Search Results (1,865)

Gout is a form of sterile inflammatory arthritis in which monosodium urate (MSU) crystals deposit and provoke a neutrophil-predominant response, primarily driven by activation of the NACHT, leucine-rich repeat, and pyrin domain-containing protein 3 (NLRP3) inflammasome. Here, we show that auranofin, a Food and Drug Administration (FDA)-approved anti-rheumatic agent, exerts anti-inflammatory effects in both in vitro and in vivo models of gout. Auranofin inhibited NLRP3 inflammasome activation in human THP-1 cells and murine macrophages, leading to reduced cleavage of caspase-1, interleukin-1β (IL-1β), and interleukin-18 (IL-18). In MSU crystal-induced mouse models, auranofin treatment reduced paw swelling, serum cytokine levels, and tissue inflammation. Notably, auranofin suppressed neutrophil migration and decreased expression of C-X-C motif chemokine ligand 1 (CXCL1) in inflamed foot tissue and air-pouch exudates. Mechanistically, auranofin disrupted the interleukin-33 (IL-33)/suppression of tumorigenicity 2 (ST2) axis, a key signaling pathway promoting neutrophil recruitment. Overexpression of IL-33 abolished the anti-inflammatory effects of auranofin, highlighting the central role of IL-33 in gout pathogenesis. Together, our findings suggest that auranofin alleviates MSU-induced inflammation by concurrently inhibiting NLRP3 inflammasome activation and IL-33-mediated neutrophil recruitment, supporting its potential as a dual-action therapeutic candidate for gout. Full article

GpsB is a conserved cell-cycle regulator in the Firmicute clade of Gram-positive bacteria that coordinates multiple aspects of envelope biogenesis. Recent studies demonstrate interactions between GpsB and the key division cytoskeleton FtsZ, suggesting that GpsB links cell division to various aspects of cell envelope biogenesis in Staphylococcus aureus and potentially other Firmicutes. We determined a 1.7 Å resolution crystal structure of the N-terminal domain of Staphylococcus aureus GpsB, revealing an asymmetric dimer with a bent conformation. This conformation is nearly identical to one of two conformations reported by Sacco et al., confirming the unique conformation of S. aureus GpsB compared to other Gram-positive bacteria. This structural agreement provides strong validation of the S. aureus GpsB fold and supports its proposed role in organizing the cell division machinery. Full article

The understanding and control of protein crystallization are crucial in structural biology, drug development, and biomaterial design. This study introduces a unified framework for modeling and comparing crystallization kinetics using selected growth functions. Experimental datasets from the literature for four proteins, Lysozyme, Thaumatin, Ribonuclease A, and Proteinase K, under Hanging Drop and Langmuir–Blodgett conditions were analyzed. Five kinetic models, Avrami, Kashchiev, Hill, Logistic, and Generalized Sigmoid (GSM), were fitted to size–time data of the four benchmark proteins. From each fit, four descriptors were extracted: crystallization half-time, time of maximum growth, width at half-maximum, and peak growth rate. These metrics summarize crystallization dynamics and enable cross-comparison of proteins and methods. Langmuir–Blodgett templating accelerated onset and improved synchrony, though the effect varied by protein and model. Logistic, Hill, and GSM models provided consistent fits across most conditions, while Avrami and Kashchiev were more sensitive to early or late deviations. Notably, descriptor extraction remained reliable even with limited or uneven sampling, revealing kinetic regimes such as synchrony, asymmetry, or prolonged nucleation, not evident in raw data. This transferable analytical framework supports quantitative evaluation of crystallization behavior, aiding screening, process optimization, and time-resolved structural studies. Full article

Background: The treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections is extremely challenging due to its antibiotic resistance, and the combination of plant active ingredients with antibiotics represents a potential strategy to address this issue. Methods: We determined the combinatorial relationship between baicalin (BA) and kanamycin (KM) using the checkerboard dilution method. The antibacterial activity of the baicalin–kanamycin (BA/KM) combination was evaluated through growth curve determination assays and scanning electron microscopy (SEM). The effects of the BA/KM combination on the cell membrane and cell wall of MRSA were analyzed using reactive oxygen species (ROS) detection assays, intracellular protein leakage experiments, alkaline phosphatase (AKP) activity assays, laser scanning confocal microscopy (LSCM) observations, and molecular docking simulations. The antibiofilm activity and related mechanisms of the BA/KM combination were elucidated via crystal violet staining, MTT assay, phenol-sulfuric acid method, congo red staining, staphyloxanthin determination assays, and quantitative real-time polymerase chain reaction (qPCR). The safety of the BA/KM combination was assessed through hemolytic activity analysis, and its anti-MRSA efficacy was evaluated on lettuce. Results: BA/KM combination showed a synergistic antibacterial effect on MRSA USA300. Mechanistic studies revealed that BA may interact with amino acid residues of peptidoglycan synthetase PBP2a to hinder peptidoglycan synthesis, thereby facilitating KM penetration through the cell wall. Subsequently, BA binds to amino acid residues of the membrane transporter NorA, leading to disruption of cell membrane homeostasis and enhancing KM’s ability to induce intracellular ROS accumulation in MRSA. Furthermore, the BA/KM combination reduced MRSA biofilm formation by 77.85% and decreased the metabolic activity of biofilm cells by 42.93% through inhibiting the synthesis of biofilm components EPS and PIA. Additionally, this combination suppressed the synthesis of staphyloxanthin and downregulated the expression of agrA and agrC genes. When 1/8 MIC BA was combined with 1/4 MIC KM, the count of MRSA on lettuce surfaces was reduced by 0.88 log CFU/cm², an effect comparable to that of 0.2% (v/v) hydrogen peroxide. Conclusions: According to these findings, the BA/KM combination may offer a promising option for enhancing antibacterial efficacy through synergism, reducing antibiotic usage concentrations, and limiting MRSA transmission in fresh agricultural products. Full article

The rising demand for convenient, nutritious foods necessitates improved freeze–thaw (F-T) stability in frozen fish balls; however, traditional thermal processing fails to prevent moisture loss, textural degradation, and oxidation. Therefore, this study systematically investigated the effect of ultra-high pressure (UHP) treatment on the quality of golden pomfret fish balls (Trachinotus ovatus) using two-step heating as a control during the F-T cycles. The results showed that compared to two-step heating, UHP significantly reduced the thawing loss (0.68 times) and centrifugal water loss (2.43 times) by enhancing the water-binding capacity (15–20%) and forming denser gel networks. Microstructural analysis revealed that UHP resulted in a more compact internal structure, reduced porosity, altered ice-crystal geometry, and a slower recrystallization rate of the fish balls. Furthermore, UHP effectively reduced protein oxidation (34.53% lower carbonyl increase) and lipid peroxidation (15.6% lower TBARS value) after five F-T cycles compared to the control. Correlation analysis confirmed the dual role of UHP in the regulation of oxidative and structural stability. These findings provide a new technological approach for processing and storing fish balls. Full article

Ice cream is a frozen aerated dessert composed of milk solids, sugars, stabilizers, and fat—with the latter being a key component in defining its structural and sensory properties. This study evaluated the influence of four fat sources—low-trans vegetable fat (T1), butter (T2), UHT cream (T3), and fresh cream (T4)—on the physical and structural characteristics of ice cream, including overrun, melting resistance, texture, color, and rheology, at different stages of processing (before and after maturation). Oscillatory rheological analysis revealed predominantly elastic behavior (G′ > G″) after maturation in all samples, indicating a stable viscoelastic solid structure. Formulations containing T3 and T1 showed the highest overrun values, indicating greater air incorporation, whereas the butter-based formulation (T2) showed the lowest overrun values. Melting resistance followed the following order: T3 > T4 > T2 > T1; therein, the UHT cream formulation exhibited the greatest thermal stability, which was likely due to protein denaturation and aggregation induced by high-temperature processing. Texture analysis showed that the T1 formulation required the lowest maximum extrusion force, while T2 required the highest, reflecting an inverse correlation with overrun values. T1 also displayed the most distinct rheological profile, which was likely due to its specific crystallization behavior and reduced destabilization of the fat globule membrane—which favored the development of a more structured internal network. These findings demonstrate that both the source and processing of fat have a significant impact on the formation of the structural matrix and the final functional properties of ice cream. The results offer technical insights for the development of formulations tailored to specific physical characteristics, optimizing texture, stability, and performance throughout the production process. Full article

Proteins and peptides are vital biomolecules, and deuterated amino acids are increasingly applied in areas such as drug discovery, metabolic tracing, and neutron scattering studies. In this study, we performed deuteration on all 20 proteinogenic amino acids, including their side chains, and established efficient methods for 13 amino acids. Using a Pt/C-catalyzed hydrogen–deuterium exchange reaction, the reaction parameters were optimized to achieve the selective and stable incorporation of deuterium. In addition, the resulting deuterated compounds, focusing on tryptophan, were characterized in order to assess their physicochemical properties. Because the deuteration reaction caused significant racemization of amino acids, deuterated D/L-tryptophan was isolated using a chiral separation method. Deuterated tryptophan characterization studies confirmed that the photostability was markedly enhanced by deuteration, whereas the acid stability showed no clear isotopic effect. The X-ray crystal structure analyses revealed minimal changes upon the hydrogen-to-deuterium substitution. These results provide a robust platform for the supply of deuterated amino acids, facilitating their application in drug development, structural analysis, and creation of advanced functional biomaterials. Full article

We have evaluated the quality of all 325 deposits in the PDB (as of December 2024) that correspond to (or contain) the catalytic domain of cAMP-dependent protein kinases (PKA). Detailed analysis was possible for 289 deposits of crystal structures that included not only the atomic coordinates but also structure factors. These structures represent 35 years of studies, and it is not surprising that the more recent structures are generally of better quality than the older ones. We did not encounter deposits with very severe problems, although some minor problems were found. To assess whether a uniform method of structure re-refinement, as implemented in the pipeline and website PDB-REDO, leads to significant improvement of structural models, we compared structure quality indicators for the originally refined structures and their counterparts resulting from PDB-REDO refinement. The re-refinement procedure significantly improved only some older structures, while its success was generally limited. We paid particular attention to the quality of small-molecule ligands, finding that most of them fit the electron density very well. This type of analysis helps identify the highest quality structures among many deposits for certain protein families and, thus, could be extended to other groups of proteins as well. Full article

Background: The mechanisms underlying fibrinolysis failure in patients with STEMI who are undergoing a pharmacoinvasive strategy appear to be multifactorial and may be associated with the thrombus’s architecture and composition. Objective: We aimed to compare the thrombus composition in patients with STEMI who were undergoing rescue percutaneous coronary intervention (rPCI) versus primary PCI (pPCI) using optical microscopy (OM) and scanning electron microscopy (SEM). Methods: Fifty-three patients were prospectively enrolled, with twenty-five undergoing rPCI and twenty-eight undergoing pPCI. After thrombus aspiration, each harvested fragment was divided into two pieces: one was analyzed using OM with a 60× magnifying lens on hematoxylin–eosin-stained samples, and the other with SEM at 5000× magnification. Results: Patients who underwent rPCI had significantly higher C-reactive protein levels and a longer ischemic interval at admission compared to those treated with pPCI (9.92 h [range: 1.58–106.17] vs. 2.14 h [range: 0–48]; p < 0.001). Optical microscopy analysis revealed that thrombi from rPCI patients exhibited a significantly higher erythrocyte area percentage (18.36% [range: 0.3–50.08] vs. 0.91% [range: 0–70.1]; p = 0.001), a lower fibrin content as assessed by optical microscopy (79.49% [range: 49.2–98.25] vs. 94.43% [range: 29.19–99.92]; p = 0.006), and a greater amount of cholesterol crystals as measured by SEM (1.73 μm² [range: 0–18.51] vs. 0.08 μm² [range: 0–0.71]; p < 0.001). Conclusions: The thrombus composition of patients with STEMI who are undergoing rPCI had higher amounts of erythrocytes and cholesterol crystals and a lesser area occupied by fibrin compared to those undergoing pPCI. The composition of thrombi in rPCI could potentially contribute to the failure of fibrinolytic therapy within a pharmacoinvasive strategy. Full article

Natural product-derived drugs represent a cornerstone of modern pharmacotherapy, with many serving as essential therapeutic agents across diverse medical conditions. Recent advances in structural biology have provided unprecedented insights into the molecular mechanisms underlying their biological activities. This review presents a comprehensive structural analysis of five representative natural product-derived drugs: digoxin, simvastatin, morphine, paclitaxel, and penicillin. Through an examination of high-resolution crystal structures and cryo-electron microscopy (cryo-EM) data, we elucidate how these compounds interact with their respective protein targets and modulate biological functions. The structural data reveal diverse binding mechanisms—ranging from competitive inhibition and covalent modification to allosteric modulation via conformational selection and induced fit—demonstrating how natural products achieve their therapeutic effects through precise molecular recognition. These structural insights provide a molecular foundation for understanding natural product pharmacology and offer valuable guidance for structure-based drug design approaches in developing next-generation therapeutics. Full article

Candida albicans (C. albicans) biofilms exhibit enhanced resistance to conventional antifungal agents; however, the underlying pathogenic mechanisms warrant deeper exploration. Protein phosphatase 2A (PP2A), especially its catalytic activity, is crucial for maintaining physiological balance. This study focused on the role of the PP2A catalytic subunit coding gene PPH21 in biofilm formation and drug resistance of C. albicans. The mutant strain (pph21Δ/Δ) was generated and identified. The oxidative stress was detected by the reactive oxygen species (ROS) and mitochondrial membrane potential (MMP). The autophagic activity was evaluated, and the autophagosomes were observed by transmission electron microscopy (TEM). The biofilm formation was measured by XTT reduction assay, crystal violet (CV) staining, and scanning electron microscopy (SEM). The susceptibility to antifungal agents was examined by XTT reduction assay and spot assay. Additionally, the antioxidant N-acetylcysteine (NAC) was applied to clarify the regulatory effect of C. albicans autophagy on oxidative stress. The pathogenicity of PPH21 in oral C. albicans infection was evaluated through in vivo experiments. We found that PPH21 deletion led to increased oxidative stress and autophagic activities, but it can be reversed by the application of NAC. Moreover, PPH21 deletion also impaired the biofilm formation ability and reduced resistance to antifungal agents. Our findings revealed that PPH21 is involved in both virulence and stress adaptation of C. albicans. Full article

Hydrogen sulfide (H₂S) exerts regulatory functions in kidney diseases. However, its protective role against kidney stone formation remains unclear. Here, we demonstrate that hyperoxaluria or oxalate exposure impairs H₂S formation, leading to tubular injury and calcium oxalate (CaOx) crystal deposition in both in vivo and in vitro models. In male rats fed 5% hydroxy-L-proline (HP), time-dependent increases in urinary supersaturation, tubular damage, and renal CaOx deposition were observed compared to controls. These changes were associated with the decreased expression of H₂S-producing enzymes and elevated urinary secretion of osteopontin (OPN) and Tamm–Horsfall protein (THP). Notably, the protein level and activity of specificity protein 1 (Sp1), a transcription factor regulating these enzymes, were markedly decreased in HP-treated kidneys. Chronic supplementation with the H₂S donor GYY4137 (GYY) significantly attenuated HP-induced tubular injury and CaOx deposition by reducing OPN and THP secretion. Consistent with in vivo results, H₂S donors mitigated oxalate-induced tubular cell damage and CaOx formation in MDCK cells. Mechanistically, oxalate activated cyclic AMP/protein kinase A (PKA) signaling, which promoted OPN and THP secretion; these effects were eradicated by the PKA inhibitor H89 or GYY. These findings indicate that hyperoxaluria impairs Sp1 transcriptional activity, resulting in H₂S deficiency and compromised anticrystallization defense in oxalate-induced tubulopathy. Full article

Cold denaturation of gluten proteins during prolonged frozen storage or repeated freeze–thaw cycles can severely affect the quality of frozen cereal products. While both processes have been studied individually, their combined effects and underlying mechanisms remain unclear. This study systematically evaluated the hydration properties and conformational changes in gluten proteins stored at −73 °C and −23 °C, with or without freeze–thaw cycling. Compared to continuous storage, freeze–thaw cycles reduced water-holding capacity by 9.1–12.2% and increased oil-holding capacity by 5.3–10.3%, indicating aggravated structural damage. Ultra-low temperature storage (−73 °C) suppressed ice crystal growth, preserved hydration, and limited hydrophobic residue exposure. Spectroscopic analyses revealed a temperature-dependent shift from α-helices to β-sheets and β-turns, which was accelerated by freeze–thaw cycles. Enhanced hydrophobic interactions and tryptophan exposure further indicated destabilization. Molecular dynamics simulations showed that increased hydrogen bonding between proteins and water contributed to unfolding at low temperatures, while temperature fluctuations intensified denaturation through repeated hydrogen bond breakage and reformation. These results underscore the critical role of thermal instability in cold denaturation and offer mechanistic insights for improving cryoprotection strategies in frozen food systems. Full article

Heparanase is the only human enzyme responsible for heparan sulfate (HS) breakdown, an activity that remodels the extracellular matrix (ECM) and strongly drives cancer metastasis and angiogenesis. Compelling evidence implies that heparanase promotes essentially all aspects of the tumorigenic process, namely, tumor initiation, vascularization, growth, metastasis, and chemoresistance. A key mechanism by which heparanase accelerates cancer progression is by enabling the release and bioavailability of HS-bound growth factors, chemokines, and cytokines, residing in the tumor microenvironment and supporting tumor growth and metastasis. The currently available heparanase inhibitors are mostly HS/heparin-like compounds that lack specificity and exert multiple off-target side effects. To date, only four such compounds have progressed to clinical trials, and none have been approved for clinical use. We have generated and characterized an anti-heparanase monoclonal antibody (A54 mAb) that specifically inhibits heparanase enzymatic activity (ECM degradation assay) and cellular uptake. Importantly, A54 mAb attenuates xenograft tumor growth and metastasis (myeloma, glioma, pancreatic, and breast carcinomas) primarily when administered (syngeneic or immunocompromised mice) in combination with conventional anti-cancer drugs. Co-crystallization of the A54 Fab fragment and the heparanase enzyme revealed that the interaction between the two proteins takes place adjacent to the enzyme HS/heparin binding domain II (HBDII; Pro271-Ala276), likely hindering heparanase from interacting with HS substrates via steric occlusion of the active site cleft. Collectively, we have generated and characterized a novel mAb that specifically neutralizes heparanase enzymatic activity and attenuates its pro-tumorigenic effects in preclinical models, paving the way for its clinical examination against cancer, inflammation, and other diseases. Full article

Background and Objective: Information about the type of kidney stones is important for informed therapeutic decisions and the prevention of urolithiasis. Urinary stones are heterogeneous, and their elemental composition and crystal structure vary between patients. The formation of urinary stone deposits depends, among other things, on physiological conditions, the concentration of promoters and inhibitors of crystallization, and proteins found in the urine. The aim of this study was to determine differences in urine osteopontin (OPN) levels between groups of different stone-formers. Methods: Urinary stone specimens (n = 44) were acquired during elective endoscopic procedures. Specimens were divided into subgroups by k-means cluster analysis depending on calcium and phosphorus concentrations. The concentration of urine OPN was determined and compared for each subgroup and the control group. Results: Cluster analysis divided the deposits into three clusters. Cluster 1 contained mainly calcium oxalate deposits; Cluster 2 contained uric acid deposits; Cluster 3 contained deposits with a high content of calcium phosphate. Urine OPN concentration in CaP stone-formers (5.77 ng/mL) differed significantly from those of controls (17.05 ng/mL, p = 0.013) and CaOx stone-formers (15.31 ng/mL, p = 0.048). Conclusions: The concentration of urine OPN varies depending on the elemental composition of renal calculi. The lowest concentration of OPN was determined in the group of patients with a high content of calcium phosphate in the deposits. Full article