Search Results (364)

Metabolic remodeling is increasingly recognized as a key component of cardiomyopathy, yet the circulating organic acid profile associated with this condition remains incompletely characterized. In this case–control study, we investigated differences in circulating organic acid profiles between patients with cardiomyopathy and control participants using targeted liquid chromatography–tandem mass spectrometry (LC-MS/MS). A total of 160 participants were enrolled, including 80 patients with cardiomyopathy and 80 age- and sex-comparable control participants. Circulating organic acids were quantitatively analyzed, and between-group differences were assessed using the two-sided Mann–Whitney U test with Benjamini–Hochberg false discovery rate correction; effect sizes were estimated using Cliff’s delta. Detection rates were also examined because several metabolites included values below the assay limit of detection. Sixteen metabolites remained significant after correction. Among these, 3-hydroxyisovaleric acid demonstrated the largest increase, followed by 2-oxoglutaric acid and 2-methylcitric acid. Additional elevations were observed in citric acid, malic acid, N-acetylaspartic acid, fumaric acid, and suberic acid, whereas 2-oxoadipic acid was reduced. These alterations are consistent with perturbations in mitochondrial intermediary metabolism, branched-chain amino acid catabolism, ketone body metabolism, and tricarboxylic acid cycle-related pathways. However, because comorbidities, renal function, glycemic status, and medication use differed between groups, the findings should be interpreted as phenotype-associated metabolic signals rather than cardiomyopathy-specific causal effects or validated diagnostic biomarkers. In conclusion, targeted LC-MS/MS-based organic acid profiling reveals an altered circulating metabolic pattern in cardiomyopathy, although further prospective studies with individual-level adjustment and external validation are required to determine its clinical relevance. Full article

Background/Objectives: Lactic acid bacteria (LAB) are essential drivers of food fermentation, yet systematic metabolic comparisons across different LAB strains remain underexplored. This study characterized and contrasted the metabolic fingerprints of Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus in vegetable fermentation and subsequently evaluated whether the same untargeted metabolomics pipeline could be applied to rapid foodborne pathogen detection. Methods: A multi-platform untargeted metabolomics strategy integrating GC-MS and UPLC-Q-TOF-MS was applied to profile four experimental conditions: non-fermented control, L. plantarum monoculture, L. rhamnosus monoculture, and mixed-culture fermentation. Multivariate statistical tools (PCA and PLS-DA) were used to identify differential metabolites and perturbed pathways. The identical analytical workflow was then applied to beef samples artificially contaminated with Escherichia coli O157:H7, Salmonella enterica, or Listeria monocytogenes. Results: Across all samples, 847 metabolites were annotated, of which 312 showed significant abundance changes upon fermentation. PLS-DA delivered robust group discrimination (R²X = 0.89, R²Y = 0.95, Q² = 0.91). Organic acids (32.0%) and amino acids (24.0%) dominated the metabolic landscape, with lactic acid, acetic acid, diacetyl, and acetoin as the most elevated compounds. KEGG analysis highlighted glycolysis/gluconeogenesis, pyruvate metabolism, and branched-chain amino acid degradation as the most heavily rewired pathways. When the same pipeline was applied to pathogen detection, it yielded AUC values of 0.89, 0.87, and 0.88 for E. coli O157:H7, S. enterica, and L. monocytogenes, respectively, with detection times of 18 h, 24 h, and 30 h. Conclusions: This work delivers a side-by-side metabolic atlas of two prominent LAB species and demonstrates the technical portability of an untargeted metabolomics pipeline from a fermentation model system to a pathogen detection scenario. The identified biomarker panels warrant further validation in diverse food matrices, and translation to routine monitoring will require matrix-specific model training and validation. Full article

Two new nitropyridine amino N-oxide derivatives were synthesized and characterized: 3-N-methylamino-4-nitropyridine N-oxide (NOPCH₃) and [(4-nitropyridine-3-yl)amino]propanoic acid N-oxide (NOPCOOH)1. Their molecular and crystal structures were determined by single-crystal X-ray diffraction, and the intermolecular contact patterns were evaluated using Hirshfeld surface analysis. Vibrational properties were investigated by FT-IR and Raman spectroscopy and interpreted with the support of quantum-chemical calculations (DFT). Electronic absorption was examined by UV–Vis measurements, while photoluminescence spectra and decay profiles were recorded under femtosecond excitation and interpreted conservatively in terms of relaxed excited-state emission. Solid-state ¹³C CP-MAS and ¹H WPMLG NMR spectroscopy provided additional support for the chemical constitution of both derivatives, with ¹H spectra interpreted conservatively because of the limitations inherent to solid-state homonuclear-decoupled measurements. A comparative analysis shows that replacing the methyl substituent (NOPCH₃) with the carboxylic-acid side chain (NOPCOOH) modifies the hydrogen-bonding landscape and the local electronic environment of the NO₂ group, which is reflected in the positions and intensities of selected NO₂-related vibrational bands and in the near-UV electronic transitions. Overall, the combined structural and spectroscopic dataset provides a consistent structure–property picture for both N-oxide derivatives and a basis for further studies of their coordination and photophysical behavior. Full article

Bioactive peptides (BPs) are widely distributed and exhibit remarkable physiological activities. However, their natural forms are frequently characterized by short half-lives, low membrane permeability, poor stability, and inadequate oral bioavailability, which severely limit their applications in the food, pharmaceutical, and biomaterial fields. Therefore, modification and engineering of natural BPs are essential to surmount these inherent limitations. Synthetic biology-based modification strategies, including amino acid substitution, sequence truncation and hybridization, side-chain functionalization, and main-chain/side-chain integration, are comprehensively summarized in this review. Chemical modification strategies, such as terminal modification, cyclization, backbone modification, polymer conjugation, lipidation, and glycosylation, are also discussed, with particular attention to their advantages, potential drawbacks, and practical limitations. Based on 122 studies identified through systematic literature searches across major scientific databases, this review also discusses the current challenges and future trends in BP modification, providing theoretical guidance and innovative insights for the further development and enhanced utilization of BPs. Full article

Peptide therapeutics offer high target selectivity and low toxicity, but their clinical utility remains constrained by rapid proteolysis in vivo and negligible oral bioavailability. Incorporating non-canonical amino acids (ncAAs) provides a robust molecular engineering framework to overcome these pharmacokinetic bottlenecks. This review analyzes the structural and biophysical design rules of ncAA-mediated peptide stabilization, categorizing them into side-chain steric shielding, backbone conformational constraint, and stereochemical evasion of L-specific proteases. We systematically evaluate the biosynthetic milestones enabling this field, focusing on engineered orthogonal translation systems (tRNA/synthetase pairs, orthogonal ribosomes, quadruplet codons) and metabolic engineering strategies that supply fluorinated and other ncAA precursors de novo. Furthermore, we examine the translation of these technologies into clinical candidates (e.g., modified antimicrobial peptides, antibody–drug conjugates, and PROTACs) and identify scaling, immunogenicity, and computational modeling as key bottlenecks. This review serves as a technical reference for designing next-generation, hyper-stable peptide therapeutics. Full article

The synthetic strategy relies on the highly diastereoselective alkylation at the C4 position of L-pyroglutamic acid derivatives, followed by a decarboxylation-allylation process that enables the incorporation of diverse substituents, including aromatic substituents, affording trans-3,5-disubstituted γ-lactams with excellent diastereiosmeric ratio (dr > 98:2). The resulting γ-lactams were efficiently transformed into a series of α,γ-disubstituted γ-amino acids through hydrogenation and acidic hydrolysis. Furthermore, cross-metathesis reactions with styrene and 1-decene enabled the introduction of structurally diverse lipophilic side chains, furnishing the corresponding γ-amino acids in good overall yields (71–77%) and high diastereoisomeric ratio from >98:2 to 92:8. In addition, N-allylation followed by ring-closing metathesis and hydrogenation provided access to a previously unexplored conformationally constrained γ-amino acid. Overall, seven α,γ-disubstituted γ-amino acids, including fluorinated and conformationally restricted derivatives, were synthesized from common intermediates with high stereocontrol. The developed methodology offers a versatile platform for the preparation of structurally diverse and underexplored γ-amino acid building blocks of potential interest in peptide synthesis, medicinal chemistry, and antimicrobial agent development. Full article

The Gram-negative bacterium Pseudomonas aeruginosa produces a family of peptide siderophores called pyoverdines that play a vital role in the mechanisms by which it acquires iron from the environment. A key component of various pyoverdines is the presence of one or more copies of L-δ-N-formyl-δ-N-hydroxyornithine (fOHOrn) as an iron-binding residue. In this study, we have developed an improved preparation of a derivative of fOHOrn that is suitable for use in solid-phase peptide synthesis, incorporating a novel N-oxidation protocol and a mild final deprotection with HCl/hexafluoroisopropanol (HFIP) that circumvents the unexpected deformylation of the fOHOrn side chain under acidic conditions. We have also devised a synthesis of the cyclic peptide component of pyoverdine D exploiting a selective side-chain deprotection strategy with HCl/HFIP that allows the application of readily available amino acids with standard tert-butyl side-chain protection and which facilitates the cyclisation step. These innovations open the way towards the convergent preparation of various pyoverdines and also other natural products that contain fOHOrn residues. Full article

Background: Recent work has revealed that protein-coding sequences encode regulatory information influencing mRNA stability and translation through a nascent peptide code. However, the evolutionary origin of this regulatory layer remains unclear. This study aims to determine when peptide-mediated translational control emerged during the evolution of the proteome and genetic code. Methods: Dipeptide-specific effects on mRNA stability and translation were integrated with a phylogenetic timeline of dipeptide emergence derived from dipeptide sequences across proteomes. Each of the 400 canonical dipeptides was assigned an evolutionary age, and experimentally derived regulatory effects were mapped onto this timeline, with associations assessed using rank-based correlation and regression analyses. Results: A weak but statistically significant negative association was observed between dipeptide age and mRNA stability, indicating that more recently evolved dipeptides tend to destabilize transcripts. This trend was stronger at the amino acid level, where later-emerging residues showed greater contributions to reduced mRNA levels. Destabilizing effects were associated with physicochemical properties such as positive charge, side-chain bulkiness, and β-strand propensity. Mapping these effects onto codon space revealed a non-random distribution aligned with the evolutionary and structural organization of the genetic code. Destabilizing effects were also enriched within specific codon exchange groups, indicating that regulatory signals are structured within the degeneracy and mutational neighborhoods of the code. Conclusions: These findings indicate that the nascent peptide code is a late evolutionary innovation linked to amino acid expansion and proteomic complexity, with regulation embedded within both peptide sequences and the degeneracy structure of the standard genetic code. Full article

Background/Objectives: Longer oligoarginines are very effective cell-penetrating peptides. It has been shown that a minimal number of positively charged side chains is necessary for efficient cellular uptake. But a highly positively charged peptide may interact with its cargo molecule, thereby reducing its efficiency. Several chemical modifications were tested to improve the internalization of short tetraarginine derivatives. Aromatic groups, such as Dabcyl at the N-terminus, Trp in the sequence, and AMBA or PABA in the backbone, were used to improve internalization. The other useful modification was the aza-glycine substitution in the case of penetratin. Methods: In this study, the effect of aza-glycine insertion into the peptide Dabcyl-RRRRK(Cf) on internalization was studied and compared with that of the Trp-modified peptide Dabcyl-RRWRRK(Cf). To explain the noticed difference in the biological activity of peptides, DFT calculations and the prediction of membrane-binding free energy (ΔΔF) from a peptide sequence were performed. Results: It turned out that the position of the aza-glycine moiety does not have an influence on the cellular uptake. The aza-glycine-containing peptide showed higher internalization than the Dabcyl-RRRRK(Cf) peptide. Besides this, these peptides have similar or higher cellular uptake than that of octaarginine at lower concentrations (c < 2 µM). The aza-glycine affected not only cellular uptake but also the entry mechanism. The structure of peptides depended on the amino acids (Trp, Gly, or azaGly) in their sequences and their positions. Conclusions: These may result in the different amphiphilicity of peptides, and thus changes in the hydrophobic moment and in the binding affinity of peptides to the negatively charged membrane surface. Full article

Driven by the demand for miniaturization, high capacitance, and enhanced reliability in high-performance multilayer ceramic capacitors (MLCCs), the continuous thinning of inner electrode layers imposes increasingly stringent requirements on the size, distribution, morphology, and dispersion of nano-nickel powders. We systematically investigate how functional additives regulate the nucleation, growth, and microstructural evolution of nano-nickel synthesized via hydrazine-driven liquid-phase reduction of nickel sulfate. The results demonstrate that the alkanolamine complexing agent (TAC) significantly refines the average particle size and morphology of the nano-nickel through coordination effects. Furthermore, inorganic sulfur salts (ISP), acting via surface adsorption to passivate growth sites and provide catalytic effects, enable a precise and continuous reduction in the average particle diameter from 330 nm down to 60 nm at a mere trace dosage of ~10⁻⁷ mol/L. Regarding dispersion optimization, highly dispersed face-centered cubic (FCC) nano-nickel was successfully prepared by introducing multidentate carboxylate (NNA). High-resolution transmission electron microscopy (HRTEM) was employed to unveil, for the first time, the crystallographic origin of the anomalous surface protrusions typically observed in conventional reaction systems. We confirmed that the family of $\left\{10\overline{1}0\right\}$ crystal planes within these regions, which exhibits interfacial angles of 58.7° and 58.3°, corresponds to a thermodynamically metastable hexagonal close-packed (HCP) nickel phase originating from atomic stacking faults induced by rapid growth kinetics. To address this microstructural defect, a thioether-based amino acid (TAA) was introduced. TAA effectively suppresses the anisotropic growth of the metastable HCP phase through the strong steric hindrance of its long side chains and its selective adsorption onto high-energy facets. Full article

Charge transport underpins essential biological processes, including cellular respiration, photosynthesis, and enzymatic catalysis. Advances in molecular electronics have enabled single-molecule measurements that unequivocally establish redox-active proteins as efficient electron conductors, with their metal cofactors serving as intrinsic redox relays. By contrast, ubiquitous non-redox proteins lacking such redox centers have long been considered poor conductors. However, recent research has challenged this view, demonstrating that efficient charge transport in non-redox proteins can be mediated through polypeptide backbones, aromatic side-chain arrays, and hydrogen bond networks. This review surveys progress in understanding the single-molecule conductance of non-redox proteins. Firstly, we elucidate the fundamental transport mechanisms, highlighting the interplay between coherent tunneling and thermally activated hopping. We then provide an overview of state-of-the-art experimental techniques for single-molecule characterization. Through analysis of diverse systems spanning short peptides to large enzymes, we illustrate how aromatic amino acid networks and dynamic conformational fluctuations govern conductance, enabling emerging applications in label-free biosensing and single-molecule protein/DNA sequencing. Finally, we discuss persistent challenges and outline future opportunities for integrating protein-based conductors into bioelectronic devices. This review aims to stimulate further research and pave the way for novel applications harnessing protein conductance. Full article

Different rhizobial strains can lead to distinct symbiotic phenotypes in alfalfa, yet molecular differences at the mature nodule stage remain unclear. Here, we analyzed 21-day post-inoculation (dpi) nodules induced by strains WE2 and WWL2. We measured nitrogenase activity (acetylene reduction assay, ARA) and performed dual RNA-seq to compare gene expression in both the alfalfa host and the rhizobia. On the host side, WE2-induced nodules showed higher expression of mature nodule marker genes (ENOD93 and leghemoglobin (Lb) genes) and higher expression of genes encoding SWEET transporters and amino acid and peptide transporters. Host differentially expressed genes were enriched in pathways related to transmembrane transport, redox and heme-related functions, and processes linked to maintaining microaerobic conditions. On the rhizobial side, WE2 nodules showed higher expression of genes involved in microaerobic respiration and nitrogen fixation (e.g., nif/fix and key respiratory chain genes), whereas WWL2 nodules showed higher expression of genes linked to transport, chemotaxis/motility, and environmental information processing. Together, these host and rhizobia expression patterns suggest coordinated differences between host pathways related to resource supply and microaerobic conditions and rhizobial expression programs for respiration and nitrogen fixation. Based on these associations, we propose a working model and provide candidate genes and pathways for functional validation and inoculant screening. Full article

The $\beta$-sheet, consisting of several $\beta$-strands, is one of the most important secondary structures of proteins. Most $\beta$-sheets differ greatly from the fully extended, all-trans form due to twisting and/or bending. When looked at in the direction of the $\beta$-strands rather than along the hydrogen bonds, the twist is usually right-handed. Although numerous studies have investigated the origin of the right-handed twist of $\beta$-sheets or $\beta$-strands in proteins, there is no common agreement about its causes. The twist can be seen from the dihedral angles in the Ramachandran plot. Here, we discuss the opposing roles of the dihedral angles $\varphi$ and $\psi$. The key role is played by the angle $\varphi$, which is controlling the distance between the carbonyl group of the backbone and the side chain of the next amino acid. There are two antisymmetric effects: the change in $\varphi$ in the clockwise direction is initiated by a ${\mathrm{C}}_{\beta }$… O clash and delimited by a subsequent ${\mathrm{C}}_{\beta }$… NH clash, while the opposite relationship holds for the counter-clockwise change in $\psi$. The impact of the twist on tertiary structures is examined. The understanding of the molecular effects within a strand is deepened by 3D computer images and ball–and–stick models. The use of (tangible) physical models is highlighted in view of teaching structural biology to undergraduate students. Full article

Background: Atherosclerosis (AS) serves as the primary pathological basis for cardiovascular disease-related deaths worldwide, posing a severe threat to public health security. Heat shock protein 90 (HSP90) plays a crucial regulatory role in the pathological progression of AS, emerging as a potential target for anti-atherosclerosis drug development in recent years. Calenduloside E (CE) is a pentacyclic triterpenoid saponin isolated from Aralia elata (Miq.) Seem. Previous studies have confirmed its anti-atherosclerotic activity, but its weak efficacy and narrow therapeutic index limit its clinical application. In this study, the CE scaffold was hybridized with a ticagrelor-derived fragment to enhance anti-atherosclerotic activity. In this study, the CE scaffold was hybridized with a ticagrelor fragment to achieve improved activity. Methods: Based on the principle of molecular hybridization, CE was linked to the active fragment of ticagrelor via a PEG chain. Ten CE derivatives were synthesized by modifying the sugar substituents. In vitro experiments were conducted to detect cytotoxicity and protective activity against ox-LDL-induced HUVECs injury. Molecular docking and Surface Plasmon Resonance (SPR) assays were used to evaluate the interaction between CE derivatives and the known target HSP90β. Combined with Microscale Thermophoresis (MST), SwissTargetPrediction, and molecular docking, other potential targets of CE derivatives were identified. Results: In the ox-LDL-induced HUVECs injury model, all compounds except C2 and C9 exhibited protective activity. Among these compounds, compound C5 exhibited the optimal protective effect, with an EC₅₀ value of 1.44 μM. Molecular docking results revealed that both C5 and CE could bind to HSP90β by forming hydrogen bonds with the key amino acid Asp93. Additionally, SPR results indicated that C5 and CE had similar binding affinities to HSP90β, with dissociation constants (K_D) of 1.73 μM and 1.72 μM, respectively. MST demonstrated that C5 binds to HSP90β with an affinity 111 times higher than that of ticagrelor. SwissTargetPrediction and molecular docking identified P2Y12 as another potential target of derivative C5. Conclusions: Compound C5 exerts protective effect against ox-LDL-induced HUVECs injury by targeting HSP90β. Its effective concentration is significantly improved compared with that of the parent CE, which provides a possibility for reducing clinical dosage and toxic side effects in subsequent studies. Furthermore, C5 may exert its effects by targeting another potential target, P2Y12, offering references for the rational design of novel anti-atherosclerotic drugs. Full article

Ultra-short peptides (USPs; ≤7–8 amino acids) emerge as minimal self-assembling building blocks for hydrogel-based biomaterials. Their intrinsic biocompatibility, straightforward synthesis, and ease of tunability make them particularly attractive candidates for potential use in bioprinting. This review provides an overview of the properties of USPs along with their applications in three-dimensional (3D) bioprinting. We first discuss how peptide sequence, terminal and side-chain modifications, and environmental triggers govern USPs’ self-assembly into nanofibers and 3D networks and how these supramolecular features translate into key rheological properties such as shear-thinning, rapid gelation, and mechanical tunability. We then survey reported applications in tissue engineering, wound healing, and organotypic models, as well as emerging ultra-short peptide-based systems for drug delivery, biosensing, and imaging, highlighting examples where printed constructs support cell viability, differentiation, and matrix deposition. Attention is given to hybrid and multi-material formulations in which USPs provide bioactivity while complementary components contribute structural robustness or additional functionality. Finally, this review outlines the main challenges that currently limit widespread adoption, including achieving high print fidelity with cytocompatible crosslinking, controlling batch-to-batch variability, and addressing the scalability, cost, and sustainability of peptide manufacturing. We conclude by discussing future opportunities such as AI-assisted peptide design, adaptive and multi-material bioprinting workflows, and greener synthetic routes, which together may accelerate the translation of ultra-short peptide-based bioinks from proof-of-concept studies to clinically and industrially relevant platforms. Full article