Search Results (176)

DNA damage requires repair via the endonuclease IV-mediated base excision repair (BER) pathway, which corrects apurinic/apyrimidinic (AP) sites. Chlamydophila pneumoniae AP endonuclease IV (CpEndoIV), the sole AP endonuclease in this pathogen, is crucial for genomic integrity. As humans lack a homologous protein, it represents a potential therapeutic target. In this study, we report the first crystal structure of CpEndoIV at 1.97 Å resolution. The structure reveals two Zn²⁺, one Mg²⁺, and a malonate molecule bound in the active site, marking the first observation of Mg²⁺ coordination in the EndoIV family. Compared to the three-Zn²⁺ model with a narrow, deep pocket for precise AP-site cleavage, the Zn²⁺/Mg²⁺-bound state has a wider, shallower pocket that might promote diverse catalytic activities. Combined with enzymatic assays, we suggest that the mixed Zn²⁺/Mg²⁺ model is better adapted for CpEndoIV to operate under host oxidative stress. Malonate binds to the metal ions, occupying the positions normally coordinated by water molecules. This binding mode may mimic the coordination of the substrate to the metal ions, and the protein conformation resembles that of the enzyme upon substrate binding at the active site. This study provides a structural basis for the functional characterization of CpEndoIV and offers a reference for the development of targeted inhibitors against diseases caused by Chlamydophila pneumoniae. Full article

Background: The ability of synthetic plastics to persist in the environment and the accumulation of microplastics has intensified the need to explore biological mechanisms capable of interacting with, and possibly degrading, polymeric materials. Microbial enzymes that have extensive catalytic flexibility represent promising candidates in this context. Aim: This study set out to examine the molecular interaction patterns and dynamical stability of Pseudomonas aeruginosa elastase (LasB) with representative structural fragments of typical synthetic plastics to assess the suitability of the enzyme to polymer-derived substrates. Methods: The crystallographic structure of LasB (PDB ID: 1EZM) was retrieved from the Protein Data Bank and pre-prepared with the help of AutoDock4.2.6 Tools. Those polymer-derived ligands that were associated with the major industrial plastics such as polyamide (PA), polyvinyl chloride (PVC), polycarbonate (PC), poly-ethylene terephthalate (PET), polymethyl methacrylate (PMMA), and polyurethane (PUR) were retrieved in the PubChem database and geometrically optimized with the help of the MMFF94 force field. AutoDock Vina, with a specific grid box around the catalytic pocket, including Zn²⁺ ion, was used to perform molecular docking simulations. PyMOL and BIOVIA Discovery Studio software were used to analyze binding conformations, interaction residues and types of intermolecular contacts. Phosphoramidon, a known metalloprotease inhibitor, served as a positive control to confirm the docking protocol. Additional assessment of the structural stability and conformational behavior of the enzyme–ligand complexes was conducted by molecular dynamics (MD) simulations with the Desmond engine and explicit solvent model in a 50 ns trajectory using the OPLS4 force field. RMSD, RMSF, radius of gyration, hydrogen bonding analysis and solvent accessibility parameters were used to measure structural stability. Results: The docking experiment showed varying binding affinities with the test polymers. Polycarbonate (−5.774 kcal/mol) and polyurethane (−5.707 kcal/mol) had the highest in-teractions with the LasB catalytic pocket, polyamide (−5.277 kcal/mol) and PET (−4.483 kcal/mol) followed PMMA and PVC, which had weaker affinities. The following were the important residues involved in interaction networks: Glu141, His140, Val137, Arg198, Tyr114, and Trp115 that were implicated in interaction networks with hydrophobic interactions, π-cation interactions and van der Waals forces that were the major stabilization forces. MD simulations had stabilized complexes, and RMSD values were found to be within acceptable ranges of stability, and ligand-specific changes (around 1.0-3.2 A), which is also in line with stable protein-ligand systems. Phosphoramidon used as a positive control had an RMSD of 1.205 A which is within this stability range. PCA determined various ligand-bound conformational states of LasB with PA in com-pact state, PC and PVC in intermediate states and PUR, PMMA and PET in ex-panded conformations, indicating structur-al stability and adaptability of the binding pocket. Conclusion: These findings show that LasB has a structurally flexible catalytic pocket that can accommodate a wide range of polymer-derived ligands. These results offer an insight into the recognition of enzymes with polymers at the molecular level and also indicate that LasB might help in the interaction of microorganisms with synthetic plastics in environmental systems. Full article

Proteins can be methylated at either of the two N atoms of the imidazole ring of histidine, yielding 1-methylhistidine (or pi-methylhistidine) or 3-methylhistidine (tau-methylhistidine). While protein histidine methylation in mammals was discovered more than 50 years ago, the first histidine methyltransferases were identified only recently. So far, four different human protein histidine methyltransferases have been uncovered, and one of these is METTL9, which is responsible for introducing 1-methylhistidine in a number of proteins. The minimal sequence motif that is required, though not always sufficient, for METTL9-mediated methylation is His-X-His (HxH), where X is preferentially a small uncharged residue. Many METTL9 substrates are methylated at stretches of alternating histidines, i.e., several adjoining HxH motifs, such as HxHxH. Histidines are frequently involved in binding metal ions, such as zinc. Accordingly, it has been shown for several sequences targeted by METTL9, for example, in the immunomodulatory and antibacterial protein S100A9 and the zinc transporter SLC39A7, that histidine methylation diminishes zinc binding and thereby modulates protein function. In this review, we present a detailed account of METTL9-mediated histidine methylation, regarding its discovery, biochemical mechanism, structural features, and biological significance. Full article

CrAlSiN nanocomposite coatings with different structures were prepared by arc ion plating. The influence of substrate bias on the composition, microstructure and properties of the coating was investigated. The nanocomposite CrAlSiN coatings all had a fcc-(Cr, Al)N phase, where Al atoms and some Si atoms were solid-dissolved in CrN phase and some Si existed in the form of amorphous phase in the coating. The coatings were preferentially grown along the (200) crystal plane. With the increase in substrate bias, the roughness of the coating gradually decreased. When the substrate bias gradually increased to 100 V, the small particles aggregated into large particles, producing more holes, so that the surface roughness of the coating increased. At the same time, with the increase in substrate bias, the hardness and adhesion of the coating first increased and then decreased. When the substrate bias voltage was 80 V, the coating had the largest hard H (31.30 GPa), elastic modulus E* (432.15 GPa), H/E* (0.0724), H³/E*² (0.1642) and binding force of 109.26 N. Full article

Crust Ash Triad Clay (CATC) is a traditional construction material commonly used for jointing coastal stone masonry in Southeast China. Its surface is prone to blackening in coastal environments. This study focused on traditional stone masonry residences within the protection area of Quanzhou Shihu Ancient Wharf. A systematic detection and analysis were conducted using combined technologies: XRD, Raman, SEM-EDS, and 16S rRNA sequencing. The results revealed that the CATC substrate is mainly composed of quartz and feldspar minerals, with calcite and other substances as binding components. The black coating on the surface is a loose material attached to the substrate, retaining some of the original minerals. The core mechanism of blackening lies in the coastal environment’s abundance of salt spray and humidity. The sulfate substances carried by rainwater react synergistically with metal ions such as Cu, Fe, and Mn in the substrate under the metabolic action of anaerobic bacteria, producing metal sulfide minerals. Photoautotrophic bacteria generate oxygen through photosynthesis, promoting the oxidation and acidification of metal sulfide. This process directly triggers the chain deterioration of the CATC substrate. Based on the principle of “minimal intervention”, physical waterproofing or laser stain removal can be implemented. This study provides scientific support for optimizing the durability and achieving precise protection of traditional building materials in coastal stone structure heritage. Full article

Snakebite envenoming remains a critical public health issue, and the molecular variability of venoms limits the cross-species efficacy of conventional antivenoms. Here, we conducted a comparative proteomic analysis of Bitis arietans venom to identify conserved peptide regions derived from enzymatic toxins and evaluate their potential relevance for complementary immunotherapeutic applications. Enzyme-enriched venom fractions were isolated through sequential affinity and ion-exchange chromatography and were subsequently characterized using fluorogenic FRET substrates and inhibitor assays. LC–MS/MS analysis identified 1099 proteins and revealed 36 conserved peptides within snake venom metalloproteinases (SVMPs), serine proteases (SVSPs), and phospholipase A₂ (PLA₂), particularly located near catalytic residues and structurally essential motifs such as the HExxHxxGxxH zinc-binding site in SVMPs, the His-Asp-Ser catalytic triad in SVSPs, and the Ca²⁺-binding loop in PLA₂, across Viperidae venoms. These conserved regions were also observed in homologous toxin isoforms from additional Viperidae genera, supporting the evolutionary conservation of key functional domains. While sequence conservation alone does not guarantee neutralization capacity, the identified regions represent strong candidates for structural epitope mapping and targeted antibody development. This study provides a peptide-level framework for advancing complementary antibody-based therapies designed to broaden cross-species toxin recognition, reduce antivenom dosage requirements, and improve clinical outcomes in snakebite envenoming. Full article

The incidence of primary liver cancer is increasing annually, with extremely high mortality and suboptimal therapeutic outcomes. The inefficient presentation of tumor antigens and low infiltration of specific cytotoxic T lymphocytes (CTLs) result in insufficient immunogenicity, which limits the efficacy of immunotherapy. Despite the popularity of immune checkpoint inhibitors (ICIs), insufficient immune activation means only a small subset of hepatocellular carcinoma (HCC) patients exhibit clinical responses to ICIs, showing significant inter-individual variability. The activation of the cyclic GMP-AMP synthase(cGAS)- stimulator of interferon genes(STING) pathway initiates the expression of type I interferons (IFNs) and inflammatory cytokines, promoting the formation of a pro-inflammatory environment at the tumor site. This pathway enhances anti-tumor immune responses by facilitating antigen processing and presentation, T cell priming and activation, and remodeling of the immunosuppressive microenvironment. Our research found that cucurbitacin B (CuB), a natural component derived from traditional Chinese medicine, had significant anti-hepatocellular carcinoma properties and exerted anti-tumor effects through the cGAS-STING pathway. Specifically, CuB regulated ferroptosis by down-regulating the expression of Solute Carrier Family 7 Member 11 (SLC7A11) and Glutathione Peroxidase 4 (GPX4) and upregulating the expression of Transferrin Receptor Protein 1 (TFR1) and Long-chain Acyl-CoA Synthetase 4 (ACSL4). These actions involved lipid substrates, iron ion homeostasis, and antioxidant defense systems. The release of mitochondrial DNA (mtDNA) triggered by ferroptosis activated the cGAS-STING immune signaling pathway, leading to the up-regulation of cGAS, phosphorylated STING (p-STING), phosphorylated TANK-binding kinase 1 (TBK1), phosphorylated Interferon regulatory factor3 (IRF3), and Interferon-β (IFN-β). This cascade activation pattern provides new insights into the drug treatment of tumors. Full article

The reliable integration of high-performance noble metal interfaces with flexible substrates is a key requirement for wearable electronics. However, achieving uniform, mechanically robust and functionally active coatings on fabric surfaces remains highly challenging. This study reports the atomic-layered-deposition (ALD) growth of platinum (Pt) on textile at low temperatures. Through ozone plasma-assisted activation technology, Pt nucleation can be achieved at 100 °C, forming a dense and defect-suppressed Pt layer that substantially increases the surface oxygen functional groups and enhances binding affinity. The resulting Pt layer also significantly enhances the adsorption behavior and sensing performance of Ti₃C₂T_x MXene gel inks on textile. At the atomic scale, the engineered Pt–MXene interface promotes stronger adsorption of MXene sheets and establishes efficient electron/ion transport pathways within the gel network. Ultimately, the conductive textile treated with Pt functionalized layers (MXene/Pt@textile) exhibits significantly enhanced sensing sensitivity and signal stability, enabling precise detection of human motions, pressure, and subtle physiological vibrations. The synergistic effect of ALD Pt layers and MXene gel inks creates a textile platform combining robustness, breathability, and high responsiveness. Full article

DapE is a highly conserved bacterial enzyme that produces L,L-diaminopimelic acid in the meso-diaminopimelic acid and lysine synthesis pathway, which is essential for peptidoglycan formation in the cell wall. DapE has been recognized as a promising antibacterial drug target and can be inhibited by captopril. The pathogenic bacterium Campylobacter jejuni expresses a DapE ortholog, cjDapE. However, the structural basis underlying the enzymatic activity of cjDapE and its inhibition by captopril is unknown. Here, we report the crystal structures of cjDapE in complexes with Zn²⁺ and with both Zn²⁺ and captopril. cjDapE consists of a catalytic domain (CD) and a dimerization domain (DD). The CD harbors a pocket, which accommodates two Zn²⁺ ions in close proximity as the catalytic active site. cjDapE assembles into a dimer primarily using DD residues, with two DD loops largely disordered in the absence of captopril. Upon captopril binding, these loops become ordered and contribute to dimer stabilization by involving both DD and CD residues. Notably, captopril binding maintains cjDapE in an open conformation that is incompatible with catalytic activity. Our comparative structural analysis suggests that captopril inhibits cjDapE primarily via substrate competition. Full article

Isothermal titration calorimetry (ITC) provides direct insight into the energetics of DNA polymerase function, including binding, catalysis, and exonuclease activity. We characterized a Phi29 mutant polymerase (SS_01) engineered to incorporate non-natural nucleotides in the presence of Mg²⁺, a function absent in the wild-type enzyme. ITC analyses revealed that SS_01 binding to the primed template was strongly influenced by metal ions. In the presence of Mg²⁺, the polymerase displayed tight binding (KD = 243 nM) and a clear exothermic signal, indicating activation of a large fraction of catalytically competent molecules. By contrast, in the presence of Ca²⁺, binding produced weaker exothermic signals (KD = 317 nM), suggesting less efficient binding complex formation. During dNTP- or oligonucleotide-tagged dNTP-driven polymerization, ITC profiles with Mg²⁺ exhibited pronounced endothermic heat changes, whereas with Ca²⁺, only minimal heat changes were observed. When binding only oligonucleotide-tagged dNTPs, the polymerases showed distinct thermodynamic behavior: in the presence of Mg²⁺, high substrate concentrations induced endothermic responses, while in the absence of catalytic ions, binding remained exothermic. Exonuclease activity monitored using unmodified oligonucleotides yielded strong exothermic signals in the presence of Mg²⁺ but weak responses in the presence of Ca²⁺, confirming strict ion dependence. Together, these data demonstrate that ITC directly captures the metal ion-dependent energetics of SS_01, providing mechanistic insight into its polymerization and exonuclease functions. Full article

In this study, we investigate the role of film thickness in modulating the properties of Cu films deposited on BaTiO₃ ceramic substrates using direct current magnetron sputtering (DCMS) and high-power pulsed magnetron sputtering (HiPIMS). While HiPIMS is known for producing dense films, and the thickness-dependent properties of sputtered Cu films are well-documented, this work uniquely explores the synergistic interplay between deposition technique and thickness on BaTiO₃ ceramic substrates, revealing novel insights into stress evolution and property optimization for advanced microelectronic and coating applications. Cu films of 300 nm, 1000 nm, and 1700 nm were systematically compared for their microstructures, surface morphologies, and electrical and mechanical properties, elucidating the critical role of thickness in densification, stress state, and overall performance. The results indicate that the target current and voltage waveforms of HiPIMS are similar to square waves, and the ionization rate is significantly higher than that of DCMS. Still, the deposition rate at the same power of 180 W is only 44.6% of that of DCMS. The films obtained by both processes present a strong (111) orientation; the crystallite size of the DCMS film grows with increasing thickness, while the HiPIMS film shows increasing and then decreasing, and its residual stress is overall lower than that of DCMS. In terms of surface morphology, DCMS films appeared porous and rough, whereas HiPIMS films were denser and smoother. In terms of properties, the resistivity of HiPIMS films is significantly lower than that of DCMS, especially at 1000 nm thickness. The binding force is also better than that of DCMS, especially at thicknesses less than 1000 nm, which is mainly attributed to the compressive stresses introduced by the energetic ion bombardment at the early deposition stage. These findings provide new mechanistic insights into thickness-dependent stress and property modulation, offering a reference for tailoring high-performance Cu films through process optimization. Full article

N-tetradecanoyl-L-homoserine lactone (C₁₄-HSL) is a long-chain signaling molecule belonging to acyl-homoserine lactones (AHLs), which is widely present in the quorum sensing (QS) system of Gram-negative bacteria. In this study, the effects of C₁₄-HSL on chalcopyrite bioleaching mediated by Acidithiobacillus ferrooxidans (A. ferrooxidans) were investigated. After cultivating A. ferrooxidans with different energy substrates and exploring the potential mechanisms of signal molecule production, chalcopyrite was selected as the energy substrate for further study. Molecular docking analysis revealed that the high binding affinity between AHL and the receptor protein AfeR in A. ferrooxidans was beneficial for the activation of transcription by the AfeR-AHL complex, promoting their biological impact. The variations in the physicochemical parameters of pH, redox potential, and copper ions revealed that after adding C₁₄-HSL, the leaching rate of chalcopyrite increased (1.15 times during the initial 12 days). Further analysis of the mechanism of extracellular polymers formation indicated that the presence of C₁₄-HSL could promote the formation of biofilms and the adhesion of bacteria, facilitating mineral leaching rate of A. ferrooxidans. This research provides a theoretical basis for regulating the biological leaching process of chalcopyrite and metal recovery using signaling molecules, which could also be used to control environmental damage caused by acid mine/rock drainage. Full article

The dynamic regulation of histone methylation is a key mechanism for epigenetic regulation of gene expression. As histone demethylases dependent on divalent iron ions and α-ketoglutarate, the JmjC family plays an important role in plant life activities. Fifty JmjC domain-containing proteins in Arabidopsis thaliana (21) and Brassica rapa (29) are divided into seven distinct groups, with each group endowed with specific functions due to unique structural domains. Some members achieve functional specificity by recognizing specific DNA motifs or interacting with transcription factors, and others exhibit special functional modes due to mutations in their binding sites. By targeting specific genes (such as FLC, FT, WRKY family, PR genes, etc.), they regulate growth and development processes, as well as responses to multiple biotic and abiotic stresses. Focusing on inter-species divergence of Arabidopsis and Brassica, this review summarized JmjC proteins’ structural classification, substrate specificity, and mechanisms, providing a basis for dissecting plant epigenetic networks and guiding Brassica crop breeding desired bolting traits (early or late bolting), high stress resistance and so on. Full article

An intracellular α-glucosidase was isolated and purified from a Pseudanabaena sp. cyanobacterial strain. Before the enzyme purification, the optimal cultural conditions were determined. Optimal culture conditions (15 g/L maltose, 2 g/L yeast extract, 23 ± 1 °C) yielded 3.3 g/L of biomass and 2186 U/L of α-glucosidase in a lab-scale bioreactor. The purified enzyme displayed a molecular mass of 52 kDa with optimum activity at 40 °C and pH 7.0, and maintained stability within an acidic and neutral range of pH 4.0 to 7.0. Enzyme activity was affected by both the concentration and interaction time of the metal ions and chelator. Kinetic constants of K_m, V_max, and k_cat for the hydrolysis of pNPG were determined as 2.0 Mm, 2.9 μmol min⁻¹, and 14.86 min⁻¹, respectively. The activation energy (E_a) was 24.2 kJ mol⁻¹ and the thermodynamic parameters of enthalpy (ΔH^*), entropy (ΔS^*) of activation, Gibbs free energy (ΔG^*), free energy of substrate binding (ΔG^*_E-S), and transition state formation (ΔG^*_Ε-Τ) were 21.6, −116, 57.8, −22.2, and −41.2 kJ mol⁻¹, respectively. Moreover, the thermodynamic parameters for thermal inactivation of the enzyme were ΔH^*= 131 kJ mol⁻¹, 105 ≤ ΔS^* ≤ 108 kJ mol⁻¹, and 96 ≤ ΔG^* ≤ 98 kJ mol⁻¹, while the thermal inactivation energy (E_(a)d) was determined to be 133 kJ mol⁻¹. This is the first detailed investigation concerning the characterization of α-glucosidase derived from cyanobacteria. The presented enzymatic characteristics provide a valuable predictive model for identifying suitable applications. Full article

Background: The rapid emergence of antibiotic resistance in Acinetobacter baumannii has led the World Health Organization (WHO) to designate it as a “high priority” pathogen. The emergence of multidrug-resistant (MDR) and pandrug-resistant (PDR) strains poses considerable treatment challenges. As antimicrobial resistance (AMR) escalates toward a post-antibiotic era, innovative therapeutic solutions are urgently needed. Objectives: To clone, over-express, and characterize a novel endolysin, LysTAC1, from Acinetobacter phage TAC1 for its antibacterial efficacy against multidrug-resistant bacteria. Methods: A 24 kDa endolysin featuring a glycoside hydrolase Family 19 chitinase domain was tested against carbapenem-resistant Acinetobacter baumannii clinical isolates and various Escherichia coli strains following outer membrane permeabilization with Ethylenediaminetetraacetic acid (EDTA). Stability assays and molecular docking studies were performed. Results: LysTAC1 demonstrated potent lytic activity against Gram-negative bacteria but showed no activity against Gram-positive bacteria (Staphylococcus aureus ATCC 29213 and Enterococcus gallinarum HCD 28-1). LysTAC1 maintained activity across pH 6–9 and temperatures 4–65 °C, with differential sensitivity to metal ions where K⁺ showed no inhibitory effect at any concentration (0.1–100 mM), and Fe²⁺ was non-inhibitory at lower concentrations (0.1–1 mM), while Mg²⁺ and Ca²⁺ demonstrated concentration-dependent inhibition across the tested range (0.1–100 mM). Molecular docking revealed LysTAC1 interactions with chitinase substrates 4-nitrophenyl N-acetyl-β-D-glucosaminide and 4-nitrophenyl N, N-Diacetyl-β-D-chitobioside, with binding energies of −5.82 and −6.85 kcal/mol, respectively. Conclusions: LysTAC1 shows significant potential as a targeted therapeutic agent against A. baumannii with robust stability under physiological conditions. Full article