conversion efficiency is significantly limited by its difficulty in the cycle of coenzymes such as NADH. In this study, we report a series of isostructural triazine covalent organic frameworks (COFs) and explore their N-substituted microenvironment-dependent photocatalytic activity for NADH regeneration. We discovered that the rational alteration of N-heterocyclic species, which are linked to the triazine center through an imine linkage, can significantly regulate both the electron band structure and planarity of a COF layer. This results in different separation efficiencies of the photoinduced electron-hole pairs and electron transfer behavior within and between individual layers. The optimal COF catalyst herein achieves an NADH regeneration capacity of 89% within 20 min, outperforming most of the reported nanomaterial photocatalysts. Based on this, an artificial photosynthesis system is constructed for the green synthesis of a high-value compound, L-glutamate, and its conversion efficiency significantly surpasses the enzymatic approach without the NADH photocatalytic cycle. This work offers new insights into the coenzyme regeneration by means of regulating the distal heterocyclic microenvironment of a COF skeleton, holding great potential for the green photosynthesis of important chemicals.

Exploring Therapeutic Potential of Catalase: Strategies in Disease Prevention and Management

The antioxidant defense mechanisms play a critical role in mitigating the deleterious effects of reactive oxygen species (ROS). Catalase stands out as a paramount enzymatic antioxidant. It efficiently catalyzes the decomposition of hydrogen peroxide (H2O2) into water and oxygen, a potentially harmful byproduct of cellular metabolism. This reaction detoxifies H2O2 and prevents oxidative damage. Catalase has been extensively studied as a therapeutic antioxidant. Its applications range from direct supplementation in conditions characterized by oxidative stress to gene therapy approaches to enhance endogenous catalase activity. The enzyme's stability, bioavailability, and the specificity of its delivery to target tissues are significant hurdles. Furthermore, studies employing conventional catalase formulations often face issues related to enzyme purity, activity, and longevity in the biological milieu. Addressing these challenges necessitates rigorous scientific inquiry and well-designed clinical trials. Such trials must be underpinned by sound experimental designs, incorporating advanced catalase formulations or novel delivery systems that can overcome existing limitations. Enhancing catalase's stability, specificity, and longevity in vivo could unlock its full therapeutic potential. It is necessary to understand the role of catalase in disease-specific contexts, paving the way for precision antioxidant therapy that could significantly impact the treatment of diseases associated with oxidative stress.

Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity

Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.

Defect-Engineering-Mediated Long-Lived Charge-Transfer Excited-State in Fe-Gallate Complex Improves Iron Cycle and Enables Sustainable Fenton-Like Reaction

Fenton reactions are inefficient because the Fe(II) catalyst cannot be recycled in time due to the lack of a rapid electron transport pathway. This results in huge H2 O2 wastage in industrial applications. Here, it is shown that a sustainable heterogeneous Fenton system is attainable by enhancing the ligand-to-metal charge-transfer (LMCT) excited-state lifetime in Fe-gallate complex. By engineering oxygen defects in the complex, the lifetime is improved from 10-90 ps. The lengthened lifetime ensures sufficient concentrations of excited-states for an efficient Fe cycle, realizing previously unattainable H2 O2 activation kinetics and hydroxyl radical (• OH) productivity. Spectroscopic and electrochemical studies show the cyclic reaction mechanism involves in situ Fe(II) regeneration and synchronous supply of oxygen atoms from water to recover dissociated Fe─O bonds. Trace amounts of this catalyst effectively destroy two drug-resistant bacteria even after eight reaction cycles. This work reveals the link among LMCT excited-state lifetime, Fe cycle, and catalytic activity and stability, with implications for de novo design of efficient and sustainable Fenton-like processes.

Histidine-Based Supramolecular Nanoassembly Exhibiting Dual Enzyme-Mimetic Functions: Altering the Tautomeric Preference of Histidine to Tailor Oxidative/Hydrolytic Catalysis

Challenges persist in replicating enzyme-like active sites with functional group arrangements in supramolecular catalysis. In this study, we present a supramolecular material comprising Fmoc-modified histidine and copper. We also investigated the impact of noncanonical amino acids (δmH and εmH), isomers of histidine, on the catalytic process. The Fmoc-δmH-based nanoassembly exhibits an approximately 15-fold increase in oxidative activity and an ∼50-fold increase in hydrolytic activity compared to Fmoc-εmH (kcat/Km). This distinction arises from differences in basicity and ligation properties between the ε- and δ-nitrogen of histidine. The addition of guanosine monophosphate further enhances the oxidative activity of the histidine- and methylated histidine-based catalysts. The Fmoc-δmH/Cu2+-based nanoassembly catalyzes the oxidation/hydrolysis cascade of 2',7'-dichlorofluorescein diacetate, benefiting from the synergistic effect between the copper center and the nonligating ε-nitrogen of histidine. These findings advance the biomimetic catalyst design and provide insights into the mechanistic role of essential residues in natural systems.

Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)

Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.

Light-gated specific oxidase-like activity of a self-assembled Pt(II) nanozyme for environmental remediation

Artificial enzyme equivalents, also known as nanozymes, are a practical tool for environmental remediation when compared to their natural counterparts due to their high operational stability, efficiency, and cost-effectiveness. Specific oxidase mimicking nanozymes are well suited to degrade toxic chemicals from industrial waste such as phenols and azo dyes. Therefore, photocatalytic nanozymes using visible/sunlight would provide a viable strategy for sustainable environmental remediation. Herein, we introduce an aggregation-induced emissive Pt(II) complex, which self-assembles in water providing NanoPtA nanotapes. These structures exhibit a specific oxidase-like nanozyme activity driven by light. The NanoPtA structure assists in the photogeneration of singlet oxygen in water via a triplet excited 3MMLCT state, leading to a specific oxidase-like activity instead of a peroxidase-like activity. The self-assembled nanozyme showed great stability under harsh environmental conditions and exhibited photo-induced specific oxidase-mimetic activity, which was considerably more efficient than the natural enzyme or other specific nanozymes. We demonstrated efficient NanoPtA-induced photocatalytic degradation of various phenolic compounds and azo dyes within 5-10 minutes of light irradiation. Notably, the system operates under sunlight and exhibits reusability over twenty cycles of catalytic reactions. Another fascinating aspect of NanoPtA is the unaltered catalytic performance for more than 75 days, providing a robust enzyme-equivalent for practical sustainable environmental remediation.

Recent theranostic applications of hydrogen peroxide-responsive nanomaterials for multiple diseases

It is well established that hydrogen peroxide (H2O2) is associated with the initiation and progression of many diseases. With the rapid development of nanotechnology, the diagnosis and treatment of those diseases could be realized through a variety of H2O2-responsive nanomaterials. In order to broaden the application prospects of H2O2-responsive nanomaterials and promote their development, understanding and summarizing the design and application fields of such materials has attracted much attention. This review provides a comprehensive summary of the types of H2O2-responsive nanomaterials including organic, inorganic and organic-inorganic hybrids in recent years, and focused on their specific design and applications. Based on the type of disease, such as tumors, bacteria, dental diseases, inflammation, cardiovascular diseases, bone injury and so on, key examples for above disease imaging diagnosis and therapy strategies are introduced. In addition, current challenges and the outlook of H2O2-responsive nanomaterials are also discussed. This review aims to stimulate the potential of H2O2-responsive nanomaterials and provide new application ideas for various functional nanomaterials related to H2O2.

Assessment of the Environmental Impact of Solid Oil Materials Based on Pyrolysis Oil

One method of managing used car tires is decomposition by thermochemical conversion methods. By conducting the process at temperatures of 450-750 °C, three fractions are obtained from tires: oil, gas, and solid. The liquid product of the pyrolysis of used car tires is pyrolysis oil, which consists of aromatic, polyaromatic, and aliphatic hydrocarbons. Unconventional building materials were obtained from tire pyrolysis oil and the environmental impact was evaluated. Blocks made from pyrolysis oil showed mechanical strength of up to about 1700 N. No heavy metals or polycyclic aromatic hydrocarbons, which were found in the crude heavy-PO fraction, were detected in the filtrates after incubation of the block obtained from the heavy-PO fraction at 240 °C. The highest inhibition of Sorghum saccharatum shoot (74.4%) and root (57.5%) growth was observed for solid materials from the medium-PO fraction obtained at 240 °C. The most favorable values of the parameters for the process of obtaining blocks based on post-PO were an annealing temperature of 180 °C, time of 20 h, and mass ratio of catalyst to catalyzed oil of 0.045.

A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function

Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.

Geometric Tuning of Single-Atom FeN4 Sites via Edge-Generation Enhances Multi-Enzymatic Properties

Single-atom nanozymes (SAzymes) are considered promising alternatives to natural enzymes. The catalytic performance of SAzymes featuring homogeneous, well-defined active structures can be enhanced through elucidating structure-activity relationship and tailoring physicochemical properties. However, manipulating enzymatic properties through structural variation is an underdeveloped approach. Herein, the synthesis of edge-rich Fe single-atom nanozymes (FeNC-edge) via an H₂ O₂ -mediated edge generation is reported. By controlling the number of edge sites, the peroxidase (POD)- and oxidase (OXD)-like performance is significantly enhanced. The activity enhancement results from the presence of abundant edges, which provide new anchoring sites to mononuclear Fe. Experimental results combined with density functional theory (DFT) calculations reveal that FeN₄ moieties in the edge sites display high electron density of Fe atoms and open N atoms. Finally, it is demonstrated that FeNC-edge nanozyme effectively inhibits tumor growth both in vitro and in vivo, suggesting that edge-tailoring is an efficient strategy for developing artificial enzymes as novel catalytic therapeutics.

Ferric heme b in aqueous micellar and vesicular systems: state-of-the-art and challenges

Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.

Hydrogen-bonded organic framework biomimetic entrapment allowing non-native biocatalytic activity in enzyme

Nature programs the structural folding of an enzyme that allows its on-demand biofunctionality; however, it is still a long-standing challenge to manually modulate an enzyme’s conformation. Here, we design an exogenous hydrogen-bonded organic framework to modulate the conformation of cytochrome c, and hence allow non-native bioactivity for the enzyme. The rigid hydrogen-bonded organic framework, with net-arranged carboxylate inner cage, is in situ installed onto the native cytochrome c. The resultant hydrogen-bonded nano-biointerface changes the conformation to a previously not achieved catalase-like species within the reported cytochrome c-porous organic framework systems. In addition, the preserved hydrogen-bonded organic framework can stabilize the encapsulated enzyme and its channel-like pores also guarantee the free entrance of catalytic substrates. This work describes a conceptual nanotechnology for manoeuvring the flexible conformations of an enzyme, and also highlights the advantages of artificial hydrogen-bonded scaffolds to modulate enzyme activity.

Heme units are immobilised in diverse heme enzymes for oxidation, and have been immobilised also in hydrogen-bonded organic frameworks. Here, the authors show the use of hydrogen-bonded organic framework to modulate the enzyme’s conformation and show different biofunction from the original.

Hemin-catalyzed oxidative oligomerization of p-aminodiphenylamine (PADPA) in the presence of aqueous sodium dodecylbenzenesulfonate (SDBS) micelles

In a previous report on the enzymatic synthesis of the conductive emeraldine salt form of polyaniline (PANI-ES) in aqueous solution using PADPA (p-aminodiphenylamine) as monomer, horseradish peroxidase isoenzyme C (HRPC) was applied as a catalyst at pH = 4.3 with H₂O₂ as a terminal oxidant. In that work, anionic vesicles were added to the reaction mixture for (i) guiding the reaction to obtain poly(PADPA) products that resemble PANI-ES, and for (ii) preventing product precipitation (known as the “template effect”). In the work now presented, instead of native HRPC, only its prosthetic group ferric heme b (= hemin) was utilized as a catalyst, and micelles formed from SDBS (sodium dodecylbenzenesulfonate) served as templates. For the elaborated optimal reaction conditions, complementary UV/vis/NIR, EPR, and Raman spectroscopy measurements clearly showed that the reaction mixture obtained after completion of the reaction contained PANI-ES-like products as dominating species, very similar to the products formed with HRPC as catalyst. HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonate) was found to have a positive effect on the reaction rate as compared to dihydrogenphosphate. This work is the first on the template-assisted formation of PANI-ES type products under mild, environmentally friendly conditions using hemin as a cost-effective catalyst.

Polyaniline emeraldine salt-type products were synthesized under mild, environmentally friendly conditions using hemin as a cost-effective catalyst, p-aminodiphenylamine (PADPA) as a monomer, and micelles formed from SDBS as templates.

Injectable multifunctional CMC/HA-DA hydrogel for repairing skin injury

Injectable Hydrogels with adhesive, antioxidant and hemostatic properties are highly desired for promoting skin injury repair. In this study, we prepared a multi-functional carboxymethyl chitosan/hyaluronic acid-dopamine (CMC/HA-DA) hydrogel, which can be crosslinked by horseradish peroxidase and hydrogen peroxide. The antioxidation, gelation time, degradability, rheology and antihemorrhagic properties of hydrogels can be finely tuned by varying composition ratio. The cytocompatibility test and hemolysis test confirmed that the designed hydrogel holds good biocompatibility. More importantly, the repair effect of the hydrogel on full-thickness skin injury model in mice was studied. The results of wound healing, collagen deposition, immunohistochemistry and immunofluorescence showed that CMC/HA-DA hydrogel could significantly promote angiogenesis and cell proliferation at the injured site. Notably, the inflammatory response can also be regulated to promote the repair of full-thickness skin defect in mice. Results indicate that this injectable CMC/HA-DA hydrogel holds high application prospect for promising wound healing.

Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC

We present an interface of the wavefunction-based quantum chemical software CFOUR to the multiscale modeling framework MiMiC. Electrostatic embedding of the quantum mechanical (QM) part is achieved by analytic evaluation of one-electron integrals in CFOUR, while the rest of the QM/molecular mechanical (MM) operations are treated according to the previous MiMiC-based QM/MM implementation. Long-range electrostatic interactions are treated by a multipole expansion of the potential from the QM electron density to reduce the computational cost without loss of accuracy. Testing on model water/water systems, we verified that the CFOUR interface to MiMiC is robust, guaranteeing fast convergence of the self-consistent field cycles and optimal conservation of the energy during the integration of the equations of motion. Finally, we verified that the CFOUR interface to MiMiC is compatible with the use of a QM/QM multiple time-step algorithm, which effectively reduces the cost of ab initio MD (AIMD) or QM/MM-MD simulations using higher level wavefunction-based approaches compared to cheaper density functional theory-based ones. The new wavefunction-based AIMD and QM/MM-MD implementations were tested and validated for a large number of wavefunction approaches, including Hartree-Fock and post-Hartree-Fock methods like Møller-Plesset, coupled-cluster, and complete active space self-consistent field.

Poly(acrylic acid)-mediated synthesis of cerium oxide nanoparticles with variable oxidation states and their effect on regulating the intracellular ROS level

Cerium oxide nanoparticles (CeNPs) possess multiple redox enzyme mimetic activities in scavenging reactive oxygen species (ROS) as a potential biomedicine. These enzymatic activities of CeNPs are closely related to their surface oxidation state. Here we have reported a synthetic method to modify CeNPs' surface oxidation state by changing the conformation of the poly(acrylic acid) (PAA) polymers adsorbed onto the CeNP surface. The synthesized PAA-CeNPs exhibited the same core size, morphology, crystal structure, and colloidal stability, with the only variation being their surface oxidation state (Ce³⁺ percentage). The modification mechanism can be attributed to the polymers chemisorbed onto the metal oxide surface forming a metal complexation structure. Such adsorption further modified CeNPs' surface oxidation state in a temperature-dependent manner. The series of PAA-CeNPs exhibited multiple redox enzyme mimetic activities (superoxide dismutase, catalase, peroxidase, and oxidase) directly related to their surface oxidation state. In vitro experiments showed no cytotoxic effect of these PAA-CeNPs on the osteoblastic cell line SAOS-2 at high loadings. Microscopic images confirmed the internalization of PAA-CeNPs in the cells. All tested PAA-CeNPs can reduce the basal and hydrogen peroxide-induced intracellular ROS level in the cells, indicating their effective intracellular ROS scavenging effect. However, we did not observe a positive correlation between the CeNP surface oxidation state and their capacities to reduce the intracellular ROS levels. We propose that CeNPs can maintain a dynamic state of Ce³⁺/Ce⁴⁺ during their catalytic activities, exhibiting a non-linear correlation between the CeNP surface oxidation state and their effect on regulating the intracellular ROS level.

A QM/MM Evaluation of the Missing Step in the Reduction Mechanism of HMG-CoA by Human HMG-CoA Reductase

Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol−1 and −40 kcal mol−1) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step.

Computing Metal-Binding Proteins for Therapeutic Benefit

Over one third of biomolecules rely on metal ions to exert their cellular functions. Metal ions can play a structural role by stabilizing the structure of biomolecules, a functional role by promoting a wide variety of biochemical reactions, and a regulatory role by acting as messengers upon binding to proteins regulating cellular metal-homeostasis. These diverse roles in biology ascribe critical implications to metal-binding proteins in the onset of many diseases. Hence, it is of utmost importance to exhaustively unlock the different mechanistic facets of metal-binding proteins and to harness this knowledge to rationally devise novel therapeutic strategies to prevent or cure pathological states associated with metal-dependent cellular dysfunctions. In this compendium, we illustrate how the use of a computational arsenal based on docking, classical, and quantum-classical molecular dynamics simulations can contribute to extricate the minutiae of the catalytic, transport, and inhibition mechanisms of metal-binding proteins at the atomic level. This knowledge represents a fertile ground and an essential prerequisite for selectively targeting metal-binding proteins with small-molecule inhibitors aiming to (i) abrogate deregulated metal-dependent (mis)functions or (ii) leverage metal-dyshomeostasis to selectively trigger harmful cells death.

Monitoring the heme iron state in horseradish peroxidase to detect ultratrace amounts of hydrogen peroxide in alcohols

Despite the importance of hydrogen peroxide (H2O2) in initiating oxidative damage and its connection to various diseases, the detection of low concentrations of H2O2 (<10 μM) is still limited using current methods, particularly in non-aqueous systems. One of the most common methods is based on examining the color change of a reducing substrate upon oxidation using UV/Vis spectrophotometry, fluorophotometry and/or paper test strips. In this study, we show that this method encounters low efficiency and sensitivity for detection of ultratrace amounts of H2O2 in non-aqueous media. Thus, we have developed a simple, fast, accurate and inexpensive method based on UV/Vis spectrophotometry to detect H2O2 in non-aqueous systems, such as alcohols. In this regard, we demonstrate that monitoring the Soret and Q-band regions of high-valent iron-oxo (ferryl heme) intermediates in horseradish peroxidase (HRP) is well suited to detect ultratrace amounts of H2O2 impurities in alcohols in the range of 0.001-1000 μM using UV/Vis spectrophotometry. We monitor the optical spectra of HRP solution for the red shift in the Soret and Q-band regions upon the addition of alcohols with H2O2 impurity. We also monitor the reversibility of this shift to the original wavelength over time to check the spontaneous decay of ferryl intermediates to the ferric state. Thus, we have found that the ferryl intermediates of HRP can be used for the detection of H2O2 in alcohols at μg L-1 levels through via UV/Vis spectrophotometric method.

Cofactor-free oxidase-mimetic nanomaterials from self-assembled histidine-rich peptides

Natural oxidases mainly rely on cofactors and well-arranged amino acid residues for catalysing electron-transfer reactions but suffer from non-recovery of their activity upon externally induced protein unfolding. However, it remains unknown whether residues at the active site can catalyse similar reactions in the absence of the cofactor. Here, we describe a series of self-assembling, histidine-rich peptides, as short as a dipeptide, with catalytic function similar to that of haem-dependent peroxidases. The histidine residues of the peptide chains form periodic arrays that are able to catalyse H₂O₂ reduction reactions efficiently through the formation of reactive ternary complex intermediates. The supramolecular catalyst exhibiting the highest activity could be switched between inactive and active states without loss of activity for ten cycles of heating/cooling or acidification/neutralization treatments, demonstrating the reversible assembly/disassembly of the active residues. These findings may aid the design of advanced biomimetic catalytic materials and provide a model for primitive cofactor-free enzymes.

Atomic engineering of single-atom nanozymes for enzyme-like catalysis

Enzyme mimics, especially nanozymes, play a crucial role in replacing natural enzymes for diverse applications related to bioanalysis, therapeutics and other enzyme-like catalysis. Nanozymes are catalytic nanomaterials with enzyme-like properties, which currently face formidable challenges with respect to their intricate structure, properties and mechanism in comparison with enzymes. The latest emergence of single-atom nanozymes (SAzymes) undoubtedly promoted the nanozyme technologies to the atomic level and provided new opportunities to break through their inherent limitations. In this perspective, we discuss key aspects of SAzymes, including the advantages of the single-site structure, and the derived synergetic enhancements of enzyme-like activity, catalytic selectivity and the mechanism, as well as the superiority in biological and catalytic applications, and then highlight challenges that SAzymes face and provide relevant guidelines from our point of view for the rational design and extensive applications of SAzymes, so that SAzyme may achieve its full potential as the next-generation nanozyme.

Molecularly imprinted peptide-based enzyme mimics with enhanced activity and specificity

We herein report the construction of peroxidase (POD)-mimicking catalysts based on the strategy of peptide assembly and molecular imprinting. Upon co-assembly of Fmoc-FFH and Hemin, we firstly fabricated CA-H/Hemin which displayed POD-like catalytic activity and showed a 21-fold rate acceleration in the oxidation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) compared to the uncatalyzed reaction. Then, upon combining CA-H/Hemin with the ABTS-imprinted polymer, the obtained imprinted catalyst (MIP-H/Hemin) showed 52-fold acceleration due to the enhanced re-binding toward ABTS. Moreover, by introducing cationic monomers, a 137-fold rate enhancement was further achieved for the positively charged imprinted catalyst (MIP+-H/Hemin), from the synergistic effect of molecular imprinting and electrostatic attraction. Remarkably, by comparing the catalytic activity of these POD mimics towards ABTS and 3,3',5,5'-tetramethylbenzidine (TMB), we also highlighted the substrate specificity of MIP-H/Hemin and MIP+-H/Hemin toward ABTS. This study provides a promising approach to improve the catalytic activity and specificity of peptide-based enzyme mimics.

Ultra-sensitive SERS detection, rapid selective adsorption and degradation of cationic dyes on multifunctional magnetic metal-organic framework-based composite

In-situ and real-time ultra-sensitive monitoring for the degradation process of environmental pollutants is always an important issue of concern to many people. Herein, a multifunctional magnetic metal-organic framework (MOF)-based composite has been successfully constructed and applied in monitoring the disposal of cationic dyes. Owing to its particular MOFs shell and internal gold particles, the composite can be used as an efficient SERS substrate to ultra-sensitively detect the cationic dyes. Furthermore, the prepared MOF-based composite is also a peroxidase-like nanozyme, which can catalytically degrade the adsorbed cationic dyes. Additionally, the magnetic core in the MOF-based composite offers a good magnetic separation capacity, which makes a facile and rapid separation of the catalyst from the reacted solution for recyclability. This work has provided a new way to monitor the catalytic degradation process by SERS technique in the co-existence of catalyst and dye molecules in the reaction system, which can effectively eliminate the absorption of the catalyst compared with the UV-vis technique, showing promising applications in in-situ and real-time pollution disposal monitoring.

Iron-Based Nanozymes in Disease Diagnosis and Treatment

Iron-based nanozymes are currently one of the few clinical inorganic nanoparticles for disease diagnosis and treatment. Overcoming the shortcomings of natural enzymes, such as easy inactivation and low yield, combined with their special nanometer properties and magnetic functions, iron-based nanozymes have broad prospects in biomedicine. This minireview summarizes their preparation, biological activity, catalytic mechanism, and applications in diagnosis and treatment of diseases. Finally, challenges to their future development and the trends of iron-based nanozymes are discussed. The purpose of this minireview is to better understand and reasonably speculate on the rational design of iron-based nanozymes as an increasingly important new paradigm for diagnostics.

A two-enzyme cascade reaction consisting of two reaction pathways. Studies in bulk solution for understanding the performance of a flow-through device with immobilised enzymes

Enzyme-catalysed cascade reactions in flow-through systems with immobilised enzymes currently are of great interest for exploring their potential for biosynthetic and bioanalytical applications. Basic studies in this field often aim at understanding the stability of the immobilised enzymes and their catalytic performance, for example, in terms of yield of a desired reaction product, analyte detection limit, enzyme stability or reaction reproducibility. In the work presented, a cascade reaction involving the two enzymes bovine carbonic anhydrase (BCA) and horseradish peroxidase (HRP) – with hydrogen peroxide (H₂O₂) as HRP “activator” – was first investigated in great detail in bulk solution at pH = 7.2. The reaction studied is the hydrolysis and oxidation of 2′,7′-dichlorodihydrofluorescein diacetate (DCFH₂-DA) to 2′,7′-dichlorofluorescein (DCF), which was found to proceed along two reaction pathways. This two-enzyme cascade reaction was then applied for analysing the performance of BCA and HRP immobilised in glass fiber filters which were placed inside a filter holder device through which a DCFH₂-DA/H₂O₂ substrate solution was pumped. Comparison was made between (i) co-immobilised and (ii) sequentially immobilised enzymes (BCA first, HRP second). Significant differences for the two arrangements in terms of measured product yield (DCF) could be explained based on quantitative UV/vis absorption measurements carried out in bulk solution. We found that the lower DCF yield observed for sequentially immobilised enzymes originates from a change in one of the two possible reaction pathways due to enzyme separation, which was not the case for enzymes that were co-immobilised (or simultaneously present in the bulk solution experiments). The higher DCF yield observed for co-immobilised enzymes did not originate from a molecular proximity effect (no increased oxidation compared to sequential immobilisation).

A cascade reaction catalysed by bovine carbonic anhydrase (BCA) and horseradish peroxidase (HRP) proceeds over two possible pathways, which explains differences in product formation for differently immobilised enzymes in flow-through reactions.

Elastic, Persistently Moisture-Retentive, and Wearable Biomimetic Film Inspired by Fetal Scarless Repair for Promoting Skin Wound Healing

An efficient and available material for promoting skin regeneration is of great importance for public health, but it remains an elusive goal. Inspired by fetal scarless wound healing, we develop a wearable biomimetic film (WBMF) composed of hyaluronan (HA), vitamin E (VE), dopamine (DA), and β-cyclodextrin (β-CD) that mimics the fetal context (FC) and fetal extracellular matrix (ECM) around the wound bed for dermal regeneration. First, the WBMF creates the FC of sterility, hypoxia, persistent moisture, and no secondary insults for wounds as the result of its seamless adhesion to the skin, optimum stress-stretch and high-cycle fatigue resistance matching the anisotropic tension of the skin, and water-triggered self-healing behavior. Thus, the WBMF modulates the early wound situation to minimize inflammatory response. In the meantime, the WBMF mimics the critical biological function of fetal ECM, inducing fibroblast migration, suppressing the overexpression of transforming growth factor β1, and mediating collagen synthesis, distribution, and reestablishment. As a result, the WBMF accelerates wound healing and gains a normal dermal collagen architecture, thereby restoring scarless appearance. Overall, the WBMF provides a new paradigm for promoting skin wound healing and may find broad utility for the field of regenerative medicine.

A novel injectable starch-based tissue adhesive for hemostasis

The starch which is modified by catechol can form hydrogel in situ so that seal the wound and reduce bleeding.

Metal and metal-oxide nanozymes: bioenzymatic characteristics, catalytic mechanism, and eco-environmental applications

Phenolic contaminants (R-OH) are a category of highly toxic organic compounds that are widespread in aquatic ecosystems and can induce carcinogenic risk to wildlife and humans; natural enzymes as green catalysts are capable of step-polymerizing these compounds to produce diverse macromolecular self-coupling products via radical-mediated C-C and C-O-C bonding at either the ortho- or para-carbon position, thereby evading the bioavailability and ecotoxicity of these compounds. Intriguingly, certain artificial metal and metal-oxide nanomaterials are known as nanozymes. They not only possess the unique properties of nanomaterials but also display intrinsic enzyme-mimicking activities. These artificial nanozymes are expected to surmount the shortcomings, such as low stability, easy inactivation, difficult recycling, and high cost, of natural enzymes, thus contributing to eco-environmental restoration. This review highlights the available studies on the enzymatic characteristics and catalytic mechanisms of natural enzymes and artificial metal and metal-oxide nanozymes in the removal and transformation of R-OH. These advances will provide key research directions beneficial to the multifunctional applications of artificial nanozymes in aquatic ecosystems.

Unraveling the Impact of Cysteine-to-Serine Mutations on the Structural and Functional Properties of Cu(I)-Binding Proteins

Appropriate maintenance of Cu(I) homeostasis is an essential requirement for proper cell function because its misregulation induces the onset of major human diseases and mortality. For this reason, several research efforts have been devoted to dissecting the inner working mechanism of Cu(I)-binding proteins and transporters. A commonly adopted strategy relies on mutations of cysteine residues, for which Cu(I) has an exquisite complementarity, to serines. Nevertheless, in spite of the similarity between these two amino acids, the structural and functional impact of serine mutations on Cu(I)-binding biomolecules remains unclear. Here, we applied various biochemical and biophysical methods, together with all-atom simulations, to investigate the effect of these mutations on the stability, structure, and aggregation propensity of Cu(I)-binding proteins, as well as their interaction with specific partner proteins. Among Cu(I)-binding biomolecules, we focused on the eukaryotic Atox1-ATP7B system, and the prokaryotic CueR metalloregulator. Our results reveal that proteins containing cysteine-to-serine mutations can still bind Cu(I) ions; however, this alters their stability and aggregation propensity. These results contribute to deciphering the critical biological principles underlying the regulatory mechanism of the in-cell Cu(I) concentration, and provide a basis for interpreting future studies that will take advantage of cysteine-to-serine mutations in Cu(I)-binding systems.

Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme

Phosphorylation by kinases enzymes is a widespread regulatory mechanism able of rapidly altering the function of target proteins. Among these are cytochrome P450s (CYP450), a superfamily of enzymes performing the oxidation of endogenous and exogenous substrates thanks to the electron supply of a redox partner. In spite of its pivotal role, the molecular mechanism by which phosphorylation modulates CYP450s metabolism remains elusive. Here by performing microsecond-long all-atom molecular dynamics simulations, we disclose how phosphorylation regulates estrogen biosynthesis, catalyzed by the Human Aromatase (HA) enzyme. Namely, we unprecedentedly propose that HA phosphorylation at Y361 markedly stabilizes its adduct with the flavin mononucleotide domain of CYP450s reductase (CPR), the redox partner of microsomal CYP450s, and a variety of other proteins. With CPR present at physiological conditions in a limiting ratio with respect to its multiple oxidative partners, the enhanced stability of the CPR/HA adduct may favor HA in the competition with the other proteins requiring CPR's electron supply, ultimately facilitating the electron transfer and estrogen biosynthesis. As a result, our work elucidates at atomic-level the post-translational regulation of CYP450s catalysis. Given the potential for rational clinical management of diseases associated with steroid metabolism disorders, unraveling this mechanism is of utmost importance, and raises the intriguing perspective of exploiting this knowledge to devise novel therapies.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.

The pivotal role of MBD4–ATP7B in the human Cu(i) excretion path as revealed by EPR experiments and all-atom simulations

Atox1–MBD4 interaction mediates the in-cell Cu(i) concentration.

Single-Molecule Studies of Allosteric Inhibition of Individual Enzyme on a DNA Origami Reactor

Unraveling the conformational changes of enzymes together with inhibition kinetics during an enzymatic reaction has great potential in screening therapeutic candidates; however, it remains challenging due to the transient nature of each intermediate step. We report our study on the noncompetitive inhibition of horseradish peroxidase with single-turnover resolution using single-molecule fluorescence microscopy. By introducing DNA origami as an addressable nanoreactor, we observe the coexistence of nascent-formed fluorescent product on both catalytic and docking sites. We further propose a single-molecule kinetic model to reveal the interplay between product generation and noncompetitive inhibition and find three distinct inhibitor releasing pathways. Moreover, the kinetic isotope effect experiment indicates a strong correlation between catalytic and docking sites, suggesting an allosteric conformational change in noncompetitive inhibition. A memory effect is also observed. This work provides an in-depth understanding of the correlation between enzyme behavior and enzymatic conformational fluctuation, substrate conversion, and product releasing pathway and kinetics.

Catalytic effect of (H2O) n (n = 1-3) on the HO2 + NH2 → NH3 + 3O2 reaction under tropospheric conditions

The effects of (H2O) n (n = 1-3) clusters on the HO2 + NH2 → NH3 + 3O2 reaction have been investigated by employing high-level quantum chemical calculations with M06-2X and CCSD(T) theoretical methods, and canonical variational transition (CVT) state theory with small curvature tunneling (SCT) correction. The calculated results show that two kinds of reaction, HO2⋯(H2O) n (n = 1-3) + NH2 and H2N⋯(H2O) n (n = 1-3) + HO2, are involved in the (H2O) n (n = 1-3) catalyzed HO2 + NH2 → NH3 + 3O2 reaction. Due to the fact that HO2⋯(H2O) n (n = 1-3) complexes have much larger stabilization energies and much higher concentrations than the corresponding complexes of H2N⋯(H2O) n (n = 1-3), the atmospheric relevance of the former reaction is more obvious with its effective rate constant of about 1-11 orders of magnitude faster than the corresponding latter reaction at 298 K. Meanwhile, due to the effective rate constant of the H2O⋯HO2 + NH2 reaction being respectively larger by 5-6 and 6-7 orders of magnitude than the corresponding reactions of HO2⋯(H2O)2 + NH2 and HO2⋯(H2O)3 + NH2, the catalytic effect of (H2O) n (n = 1-3) is mainly taken from the contribution of the water monomer. In addition, the enhancement factor of the water monomer is 10.06-13.30% within the temperature range of 275-320 K, which shows that at whole calculated temperatures, a positive water effect is obvious under atmospheric conditions.