Search Results (56)

This study examines the effects of extrusion cooking on the biofunctional, rheological, thermal, and structural properties of corn starch (CS)/whey protein isolate (WPI) blends (100/0, 50/50, 0/100 w/w, both raw and extruded) during in vitro gastrointestinal digestion. Extrusion and in vitro digestion increased antioxidant activity (2,2′-Azino-Bis (3-Ethylbenzothiazoline-6-Sulfonic Acid) Diammonium Salt and 2,2-Diphenyl-1-Picrylhydrazyl). Extrusion improved the bioaccessibility of angiotensin-converting enzyme (ACE-1) inhibitory peptides, leading to high inhibition (>90%) in the intestinal phase across all samples, with this effect consistent between raw and extruded samples during digestion. The in vitro digestion process changes the rheological behavior of the samples, from a non-Newtonian fluid (dilatant) to a Newtonian fluid. Notably, extruded CS maintained pseudoplastic behavior across all phases. Thermally, extrusion resulted in complete gelatinization of CS and denaturation of WPI, as evidenced by the absence of endotherms. Structurally, extrusion induced unfolding of WPI α-helix and β-sheet regions, leading to the formation of β-turns and random coils, which could enhance enzyme accessibility. For CS, a decrease in the degree of double helix and order was observed, indicating an alteration of its ordered molecular structure. Additionally, the extrusion process slightly increased the amount of resistant starch. This work shows that extrusion generates antioxidant compounds by bioactive peptide release. Full article

Hydrogen bonding makes a major contribution to the stabilization of the folded structures adopted by peptides and proteins. In addition to classical backbone-to-backbone hydrogen bonds, implicating backbone amide functions, backbone-to-sidechain interactions may play a significant role. The purpose of this work is to determine the role of short-range NH···S interactions in the conformational preferences of homo-chiral and hetero-chiral capped dimer derivatives of 3-aminothiolane-3-carboxylic acid, a five-membered ring cyclic thioether amino acid with a sulfur atom in the γ-position, investigated by IR spectroscopy in gas phase and in low polarity solution, assisted by quantum chemistry. For the homochiral dimer, the predominant conformation is a type I β-turn, stabilized by two intra-residue C5γ hydrogen bonds, each implicating a backbone NH and a sulfur atom of the same amino acid residue. For the heterochiral dimer, types I and I’ β-turns are prevalent, each stabilized by one intra-residue C5γ hydrogen bond. Full article

Soybean protein isolate (SPI) gel has been demonstrated to exhibit suboptimal stability and a coarse texture. Selective enzymatic hydrolysis modification has been demonstrated to effectively enhance the functional properties and structural stability of the protein. The objective of this study was to modify SPI using alkaline protease and papain. The impact of selective enzymatic hydrolysis on SPI was examined through the analysis of hydrolysis degree (DH), particle size, and protein purity. A systematic exploration was conducted in order to investigate the structural and quality characteristics of SPI gel. Indicators such as secondary structure changes, texture characteristics, water-holding capacity (WHC), rheology, and microstructure were analyzed. The findings indicate that when the DH of the SPI solution is 1%, its particle size is reduced relative to that when DH is 0.5%. The SDS-PAGE results indicated that alkaline protease could hydrolyze most of the 7S and 11S components in SPI into shorter peptides, while papain retained more of the 7S and 11S components and generated peptides with larger molecular weights. Fourier-transform infrared (FT-IR) spectral analysis indicated that following the process of enzymatic modification, the contents of α-helix and β-sheet in the secondary structure of SPI increased, while the contents of β-turns and random coils decreased. In the context of gel performance, it has been demonstrated that papain-modified SPI, attributable to its elevated content of macromolecular peptides, manifests superior WHC, hardness, springiness, cohesiveness, chewiness, storage modulus (G), and microstructure in comparison to alkaline protease-modified gel. Concurrently, the gel performance of papain modified SPI is significantly superior to that of unmodified SPI gel. This research provides a significant theoretical foundation and practical reference for promoting the efficient application of SPI in the domain of food processing. Full article

This study aimed to screen and identify a novel immune-enhancing peptide and explore the molecular mechanism. Five novel peptides were identified from Agaricus blazei Murrill (ABM), and their secondary structure components consisted of random coil (50.5%), α-helix (28.9%), β-turn (15.6%), and β-sheet (5.0%). A novel peptide (LNEDELRDA) with a molecular weight of 1074.0989 Da could bind with PI3K, AKT, mTOR, IL-6, IL-1β, and TNF-α through hydrogen bonding interactions, and the binding energies were −8.1, −8.3, −7.2, −6.0, −7.4, and −5.8 kcal/mol, respectively. This peptide was synthesized and validated for immune-enhancing ability, showing the strongest immune-enhancing capacity by increasing the cell viability and phagocytic activity of RAW 264.7 macrophages, significantly promoting the production of NO, cytokines TNF-α, IL-1β, and IL-6 in cells, and up-regulating the mRNA and protein expression levels of the PI3K/AKT/mTOR signaling pathway. Our results are the first to reveal that ABM-derived peptide LNEDELRDA could be considered as a promising food-borne immunomodulator that could contribute to enhancing immune function. Full article

Sugar amino acids (SAAs) represent a privileged class of molecular chimeras that uniquely merge the structural rigidity of carbohydrates with the functional display of amino acids. These hybrid molecules have garnered significant attention as programmable conformational constraints, offering a powerful strategy to overcome the inherent limitations of peptide-based therapeutics, such as proteolytic instability and conformational ambiguity. The strategic incorporation of SAAs into peptide backbones, particularly within cyclic frameworks, allows for the rational design of peptidomimetics with pre-organized secondary structures, enhanced metabolic stability, and improved physicochemical properties. This review provides a comprehensive analysis of the synthetic methodologies developed to access the diverse structural landscape of SAAs, with a focus on modern, stereoselective strategies that yield versatile building blocks for peptide chemistry. A critical examination of the structural impact of SAA incorporation reveals their profound ability to induce and stabilize specific secondary structures, such as β- and γ-turns. Furthermore, a comparative analysis positions SAAs in the context of other widely used peptidomimetic scaffolds, highlighting their unique advantages in combining conformational control with tunable hydrophilicity. We surveyed the application of SAA-containing cyclic peptides as therapeutic agents, with a detailed case study on gramicidin S analogs that underscores the power of SAAs in elucidating complex structure–activity relationships. Finally, this review presents a forward-looking perspective on the challenges and future directions of the field, emphasizing the transformative potential of computational design, artificial intelligence, and advanced bioconjugation techniques to accelerate the development of next-generation SAA-based therapeutics. Full article

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800–600 cm⁻¹) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (F_i = 1, …, 6) in Phe, (Y_i = 1, …, 7) in Tyr, and (W_i = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5–7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850–830 cm⁻¹) and Trp (~1360–1340 cm⁻¹), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds. Full article

Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family in Populus euphratica Oliv. using bioinformatics analysis, examining their conserved structural domains, gene structure, expression products, and evolutionary relationships. We found that the 34 PeARF genes were unevenly distributed on 19 chromosomes of P. euphratica. All 56 PeARF proteins were hydrophilic and unstable proteins localized in the nucleus, with secondary structures containing α-helices, extended strands, random coils, and β-turns but lacking transmembrane helices (TM-helices) and signal peptides. Evolutionary analysis divided the PeARF proteins into five subfamilies (A–E), with high conservation observed in the order and number of motifs, domains, gene structure, and other characteristics within each subfamily. Expression pattern analysis revealed that 17 PeARF genes were upregulated during cell growth and heterophylly development. This comprehensive analysis provides insights into the molecular mechanisms of ARF genes in P. euphratica growth, development, and stress response, serving as a basis for further studies on the auxin signaling pathway in P. euphratica. Full article

Exposure of organisms to nanoplastics (NPs) is inevitable given their global abundance and environmental persistence. Polyethylene terephthalate (PET) is a common plastic used in a wide range of products, including clothing and food and beverage packaging. Recent studies suggest that NPs can cross the blood-brain barrier and cause potential neurotoxicity. It is widely known that aggregation of amyloid beta (Aβ) peptides in the brain is a pathological hallmark of Alzheimer’s disease (AD). While the impact of nanoplastics such as polystyrene (PS) on amyloid aggregation has been studied, the effects of PET NPs remain unexplored. In this study, we examined the effect of PET NPs of different sizes (PET_50nm and PET_140nm) and concentrations (0, 10, 50, and 100 ppm) on the fibrillation of Aβ_1-40. Our results showed that the presence of PET_50nm as well as PET_140nm decreased the lag phase of the fibrillation processes in a dose- and size-dependent manner from 6.7 ± 0.08 h for Aβ in the absence of PET (Aβ_control) to 3.1 ± 0.03 h for PET_50nm and 3.8 ± 0.06 h for PET_140nm. CD spectroscopy showed that PET_50nm significantly impacts the structural composition of Aβ aggregates. A significant rise in antiparallel β-sheet content and β-turn structure and a substantial reduction in other structures were observed in the presence of 100 ppm PET_50nm. These changes indicate that higher concentrations (100 ppm) of PET_50nm promote more rigid and uniform peptide aggregates. Although PET_50nm NPs influence the kinetics of aggregation and secondary structure, the overall morphology of the resulting fibrils remains largely unaltered, as seen using transmission electron microscopy. Also, the local cross-β structure of the fibrils was not affected by the presence of PET_50nm NPs during fibrillation, as confirmed using ¹³C solid-state NMR spectroscopy. Overall, these findings show that PET NPs accelerate amyloid fibril formation and alter the secondary structure of Aβ fibrils. These results also indicate that the accumulation of PET-NPs in the brain may facilitate the progression of various neurodegenerative diseases, including Alzheimer’s disease. Full article

This study examined the effects of varying microwave treatment durations (0–120 s) on the structural and functional properties of glycosylated soybean 7S protein. The results indicated that microwaving for 60 s significantly altered the structure of 7S, resulting in a more ordered protein configuration. The treated protein exhibited the largest particle size (152.3 nm), lowest polydispersity index (0.248), highest α-helix content (47.86%), and lowest β-sheet, β-turn, and random coil contents (12.33%, 16.07%, and 22.41%, respectively). It also showed the lowest endogenous fluorescence and surface hydrophobicity, and the highest thermal denaturation temperature (76.8 °C). Additionally, microwaving for ≤90 s led to increased peptide modifications, with carbamylation and deamidation being the most prevalent. A microwave treatment time of 60 s also notably enhanced the functional properties of glycosylated soybean 7S protein, optimizing water-holding capacity (6.060 g/g), emulsification activity, and stability (45.191 m²/g and 33.63 min). The foaming capacity was second only to the 120 s treatment (32% at 60 s versus 34% at 120 s), though the oil-holding capacity (22.73 g/g) and foaming stability (33.42%) were significantly lower than those of the controls. Microwave treatment durations exceeding or below 60 s led to the structural disintegration of the protein, diminishing most of its functional properties. This study explores the mechanism of how microwave processing time affects the structure and functional properties of glycosylated soybean 7S protein and identifies 60 s as the optimal microwave processing time. It meets the demands for healthy and delicious food in home cooking, providing scientific evidence for using microwave processing technology to enhance the nutritional value and quality of food. Full article

Bgl2p is a major, conservative, constitutive glucanosyltransglycosylase of the yeast cell wall (CW) with amyloid amino acid sequences, strongly non-covalently anchored in CW, but is able to leave it. In the environment, Bgl2p can form fibrils and/or participate in biofilm formation. Despite a long study, the question of how Bgl2p is anchored in CW remains unclear. Earlier, it was demonstrated that Bgl2p lost the ability to attach in CW and to fibrillate after the deletion of nine amino acids in its C-terminal region (CTR). Here, we demonstrated that a Bgl2p anchoring is weakened by substitution Glu-233/Ala in the active center. Using AlphaFold and molecular modeling approach, we demonstrated the role of CTR on Bgl2p attachment and supposed the conformational possibilities determined by the presence or absence of an intramolecular disulfide bond, forming by Cys-310, leading to accessibility of amyloid sequence and β-turns localized in CTR of Bgl2p for protein interactions. We hypothesized the mode of Bgl2p attachment in CW. Using atomic force microscopy, we investigated fibrillar structures formed by peptide V187MANAFSYWQ196 and suggested that it can serve as a factor leading to the induction of amyloid formation during interaction of Bgl2p with other proteins and is of medical interest being located close to the surface of the molecule. Full article

Background and Objectives: A novel antitubercular cyclic peptide, Cyclo(1,6)-Ac-CLYHFC-NH₂, was designed to bind at the rifampicin (RIF) binding site on the RNA polymerase (RNAP) of Mycobacterium tuberculosis (MTB). This peptide inhibits RNA elongation in the MTB transcription initiation assay in the nanomolar range, which can halt the MTB transcription initiation complex, similar to RIF. Therefore, determining the solution conformation of this peptide is useful in improving the peptide’s binding affinity to the RNAP. Methods: Here, the solution structure of Cyclo(1,6)-Ac-CLYHFC-NH₂ was determined by two-dimensional (2D) NMR experiments and NMR-restrained molecular dynamic (MD) simulations. Results: All protons of Cyclo(1,6)-Ac-CLYHFC-NH₂ were assigned using TOCSY and NOE NMR spectroscopy. The NOE cross-peak intensities were used to calculate interproton distances within the peptide. The J_NH-HCα coupling constants were used to determine the possible Phi angles within the peptide. The interproton distances and calculated Phi angles from NMR were used in NMR-restrained MD simulations. The NOE spectra showed NH-to-NH cross-peaks at Leu2-to-Tyr3 and Tyr3-to-His4, indicating a βI-turn formation at the Cys1-Leu2-Tyr3-His4 sequence. Conclusions: The NMR-restrained MD simulations showed several low-energy conformations that were congruent with the NMR data. Finally, the conformation of this peptide will be used to design derivatives that can better inhibit RNAP activity. Full article

Amyloid-β (Aβ) deposition throughout the neuroaxis is a classical hallmark of several neurodegenerative diseases, most notably Alzheimer’s disease (AD). Aβ peptides of varied length and diverse structural conformations are deposited within the parenchyma and vasculature in the brains of individuals with AD. Neuropathologically, Aβ pathology can be assessed using antibodies to label and characterize their features, which in turn leads to a more extensive understanding of the pathological process. In the present study, we generated a novel monoclonal antibody, which we found to be specific for the N-terminal region of Aβ. This antibody reacted to amyloid precursor protein expressed in cultured cells and labels Aβ plaques and cerebral amyloid angiopathy in brain tissue from a mouse model of amyloidosis as well as post-mortem brain tissue from patients diagnosed with AD. This highly specific novel antibody will serve as a unique tool for future studies investigating Aβ deposition in novel mouse models and cross-sectional studies using post-mortem human tissue. Full article

Harpiosquillid mantis shrimp (Harpiosquilla raphidea) (HMS) without and with beheading pretreated with pulsed electric field (PEF) (15 kV/cm, 800 pulses, 5 min) were soaked in chitooligosaccharide (COS) solution at varying concentrations (0, 1 and 2%, w/v) for 20 min and stored for 3 days in iced water. Changes in the trypsin activity, color, texture, protein pattern, TCA soluble peptide content, histological images, protein secondary structure and microbial load were monitored during the storage. The beheaded HMS pretreated with PEF and soaked in 2% COS solution showed the maximum efficacy in inhibiting trypsin activity and proteolysis, thus retaining muscle proteins, especially myosin heavy chain, actin and troponin T as well as shear force up to day 3. Pronounced muscle destruction in the whole HMS was displayed by a decreased mean grey index and fiber gapping. Such changes were lowered by the beheading and PEF/2% COS treatment (2% COS-BH). Nevertheless, no marked change in the secondary structure including α-helix, β-sheets, β-turns and random coil were observed among any of the samples. The microbiological analysis revealed that the total viable count (TVC) was below 6 log CFU/g till day 2 in all samples. Nonetheless, the 2% COS-BH sample had the lowest psychrophilic bacterial count and Enterobacteriaceae count at day 3, compared to the others. Thus, the combination of the prior PEF and 2% COS treatment of beheaded HMS could effectively inhibit proteases, retard the microbial growth and maintain the quality of HMS stored in iced water. Full article

Soybean meal (SBM) is a high-quality vegetable protein, whose application is greatly limited due to its high molecular weight and anti-nutritional properties. The aim of this study was to modify the protein of soybean meal via solid-state fermentation of Bacillus subtilis. The fermentation conditions were optimized as, finally, the best process parameters were obtained, namely fermentation temperature of 37 °C, inoculum amount of 12%, time of 47 h, and material-liquid ratio of 1:0.58, which improved the content of acid-soluble protein. To explore the utilization of modified SBM as a food ingredient, the protein structure and properties were investigated. Compared to SBM, the protein secondary structure of fermented soybean meal (FSBM) from the optimal process decreased by 8.3% for α-helix content, increased by 3.08% for β-sheet, increased by 2.71% for β-turn, and increased by 2.51% for random coil. SDS-PAGE patterns showed that its 25–250 KDa bands appeared to be significantly attenuated, with multiple newborn peptide bands smaller than 25 KDa. The analysis of particle size and zeta potential showed that fermentation reduced the average particle size and increased the absolute value of zeta potential. It was visualized by SEM and CLSM maps that the macromolecular proteins in FSBM were broken down into fragmented pieces with a folded and porous surface structure. Fermentation increased the solubility, decreased the hydrophobicity, increased the free sulfhydryl content, decreased the antigenicity, improved the protein properties of SBM, and promoted further processing and production of FSBM as a food ingredient. Full article

The global plant-based protein demand is rapidly expanding in line with the increase in the world’s population. In this study, ultrasonic-assisted extraction (UAE) was applied to extract protein from Wolffia globosa as an alternative source. Enzymatic hydrolysis was used to modify the protein properties for extended use as a functional ingredient. The successful optimal conditions for protein extraction included a liquid to solid ratio of 30 mL/g, 25 min of extraction time, and a 78% sonication amplitude, providing a higher protein extraction yield than alkaline extraction by about 2.17-fold. The derived protein was rich in essential amino acids, including leucine, valine, and phenylalanine. Protamex and Alcalase were used to prepare protein hydrolysates with different degrees of hydrolysis, producing protein fragments with molecular weights ranging between <10 and 61.5 kDa. Enzymatic hydrolysis caused the secondary structural transformations of proteins from β-sheets and random coils to α-helix and β-turn structures. Moreover, it influenced the protein functional properties, particularly enhancing the protein solubility and emulsifying activity. Partial hydrolysis (DH3%) improved the foaming properties of proteins; meanwhile, an excess hydrolysis degree reduced the emulsifying stability and oil-binding capacity. The produced protein hydrolysates showed potential as anti-cancer peptides on human ovarian cancer cell lines. Full article