Catalytic Site Research Articles

Nano-enzyme hydrogels for cartilage repair effectiveness based on ternary strategy therapy.

Designing artificial nano-enzymes for scavenging reactive oxygen species (ROS) in chondrocytes (CHOs) is considered the most feasible pathway for the treatment of osteoarthritis (OA). However, the accumulation of ROS due to the amount of nano-enzymatic catalytic site exposure and insufficient oxygen supply seriously threatens the clinical application of this therapy. Although metal-organic framework (MOF) immobilization of artificial nano-enzymes to enhance active site exposure has been extensively studied, artificial nano-enzymes/MOFs for ROS scavenging in OA treatment are still lacking. In this study, a biocompatible lubricating hydrogel-loaded iron-doped zeolitic imidazolate framework-8 (Fe/ZIF-8/Gel) centrase was engineered to scavenge endogenous overexpressed ROS synergistically generating dissolved oxygen and enhancing sustained lubrication for CHOs as a ternary artificial nano-enzyme. This property enabled the nano-enzymatic hydrogels to mitigate OA hypoxia and inhibit oxidative stress damage successfully. Ternary strategy-based therapies show excellent cartilage repair in vivo. The experimental results suggest that nano-enzyme-enhanced lubricating hydrogels are a potentially effective OA treatment and a novel strategy.

Arg1 from Cryptococcus neoformans lacks PI3 kinase activity and conveys virulence roles via its IP3-4 kinase activity.

Inositol tris/tetrakis phosphate kinases (IP3-4K) in the human fungal priority pathogens, Cryptococcus neoformans (CnArg1) and Candida albicans (CaIpk2), convey numerous virulence functions, yet it is not known whether the IP3-4K catalytic activity or a scaffolding role is responsible. We therefore generated a C. neoformans strain with a non-functional kinase, referred to as the dead-kinase (dk) CnArg1 strain (dkArg1). We verified that, although dkARG1 cDNA cloned from this strain produced a protein with the expected molecular weight, dkArg1 was catalytically inactive with no IP3-4K activity. Using recombinant CnArg1 and CaIpk2, we confirmed that, unlike the IP3-4K homologs in humans and Saccharomyces cerevisiae, CnArg1 and CaIpk2 do not phosphorylate the lipid-based substrate, phosphatidylinositol 4,5-bisphosphate, and therefore do not function as class I PI3Ks. Inositol polyphosphate profiling using capillary electrophoresis-electrospray ionization-mass spectrometry revealed that IP3 conversion is blocked in the dkArg1 and ARG1 deletion (Cnarg1Δ) strains and that 1-IP7 and a recently discovered isomer (4/6-IP7) are made by wild-type C. neoformans. Importantly, the dkArg1 and Cnarg1Δ strains had similar virulence defects, including suppressed growth at 37°C, melanization, capsule production, and phosphate starvation response, and were avirulent in an insect model, confirming that virulence is dependent on IP3-4K catalytic activity. Our data also implicate the dkArg1 scaffold in transcriptional regulation of arginine metabolism but via a different mechanism to S. cerevisiae since CnArg1 is dispensable for growth on different nitrogen sources. IP3-4K catalytic activity therefore plays a dominant role in fungal virulence, and IPK pathway function has diverged in fungal pathogens.IMPORTANCEThe World Health Organization has emphasized the urgent need for global action in tackling the high morbidity and mortality rates stemming from invasive fungal infections, which are exacerbated by the limited variety and compromised effectiveness of available drug classes. Fungal IP3-4K is a promising target for new therapy, as it is critical for promoting virulence of the human fungal priority pathogens, Cryptococcus neoformans and Candida albicans, and impacts numerous functions, including cell wall integrity. This contrasts to current therapies, which only target a single function. IP3-4K enzymes exert their effect through their inositol polyphosphate products or via the protein scaffold. Here, we confirm that the IP3-4K catalytic activity of CnArg1 promotes all virulence traits in C. neoformans that are attenuated by ARG1 deletion, reinforcing our ongoing efforts to find inositol polyphosphate effector proteins and to create inhibitors targeting the IP3-4K catalytic site, as a new antifungal drug class.

Active Oxygenated Structure‐Intensified CO2 Capture Enables Efficient Electrochemical Ethylene Production Over Carbon Nanofibers

AbstractThe pursuit of high efficacy C−C coupling during the electrochemical CO2 reduction reaction remains a tremendous challenge owing to the high energy barrier of CO2 activation and insufficient coverage of the desired intermediates on catalytic sites. Inspired by the concept of capture‐coupled CO2 activation, we fabricated quinone‐grafted carbon nanofibers via an in situ oxidative carbonylation strategy. The quinone functionality of carbon nanofibers promotes the capture of CO2 followed by activation. At a current density of 400 mA cm−2, the Faradaic efficiency of ethylene reached 62.9 %, and a partial current density of 295 mA cm−2 was achieved on the quinone‐rich carbon nanofibers. The results of in situ spectroscopy and theoretical calculations indicated that the remarkable selectivity enhancement in ethylene originates from the quinone structure, rather than the electronic properties of Cu particles. The interaction of quinone with CO2 increases the local *CO coverage and simultaneously hinders the co‐adsorption of *H on Cu sites, which greatly reduces the energy barrier for C−C coupling and restrains subsequent *CO protonation. The modulation strategy involving specific oxygenated structure, as an independent degree of freedom, guides the design of functionalized carbon materials for tailoring the selectivity of desired products during the CO2 capture and reduction.

Active Oxygenated Structure-Intensified CO2 Capture Enables Efficient Electrochemical Ethylene Production Over Carbon Nanofibers.

The pursuit of high efficacy C-C coupling during the electrochemical CO2 reduction reaction remains a tremendous challenge owing to the high energy barrier of CO2 activation and insufficient coverage of the desired intermediates on catalytic sites. Inspired by the concept of capture-coupled CO2 activation, we fabricated quinone-grafted carbon nanofibers via an in situ oxidative carbonylation strategy. The quinone functionality of carbon nanofibers promotes the capture of CO2 followed by activation. At a current density of 400 mA cm-2, the Faradaic efficiency of ethylene reached 62.9%, and a partial current density of 295 mA cm-2 was achieved on the quinone-rich carbon nanofibers. The results of in situ spectroscopy and theoretical calculations indicated that the remarkable selectivity enhancement in ethylene originates from the quinone structure, rather than the electronic properties of Cu particles. The interaction of quinone with CO2 increases the local *CO coverage and simultaneously hinders the co-adsorption of *H on Cu sites, which greatly reduces the energy barrier for C-C coupling and restrains subsequent *CO protonation. The modulation strategy involving specific oxygenated structure, as an independent degree of freedom, guides the design of functionalized carbon materials for tailoring the selectivity of desired products during the CO2 capture and reduction.

Aquivion-based spray freeze-dried composite materials for the cascade production of γ-valerolactone.

The development of multifunctional catalysts is a necessary step to effectively carry out cascade reactions, such as that from furfural to γ-valerolactone. This research effort faces the challenge posed by the intrinsic limit of how many kinds of catalytic sites a single material can bear. In this work, the application of Spray-Freeze Drying (SFD) as a synthetic technique for the preparation of a wide range of composite multi-functional catalysts is reported. Herein we show that by the proper combination of Aquivion as a highly active Brønsted acid catalyst and metal oxides as Lewis acids (LAS) enable to achieve highly unique efficient and effective dual acid composite catalysts that are able to carry out the cascade reaction from furfural to γ-valerolactone. The dual catalytic system comprised of Aq/ZrO2 with 30% polymer content prepared via spray-freeze drying exhibited GVL yields of 25% after only 2 h at 180 °C and a remarkably high productivity of 4470 µmolGVL gCat-1 h-1, one of the highest reported results. Mechanistic studies based on experimental and advanced characterisation and spectroscopic techniques, such as, SEM, TEM, 15N MAS NMR and 19F MAS NMR indicate that activity arises from the proper tuning of BAS/LAS acidic properties.

Ceria-Optimized Oxygen-Species Exchange in Hierarchical Bimetallic Hydroxide for Electrocatalytic Water Oxidation.

The utilization of rare earth elements to regulate the interaction between catalysts and oxygen-containing species holds promising prospects in the field of oxygen electrocatalysis. Through structural engineering and adsorption regulation, it is possible to achieve high-performance catalytic sites with a broken activity-stability tradeoff. Herein, we fabricate a hierarchical CeO2/NiCo hydroxide for electrocatalytic oxygen evolution reaction (OER). This material exhibits superior overpotentials and enhanced stability. Multiple potential-dependent experiments reveal that CeO2 promotes oxygen-species exchange, especially OH- ions, between catalyst and environment, thereby optimizing the redox transformation of hydroxide and the adsorption of oxygen-containing intermediates during OER. This is attributed to the reduction in the adsorption energy barrier of Ni to *OH facilitated by CeO2, particularly the near-interfacial Ni sites. The less-damaging adsorbate evolution mechanism and the CeO2 hierarchical shell significantly enhance the structural robustness, leading to exceptional stability. Additionally, the observed "self-healing" phenomenon provides further substantiation for the accelerated oxygen exchange. This work provides a neat strategy for the synthesis of ceria-based complex hollow electrocatalysts, as well as an in-depth insight into the co-catalytic role of CeO2 in terms of oxygen transfer. This article is protected by copyright. All rights reserved.

Advances on Single‐Atom‐Based Dual‐Site Photocatalysts: Fundamentals, Mechanisms, and Applications

Single‐atom catalysts (SACs) have emerged as leading‐edge research in the field of photocatalysis due to outstanding photocatalytic performance, maximum atomic utilization efficiency, and well‐defined catalytic active sites. However, the singular functionality of active sites in SACs restricts their applications in complex redox reactions involving multiple intermediates and reaction pathways. To circumvent this limitation, a second site comprising single atoms (SA), alloys, clusters, or nanoparticles is proposed to establish SA‐based dual‐site photocatalysts (SA DSPs). While maintaining 100% atomic utilization, the second site and site–site collaboration endow SA DSPs with superior photocatalytic activities to surpass those of SACs. In this review, the latest investigations on SA DSPs featuring diverse compositions, electronic and geometric configurations, site–site collaboration, and metal–support interactions are summarized. Thereafter, the mechanisms underlying enhanced photocatalytic activities are elucidated regarding the roles of the dual sites in charge‐carrier dynamics and surface reactivity. Furthermore, the state‐of‐the‐art applications in photocatalytic hydrogen evolution, CO2 reduction, and methane oxidation, etc., over SA DSPs are discussed. It is anticipated that this review will offer insights into precise control and design of dual sites in photocatalysts, thereby advancing photocatalysis toward commercial viability.

Kinetic study of p-nitrophenol degradation with zinc oxide nanoparticles prepared by sol–gel methods

Three zinc oxides (ZnO A, B, C) with similar spherical morphology but different sizes are synthesized by sol–gel methods. A kinetic study is carried out on the photocatalytic activity of these three ZnO, through the degradation of p-nitrophenol (PNP). A mathematical model is developed and the rate constants of the three catalysts are determined. To understand the parameters influencing the kinetics, the catalysts are reduced to the surface of an isolated particle (assuming perfect dispersion conditions where all catalytic active sites are available) whose size is determined by X-ray diffraction (XRD) and transmission electron microscopy (TEM). However, by considering the real case (not a perfect dispersion), it appears that the size of the aggregates induced by the synthesis methods play a more important role in the catalytic activity of the three ZnO samples than defects. A discussion on the formation of these aggregates highlights the importance of the synthesis parameters, like the solvent or the surfactant used to obtain a high dispersion. The dispersion plays a crucial role in photocatalytic efficiency, with kinetics three times higher for the catalyst with the best dispersion. Also, as shown by photoluminescence and X-ray photoelectron spectroscopy (XPS), the type and amount of defects play an important role in the photocatalytic performance. ZnO A and B show a defect peak at 620 nm whereas ZnO C shows a defect peak at 680 nm, suggesting a different type of defect on the surface of the catalyst that reduces the photocatalytic performance. Electron paramagnetic resonance (EPR) measurements are performed to identify the type of radicals involved in PNP degradation. The results show that the catalyst with the best dispersion produces the highest amount of hydroxyl radicals. Finally, photoluminescence and XPS analyses underline the type and the amount of defects for the three photocatalysts.

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB.

Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli, indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase.IMPORTANCEStenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa. We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

Improving the enzymatic activity and stability of N-carbamoyl hydrolase using deep learning approach

BackgroundOptically active D-amino acids are widely used as intermediates in the synthesis of antibiotics, insecticides, and peptide hormones. Currently, the two-enzyme cascade reaction is the most efficient way to produce D-amino acids using enzymes DHdt and DCase, but DCase is susceptible to heat inactivation. Here, to enhance the enzymatic activity and thermal stability of DCase, a rational design software “Feitian” was developed based on kcat prediction using the deep learning approach.ResultsAccording to empirical design and prediction of “Feitian” software, six single-point mutants with high kcat value were selected and successfully constructed by site-directed mutagenesis. Out of six, three mutants (Q4C, T212S, and A302C) showed higher enzymatic activity than the wild-type. Furthermore, the combined triple-point mutant DCase-M3 (Q4C/T212S/A302C) exhibited a 4.25-fold increase in activity (29.77 ± 4.52 U) and a 2.25-fold increase in thermal stability as compared to the wild-type, respectively. Through the whole-cell reaction, the high titer of D-HPG (2.57 ± 0.43 mM) was produced by the mutant Q4C/T212S/A302C, which was about 2.04-fold of the wild-type. Molecular dynamics simulation results showed that DCase-M3 significantly enhances the rigidity of the catalytic site and thus increases the activity of DCase-M3.ConclusionsIn this study, an efficient rational design software “Feitian” was successfully developed with a prediction accuracy of about 50% in enzymatic activity. A triple-point mutant DCase-M3 (Q4C/T212S/A302C) with enhanced enzymatic activity and thermostability was successfully obtained, which could be applied to the development of a fully enzymatic process for the industrial production of D-HPG.

The Importance of Structured Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules.

Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site. Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "Re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest. In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB. Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand. These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals. The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

Liquid phase oxidation of cyclopentanone over metal-free carbon catalysts

AbstractOxidation of cyclopentanone (CPO) was studied over metal-free carbon catalysts in solvent-free conditions. Norit SX plus (900 m2 g−1) and Vulcan XC72 (240 m2 g−1) were used as pristine materials. Catalysts were prepared by activation in nitrogen and by treatment with urea, calcined in nitrogen at 500 °C and 950 °C. SEM, EDX, XPS, X-ray powder diffraction, nitrogen adsorption–desorption isotherms, acid–base titration, FTIR and Raman techniques were used for characterization. Catalytic tests carried out at 0.45 MPa and 80–110 °C enabled to find the best results: 30% selectivity to glutaric acid (GA) and 3% to succinic acid at 25% conversion of CPO, over Vulcan type catalysts. A low activity, selectivity and strong deactivation of Norit type catalysts can be ascribed to a higher specific surface in a disordered arrangement providing a high concentration of unselective catalytic sites. A higher extent of side reactions can yield in higher molar mass products, which stick on the surface and block catalytic sites. Optimum amount of accessible planar domains, represented by graphene and/or graphitic plates with some disorders present in Vulcan type catalysts classified them superior to Norit catalysts. A redox reaction scheme of oxidation of CPO to GA is also proposed. Graphical abstract

Advanced Development of In situ Characterization Technique for Electrocatalytic Hydrogen Evolution Reaction

AbstractHydrogen evolution reaction (HER) from water splitting using renewable energy provides a promising solution to the global energy crisis and environmental problems. However, the lack of in‐depth understanding of the reaction mechanism and clear identification of the catalytic active site has hindered the further development of low‐cost, high‐performance, and long‐life efficient electrocatalysts. Through in situ characterization techniques, the activity and stability of catalysts can be monitored in real‐time, track the structural evolution of catalytic reaction intermediates, and obtain a deep understanding of catalytic reaction mechanism, so as to feedback and guide the development and utilization of the catalyst. In this review, advanced development of in situ characterization techniques in electrocatalytic HER in recent years is summarized. In situ spectroscopy can be used to track the behavior of reaction intermediates such as adsorption, desorption, and structural evolution at the molecular level to reveal the electrocatalytic HER mechanism. The imaging techniques can be used to observe the evolution of material structure during HER in situ, which provides valuable information for the understanding of visualization of catalytic hydrogen evolution at atomic level. This review contributes to theadvanced development of in situ characterization technique for electrocatalytic HER.

Reaction Mechanisms of Single Metal Site Catalysts Supported on Covalent Organic Frameworks

Covalent organic frameworks (COFs) have become a versatile platform to immobilize a wide variety of single‐atom metal catalysts. The resulting post‐synthetic modified materials present a spectrum of valuable properties ranging from homogeneous to heterogeneous systems, such as well‐defined catalytic sites, selectivity, recyclability, and stability. In this minireview, we discuss selected contributions that provide experimental and computational details on reaction mechanisms (e.g., via EXAFS, TEM, and DFT) catalyzed by single‐atom metals embedded within the COF structure. When applicable, we highlight the different behaviour between molecular (homogeneous) and COF‐supported (heterogeneous) sites regarding catalytic performance. With this survey, we aim to decipher the key features that aid in seeing COFs as not merely passive supports but as active items in catalysis.

Step-by-step transfer of photoexcited electron in donor-acceptor-catalyst configuration covalent triazine framework for efficient photoreduction CO2 to formic acid

Covalent triazine frameworks (CTFs) have great potential for photocatalysis. However, the electron-hole recombination and the lack of efficient catalytic sites constrain the activity and selectivity. Herein, a novel design strategy of donor–acceptor-catalyst (D-A-C) configuration is proposed. This configuration enables the photoexcited electron undergoes stepwise transfer from donor unit to acceptor unit and ultimately reaches catalytic center, effectively inhibiting electron-hole recombination. The proof-of-concept model CTF-TT-Ir, in which thieno[3,2-b]thiophene (TT) serves as the donor unit, triazine as the acceptor unit, and Cp*Ir(bpy) (Ir) as the built-in catalytic site, was prepared for the photocatalytic reduction of CO2 to HCOOH. The stepwise transfer of photoexcited electrons in the ternary structure has been demonstrated through the in-situ XPS measurements and the theoretical calculations. Photoluminescence and photocurrent tests have indicated CTF-TT-Ir exhibits superior charge separation efficiency. Without additional photosensitizer and co-catalyst, the photocatalytic HCOOH yield rate of CTF-TT-Ir reached 245 μmol g−1h−1 (selectivity of 97 %).

Co-pyrolysis of fly ash with sewage sludge for PCDD/F removal.

Fly ash generated from municipal waste incineration (MWI) contains various toxic substances, and it has to be properly treated before disposal or reuse. Water washing and thermal pyrolysis can improve the destruction efficiency of PCDD/Fs in fly ash generated from municipal solid waste incinerators. Since sulfur oxides and nitrogen compounds generated by the heating of the sewage sludge poison the catalytic active sites for PCDD/Fs formation on fly ash surface, co-pyrolysis of fly ash with sewage sludge effectively inhibits precursor formation and de novo synthesis reaction, resulting in the great reduction of PCDD/F formation. The results of the pyrolysis at 350 °C show that the PCDD/Fs removal efficiencies based on mass concentration are over 99%. The results at 350 °C of different reaction times show that the reaction time of 10 min is sufficient to reach the European End of Waste criteria (≤ 20 pg TEQ/g) when the ratio of fly ash/sewage sludge is controlled at 1:1.

Comparative study of organic removal by pre-adsorption oxidation and synchronous adsorption oxidation processes: Performance and mechanism

Both adsorption and oxidation occur and contribute to organics removal in carbonaceous materials based advanced oxidation processes, while the correction of adsorption and oxidation, and the role of adsorption in the veritable removal of organic are not clear. Herein, we investigated the performance of carbamazepine (CBZ) removal by peroxymonosulfate (PMS) activated by magnetic Fe-doped biochar through two models of pre-adsorption oxidation and synchronous adsorption oxidation processes. The adsorption process was better fitted by pseudo-second-order kinetic model and the adsorption mechanism was obtained by comprehensive analysis of equilibrium adsorption capacities, surface functional groups, specific surface area, pore volume, and ID/IG value. It is noted that pre-adsorption highly inhibited the further oxidation of CBZ in 0.5Fe@LSBC700/PMS system due to the occupied catalytic active sites. Total CBZ removal in pre-adsorption oxidation (45 %) was inferior to synchronous adsorption oxidation (∼100 %), as well as the veritable CBZ oxidation removal of 27 % for pre-adsorption oxidation vs ∼100 % in synchronous adsorption oxidation at 30 min. Oxidation degradation of CBZ based on radical oxidation was identified by quenching experiments and electron paramagnetic resonance measurements. This work is conducive to identifying the role of adsorption during the removal of organics in the adsorption-oxidation process, as well as veritable adsorption and oxidation removal of organics.

Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel

The kinetics of the protein elongation cycle by the ribosome depends on intertwined factors. One of these factors is the electrostatic interaction of the nascent protein with the ribosome exit tunnel. In this computational biology theoretical study, we focus on the rate of the peptide bond formation and its dependence on the ribosome exit tunnel electrostatic potential profile. We quantitatively predict how oligopeptides of variable lengths can affect the peptide bond formation rate. We applied the Michaelis-Menten model as previously extended to incorporate the mechano-biochemical effects of forces on the rate of reaction at the catalytic site of the ribosome. For a given pair of carboxy-terminal amino acid substrate at the P- and an aminoacyl-tRNA at the A-sites, the relative time courses of the peptide bond formation reaction can be reversed depending on the oligopeptide sequence embedded in the tunnel and their variable lengths from the P-site. The reversal is predicted to occur from a shift in positions of charged amino acids upstream in the oligopeptidyl-tRNA at the P-site. The position shift must be adjusted by clever design of the oligopeptide probes using the electrostatic potential profile along the exit tunnel axial path. These predicted quantitative results bring strong evidence of the importance and relative contribution of the electrostatic interaction of the ribosome exit tunnel with the nascent peptide chain during elongation.

Rational design of waste anode graphite-derived carbon catalyst to activate peroxymonosulfate for atrazine degradation

As the rapidly growing number of waste lithium-ion batteries (LIBs), the recycling and reutilization of anode graphite is of increasing interest. Converting waste anode graphite into functional materials may be a sensible option. Herein, a series of carbonaceous catalysts (TG) were successfully prepared using spent anode graphite calcined at various temperatures and applied for activating peroxymonosulfate (PMS) to degrade atrazine (ATZ). The catalyst obtained at 800 °C (TG-800) showed the optimum performance for ATZ removal (99.2% in 6 min). Various experimental conditions were explored to achieve the optimum efficiency of the system. In the TG-800/PMS system, free radicals (e.g., SO4·−, HO·), singlet oxygen (1O2), together with a direct electron transfer pathway all participated in ATZ degradation, and the ketonic (CO) group was proved as the leading catalytic site for PMS activation. The potential degradation routes of ATZ have also been presented. According to the toxicity assessment experiments, the toxicity of the intermediate products decreased. The reusability and universal applicability of the TG-800 were also confirmed. This research not only provides an efficient PMS activator for pollutant degradation, but also offers a meaningful reference for the recovery of waste anode graphite to develop environmentally functional materials.

Medium entropy FeCoNi nanoalloy supported on reduced graphene oxide for efficient electrochemical detection of roxarsone in food samples

Herein, a novel FeCoNi(b)-800 ternary metal nanoalloy was uniformly mixed with reduced graphene oxide (RGO) to synthesize the FeCoNi(b)-800@RGO(2:1) composite. The addition of RGO not only stopped the accumulation of FeCoNi(b)-800 alloy, but also heightened the electrocatalytic activity of composite. Particularly, the FeCoNi(b)-800@RGO(2:1) composite displayed the significantly strong electrocatalytic capacity for the reduction of roxarsone (ROX). Furthermore, the FeCoNi(b)-800@RGO(2:1) composite possessed enough porosity and metal catalytic sites, facilitating the transport and electrochemical reduction of the ROX. Thus, the FeCoNi(b)-800@RGO(2:1) composite modified glassy carbon electrode (FeCoNi(b)-800@RGO(2:1)/GCE) showed the superb electrochemical detection effect for ROX with relatively wide working range (0.1–1500 μM) and low detection limit (0.013 μM). Importantly, the FeCoNi(b)-800@RGO(2:1)/GCE sensor could accurately determine the contents of ROX in actual pork, chicken, duck and egg samples, indicating that it had good suitability in food safety monitoring.