Search Results (106)

Pangasius (Pangasianodon hypophthalmus) minced muscle with 1 and 2% salt was treated with different high-pressure processing and thermal methods, including conventional heat-induced gels (HIGs), high-pressure processing (HPP) prior to cooking (PC), HPP prior to setting (PS), and setting prior to HPP (SP), to evaluate for their effects on the selected physicochemical properties. The results showed that the PC treatment produced gels with a significantly higher gel strength (496.72–501.26 N·mm), hardness (9.62–10.14 N), and water-holding capacity (87.79–89.74%) compared to the HIG treatment, which showed a gel strength of 391.24 N·mm, a hardness of 7.36 N, and a water-holding capacity of 77.98%. PC gels also exhibited the typical microstructure of pressure-induced gels, with a denser and homogeneous microstructure compared to the rough and loosely connected structure of HIGs. In contrast, SP treatment exhibited the poorest gel quality in all parameters, with gel strength ranging from 319.79 to 338.34 N·mm, hardness from 5.87 to 6.31 N, and WHC from 71.91 to 73.72%. Meanwhile, the PS treatment showed a comparable gel quality to HIGs. SDS-PAGE analysis revealed protein degradation and aggregation in HPP-treated samples, with a decrease in the intensity of myosin heavy chains and actin bands. Fourier-transform infrared spectroscopy (FTIR) analysis showed minor shifts in protein secondary structures, with the PC treatment showing a significant increase in α-helices (28.09 ± 0.51%) and a decrease in random coil content (6.69 ± 0.92%) compared to α-helices (23.61 ± 0.83) and random coil structures (9.47 ± 1.48) in HIGs (p < 0.05). Only the PC treatment resulted in a significant reduction in total plate count (TPC) (1.51–1.58 log CFU/g) compared to 2.33 ± 0.33 log CFU/g in the HIG treatment. These findings suggest that HPP should be applied prior to thermal treatments (cooking or setting) to achieve an improved gel quality in reduced-salt pangasius products. Full article

Microfluidic modulation spectroscopy-infrared (MMS) offers a label-free, high-sensitivity approach for quantifying changes in protein secondary structures under native solution conditions. MMS subtracts the solvent backgrounds from sample signals by alternately flowing proteins and matched buffers through a microfluidic chamber, yielding clear amide I spectra from microliter volumes. In this study, we validated MMS on canonical globular proteins, bovine serum albumin, mCherry, and lysozyme, demonstrating accurate detection and resolution of α-helix, β-sheet, and mixed-fold structures. Applying MMS to the intrinsically disordered protein Tau, we detected environment-driven shifts in transient conformers: both the acidic (pH 2.5) and alkaline (pH 10) conditions increased the turn/unordered structures and decreased the α-helix content relative to the neutral pH, highlighting the charge-mediated destabilization of the labile motifs. Hyperphosphorylation of Tau yielded a modest decrease in the α-helical fraction and an increase in the turn/unordered structures. Comparison of monomeric and aggregated hyperphosphorylated Tau revealed a dramatic gain in β-sheet and a loss in turn/unordered structures upon amyloid fibril formation, confirming MMS’s ability to distinguish disordered monomers from amyloids. These findings establish MMS as a robust platform for detecting protein secondary structures and monitoring aggregation pathways in both folded and disordered systems. The sensitive detection of structural transitions offers opportunities for probing misfolding mechanisms and advancing our understanding of aggregation-related diseases. Full article

Elephant grass (Cenchrus purpureus) is an important forage crop hindered by high lignin content. Although MYB transcription factors (TFs) regulate lignin biosynthesis, their roles in elephant grass remain unclear. In this study, we identified 247 CpMYB TFs through whole-genome bioinformatic analysis of elephant grass and classified them into 23 phylogenetic subgroups. Among them, 233 were mapped to 14 chromosomes, and 14 to unanchored contigs. Gene structure, conserved motifs, and domain analyses revealed subgroup-specific conservation and CpMYB proteins dominated by random coils and α-helices. Gene duplication and selection pressure analyses indicated that segmental duplication predominantly contributed to family expansion. Transcriptome analysis identified 48 CpMYB genes differentially expressed in internodes at least one of three developmental stages, with promoters containing various growth-, phytohormone-, and stress-related cis-elements. Additionally, nine CpMYB genes were consistently differentially expressed across all three stages, and predicted protein–DNA interaction suggested that four of them (CpMYB094, CpMYB131, CpMYB145, and CpMYB148) potentially regulate key lignin biosynthetic genes, including 4-coumarate:CoA ligase 1 (4CL1), hydroxycinnamoyl transferase (HCT), caffeoyl-CoA O-methyltransferase 1/7 (CCoAOMT1/7), and reduced epidermal fluorescence 3 (REF3). However, their regulatory functions require further experimental validation. Overall, this study characterizes the CpMYB family in elephant grass and highlights their potential roles in lignin biosynthesis. Full article

The aim of this study was to investigate the structural characteristics of four polysaccharides derived from Citri grandis fructus immaturus and their antioxidant and expectorant activities. ECP1 fraction passing through a 500 kDa dialysis bag (ECP1A) and ECP2 fraction retained in a 300 kDa dialysis bag (ECP2B) had molecular weights of 340 and 1217 kDa, respectively. All four polysaccharides were composed of six monosaccharides, including l-rhamnose, d-arabinose, d-xylose, d-mannose, d-glucose, and d-galactose, with molar ratios of 1.99:52.38:6.99:2.64:5.15:31.15 for ECP1A and 1.54:65.13:6.34:2.51:3.58:22.07 for ECP2B. ECP1A had an α/β-glucopyranose ring, and the glycosyl groups were linked mainly by 1→4, 1→2, or 1→6 glycosidic bonds. It likely adopted a single-stranded helical conformation. ECP2B had a β-glucopyranose ring, and the glycosyl groups were linked mainly by 1→4, 1→2, or 1→6 glycosidic bonds. Furthermore, in vitro experiments showed that ECP1A displayed excellent antioxidant activity (IC₅₀ = 0.4614 mg/mL). ECP2B significantly inhibited MUC5AC mucin content expression in the mucus hypersecretion model of BEAS-2B cells, thus exerting an expectorant effect. A significant negative correlation was observed between the molecular weight of Citri grandis fructus immaturus polysaccharides and their antioxidant activity, and the uronic acid and d-arabinose contents of these polysaccharides exhibited strong negative trends with both antioxidant and expectorant activities. This study shows the potential for developing and utilizing polysaccharides from Citri grandis fructus immaturus as an antioxidant and expectorant agent. Full article

Lactic acid bacteria exopolysaccharides (EPS) have a variety of excellent biological functions and are widely used in the food and pharmaceutical industries. The complex metabolic system of lactic acid bacteria and the mechanism of EPS biosynthesis have not been fully analyzed, which limits the wider application of EPS. EPS synthesis is regulated by cyclic diadenosine monophosphate (c-di-AMP), but the exact mechanism remains unclear. Dac and pde are c-di-AMP anabolic genes, gtfA, gtfB and gtfC are EPS synthesis gene clusters, among which gtfC was the key gene for EPS synthesis in Leuconostoc mesenteroides DRP105. In order to explore whether diadenylate cyclase (DAC) can catalyze the synthesis of c-di-AMP from ATP, the sequence of DAC was analyzed by bioinformatics based on the whole genome sequence. DAC was a CdaA type diadenylate cyclase containing the classical domain DisA_N and DGA and RHR motifs. The secondary structure was mainly composed of α-helices, and AlphaFold2 was used to model the 3D structure of the protein and evaluate the rationality of the DAC protein structure model. A total of 8 salt bridges, 21 hydrogen bonds and 221 non-bonded interactions were found between DAC and GtfC. Molecular docking simulations revealed ATP1 and ATP2 fully occupied the binding pocket of DAC and interacted directly with the binding site residues of DAC. The molecular dynamics simulations showed that the binding of DAC to ATP molecules was relatively stable. Gene and enzyme correlation analysis found that dac and gtfC gene expression were significantly positively correlated with DAC enzyme activity, c-di-AMP content and EPS production, and had no significant correlation with PDE enzyme activity responsible for c-di-AMP degradation. Bioinformatics analysis of the regulatory role of DAC in the synthesis of EPS by lactic acid bacteria was helpful to fully reveal the biosynthetic mechanism of EPS and provide theoretical basis for large-scale industrial production of EPS. Full article

α-Synuclein (αS) interacts with lipid membranes in neurons to form amyloid fibrils that contribute to Parkinson’s disease, and its non-amyloid-β component domain is critical in the fibrillation. In this study, the salt (NaCl) effect on the membrane interaction and fibril formation of αS_57–102 peptide (containing the non-amyloid-β component domain) was characterized at the molecular level because the αS_57–102 fibrils exhibited structural polymorphism with two morphologies (thin and thick) in the presence of NaCl but showed one morphology (thin) in the absence of NaCl. The membrane-bound conformation (before fibrillation) of αS_57–102 had two helical regions (first and second) on the membrane regardless of salt, but the length of the first region largely shortened when NaCl was present, exposing its hydrophobic area to the solvent. The exposed region induced two distinct pathways of fibril nucleation, depending on the molar ratios of free and membrane-bound αS_57–102: one from the association of free αS_57–102 with membrane-bound αS_57–102 and the other from the assembly among membrane-bound αS_57–102. The differences mainly affected the β-strand orientation and helical content within the fibril conformations, probably contributing to the thickness degree, leading to structural polymorphism. Full article

The class III peroxidase (POD) gene family encodes redox enzymes involved in the catalytic processes of hydrogen peroxide, phenolic compounds, and reactive oxygen species. These enzymes play crucial roles in lignin biosynthesis and stress responses. To explore the functions of the oat (Avena sativa) POD (AsPOD) gene family in resistance to powdery mildew, we performed a genome-wide analysis and bioinformatics characterization. A total of 97 AsPOD genes were identified, unevenly distributed across 21 chromosomes. Structural predictions indicated that α-helices are the predominant structural components of AsPOD proteins, and phylogenetic analysis revealed six clades of AsPOD proteins, with high homology to POD proteins in the Poaceae family. Cis-regulatory element analysis revealed that three AsPOD genes are associated with hormone signaling, light response, and stress resistance. Analysis of duplication events in the oat POD gene family indicates that there are a total of 55 pairs of gene segment duplications among the 69 AsPOD genes. Expression profiling of powdery mildew-infected oat varieties showed significant up- or downregulation of several AsPOD genes (AsPOD51, AsPOD55, AsPOD63, AsPOD89), identifying them as key candidates for disease resistance studies. Furthermore, resistant oat varieties exhibited higher lignin content than susceptible ones. Correlation analysis indicated that AsPOD51, AsPOD55, AsPOD63, AsPOD88, and AsPOD89 showed a stronger positive association with lignin content in resistant varieties. After inoculation with the powdery mildew pathogen, the H₂O₂ content rapidly increases, and POD activity first rises and then decreases. Those findings provide a foundation for further research into the role of AsPOD genes in oat disease resistance. Full article

Marine-derived proteins, rich in amino acids and bioactivity, serve as a natural and safe alternative to chemical haircare products. This study selected three highly bioactive fish-derived protein peptides and determined their optimal repair ratio using FTIR structural analysis and response surface methodology (RSM). A collagen peptide-based composite human hair repair emulsion (CHFRE) was formulated, and its repair efficacy on damaged hair (DH) was evaluated using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and amino acid analysis. Following CHFRE treatment, the physical and chemical properties of damaged hair improved significantly. SEM analysis revealed enhanced hair luster, aligned cuticle scales, and a denser cortex. FTIR and DSC analyses showed a 5.94% increase in α-conformation content and a 28.44% rise in relative helical content (RHC), indicating enhanced protein stability and a conformation closer to that of normal hair. Additionally, the 14.63% increase in S=O transmittance suggested reduced oxidative damage. Amino acid analysis and hydrophobic amino acids, with specific increments of 16.77 g/100 g and 2.47 g/100 g, respectively, enhance hair affinity and keratin stability. This bio-based repair material effectively restores damaged hair structure, strengthens resistance to chemical damage, and ensures sustainability, safety, and biocompatibility, providing a promising approach for the development of natural hair repair products. Full article

The first luciferase from Antarctic krill (LAK) was cloned and successfully expressed in Escherichia coli BL21(DE3). LAK exhibits the unique ability to emit bright violet fluorescence at an emission wavelength of 350 nm, which represents the lowest reported bioluminescence wavelength for luciferases. However, its low thermal stability poses a limitation to its broader application. In this study, we employed a rational design approach to introduce three pairs of artificial disulfide bonds into LAK. Circular dichroism (CD) analysis revealed that the introduction of artificial disulfide bonds resulted in a significant increase in the secondary structural content of α-helices and β-sheets compared to the wild-type (WT) enzyme. However, these modifications did not influence the emission spectrum. Among the resultant mutant strains, two exhibited markedly enhanced thermal stability. Notably, Mut2 demonstrated a 6.18-fold increase in half-life at 50 °C. Molecular docking studies indicated that D-fluorescein can form additional hydrogen bonds with surrounding amino acid residues (A323, T347, and K534). The docking energies between the enzyme and substrate for WT and Mut2 were −19.5 kcal/mol and −23.4 kcal/mol, respectively, thereby establishing strong interactions within the catalytic pocket region. These interactions likely contribute to a 2.92-fold improvement in substrate affinity, as evidenced by a reduced Michaelis–Menten constant (Km). Our thermal stability and catalytic activity analyses revealed that the linker region between the N- and C-domains plays a crucial role in the overall stability of the enzyme. Furthermore, the C-terminus of LAK does not participate in substrate-binding and catalysis; its local excessive rigidity was found to restrict the release of the AMP product, thereby negatively impacting catalytic activity. These findings offer new insights into the mutagenesis of luciferases and pave the way for the further optimization of LAK for various biotechnological applications. Full article

To enhance and stabilise the edible quality of coated tofu, this study explored the changes in the microstructure and intermolecular forces of coated tofu gel and sol under different heat treatments. It elucidated the phase transformation mechanism of coated tofu gel and sol under heat treatment. The results showed that the protein structure unfolded, the fluorescence intensity decreased, and the protein solubility, surface hydrophobicity, and free sulfhydryl group content increased as the coated tofu gel transformed to sol. Disulfide bonding and hydrophobic interactions were the primary intermolecular forces in the heat-induced gel–sol transition. FTIR showed that the content of β-sheets decreased significantly during gel–sol transformation, while the content of β-turns, α-helices and random coils increased significantly. Most remained relatively stable during the gel–sol transformation process, with only the A and B subunits of the 11S protein decreasing slightly. Their reduction became significant when the temperature reached 200 °C. Additionally, the high-temperature heat treatment promoted the gel–sol transition of the coated tofu, with its cross-section gradually transforming from a porous network structure to a more uniform and smooth texture during heat treatment process. The findings of this study provide a theoretical basis for improving the quality of coated tofu by optimising heat treatment parameters, laying the groundwork for future advancements in the development of pre-heat-treated coated tofu. Full article

High-temperature cooking can induce oxidation and structural changes in myofibrillar protein (MP), harming meat product quality. 6-gingerol is a key part of ginger and a natural antioxidant. In this study, MP was mixed with 6-gingerol and cooked at different temperatures. Chemical methods, fluorescence spectroscopy, Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and molecular docking were used to study the effects on protein aggregation, oxidation, molecular structure, and the microstructure of muscle fibers. The results showed that 40 μg/mL of 6-gingerol significantly optimized the indexes of beef MP. For example, 6-gingerol inhibited the decrease in MP sulfhydryl content and solubility, delayed the rise in surface hydrophobicity and carbonyl content, decreased the particle size of MP, and elevated the absolute value of Zeta potential, which, in turn, hindered oxidative denaturation and the aggregation of proteins. 6-gingerol could maintain the stability of the spatial conformational structure and microstructure of the protein. The protein secondary structure changed, and the α-helical might have been transformed into the β-folded one. The binding of 6-gingerol to MP mainly relied on hydrogen bonds, van der Waals forces, and hydrophobic interactions. Thus, 6-gingerol had a positive effect on the antioxidant properties and structural stability of beef MP during heating. Full article

Drawing soy protein (DSP) exhibits a well-defined fibrous structure, conferring significant market potential. This study investigates the interactions between DSP and myofibrillar proteins (MP) and their effects on gel properties. Porcine myofibrillar protein (MP) was used as the raw material, and mixed systems were prepared by incorporating different concentrations of DSP at 0%, 2%, 4%, 6%, and 8% to evaluate their physicochemical properties and gel characteristics. The results demonstrated that the addition of DSP enhanced the gel strength, hardness, and water-holding capacity (WHC) of MP, thereby improving the overall properties and water retention of the gels. Among them, the trend of change was most obvious when the addition amount was 6%. The gel strength increased by 196.5%, the water retention capacity improved by 68.3%, and the hardness rose by 33.3%. Furthermore, as the addition amount of DSP increases, the total thiol content decreases, the hydrogen bond content increases, and the surface hydrophobicity enhances. This leads to a more compact arrangement of protein molecules, which is conducive to a denser and more stable solution and improves the stability of the protein solution. The α-helical structures in the proteins progressively transformed into β-turn structures, exposing more amino acid side chains and inducing conformational changes in MP, resulting in denser and more uniform gel network structures. The most pronounced changes were observed at a 6% addition level. These findings contribute to diversifying meat products and provide a theoretical basis for improving the WHC and yield of emulsified meat products in pork processing. Full article

Background/Objectives: The GARP transcription factor superfamily is crucial for plant growth, development, and stress responses. This study systematically identified and analyzed the GARP family genes in Populus deltoides to explore their roles in plant development and abiotic stress responses. Methods: A total of 58 PdGARP genes were identified using bioinformatics tools. Their physicochemical properties, genomic locations, conserved motifs, gene structures, and phylogenetic relationships were analyzed. Expression patterns under phosphorus and nitrogen deficiency, as well as tissue-specific expression, were investigated using RT-qPCR. Transgenic RNAi lines were generated to validate the function of GLK genes in chlorophyll biosynthesis. Results: The 58 PdGARP genes were classified into five subfamilies based on their evolutionary relationships and protein sequence similarity. Segmental duplication was found to be the primary driver of the PdGARP family’s expansion. Cis-regulatory elements (CREs) related to light, hormones, and abiotic stresses were identified in the promoters of PdGARP genes. Differential expression patterns were observed for NIGT1/HRS1/HHO and PHR/PHL subfamily members under phosphorus and nitrogen deficiency, indicating their involvement in stress responses. KAN subfamily members exhibited tissue-specific expression, particularly in leaves. Structural analysis of the GLK subfamily revealed conserved α-helices, extended chains, and irregular coils. Transgenic RNAi lines targeting GLK genes showed significant reductions in chlorophyll and carotenoid content. Conclusions: This study provides a comprehensive analysis of the GARP transcription factor superfamily in P. deltoides, highlighting their potential roles in nutrient signaling and stress response pathways. The findings lay the foundation for further functional studies of PdGARP genes and their application in stress-resistant breeding of poplar. Full article

Silver(I) ions and organometallic complexes thereof are well-established antimicrobial agents. They have been employed in medical applications for centuries. It is also known that some bacteria can resist silver(I) treatments through an efflux mechanism. However, the exact mechanism of action remains unclear. All-atom force-field simulations can provide valuable structural and thermodynamic insights into the molecular processes of the underlying mechanism. Lennard-Jones parameters of silver(I) have been available for quite some time; their applicability to properly describing the binding properties (affinity, binding distance) between silver(I) and peptide-based binding motifs is, however, still an open question. Here, we demonstrate that the standard 12-6 Lennard-Jones parameters (previously developed to describe the hydration free energy with the TIP3P water model) significantly underestimate the interaction strength between silver(I) and both methionine and histidine. These are two key amino-acid residues in silver(I)-binding motifs of proteins involved in the efflux process. Using free-energy calculations, we calibrated non-bonded fix (NBFIX) parameters for the CHARMM36m force field to reproduce the experimental binding constant between amino acid sidechain fragments and silver(I) ions. We then successfully validated the new parameters on a set of small silver-binding peptides with experimentally known binding constants. In addition, we monitored how silver(I) ions increased the α-helical content of the LP1 oligopeptide, in agreement with previously reported Circular Dichroism (CD) experiments. Future improvements are outlined. The implementation of these new parameters is straightforward in all simulation packages that can use the CHARMM36m force field. It sets the stage for the modeling community to study more complex silver(I)-binding processes such as the interaction with silver(I)-binding-transporter proteins. Full article

In this study, pepper (Zanthoxylum bungeanum Maxim.) leaf (ZL) extract was added to larou to investigate the improvement in the quality of physicochemical properties, texture, water distribution, and microorganism growth during storage for 20 days. Based on the results, the addition of ZL extract significantly retarded the increase in cooking loss, TBARS value, hardness, and microorganism growth. Moreover, the addition of ZL extract decreased the pH value, lightness, and microorganism counts, and increased the moisture content, total soluble protein content, a* value, b* value, and chewiness. The LF-NMR results showed that the addition of ZL extract shortened the T₂ relaxation time and boosted the proportion of immobilized water, facilitating the validation of the improvement in water retention of larou during storage. The FT-IR results indicated that the addition of ZL extract influenced the protein secondary structure by inducing the conversion of α-helices to β-sheet structures. Accordingly, ZL extract has the potential to serve as a natural antioxidant, effectively helping to ameliorate the quality properties of cured meat products during storage. Full article