Caspase-1 Engages Full-Length Gasdermin D through Two Distinct Interfaces That Mediate Caspase Recruitment and Substrate Cleavage.

The recognition and cleavage of gasdermin D (GSDMD) by inflammatory caspases-1, 4, 5, and 11 are essential steps in initiating pyroptosis after inflammasome activation. Previous work has identified cleavage site signatures in substrates such as GSDMD, but it is unclear whether these are the sole determinants for caspase engagement. Here we report the crystal structure of a complex between human caspase-1 and the full-length murine GSDMD. In addition to engagement of the GSDMD N- and C-domain linker by the caspase-1 active site, an anti-parallel ß sheet at the caspase-1 L2 and L2' loops bound a hydrophobic pocket within the GSDMD C-terminal domain distal to its N-terminal domain. This "exosite" interface endows an additional function for the GSDMD C-terminal domain as a caspase-recruitment module besides its role in autoinhibition. Our study thus reveals dual-interface engagement of GSDMD by caspase-1, which may be applicable to other physiological substrates of caspases.

Surface atom knockout for the active site exposure of alloy catalyst.

The fine regulation of catalysts by the atomic-level removal of inactive atoms can promote the active site exposure for performance enhancement, whereas suffering from the difficulty in controllably removing atoms using current micro/nano-scale material fabrication technologies. Here, we developed a surface atom knockout method to promote the active site exposure in an alloy catalyst. Taking Cu3Pd alloy as an example, it refers to assemble a battery using Cu3Pd and Zn as cathode and anode, the charge process of which proceeds at about 1.1 V, equal to the theoretical potential difference between Cu2+/Cu and Zn2+/Zn, suggesting the electricity-driven dissolution of Cu atoms. The precise knockout of Cu atoms is confirmed by the linear relationship between the amount of the removed Cu atoms and the battery cumulative specific capacity, which is attributed to the inherent atom-electron-capacity correspondence. We observed the surface atom knockout process at different stages and studied the evolution of the chemical environment. The alloy catalyst achieves a higher current density for oxygen reduction reaction compared to the original alloy and Pt/C. This work provides an atomic fabrication method for material synthesis and regulation toward the wide applications in catalysis, energy, and others.

Novel exported fusion enzymes with chorismate mutase and cyclohexadienyl dehydratase activity: Shikimate pathway enzymes teamed up in no man's land.

Chorismate mutase (CM) and cyclohexadienyl dehydratase (CDT) catalyze two subsequent reactions in the intracellular biosynthesis of l-phenylalanine (Phe). Here, we report the discovery of novel and extremely rare bifunctional fusion enzymes, consisting of fused CM and CDT domains, which are exported from the cytoplasm. Such enzymes were found in only nine bacterial species belonging to non-pathogenic γ- or ß-Proteobacteria. In γ-proteobacterial fusion enzymes, the CM domain is N-terminal to the CDT domain, whereas the order is inverted in ß-Proteobacteria. The CM domains share 15% to 20% sequence identity with the AroQγ class CM holotype of Mycobacterium tuberculosis (∗MtCM), and the CDT domains 40% to 60% identity with the exported monofunctional enzyme of Pseudomonas aeruginosa (PheC). In vitro kinetics revealed a Km <7 µM, much lower than for ∗MtCM, whereas kinetic parameters are similar for CDT domains and PheC. There is no feedback inhibition of CM or CDT by the pathway's end product Phe, and no catalytic benefit of the domain fusion compared with engineered single-domain constructs. The fusion enzymes of Aequoribacter fuscus, Janthinobacterium sp. HH01, and Duganella sacchari were crystallized and their structures refined to 1.6, 1.7, and 2.4 Å resolution, respectively. Neither the crystal structures nor the size-exclusion chromatography show evidence for substrate channeling or higher oligomeric structure that could account for the cooperation of CM and CDT active sites. The genetic neighborhood with genes encoding transporter and substrate binding proteins suggests that these exported bifunctional fusion enzymes may participate in signaling systems rather than in the biosynthesis of Phe.

Tuning Electrocatalytic Water Oxidation Activity: Insights from the Active-Site Distance in LnCu6 Clusters.

Atomically precise metal clusters serve as a unique model for unraveling the intricate mechanism of the catalytic reaction and exploring the complex relationship between structure and activity. Herein, three series of water-soluble heterometallic clusters LnCu6, abbreviated as LnCu6-AC (Ln = La, Nd, Gd, Er, Yb; HAC = acetic acid), LnCu6-IM (Ln = La and Nd; IM = Imidazole), and LnCu6-IDA (Ln = Nd; H2IDA = Iminodiacetic acid) are presented, each featuring a uniform metallic core stabilized by distinct protected ligands. Crystal structure analysis reveals a triangular prism topology formed by six Cu2+ ions around one Ln3+ ion in LnCu6, with variations in Cu···Cu distances attributed to different ligands. Electrocatalytic oxygen evolution reaction (OER) shows that these different LnCu6 clusters exhibit different OER activities with remarkable turnover frequency of 135 s-1 for NdCu6-AC, 79 s-1 for NdCu6-IM and 32 s-1 for NdCu6-IDA. Structural analysis and Density Functional Theory (DFT) calculations underscore the correlation between shorter Cu···Cu distances and improves OER catalytic activity, emphasizing the pivotal role of active-site distance in regulating electrocatalytic OER activities. These results provide valuable insights into the OER mechanism and contribute to the design of efficient homogeneous OER electrocatalysts.

Anionic Coordination Control in Building Cu-Based Electrocatalytic Materials for CO2 Reduction Reaction.

Renewable energy-driven conversion of CO2 to value-added fuels and chemicals via electrochemical CO2 reduction reaction (CO2RR) technology is regarded as a promising strategy with substantial environmental and economic benefits to achieve carbon neutrality. Because of its sluggish kinetics and complex reaction paths, developing robust catalytic materials with exceptional selectivity to the targeted products is one of the core issues, especially for extensively concerned Cu-based materials. Manipulating Cu species by anionic coordination is identified as an effective way to improve electrocatalytic performance, in terms of modulating active sites and regulating structural reconstruction. This review elaborates on recent discoveries and progress of Cu-based CO2RR catalytic materials enhanced by anionic coordination control, regarding reaction paths, functional mechanisms, and roles of different non-metallic anions in catalysis. Finally, the review concludes with some personal insights and provides challenges and perspectives on the utilization of this strategy to build desirable electrocatalysts.

Nickel Single Atom Density-Dependent CO2 Efficient Electroreduction.

The transition metal-nitrogen-carbon (M─N─C) with MNx sites has shown great potential in CO2 electroreduction (CO2RR) for producing high value-added C1 products. However, a comprehensive and profound understanding of the intrinsic relationship between the density of metal single atoms and the CO2RR performance is still lacking. Herein, a series of Ni single-atom catalysts is deliberately designed and prepared, anchored on layered N-doped graphene-like carbon (x Ni1@NG-900, where x represents the Ni loading, 900 refers to the temperature). By modulating the precursor, the density of Ni single atoms (DNi) can be finely tuned from 0.01 to 1.19 atoms nm-2. The CO2RR results demonstrate that the CO faradaic efficiency (FECO) predominantly increases from 13.4% to 96.2% as the DNi increased from 0 to 0.068 atoms nm-2. Then the FECO showed a slow increase from 96.2% to 98.2% at -0.82 V versus reversible hydrogen electrode (RHE) when DNi increased from 0.068 to 1.19 atoms nm-2. The theoretical calculations are in good agreement with experimental results, indicating a trade-off relationship between DNi and CO2RR performance. These findings reveal the crucial role of the density of Ni single atoms in determining the CO2RR performance of M─N─C catalysts.

Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin.

Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.

Thirty years with three-dimensional structures of lipoxygenases.

The X-ray crystal structures of soybean lipoxygenase (LOX) and rabbit 15-LOX were reported in the 1990s. Subsequent 3D structures demonstrated a conserved U-like shape of the substrate cavities as reviewed here. The 8-LOX:arachidonic acid (AA) complex showed AA bound to the substrate cavity carboxylate-out with C10 at 3.4 Å from the iron metal center. A recent cryo-electron microscopy (EM) analysis of the 12-LOX:AA complex illustrated AA in the same position as in the 8-LOX:AA complex. The 15- and 12-LOX complexes with isoenzyme-specific inhibitors/substrate mimics confirmed the U-fold. 5-LOX oxidizes AA to leukotriene A4, the first step in biosynthesis of mediators of asthma. The X-ray structure showed that the entrance to the substrate cavity was closed to AA by Phe and Tyr residues of a partly unfolded α2-helix. Recent X-ray analysis revealed that soaking with inhibitors shifted the short α2-helix to a long and continuous, which opened the substrate cavity. The α2-helix also adopted two conformations in 15-LOX. 12-LOX dimers consisted of one closed and one open subunit with an elongated α2-helix. 13C-ENDOR-MD computations of the 9-MnLOX:linoleate complex showed carboxylate-out position with C11 placed 3.4 ± 0.1 Å from the catalytic water. 3D structures have provided a solid ground for future research.

Advances in Naked Metal Clusters for Catalysis.

The properties of sub-nano metal clusters are governed by quantum confinement and their large surface-to-bulk ratios, atomically precise compositions and geometric/electronic structures. Advances in metal clusters lead to new opportunities in diverse aspects of sciences including chemo-sensing, bio-imaging, photochemistry, and catalysis. Naked metal clusters having synergic multiple active sites and coordinative unsaturation and tunable stability/activity enable researchers to design atomically precise metal catalysts with tailored catalysis for different reactions. Here we summarize the progress of ligand-free naked metal clusters for catalytic applications. It is anticipated that this review helps to better understand the chemistry of small metal clusters and facilitates the design and development of new catalysts for potential applications.

Enhancing catalytic efficiency of Bacillus subtilis laccase BsCotA through active site pocket design.

BsCotA laccase is a promising candidate for industrial application due to its excellent thermal stability. In this research, our objective was to enhance the catalytic efficiency of BsCotA by modifying the active site pocket. We utilized a strategy combining the diversity design of the active site pocket with molecular docking screening, which resulted in selecting five variants for characterization. All five variants proved functional, with four demonstrating improved turnover rates. The most effective variants exhibited a remarkable 7.7-fold increase in catalytic efficiency, evolved from 1.54 × 105 M-1 s-1 to 1.18 × 106 M-1 s-1, without any stability loss. To investigate the underlying molecular mechanisms, we conducted a comprehensive structural analysis of our variants. The analysis suggested that substituting Leu386 with aromatic residues could enhance BsCotA's ability to accommodate the 2,2'-azino-di-(3-ethylbenzothiazoline)-6-sulfonate (ABTS) substrate. However, the inclusion of charged residues, G323D and G417H, into the active site pocket reduced kcat. Ultimately, our research contributes to a deeper understanding of the role played by residues in the laccases' active site pocket, while successfully demonstrating a method to lift the catalytic efficiency of BsCotA. KEY POINTS: • Active site pocket design that enhanced BsCotA laccase efficiency • 7.7-fold improved in catalytic rate • All tested variants retain thermal stability.

Aptamer-based fluorescent sensor for highly sensitive detection of methamphetamine.

The construction of a fluorescence aptamer sensor was achieved by employing the fundamental principle of fluorescence resonance energy transfer. By employing molecular modeling technologies to identify the binding site, the high-affinity aptamer APT-40nt was derived from the whole sequence and utilized on the graphene oxide (GO) fluorescent platform for the purpose of achieving a highly sensitive detection of methamphetamine (METH). The aptamer tagged with fluorescein (FAM) dye undergoes quenching in the presence of GO due to π-stacking interaction. With the addition of the target, the aptamer that has been tagged was detached from the GO surface, forming a stable complex with METH. This process resulted in fluorescence restoration of the system, and the degree of fluorescence restoration was proportional to METH concentration in the linear range of 1-50 and 50-200 nM. Notably, under optimized conditions, the detection limit of this aptasensor was as low as 0.78 nM, which meets the detection limit requirements of METH detection in saliva and urine in some countries and regions. Moreover, other common illicit drugs and metabolites had minimizing interference with the determination. The established aptasensor, therefore, has been successfully applied to detect METH in saliva and urine samples and exhibited satisfactory recoveries (87%-111%). This aptasensor has the advantages of low detection limit, excellent selectivity, ease of operation, and low cost, providing a promising strategy for on-site detection of METH in saliva and urine.

Structure-Function Analysis of the Essential Mycobacterium tuberculosis P450 Drug Target, CYP121A1.

Cytochrome P450 CYP121A1 is a well-known drug target against Mycobacterium tuberculosis, the human pathogen that causes the deadly disease tuberculosis (TB). CYP121A1 is a unique P450 enzyme because it uses classical and non-classical P450 catalytic processes and has distinct structural features among P450s. However, a detailed investigation of CYP121A1 protein structures in terms of active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 53 CYP121A1 crystal structures were investigated in this study. Critical amino acids required for CYP121A1's overall activity were identified and highlighted this enzyme's rigid architecture and substrate selectivity. The CYP121A1-fluconazole crystal structure revealed a novel azole drug-P450 binding mode in which azole heme coordination was facilitated by a water molecule. Fragment-based inhibitor approaches revealed that CYP121A1 can be inhibited by molecules that block the substrate channel or by directly interacting with the P450 heme. This study serves as a reference for the precise understanding of CYP121A1 interactions with different ligands and the structure-function analysis of P450 enzymes in general. Our findings provide critical information for the synthesis of more specific CYP121A1 inhibitors and their development as novel anti-TB drugs.

A Fine Analysis of Zn Species Structure and Distribution in Zn/ZSM-5 Catalysts by Linear Combination Fitting Analysis of XANES Spectra.

Investigating the distribution of different Zn species on Zn-containing zeolite catalysts is crucial for identifying the active sites and establishing the relationship between the catalyst's structure and its activity in the process of ethylene aromatization. By utilizing X-ray absorption near edge spectra (XANES) of various reference samples, this study employed linear combination fitting (LCF) analysis on XANES spectra of real samples to accurately measure the changes in the distribution of Zn species in Zn-containing HZSM-5 zeolites under different Zn sources and loadings. The results showed that ZnOH+, ZnO clusters, and ZnO crystalline structures coexist in Zn/HZSM-5 catalysts prepared through physical mixing and incipient wet impregnation methods. A similar trend was observed for catalysts prepared using different methods, with an increase in Zn content resulting in a decrease in the proportion of ZnOH+ and a significant increase in the amount of larger ZnO crystals. Furthermore, ZnO clusters were confined within the zeolite pores. The findings of this study established a direct correlation between the amount of ZnOH+ determined through LCF analysis and both the rate of hydrogen production and the rate of aromatics formation, providing strong evidence for the catalytic role of ZnOH+ as an active center for dehydrogenation, which plays a key role in promoting the formation of aromatics. The method of LCF analysis on XANES spectra allows for the determination of the local structure of Zn species, facilitating a more precise analysis based on the distribution of these species. This method not only provides detailed information about the Zn species but also enhances the accuracy of the overall analysis.

Insights into the Understanding of the Nickel-Based Pre-Catalyst Effect on Urea Oxidation Reaction Activity.

Nickel-based catalysts are regarded as the most excellent urea oxidation reaction (UOR) catalysts in alkaline media. Whatever kind of nickel-based catalysts is utilized to catalyze UOR, it is widely believed that the in situ-formed Ni3+ moieties are the true active sites and the as-utilized nickel-based catalysts just serve as pre-catalysts. Digging the pre-catalyst effect on the activity of Ni3+ moieties helps to better design nickel-based catalysts. Herein, five different anions of OH-, CO32-, SiO32-, MoO42-, and WO42- were used to bond with Ni2+ to fabricate the pre-catalysts ß-Ni(OH)2, Ni-CO3, Ni-SiO3, Ni-MoO4, and Ni-WO4. It is found that the true active sites of the five as-fabricated catalysts are the same in situ-formed Ni3+ moieties and the five as-fabricated catalysts demonstrate different UOR activity. Although the as-synthesized five catalysts just serve as the pre-catalysts, they determine the quantity of active sites and activity per active site, thus determining the catalytic activity of the catalysts. Among the five catalysts, the amorphous nickel tungstate exhibits the most superior activity per active site and can catalyze UOR to reach 158.10 mA·cm-2 at 1.6 V, exceeding the majority of catalysts. This work makes for a deeper understanding of the pre-catalyst effect on UOR activity and helps to better design nickel-based UOR catalysts.

Structural Catalytic Core of the Members of the Superfamily of Acid Proteases.

The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a structural marker of four individual protease families. The SCC is a dimer of several structural blocks, such as the DD-link, D-loop, and G-loop, around two catalytic aspartates in each protease subunit or an individual chain. A dimer made of two (D-loop + DD-link) structural elements makes a DD-zone, and the D-loop + G-loop combination makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation, and protein engineering.

Tuning Active Site Flexibility by Defect Engineering of Graphene Ribbon Edge-hosted Fe-N3 Sites.

Nitrogen-doped, carbon-supported transition metal catalysts are excellent for several reactions. Structural engineering of M-Nx sites to boost catalytic activity is rarely studied. Here, we demonstrate that the structural flexibility of Fe-N3 site is vital for tuning the electronic structure of Fe atoms and regulating the catalytic transfer hydrogenation (CTH) activity. By introducing carbon defects, we construct Fe-N3 sites with varying Fe-N bond lengths distinguishable by X-ray absorption spectroscopy. We investigate the CTH activity by density-functional theory and microkinetic calculations and reveal that the vertical displacement of the Fe atom out of the plane of the support, induced by the Fe-N3 distortion, raises the Fe 3 d z 2 ${3{d}_{{z}^{2}}{\rm \ }}$ orbital and strengthens binding. We propose that the activity is controlled by the relaxation of the reconstructed site, which is further affected by Fe-N bond length, an excellent activity descriptor. We elucidate the origin of the CTH activity and principles for high-performing Fe-N-C catalysts by defect engineering.

All-in-One: Plasmonic Janus Heterostructures for Efficient Cooperative Photoredox Catalysis.

Janus heterostructures consisting of multiple jointed components with distinct properties have gained growing interest in the photoredox catalytic field. Herein, we have developed a facile low-temperature method to gain anisotropic one-dimensional Au-tipped CdS (Au-CdS) nanorods (NRs), followed by assembling Ru molecular co-catalyst (RuN5) onto the surface of the NRs. The CdS NRs decorated with plasmonic Au nanoparticles (NPs) and RuN5 complex harness the virtues of metal-semiconductor and inorganic-organic interface, giving directional charge transfer channels, spatially separated reaction sites, and enhanced local electric field distribution. As a result, the Au-CdS-RuN5 can act as an efficient dual-function photocatalyst for simultaneous H2 evolution and valorization of biomass-derived alcohols. Benefiting from the interfacial charge decoupling and selective chemical bond activation, the optimal all-in-one Au-CdS-RuN5 heterostructure shows greatly enhanced photoactivity and selectivity as compared to bare CdS NRs, along with a remarkable apparent quantum yield of 40.2 % at 400 nm. The structural evolution and working mechanism of the heterostructures are systematically analyzed based on experimental and computational results.

Stabilizing Diluted Active Sites of Ultrasmall High-Entropy Intermetallics for Efficient Formic Acid Electrooxidation.

The poisoning of undesired intermediates or impurities greatly hinders the catalytic performances of noble metal-based catalysts. Herein, high-entropy intermetallics i-(PtPdIrRu)2FeCu (HEI) are constructed to inhibit the strongly adsorbed carbon monoxide intermediates (CO*) during the formic acid oxidation reaction. As probed by multiple-scaled structural characterizations, HEI nanoparticles are featured with partially negative Pt oxidation states, diluted Pt/Pd/Ir/Ru atomic sites and ultrasmall average size less than 2 nm. Benefiting from the optimized structures, HEI nanoparticles deliver more than 10 times promotion in intrinsic activity than that of pure Pt, and well-enhanced mass activity/durability than that of ternary i-Pt2FeCu intermetallics counterpart. In situ infrared spectroscopy manifests that both bridge and top CO* are favored on pure Pt but limited on HEI. Further theoretical elaboration indicates that HEI displayed a much weaker binding of CO* on Pt sites and sluggish diffusion of CO* among different sites, in contrast to pure Pt that CO* bound more strongly and was easy to diffuse on larger Pt atomic ensembles. This work verifies that HEIs are promising catalysts via integrating the merits of intermetallics and high-entropy alloys.

Synergistic Effect of Oxygen Vacancy and High Porosity of Nano MIL-125(Ti) for Enhanced Photocatalytic Nitrogen Fixation.

This work reports that a low-temperature thermal calcination strategy was adopted to modulate the electronic structure and attain an abundance of surface-active sites while maintaining the crystal morphology. All the experiments demonstrate that the new photocatalyst nano MIL-125(Ti)-250 obtained by thermal calcination strategy has abundant Ti3+ induced by oxygen vacancies and high specific surface area. This facilitates the adsorption and activation of N2 molecules on the active sites in the photocatalytic nitrogen fixation. The photocatalytic NH3 yield over MIL-125(Ti)-250 is enhanced to 156.9 µmol g-1 h-1 , over twice higher than that of the parent MIL-125(Ti) (76.2 µmol g-1 h-1 ). Combined with density function theory (DFT), it shows that the N2 adsorption pattern on the active sites tends to be from "end-on" to "side-on" mode, which is thermodynamically favourable. Moreover, the electrochemical tests demonstrate that the high atomic ratio of Ti3+ /Ti4+ can enhance carrier separation, which also promotes the efficiency of photocatalytic N2 fixation. This work may offer new insights into the design of innovative photocatalysts for various chemical reduction reactions.

Unlocking Double Redox Reaction of Metal-Organic Framework for Aqueous Zinc-Ion Battery.

Metal-organic frameworks (MOFs) show wide application as the cathode of aqueous zinc-ion batteries (AZIBs) in the future owning to their high porosity, diverse structures, abundant species, and controllable morphology. However, the low energy density and poor cycling stability hinder the feasibility in practical application. Herein, an innovative strategy of organic/inorganic double electroactive sites is proposed and demonstrated to obtain extra capacity and enhance the energy density in a manganese-based metal-organic framework (Mn-MOF-74). Simultaneously, its energy storage mechanism is systematically investigated. Moreover, profiting from the coordination effect, the Mn-MOF-74 features with stable structure in ZnSO4 electrolyte. Therefore, the Zn/Mn-MOF-74 batteries exhibit a high energy density and superior cycling stability. This work aids in the future development of MOFs in AZIBs.