Search Results (196)

While there is a consensus that the cytochrome b₆f complex (cytb₆f) in algae and plants is involved in the regulatory mechanism of oxygenic photosynthesis known as light-induced state transitions (STs), no such consensus exists for cyanobacteria. Here, we provide the first direct functional evidence for cytb₆f using single-point mutation data. We introduced a PetD-Phe124Ala substitution in the cyanobacterium Synechocystis sp. PCC 6803 to test the key predictions of the hydrophobic-mismatch (HMM) model for cytb₆f-driven STs in all oxygenic photosynthetic species. These predictions concern the role of the Phe/Tyr124^fg-loop-PetD and the extent and kinetic characteristics of STs. The effects of PetD-F124A mutation on STs were monitored using 77K and Pulse-Amplitude-Modulated (PAM) fluorescence. For comparison, we employed a phycobilisome (PBS)-less Synechocystis mutant and wild-type (WT) strain, as well as the stn7 mutant and WT of Arabidopsis plant. The PetD-F124A mutation reduced the extent of STs and selectively affected the two-exponential kinetics components of the transitions. Under State 1 conditions, the mutant exhibited ~60% less energetic decoupling of PBS from photosystem I (PSI) compared to the WT. It is explainable by the HMM model with the inability of the PetD-F124A mutant, during the induction phase of the State 2→State 1 transition to adopt the cytb₆f conformation with minimal hydrophobic thickness. PAM-derived parameters indicated that PSII electron transport function is not inhibited, and no detectable effect on cyclic electron transport around PSI was observed under low-light conditions. Circular dichroism and differential scanning calorimetry confirmed that both the PSI trimer/monomer ratio and the structural integrity of the PBSs are preserved in the mutant. The compensatory response to the mutation includes decreased PSI content and an increase in PBS rod size. In conclusion, (1) cytb₆f is involved in cyanobacterial STs; (2) evidence is provided supporting the HMM model; (3) the electron transfer and signal transduction functions of cytb₆f are separated into distinct domains; and (4) the signaling pathway regulating STs and pigment-protein composition in Synechocystis involves PetD-Phe124. Full article

Background/Objectives: Thyroid hormones (THs) regulate almost all physiological processes in vertebrates via specific mechanisms exercised spatiotemporally throughout the lifespan. The TH signalling can be impaired by thyroid-disrupting chemicals (TDCs) capable of disrupting the hypothalamic–pituitary–thyroid (HPT) axis. Octyl methoxycinnamate (OMC) (also designated octinoxate), one of the most widely used ultraviolet (UV) filters, has emerged as an environmental contaminant and has raised significant concerns recently due to its disruptive effects as TDC on humans and animals. Although the disruption of TH homeostasis has been reported, its exact modes of action (MoA) remain largely unknown. Our study aimed to provide a comparative information on the molecular interactions of OMC on TH signalling in humans and zebrafish. Methods: In silico approaches were performed comparing OMC with endogenous thyroid hormone T3 and the anti-thyroid drug propylthiouracil (PTU). Results: Our findings suggested a key role of OMC on the corticotrophin-releasing hormone receptor (crhr2), thyrotropin receptor (TSHR/tshr), and thyroid nuclear receptors (TR/tr-α and -β). At the hypothalamic level, a favourable binding of OMC to zebrafish crhr2 was found, involving ALA86, CYS44, HIS89, ILE63, ILE64, LEU92, PRO87, PRO88, SER48, and THR47. At the pituitary level, OMC was bound to human TSHR by the amino acid residues ASN590, GLU506, ILE583, ILE640, LEU570, MET572, PRO571, SER505, TYR667, VAL502, VAL586, ALA644, LEU587, MET637, SER641, and TYR582 and to zebrafish tsrh by ASN589, ILE639, MET636, ILE582, LEU569, LEU586, VAL501, and VAL585. Concerning nuclear receptors, OMC showed a more favourable binding energy of T3, involving the shared residues PHE218 and MET259 with T3 in both species. For human TRβ, OMC shared T3 with residues ILE 275, ILE276, LEU346, PHE269, PHE272, THR273, ALA279, ASN331, HIS435, LEU330, MET310, MET313, and PHE455. No similar residues were obtained for zebrafish trβ compared with the humans. Conclusions: Overall, the action of OMC seems to agree with primary hypothyroidism (anti-thyroid action) mimicking the T3 hormone. This investigation demonstrates that OMC acts as a potential TDC and provides new insights into its disruptive action on the HPT axis. Full article

Background/Objectives: Carvacrol, a major active component of oregano oil and common feed additive, has been widely studied for its effects on fish growth, immunity, and intestinal health. But its transcriptional/metabolic impacts on fish liver remain unclear. This study investigated these effects in Pengze crucian carp (Carassius auratus var. Pengze). Methods: Fish were fed a basal diet (control) or basal diet supplemented with 10% microencapsulated carvacrol (600 mg/kg) for 56 days; liver samples were analyzed via transcriptomics and metabolomics. Results: Transcriptomic analysis revealed 482 differentially expressed genes (DEGs) in the liver of Pengze crucian carp following carvacrol supplementation, with 158 upregulated and 324 downregulated genes. Functional annotation highlighted enrichment in translation, signal transduction, amino acid metabolism, and posttranslational modification pathways. GO analysis further identified key processes, including carboxylic acid transport, tRNA aminoacylation, and mitochondrial nucleoid function, while KEGG pathways were implicated in amino acid biosynthesis, lipid metabolism (e.g., alpha-linolenic acid), and insulin signaling. Metabolomic profiling identified 679 significantly altered metabolites, including 113 upregulated and 566 downregulated ones. Among these, upregulated compounds like L-asparaginyl-L-lysine (Log₂FC = 4.36) and 2′-Deoxyadenosine-5′-diphosphate (Log₂FC = 4.31) are linked to nucleotide metabolism, and downregulated peptides (e.g., Ala-Phe-Tyr-Arg) suggesting modulated protein turnover. Joint omics analysis revealed convergent pathways in glycerophospholipid metabolism, aminoacyl-tRNA biosynthesis, and autophagy. Notably, the chaperone gene dnaja3b was correlated strongly with neuroactive metabolites (e.g., normetanephrine), potentially implicating carvacrol in stress response regulation. Conclusions: Our findings demonstrate that carvacrol modulates liver gene expression and metabolic profiles, primarily influencing amino acid and lipid metabolism pathways, autophagy, and stress responses. The observed correlations between dnaja3b and specific metabolites offer mechanistic insights into the action of carvacrol in fish liver. Full article

The ability of plants to survive oxygen deficiency is associated with significant changes in metabolism. Metabolic profiling of wheat seedlings under anoxia and subsequent reoxygenation conditions was performed using GC-MS. A total of 374 and 298 compounds were detected in root and shoot metabolomes, respectively. All intermediates of central metabolism were identified. Early anoxic responses of root and shoot metabolomes showed similarity, leading to the accumulation of amino acids (Ala, GABA and Tyr), carboxylates (lactate and succinate), nucleotides and amines, together with a decrease in sugars. The metabolic response to long-term anoxia varied significantly in the roots and shoots of wheat seedlings and was related to the redistribution of carbon flux from glycolysis predominantly to lipids in the roots, while it was directed to carboxylates and GABA in the shoots. Imposition of 24 h of reaeration after short-term anoxia (6 h) switched the metabolome toward a normoxic profile, predominantly in roots. Anaerobically down-regulated metabolites were accumulated, while anaerobic intermediates were depleted post-anoxia. The effects of more prolonged anoxia on wheat seedling metabolomes were less reversible, particularly in shoots. Interestingly, several metabolites with not fully understood roles (e.g., hydroxyl carboxylates, α,ω-dicarboxylic acids, polyols) were detected under anoxic conditions in wheat seedlings, which could potentially serve as markers of plant sensitivity to oxygen deficiency. Full article

Flavor is a pivotal indicator influencing the meat quality and palatability of premium broiler chickens, shaped by multiple factors. The flavor differences among broiler chicken breeds/lines stem from the specificity of their metabolite profiles and volatile flavor compounds. This study aims to identify key metabolites and pathways that regulate flavor variations in high-quality broilers, providing data support and theoretical references for breeding superior broiler lines and developing technologies to enhance flavor quality. Breast Muscle tissue from 15-week-old roosters of the S3 and H lines (n = 6) was used as experimental material. Broad-targeted metabolomics and volatile metabolomics technologies were employed to identify key metabolites and volatile organic compounds (VOCs) influencing the flavor of breast meat in these two high-quality broiler lines. Broad-target metabolomics identified 167 differentially expressed metabolites (VIP > 1, p < 0.05) between the two strains, including 141 upregulated and 26 downregulated metabolites. These metabolites were primarily amino acids and their derivatives, and were significantly enriched in metabolic pathways such as ABC transporters (p < 0.05). Leu-Tyr, Ile-Tyr, Val-Leu, Val-Ile, and Tyr-Ala were identified as key metabolites influencing the flavor formation of breast meat from both high-quality broiler lines. Volatile metabolomics results identified 33 downregulated VOCs (VIP > 1 and p < 0.05). The flavor differences between the two strains primarily involved fatty and grassy flavor. Key flavor markers included 2-Nonanone, 2-Nonanone, 3-hydroxymethyl, 2-Methylheptanoic acid, and Hexanoic acid, butyl ester as the primary flavor markers. These significantly downregulated volatiles are formed through lipid oxidation and amino acid degradation pathways, respectively, collectively shaping the more pronounced fatty and grassy aromas in the S3 strain. Correlation analysis revealed a significant negative correlation between Met-Asn and Hexanoic acid, butyl ester, suggesting it may represent a key regulatory pathway influencing green flavor formation. In summary, this study elucidates key metabolites and pathways governing flavor differences in high-quality broiler rooster breast meat, providing a scientific foundation for poultry breeding, optimization of farming practices, and flavor regulation in meat products. Full article

Among many metal ions in biological systems, iron plays a fundamental role. Transferrins are iron-binding glycoproteins responsible for transporting Fe³⁺ in vertebrate blood. Neisseria meningitidis, a Gram-negative pathogen causing meningitis, relies on iron for survival and acquires it from human transferrin (hTf) using two surface proteins, TbpA and TbpB. These proteins interact with hTf to form a ternary TbpA–TbpB–hTf complex, enabling iron capture from the host. The absence of an experimental crystal structure for this complex has hindered computational studies, a detailed understanding of Fe³⁺ dissociation, and designing efficient therapeutics. This study presents the first computational model of the ternary complex, its validation, and molecular dynamics simulations. Structural analyses revealed key electrostatic interactions regulating Fe³⁺ coordination and essential contact regions between proteins. The role of Lys359 from TbpA was investigated via QM/MM calculations by evaluating Fe³⁺ binding energies of isolated hTf, the ternary complex, and Lys359Ala, Lys359Arg, Lys359Asp mutant models. Results revealed that the proton transfer from Lys359 leads to disruption of Tyr517–Fe³⁺ coordination, facilitating iron transfer to the bacterial system. Natural bond orbital analysis confirmed this mechanism. The findings provide new molecular insight into N. meningitidis iron acquisition and identify Lys359 as a potential target for covalent inhibitor design, guiding the development of novel therapeutics against meningococcal infection. Full article

A thiazole–thiophene derivative, (E)-4-(2-(2-(1-(5-chlorothiophen-2-yl)ethylidene)hydrazinyl)thiazol-4-yl)benzonitrile (CTHTBN), was synthesized via a one-pot multicomponent reaction involving 5-chloro-2-acetylthiophene, thiosemicarbazide, and 4-(2-bromoacetyl)benzonitrile. The synthesized compound was characterized by FT-IR, ¹H NMR, and ¹³C NMR spectroscopy, confirming the formation of the title compound. Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d,p) level were performed to explore the electronic structure and reactivity of CTHTBN. The HOMO and LUMO energies were found to be −5.75 eV and −2.03 eV, respectively, with an energy gap (E_g) of 3.72 eV, suggesting a balanced chemical stability and reactivity. The dipole moment of 7.9381 Debye indicated substantial polarity, favorable for biological interactions. Global reactivity descriptors, including chemical hardness (η = 1.86 eV), chemical softness (σ = 0.5376 eV⁻¹), electronegativity (χ = 3.89 eV), electrophilicity index (ω = 4.07 eV), and maximum charge transfer capacity (ΔN_max = 2.09), further supported the molecule’s electronic competence. Molecular docking against M. tuberculosis CYP51 revealed a strong binding affinity (−8.8 kcal/mol), stabilized by π–sulfur contacts with MET79 and PHE83, π–π stacking with TYR76, and π–π T-shaped interactions with PHE83 and the heme cofactor. Additional π–alkyl interactions with LEU321, ALA325, and the heme group reinforced hydrophobic complementarity, confirming efficient accommodation of CTHTBN in the active site. These findings suggest that CTHTBN holds promising potential as an antimycobacterial agent targeting CYP51 and may be explored in future biological studies. Full article

Background: Levofloxacin is a broad-spectrum third-generation fluoroquinolone with bactericidal activity against Streptococcus species. We aimed to investigate the susceptibility rates of levofloxacin, the genetic determinants contributing to resistance, the serotype distribution, and the population structure of levofloxacin-resistant Streptococcus agalactiae (GBS) isolates. Methods: Antibiotic susceptibility testing was conducted according to the EUCAST criteria. PCR-serotyping, determination of mutations in the quinolone resistance-determining regions (QRDRs), and multi-locus sequence typing (MLST) were performed on all levofloxacin-resistant strains. Results: Among the 328 GBS isolates, 11.9% exhibited resistance to levofloxacin. We categorized the samples into two main groups: vaginal (64.1%) and extra-vaginal. The latter was further subdivided into invasive (10.3%) and non-invasive (25.6%) ones. The most common serotypes identified were V (30.8%) and III (25.6%). All examined resistant strains possessed missense mutations in the QRDR of parC (Ser79Phe/Tyr and Asp83Asn), whereas 59.0% of them exhibited additional mutation in gyrA (Ser81Leu and Glu85Lys/Ala). The MLST results disclosed six clonal complexes: CC19(64.1%), followed by CC1 (10.3%), CC452 (7.7%), and CC459 (5.1%), and CC12 and CC23, represented by single strains. Conclusions: We observed a growing resistance to fluoroquinolones that appears to exceed the average in Europe. More than half of the isolates exhibited the accumulation of mutations within the QRDRs. Rigorous monitoring is needed to prevent the emergence of MDR GBS and preserve the effectiveness of the newer generations of fluoroquinolones. Full article

This study employed a combined computational and experimental approach to investigate the molecular recognition mechanism of 4-methylphenol by human olfactory receptor hOR9Q2. The strategy integrated molecular docking using BIOVIA Discovery Studio, structural modeling of hOR9Q2 based on the AlphaFold2-predicted, molecular dynamics simulations with GROMACS software employing the AMBER14SB force field, and systematic site-directed mutagenesis validation. Computational simulations revealed that the binding cavity formed by transmembrane domains TM3, TM5, and TM6 serves as the key interaction region, with van der Waals, hydrophobic, and Pi-sulfur interactions driving stable binding (ΔG = −40.173 ± 0.34 kJ/mol). Functional characterization identified six critical residues (Cys112, Val158, Met207, Phe251, Leu255, and Tyr259) as essential for receptor activation, while mutations at Ile71 and Ala108 resulted in partial functional impairment. This study reveals the structural basis for hOR9Q2’s selective response to 4-methylphenol, while establishing a computational–experimental framework for precisely locating functional sites on olfactory receptors. These findings elucidate the molecular mechanism of odorant recognition and provide insights for developing odorant prediction models and designing specific olfactory receptor modulators. Full article

Plasmid DNA (pDNA) purification plays a key role in the development of vaccines and gene therapies. Affinity chromatography stands out as a promising method for plasmid purification, leveraging a range of biological and synthetic ligands to achieve selectivity. This study investigates the potential of a synthetic ligand library consisting of triazine-based bifunctional compounds designed to mimic the side chains of amino acids that are known to bind nucleic acids. A high-throughput screening method was employed to assess the binding ability of 158 ligands within the library to single-stranded, FITC-labeled homo-oligonucleotides (G and T), each comprising 20 nucleotides, under both hydrophilic and hydrophobic conditions. High-affinity ligands were identified for both T and G oligonucleotides. Follow-up microscale chromatographic screening uncovered some false positives from the initial FITC-based screening, narrowing the selection to 22 ligands for further investigation. In the next phase of the study, the binding affinity of these ligands towards double-stranded oligonucleotides (AT and CG) was assessed. Ligand 1/2, a mimic of Ala-Lys or Gly-Lys, and ligand 2/3, a mimic of Lys-Tyr, were chosen as initial candidates for evaluating plasmid DNA purification from an Escherichia coli crude extract. The results obtained with 0.4 M ammonium sulfate in 20 mM Tris-HCl (pH 8.0) as the binding buffer were similar to those observed when purifying plasmid DNA from E. coli clarified lysates by hydrophobic interaction chromatography. The affinity resins retained RNA, while the less hydrophobic plasmid DNA was excluded in the initial fractions. Future research will be directed towards exploring the potential of the most promising ligands to separate pDNA isoforms. Full article

In order to innovatively develop high-activity ACE inhibitory peptides from edible fungi, the conditions for a double-enzymatic hydrolysis preparation of ACE inhibitory peptides from Flammulina velutipes were optimized by response surface methodology. After purification by macroporous resin, gel chromatography, and RP-HPLC, a crude peptide fraction was obtained; its ACE inhibition rate was 85.73 ± 0.95% (IC₅₀ = 0.83 ± 0.09 mg/mL). Based on LC-MS/MS sequencing, the four novel peptides, namely, FAGGP, FDGY, FHPGY, and WADP, were screened by computer analysis and molecular docking technology. The four peptides exhibited a binding energy between −9.4 and −10.3 kcal/mol, and formed hydrogen bonds with Tyr523, Ala354, and Glu384 in the S1 pocket, Tyr520 and His353 in the S2 pocket, and His383 in the HEXXH zinc-coordinating motif of ACE, indicating their good affinity with the ACE active site. The IC₅₀ values of the four ACE inhibitory peptides were 29.17, 91.55, 14.79, and 41.27 μM, respectively, suggesting that these peptides could potentially contribute to the development of new antihypertensive products. Full article

Gonadotropin-Releasing Hormone (GnRH) is a crucial neuropeptide that regulates reproductive functions in vertebrates. The study identifies and characterizes (GnRH) in the brain of Tenualosa ilisha, an iconic and lucrative Clupeiform fish from River Ganga, India. The current study aimed to analyze the GnRH gene in T. ilisha using an in silico study. The GnRH gene of T. ilisha comprises a full-length nucleotide sequence of 605 base pairs with an open reading frame of 312 base pairs, which encodes 103 deduced amino acids (aa), respectively. It was found that leucine (L) is the most abundant amino acid in the GnRH protein. Additionally, the ligand interactions of the GnRH were analyzed using computational approaches. The structural validation showed an excellent stereochemical quality of the GnRH protein sequence, with over 88% of residues in Ramachandran plot-favored regions. The binding site prediction revealed 6 ligand-binding pockets, with the largest pocket containing 12 amino acids. After ADME screening, 16 drug-like compounds were docked to GnRH protein. Top five ligands N-Ac-(4-Cl-Phe)-Trp-Lys-AlaNH2, LHRH_LYS (6), Seabream_GnRH, Leuprolide, and LHRH_Des-tyr (5) had binding affinities ranging from −7.5 to −5.6 kcal/mol. The stable binding site was confirmed by 100 ns molecular dynamics simulations, with RMSD values below 10 Å and key residues retaining ligand contacts. The GnRH-protein resulted in the development of a suitable peptide sequence of T. ilisha, showing similarity with the similar anadromous American shad (Alosa sapidissima). This will certainly aid in future therapeutic and captive breeding advances, thereby fostering the culture and conservation of the wild species. Full article

Seliciclib, a cyclin-dependent kinase 5 (CDK5) inhibitor, has demonstrated neuroprotective potential. However, its therapeutic application is limited by poor permeability across the blood–brain barrier (BBB). In this study, polymeric nanoparticles (NPs) modified with a BBB-targeting peptide ligand (His-Ala-Ile-Tyr-Pro-Arg-His) were employed to encapsulate seliciclib. In vitro transport studies showed that the peptide-modified NPs exhibited significantly greater translocation across a bEnd.3 cell monolayer compared to unmodified NPs. Furthermore, in vivo biodistribution analysis revealed that the brain accumulation of peptide-modified NPs was 3.38-fold higher than that of unmodified NPs. Notably, the peptide-conjugated, seliciclib-loaded NPs demonstrated a significant neuroprotective effect against the neurotoxin 1-methyl-4-phenylpyridinium (MPP⁺) in differentiated SH-SY5Y cells. Full article

This study presents a detailed Raman spectroscopic investigation of hydrogels composed of sodium hyaluronate and two N-terminally blocked dipeptides: N-acetyl-L-alanine-methyl-amide (NAcAlaNHMA) and N-acetyl-L-tyrosine-methyl-amide (NAcTyrNHMA). Vibrational spectra of the dipeptides in both crystalline and aqueous forms were analyzed and supported by density functional theory (DFT) calculations. Spectral features of the hyaluronan component were elucidated by simulating the vibrational modes of its two principal disaccharide building blocks. Gels were prepared with varying dipeptide-to-hyaluronan ratios, and their structural characteristics were examined using Raman spectroscopy and atomic force microscopy. The results showed that while NAcAlaNHMA exhibited no significant interaction with the HA matrix, NAcTyrNHMA demonstrated specific binding behavior, as evidenced by notable shifts in its N–H and C–O–H vibrational bands. These findings indicate that NAcTyrNHMA binds to hyaluronic acid via hydrogen bonding, likely involving carboxyl and hydroxyl functional groups. This study highlights the potential for selective tuning of HA-based hydrogels using dipeptides, with implications for biomedical applications such as drug delivery, antimicrobial gels and biomaterial design. Full article

Rhodotorula mucilaginosa plays a key role in developing the taste of dry-cured ham, while the mechanism of Rhodotorula mucilaginosa proteases on myofibrillar protein (MP) hydrolysis and the evolution of taste substances has not been studied. The enzymatic characteristics, hydrolysis capacities for MPs, free amino acid contents, metabolite compositions, and taste attributes were investigated during the interactions of MPs and proteases. The proteases of R. mucilaginosa EIODSF019 (RE) and R. mucilaginosa XZY63-3 (RX) showed high hydrolytic activities at the conditions of pH 5.0~7.0 and 30~40 °C. Compared with RX, RE showed a lower Michaelis constant (Km) value and a better affinity for protein substrates. RE showed a higher capability to degrade myosin and actin compared with RX and P. kudriavzevii XS-5 proteases (PK). The microtopography of enzyme-treated MPs in RE presented a smoother surface and lower root mean square roughness than that in RX and PK. The total content of free amino acids significantly increased from 0.34 mg/100 mL of CK to 17.10 mg/100 mL of RE after 4 h of hydrolysis of MPs. Sixty-two metabolites were identified by LC-MS/MS, and γ-glutamyl peptides were the main components of MP hydrolysates. Sensory scores of umami, richness, and aftertaste showed the largest values in RE among these groups. Partial least squares discriminant analysis and correlation network demonstrated that γ-Glu-Lys, γ-Glu-Tyr, γ-Glu-Glu, γ-Glu-His, γ-Glu-Leu, γ-Glu-Cys, γ-Glu-Ala, and γ-Glu-Gln were positively correlated with the improvements of umami, richness, and aftertaste in RE. Full article