Search Results (681)

Diabetes mellitus poses a global health challenge, necessitating natural adjuvants with minimal side effects. The aims of this study were to optimize the concentrations of chromium (Cr), zinc (Zn), and germanium (Ge) in the liquid fermentation media of Pleurotus citrinopileatus and Hericium erinaceus and to evaluate the hypoglycemic efficacy of buccal tablets in diabetic mice. The results showed that the optimal ion concentrations in the liquid fermentation medium were Cr 200 mg/L, Zn 200 mg/L, and Ge 50 mg/L for P. citrinopileatus, and Cr 200 mg/L, Zn 100 mg/L, and Ge 100 mg/L for H. erinaceus. After 3 weeks of administration of high-dose (6 g/kg) P. citrinopileatus and H. erinaceus buccal tablets, a 29.1% reduction in the blood glucose levels of diabetic mice was observed compared with pre-administration. High-dose tablets decreased the levels of total cholesterol, triglyceride, and low-density lipoprotein cholesterol while increasing high-density lipoprotein cholesterol. Compared with negative control, high-dose tablets increased catalase and superoxide dismutase activities by 31.2% and 34.1%, respectively. Moreover, the buccal tablets modulated the diversity and structure of the gut microbiota in mice. Relative abundance of beneficial genera (Lactobacillus, Akkermansia, Bifidobacterium, and Ruminococcus) in the high-dose group were increased, while diabetogenic taxa (Prevotella, Desulfovibrio, and Enterococcus) were inhibited. It is concluded that buccal tablets combining P. citrinopileatus and H. erinaceus treated with Cr, Zn, and Ge significantly ameliorated hyperglycemia, dyslipidemia, and oxidative stress, and reshaped the gut microbiota in diabetic mice, demonstrating the potential of edible mushrooms and trace elements as a natural antidiabetic therapy. Full article

Crystallography plays a crucial role in understanding the functions of macromolecules by determining their three-dimensional structures at the atomic level. This review outlines the history of crystallization, explains the principles of crystallization, and provides a comprehensive retrospective on the role of crystallography in enzymology, with a particular focus on the seven Enzyme Commission (EC) classes. For each class, we highlight representative enzymes and the specific mechanistic insights enabled by crystal structures, oxidoreductases (the “yellow enzyme” lineage), transferases (phosphotransferase systems), hydrolases (RNase III and chymotrypsin), lyases (fumarase), isomerases (pseudouridine synthases), ligases (E3 ubiquitin ligases), and translocases (ATP synthase), emphasizing cofactor usage, conformational change, regulation, and implications for disease and drug discovery. We also compile EC-wide statistics from the Protein Data Bank (PDB) to quantify structural coverage. The limitations and challenges of current crystallization techniques are addressed, along with alternative experimental methods for structural elucidation. In addition, emerging computational tools and biomolecular design are also discussed. By reviewing the trajectory of enzymology and crystallography, we demonstrated their profound impact on biochemistry and therapeutic discovery. Full article

Fucoidan is of considerable interest for the development of drug carriers. The inclusion of fucoidan allows calcium carbonate microparticles in the form of vaterite to acquire new properties, enabling their use in the immobilization of protein preparations. In this work, we investigated the properties of hybrid vaterite microparticles with fucoidan from Fucus vesiculosus obtained by co-precipitation and loaded with recombinant human lactoferrin from goats. The hybrid microparticles had a smaller diameter (3–4 µm), larger surface area (35–36 m²g⁻¹), smaller pore size (5–10 nm average), and more negative ζ-potential (−(11–13) mV) than the control vaterite microparticles. The incorporation of lactoferrin into the microparticles by co-precipitation in complex with fucoidan was greater than when the protein was adsorbed onto the hybrid microparticles. Microparticles with fucoidan and lactoferrin were stable in acidic environments, released both components over a prolonged period at pH 7.4, and possessed mucoadhesive properties and anticoagulant activity. The antibacterial properties of hybrid microparticles with fucoidan and lactoferrin against Bacillus subtilis were characterized. Microparticles of vaterite with fucoidan can serve as a platform for the microfabrication of effective means of delivering therapeutic proteins. Full article

Akkermansia muciniphila (AKK) is a mucin-degrading gut symbiont with emerging probiotic potential. Among its carbohydrate-active enzymes, Amuc_0517, a glycoside hydrolase family 36 (GH36) protein, has been identified as a highly specific α-galactosidase. In this study, the Amuc_0517 gene was cloned into pET-28a(+), expressed in Escherichia coli BL21, and purified via Ni²⁺-NTA affinity chromatography. Bioinformatic analysis indicated the presence of a signal peptide and α-galactosidase domain. Enzyme assays confirmed its ability to cleave α-1,6-glycosidic bonds in pNPGal, with no detectable activity toward pNPGlu, and molecular dynamics simulations revealed stronger binding affinity and lower free energy with pNPGal, supporting its substrate specificity. Given that α-galactosidases are widely applied in the dairy industry to hydrolyze galactose-containing oligosaccharides in milk and whey, the biochemical features of Amuc_0517 suggest its potential as a novel biocatalyst for functional dairy processing and probiotic-enriched dairy product development. Full article

Polystyrene microplastics (PS-MPs) are microplastic particles produced during plastic manufacturing and environmental degradation, accumulating over time and entering ecosystems through various pathways, ultimately affecting organisms and inducing toxic effects. Current research on the impact of PS-MPs on mammalian oocyte quality, along with potential preventive mechanisms and strategies to mitigate toxicity, remains limited. This study investigates the effects of antioxidant melatonin on oocyte quality in the presence of PS-MPs, focusing on their influence on oocyte meiotic maturation and embryonic developmental potential. PS-MPs at a concentration of 30 μg/mL significantly impaired first polar body extrusion and reduced the success rate of parthenogenetic activation of mature oocytes in vitro. Furthermore, exposure to PS-MPs exacerbated oxidative stress, mitochondrial dysfunction, apoptosis, and autophagy impairment. Additionally, PS-MPs exposure led to a reduction in antioxidant gene expression and an increase in apoptosis-related gene expression in porcine oocytes. Immunofluorescence assays revealed that PS-MPs may induce oxidative stress, mitochondrial damage, and inflammation through the NF-KB/Nrf2/JNK MAPK signaling pathway crosstalk. Further investigation demonstrated that melatonin supplementation alleviated the toxic effects of PS-MPs exposure, offering potential as a therapeutic approach for mitigating PS-MP-induced reproductive toxicity and preserving oocyte quality. Full article

Malate dehydrogenase (MDH) is a key energy metabolic enzyme with distinct coenzyme specificity for either NAD⁺ or NADP⁺ in all domains of life. Here, we characterize a novel MDH from the bloom-forming cyanobacterium Microcystis aeruginosa PCC7806 (MaMDH), which displays dual-coenzyme specificity with comparable efficiency for both NAD⁺ and NADP⁺, albeit with a slight preference for NAD⁺. MaMDH exists as a 72.1 kDa homodimer with a subunit mass of 36.2 kDa in solution. Kinetic measurements yielded K_m values of 33.140 μM for NAD⁺ and 113.200 μM for NADP⁺, with a k_cat ratio (NAD⁺/NADP⁺) of 3.64. The enzyme exhibited optimal activity at pH 8.0 and 40 °C, along with notable thermostability, retaining over 90% activity after incubation at 70 °C for 20 min. Through structure-guided mutagenesis of the predicted coenzyme-binding motif, we shifted MaMDH cofactor preference from NAD⁺ toward NADP⁺, supporting the hypothesis that dual-specificity MDHs may represent evolutionary intermediates in the emergence of NADP⁺-dependent chloroplast MDHs. This study provides new insights into the molecular evolution mechanisms of coenzyme specificity within the MDH family. Full article

Central nervous system (CNS) diseases exhibit high incidence rates, and the blood–brain barrier (BBB) poses a major obstacle to drug delivery. Conventional drug delivery methods not only show limited therapeutic efficacy but also cause significant side effects. Intranasal administration offers a new strategy for CNS therapy by bypassing the BBB through the unique nasal-brain pathway, while nanodrug delivery systems (NDDSs) can improve drug delivery efficiency. On this basis, biomimetic drug delivery systems (BDDSs) based on cell membrane structure have been developed. The combination of nanoparticles modified by cell membranes or cell membrane-derived vesicles with carriers such as hydrogels creates a drug delivery system that utilizes a unique transnasal-to-brain pathway, opening new avenues for treating CNS disorders. This paper systematically reviews the classification, characteristics, and preparation strategies of BDDSs, while analyzing the anatomical pathways and physiological mechanisms of nasal–cerebral delivery. Furthermore, it delves into the biogenesis mechanisms of extracellular vesicles (EVs) and bacterial extracellular vesicles (BEVs). For CNS disorders, including glioblastoma multiforme (GBM), ischemic stroke (IS), Alzheimer’s disease (AD), and Parkinson’s disease (PD), this paper presents diverse applications and challenges of BDDSs in nasal–cerebral delivery. Full article

Exposure of the plant cell wall to biotic and abiotic stresses results in structural and chemical changes. Russian wheat aphid (RWA) infestation severely damages wheat plants, releasing cell wall-degrading enzymes that compromise cell wall integrity. This study aims to elucidate the cell wall modifications in resistant wheat cultivars during RWA infestation. Three wheat cultivars with distinct resistance phenotypes to the RWA South African biotype 2 (RWASA2) were grown in the glasshouse. At the three-leaf stage, the seedlings were infested with RWASA 2 for 14 days. The leaf samples harvested at 2, 7, and 14 days post-infestation (dpi) were used to study cell wall modifications in the RWASA 2-infested cultivars, focusing on cellulose, hemicellulose, callose, and lignin contents. The results showed that post-RWASA2 infestation, the resistant Tugela-Dn5 significantly increased the hemicellulose content by 2.8- and 1.3-folds at 2 and 14 dpi, respectively, while the Tugela and Tugela-Dn1 significantly decreased the hemicellulose content at 2, 7, and 14 dpi. Tugela-Dn5 also increased the cellulose content by 1.4-fold and 2.2-fold at 7 and 14 dpi, respectively. The acid-soluble lignin content significantly increased in the infested Tugela-Dn5 compared to uninfested at 2 and 14 dpi, while it significantly decreased in Tugela and Tugela-Dn1. Callose levels also increased in all cultivars at 2 dpi, but only the infested Tugela-Dn5 exhibited an increase in callose content compared to the uninfested at 14 dpi. The extracted contents of the increased cellulose, hemicellulose, and lignin in Tugela-Dn5 were corroborated by FTIR analysis, which showed broad peaks at 3300 cm⁻¹ representing the OH functional group and inter- and intra-hydrogen bonds within the increased cellulose in Tugela-Dn5. No significant reduction of lignin peaks at 1600 to 1578. 99 cm⁻¹ assigned to the phenolic groups was observed in Tugela-Dn5. These findings place cell wall modifications at the centre of the wheat’s physiological resistance response to aphid infestation, particularly the reinforcement of the cell wall that persists for 14 dpi. Full article

The investigation of the structure–function relationship in hypoxanthine-guanine phosphoribosyltransferases (HGPRT) is a direction that is relevant for the development of drugs and approaches of enzymatic synthesis of modified nucleosides and nucleotides. This research paper is dedicated to the investigation of binding of sulphonate molecules, such as HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) in the active sites of HGPRT and similar proteins. We report the crystal structure of HGPRT from Escherichia coli (EcoHGPRT) in a complex with HEPES. In the obtained X-ray structure, a HEPES molecule binds to the active site in a position that mimics one of the HGPRT substrates, namely phosphoribosylpyrophosphate (PRPP). Enzymological study has shown that HEPES is an inhibitor of EcoHGPRT, along with two structurally similar molecules, namely MES and PIPES. Comparison of the observed EcoHGPRT/HEPES complex to other reported structures in the context of inhibition study results provides an opportunity to explore the variety of binding modes of HEPES and similar molecules and to discuss the structure–function relationship in this enzyme and similar proteins. Full article

Leghemoglobin (LegH), a plant-derived hemoprotein, is engineered for the first time as a standalone biocatalyst for carbene N–H insertion. Through semi-rational design, the K65P mutation in the heme pocket significantly enhances catalytic efficiency. Under mild aqueous conditions (PBS buffer, 25 °C), the K65P variant achieves 92% yield in the model reaction between benzylamine and ethyl α-diazoacetate—surpassing wild-type LegH by >1.6-fold in initial reaction rate. The mutant also exhibits markedly improved thermostability. This work establishes engineered LegH as a high-performance, cofactor-free biocatalyst for C–N bond formation, providing a sustainable platform for synthesizing chiral amine derivatives. The catalytic proficiency and inherent stability of the K65P mutant demonstrate the potential of plant hemoproteins in non-natural carbene transfer reactions without requiring immobilization supports. Full article

Inorganic pyrophosphatase (PPase) is an enzyme that catalyzes the hydrolysis of pyrophosphate (PPi) into two phosphates. Ton1914, a thermophilic inorganic pyrophosphatase derived from Thermococcus onnurineus NA1, has good thermal stability and an extremely high optimum temperature and has been shown to reduce pyrophosphate inhibition. In this study, eight sites were selected based on sequence alignment and software calculations, and multiple single mutants were successfully constructed. After saturation and superposition mutations, six superior mutants were obtained. The enzyme activities of E97Y, D101K and L42F were increased 2.57-, 2.47- and 2.15-fold, respectively, while those of L42F/E97Y, L42F/D101K and E97Y/D101K were increased 2.60-, 2.63- and 1.88-fold, respectively, relative to the wild-type enzyme. Compared to Ton1914, all mutants more effectively increased PCR product quantity, reduced the number of qPCR cycles required to reach the threshold, and improved the efficiency of gene amplification. In the UDP-Galactose (UDP-Gal) synthesis reaction, the addition of mutants could further improve yield. When Ton1914 and mutants with the same activity were added, the yield of UDP-Gal was almost identical, effectively reducing the dosage of pyrophosphatase. Overall, the mutants showed greater prospects for industrial application. Full article

RNA polymerases are essential enzymes that catalyze DNA transcription into RNA, vital for protein synthesis, gene expression regulation, and cellular responses. Non-template-dependent RNA polymerases, which synthesize RNA without a template, are valuable in biological research due to their flexibility in producing RNA without predefined sequences. However, their substrate polymerization mechanisms are not well understood. This study examines Poly (A) polymerase (PAP), a nucleotide transferase superfamily member, to explore its substrate selectivity using computational methods. Previous research shows PAP’s polymerization efficiency for nucleoside triphosphates (NTPs) ranks ATP > GTP > CTP > UTP, though the reasons remain unclear. Using 500 ns Gaussian accelerated molecular dynamics simulations, stability analysis, secondary structure analysis, MM-PBSA calculations, and Markov state modeling, we investigate PAP’s differential polymerization efficiencies. Results show that ATP binding enhances PAP’s structural flexibility and increases solvent-accessible surface area, likely strengthening protein–substrate or protein–solvent interactions and affinity. In contrast, polymerization of other NTPs leads to a more open conformation of PAP’s two domains, facilitating substrate dissociation from the active site. Additionally, ATP binding induces a conformational shift in residues 225–230 of the active site from a loop to an α-helix, enhancing regional rigidity and protein stability. Both ATP and GTP form additional π–π stacking interactions with PAP, further stabilizing the protein structure. This theoretical study of PAP polymerase’s substrate selectivity mechanisms aims to clarify the molecular basis of substrate recognition and selectivity in its catalytic reactions. These findings offer valuable insights for the targeted engineering and optimization of polymerases and provide robust theoretical support for developing novel polymerases for applications in drug discovery and related fields. Full article

Oxidative stress, caused by excessive free radicals, leads to cellular damage and various diseases. Antioxidant peptides from natural proteins offer potential in alleviating this stress. In this study, antioxidant peptides were identified from deer antler proteins using in silico enzymatic hydrolysis and machine learning. Peptides with high prediction scores and non-toxic profiles were selected for evaluation. The antioxidant activities of top candidates, PHPAPTL and VPHGL, were confirmed by radical scavenging assays and their protective effects in HepG2 cells. Molecular dynamics simulations revealed stable binding of these peptides to Keap1, enhancing system stability and reducing residue fluctuations at the ligand-binding interface. Key interactions involved Arg415, Arg483, Arg380, and Ser555. Secondary structure analysis showed peptide binding induced local conformational transitions, notably increasing parallel β-sheet formation near active sites. These findings provide mechanistic insight into their antioxidant effects and support their potential application in functional food development. Full article

Cid1 protein is a crucial component in the RNA interference pathway and abnormal nuclear RNA turnover processes, primarily responsible for adding uridine to the 3′ end of RNA. Cid1 exhibits selective polymerization of UTP over other nucleoside triphosphates. To explore the mechanism of this selectivity, five systems: free-Cid1, Cid1-ATP, Cid1-UTP, Cid1-CTP, and Cid1-GTP with 500 ns Gaussian accelerated molecular dynamics (GaMD) simulations were performed to investigate conformational changes and binding affinities between substrates and Cid1. The results showed that UTP formed stronger and more numerous non-covalent interactions with Cid1 compared to the other three substrates. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energy analysis revealed a substrate preference for Cid1 polymerase in the order of UTP, followed by ATP, CTP, and GTP. These findings provide theoretical insights into the substrate selectivity mechanism of Cid1 and provide theoretical clues for the design and modification of Cid1 polymerase. Full article

Although mulberry leaf (Morus alba L., ML) and Siraitia grosvenorii (SG) individually demonstrate anti-diabetic properties, their combined efficacy against type 2 diabetes mellitus (T2DM) remains unexplored. This study systematically explored the multi-target mechanisms and synergistic potential of the MLSG combination (MLSG) for T2DM intervention. We evaluated the in vitro inhibitory activities of MLSG, ML, and SG on α-amylase and α-glucosidase, alongside antioxidant capacity assessments through DPPH/ABTS radical scavenging, reducing power, and FRAP assays. Bioactive metabolites were identified using non-targeted metabolomics, while core targets and pathways were predicted using network pharmacology and validated through molecular docking. The results reveal MLSG’s significantly enhanced inhibition of α-amylase (IC₅₀ = 14.06 mg/mL) and α-glucosidase (IC₅₀ = 0.02 mg/mL) compared to individual extracts, exhibiting 1.3–15.5-fold higher potency with synergistic effects (combination index < 1). MLSG also showed improved antioxidant capacity, outperforming SG in DPPH/ABTS⁺ scavenging and reducing power (p < 0.05), and surpassing ML in ABTS⁺ scavenging, reducing power, and FRAP values (p < 0.05). Metabolomics identified 26 MLSG-derived metabolites with anti-T2DM potential, and network analysis pinpointed 26 active components primarily targeting STAT3, AKT1, PIK3CA, EGFR, and MAPK1 to regulate T2DM pathways. Molecular docking confirmed strong binding affinities between these components and core targets. Collectively, MLSG exerts potent synergistic anti-T2DM effects through dual-enzyme inhibition, elevated antioxidant activity, and multi-target pathway regulation, providing a solid foundation for developing MLSG as functional food ingredients. Full article