Cross-linked Peptides Research Articles

Dinickel-Catalyzed N=N Coupling Reactions for the Synthesis of Hindered Azoarenes.

Azoarenes are the largest class of photoswitching molecules, and they have a broad range of applications in photopharmacology and materials science. Azoarenes possessing ortho-substitution often display improved properties, including isomerization under visible light irradiation, near-quantitative switching, and long thermal half-lives in the cis form. The synthesis of hindered ortho-substituted azoarenes is often low-yielding using established oxidative or reductive coupling methods. Here, we describe the design and synthesis of a new dinickel complex that catalyzes the dimerization of ortho-substituted aryl azides in high yield. Applications of this method in the synthesis of high-performance photoswitches, photoactive peptide cross-linkers, hindered diazocines, and main-chain azoarene polymers are described.

Functional characterization of a nanobody-based glycoprotein VI-specific platelet agonist

BackgroundGlycoprotein (GP)VI is a platelet-specific collagen receptor required for platelet activation during hemostasis. Platelet reactivity toward collagen is routinely assessed during diagnostic workup of platelet disorders. GPVI can be activated by inducing receptor clustering with suspensions of fibrillar collagen or synthetic cross-linked collagen-related peptide (CRP-XL). However, these suspensions are poorly standardized or difficult to produce. Nanobodies are small recombinant camelid-derived heavy-chain antibody variable regions. They are highly stable, specific, and ideal candidates for developing a stable GPVI agonist for diagnostic assays. ObjectivesDevelop a stable nanobody-based GPVI agonist. MethodsNanobody D2 (NbD2) was produced as dimers and purified. Tetramers were generated via C-terminal fusion of dimers with click chemistry. Nanobody constructs were functionally characterized with light transmission aggregometry (LTA) in platelet-rich plasma and whole blood flow cytometry. Diagnostic performance was assessed in patients with inherited platelet function disorders with LTA and flow cytometry. ResultsNbD2 was specific for human platelet GPVI. Dimers did not result in platelet activation in LTA or flow cytometry settings and fully inhibited CRP-XL-induced P-selectin expression and fibrinogen binding in whole blood and attenuated collagen-induced platelet aggregation in platelet-rich plasma. However, NbD2 tetramers caused full platelet aggregation, as well as P-selectin expression and fibrinogen binding. NbD2 tetramers were able to discriminate between inherited platelet function disorder patients and healthy controls based on fibrinogen binding, similar to CRP-XL. ConclusionNanobody tetramers to GPVI induce platelet activation and can be used to assess the GPVI pathway in diagnostic assays.

Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells

Unlocking the intricacies of protein structures and interactions within the dynamic landscape of subcellular organelles presents a significant challenge. To address this, we introduce SPACX, a method for spatially resolved protein complex profiling via biocompatible chemical cross(x)-linking with subcellular isolation, designed to monitor protein conformation, interactions, and translocation in living cells. By rapidly capturing protein complexes in their native physiological state and efficiently enriching cross-linked peptides, SPACX allows comprehensive analysis of the protein interactome within living cells. Leveraging structure refinement with cross-linking restraints, we identify subcellular-specific conformation heterogeneity of PTEN, revealing dynamic differences in its dual specificity domains between the nucleus and cytoplasm. Furthermore, by discerning conformational disparities, we identify 83 cytoplasm-exclusive and 109 nucleus-exclusive PTEN-interacting proteins, each associated with distinct biological functions. Upon induction of ubiquitin-proteasome system stress, we observe dynamic alterations in PTEN assembly and its interacting partners during translocation. These changes, including the identification of components and interaction sites, are characterized using the SPACX approach. Notably, SPACX enables identification of unique interacting proteins specific to PTEN isoforms, including PTEN and PTEN-Long, through the determination of sequence-specific cross-linking interfaces. These findings underscore the potential of SPACX to elucidate the functional diversity of proteins within distinct subcellular sociology.

Mechanisms conferring bacterial cell wall variability and adaptivity.

The bacterial cell wall, a sophisticated and dynamic structure predominantly composed of peptidoglycan (PG), plays a pivotal role in bacterial survival and adaptation. Bacteria actively modify their cell walls by editing PG components in response to environmental challenges. Diverse variations in peptide composition, cross-linking patterns, and glycan strand structures empower bacteria to resist antibiotics, evade host immune detection, and adapt to dynamic environments. This review comprehensively summarizes the most common modifications reported to date and their associated adaptive role and further highlights how regulation of PG synthesis and turnover provides resilience to cell lysis.

Enhanced rare earth element recovery with cross-linked glutaraldehyde-lanthanide binding peptides in foam-based separations

HypothesisLanthanide Binding Tag (LBT) peptides that coordinate selectively with lanthanide ions can be used to replace the energy intensive processes used for the separation of rare earth elements (REEs). These surface-active biomolecules, once selectively complexed with the trivalent REE cations, can adsorb to air/aqueous interfaces of bubbles for foam-based REEs recovery. Glutaraldehyde, an organic compound that is a homobifunctional crosslinker for proteins and peptides, can be used to enhance the adsorption and interfacial stabilization of lanthanide-bound peptides films. ExperimentsThe stability of the interfacial cross-linked films was tested by measuring their dilational and shear surface rheological properties. Surface activity of the adsorbed species was analyzed using pendant drop tensiometry, while surface density and molecular arrangement were determined using x-ray reflectivity and x-ray fluorescence near total reflection. FindingsGlutaraldehyde cross-linked REE-peptide complexes enhance the adsorption of lanthanides to air-water interfaces, resulting in thicker interfacial structures. Subsequently, these thicker layers enhance the dilational and shear interfacial rheological properties. The interfacial film stabilization and REEs extraction promoted by the cross-linker presented in this work provides an approach to integrate glutaraldehyde as a substitute of common foam stabilizers such as polymers, surfactants, and particles to optimize the recovery of REEs when using biomolecules as extractants.

Identification of a family of peptidoglycan transpeptidases reveals that Clostridioides difficile requires noncanonical cross-links for viability

Most bacteria are surrounded by a cell wall that contains peptidoglycan (PG), a large polymer composed of glycan strands held together by short peptide cross-links. There are two major types of cross-links, termed 4-3 and 3-3 based on the amino acids involved. 4-3 cross-links are created by penicillin-binding proteins, while 3-3 cross-links are created by L,D-transpeptidases (LDTs). In most bacteria, the predominant mode of cross-linking is 4-3, and these cross-links are essential for viability, while 3-3 cross-links comprise only a minor fraction and are not essential. However, in the opportunistic intestinal pathogen Clostridioides difficile, about 70% of the cross-links are 3-3. We show here that 3-3 cross-links and LDTs are essential for viability in C. difficile. We also show that C. difficile has five LDTs, three with a YkuD catalytic domain as in all previously known LDTs and two with a VanW catalytic domain, whose function was until now unknown. The five LDTs exhibit extensive functional redundancy. VanW domain proteins are found in many gram-positive bacteria but scarce in other lineages. We tested seven non-C. difficile VanW domain proteins and confirmed LDT activity in three cases. In summary, our findings uncover a previously unrecognized family of PG cross-linking enzymes, assign a catalytic function to VanW domains, and demonstrate that 3-3 cross-linking is essential for viability in C. difficile, the first time this has been shown in any bacterial species. The essentiality of LDTs in C. difficile makes them potential targets for antibiotics that kill C. difficile selectively.

Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks.

Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric cross-links can offer enhanced spatial resolution to facilitate the characterization of dynamic and heterogeneous protein complexes. However, the identification of multimeric cross-links remains extremely challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MS n analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks. The trimeric interactions captured by TSTO have uncovered new structural details that cannot be easily revealed by existing reagents, allowing in-depth description of PPIs to facilitate structural modeling. This development not only advances XL-MS technologies for global PPI profiling from living cells, but also offers a new direction for creating multifunctional MS-cleavable cross-linkers to further push structural systems biology forward in the future.

An Optimized Miniaturized Filter-Aided Sample Preparation Method for Sensitive Cross-Linking Mass Spectrometry Analysis of Microscale Samples.

Cross-linking mass spectrometry (XL-MS) is a powerful tool for elucidating protein structures and protein-protein interactions (PPIs) at the global scale. However, sensitive XL-MS analysis of mass-limited samples remains challenging, due to serious sample loss during sample preparation of the low-abundance cross-linked peptides. Herein, an optimized miniaturized filter-aided sample preparation (O-MICROFASP) method was presented for sensitive XL-MS analysis of microscale samples. By systematically investigating and optimizing crucial experimental factors, this approach dramatically improves the XL identification of low and submicrogram samples. Compared with the conventional FASP method, more than 7.4 times cross-linked peptides were identified from single-shot analysis of 1 μg DSS cross-linked HeLa cell lysates (440 vs 59). The number of cross-linked peptides identified from 0.5 μg HeLa cell lysates was increased by 58% when further reducing the surface area of the filter to 0.058 mm2 in the microreactor. To deepen the identification coverage of XL-proteome, five different types of cross-linkers were used and each μg of cross-linked HeLa cell lysates was processed by O-MICROFASP integrated with tip-based strong cation exchange (SCX) fractionation. Up to 2741 unique cross-linked peptides were identified from the 5 μg HeLa cell lysates, representing 2579 unique K-K linkages on 1092 proteins. About 96% of intraprotein cross-links were within the maximal distance restraints of 26 Å, and 75% of the identified PPIs reported by the STRING database were with high confidence (scores ≥0.9), confirming the high validity of the identified cross-links for protein structural mapping and PPI analysis. This study demonstrates that O-MICROFASP is a universal and efficient method for proteome-wide XL-MS analysis of microscale samples with high sensitivity and reliability.

On the utility of the extracted ion chromatograms for assigning the conjugation sites and side reactions in bioconjugates synthesized by the maleimide-thiol chemistry

Maleimide-thiol chemistry is widely used in the synthesis of protein–protein conjugate vaccines. In this reaction, thiol and maleimide groups, either in the carrier protein or in the antigen molecules, are linked via a thiosuccinimide linker. The assignment of the conjugation sites is key and is usually done by LC-MS/MS analysis of the conjugate proteolytic digestion, resulting in a very complex mixture of linear peptides and cross-linked peptide pairs. During proteolysis, the thiosuccinimide linker is converted to its hydrolyzed and transcyclized forms. The set of MS/MS spectra assigned to cross-linked peptide pairs contains valuable information about the conjugation sites that must be validated using objective criteria for more reliable assignment. The extracted ion chromatograms (XICs) have not previously been considered for these validation purposes. In the LC-MS/MS analysis, linear peptides eluted with a single-peak XIC pattern, while the cross-linked peptide pairs with a transcyclized linker (consisting of a mixture of diastereomers) eluted with a two-peak XIC pattern in 68–100 % of cases. Cross-linked peptide pairs with the hydrolyzed linker were detected with a multi-peak XIC pattern consisting of two, three and four peaks in 77 %, 15 % and 8 % of cases, respectively. The four-peak XIC pattern corresponds to cross-linked peptide pairs with two positional isomers of the hydrolyzed linker containing a mixture of diastereomers. Tandem digestions increased the analytical value of the XICs by converting the large and hydrophobic cross-linked peptide pairs, that show a single-peak XIC pattern, to more hydrophilic species eluting in multi-peak XIC patterns. XICs are easily obtained in any LC-MS/MS analysis, contain valuable information about conjugation sites and side reaction detection, and are worthy of routine inclusion in bioconjugate characterization.

Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids

Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.

Epimedii Folium decoction ameliorates osteoporosis in mice through NLRP3/caspase-1/IL-1β signalling pathway and gut-bone axis

Aim of the studyThis study aimed to determine the effect of Epimedium brevicornu Maxim. (EF) on osteoporosis (OP) and its underlying molecular mechanisms, and to explore the existence of the “Gut-Bone Axis”. Material and methodsThe impact of EF decoction (EFD) on OP was evaluated using istopathological examination and biochemical assays. Targeted metabolomics was employed to identify key molecules and explore their molecular mechanisms. Alterations in the gut microbiota (GM) were evaluated by 16S rRNA gene sequencing. The role of the GM was clarified using an antibiotic cocktail and faecal microbiota transplantation. ResultsEFD significantly increased the weight (14.06%), femur length (4.34%), abdominal fat weight (61.14%), uterine weight (69.86%), and insulin-like growth factor 1 (IGF-1) levels (59.48%), while reducing serum type I collagen cross-linked carboxy-terminal peptide (CTX-I) levels (15.02%) in osteoporotic mice. The mechanism of action may involve the regulation of the NLRP3/cleaved caspase-1/IL-1β signalling pathway in improving intestinal tight junction proteins and bone metabolism. Additionally, EFD modulated the abundance of related GM communities, such as Lactobacillus, Coriobacteriaceae, bacteria of family S24-7, Clostridiales, and Prevotella, and increased propionate and butyrate levels. Antibiotic-induced dysbiosis of gut bacteria disrupted OP regulation of bone metabolism, which was restored by the recovery of GM. ConclusionsOur study is the first to demonstrate that EFD works in an OP mouse model by utilising GM and butyric acid. Thus, EF shows promise as a potential remedy for OP in the future.

Strong and Thermo-Switchable Gel Adhesion Based on UCST-Type Phase Transition in Deep Eutectic Solvent.

It remains a great challenge to achieve strong and reversible hydrogel adhesion. Hydrogel adhesives also suffer from poor environmental stability due to dehydration. To overcome these problems, here reversible adhesive gels are designed using a new switching mechanism and new solvent. For the first time, the study observes UCST (upper critical solution temperature)-type thermosensitive behaviors of poly(benzyl acrylate) (PBnA) polymer and gel in menthol:thymol deep eutectic solvents (DESs). The temperature-induced phase transition allows adjusting cohesive force, and hence adhesion strength of PBnA gels by temperature. To further improve the mechanical and adhesion properties, a peptide crosslinker is used to allow energy dissipation when deforming. The resulting eutectogel exhibits thermal reversible adhesion with a high switching ratio of 14.0. The adhesion strength at attachment state reaches 0.627MPa, which is much higher than most reversible adhesive hydrogels reported before. The low vapor pressure of DES endows the gel excellent environmental stability. More importantly, the gel can be repeatedly switched between attachment and detachment states. The strong and reversible gel adhesive is successfully used to design soft gripper for the transport of heavy cargos and climbing robot capable of moving on vertical and inverted surface in a manner similar to gecko.

Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines.

Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.

Molecularly imprinted polymer for selective insulin capture and separation

Human insulin production was severely limited by its complex downstream processing. Herein, an insulin-imprinted polymer with shape-memorable imprint cavities was designed for the separation and purification of insulin from complex biofluids. N-isopropylacrylamide (NIPAM) was chosen as main monomer, and acrylamide (AAm) and (3-acrylamidopropyl)trimethylammonium chloride (AAPTAC) as functional monomers. A poly(l-lysine)-based peptide crosslinker, instead of the commonly used crosslinkers, was used to introduce poly(l-lysine) segments into the polymer. Because of the reversible and precise pH-induced helix-coil transition of the poly(l-lysine) segments, the imprint cavities in the polymer are shape-memorable. For this reason, the insulin template can be removed completely under mild conditions, meanwhile the imprinting efficiency is significantly improved. A high adsorption capacity (595 mg/g) and a high imprinting factor (5.83) were obtained, both of which are significantly higher than the previously developed insulin-imprinted polymers. The polymer also exhibits a high selectivity towards insulin and can be used repeatedly. Using this polymer insulin spiked in human serum was selectively captured and separated, demonstrating its ability for separation and purification of insulin from complex biofluids.

Rare-Earth-Metal-Free Solid-State Fluorescent Carbonized-Polymer Microspheres for Unclonable Anti-Counterfeit Whispering-Gallery Emissions from Red to Near-Infrared Wavelengths.

Colloidal carbon dots (CDs) have garnered much attention as metal-free photoluminescent nanomaterials, yet creation of solid-state fluorescent (SSF) materials emitting in the deep red (DR) to near-infrared (NIR) range poses a significant challenge with practical implications. To address this challenge and to engineer photonic functionalities, a micro-resonator architecture is developed using carbonized polymer microspheres (CPMs), evolved from conventional colloidal nanodots. Gram-scale production of CPMs utilizes controlled microscopic phase separation facilitated by natural peptide cross-linking during hydrothermal processing. The resulting microstructure effectively suppresses aggregation-induced quenching (AIQ), enabling strong solid-state light emission. Both experimental and theoretical analysis support a role for extended π-conjugated polycyclic aromatic hydrocarbons (PAHs) trapped within these microstructures, which exhibit a progressive red shift in light absorption/emission toward the NIR range. Moreover, the highly spherical shape of CPMs endows them with innate photonic functionalities in combination with their intrinsic CD-based attributes. Harnessing their excitation wavelength-dependent photoluminescent (PL) property, a single CPM exhibits whispering-gallery modes (WGMs) that are emission-tunable from the DR to the NIR. This type of newly developed microresonator can serve as, for example, unclonable anti-counterfeiting labels. This innovative cross-cutting approach, combining photonics and chemistry, offers robust, bottom-up, built-in photonic functionality with diverse NIR applications.

Secondary Structure Stabilization of Macrocyclic Antimicrobial Peptides via Cross-Link Swapping.

Lactam cross-links have been employed to stabilize the helical secondary structure and enhance the activity and physiological stability of antimicrobial peptides; however, stabilization of β-sheets via lactamization has not been observed. In the present study, lactams between the side chains of C- and N-terminal residues have been used to stabilize the β-sheet conformation in a short ten-residue analogue of chicken angiogenin-4. Designed using a combination of molecular dynamics simulations and Markov state models, the lactam cross-linked peptides are shown to adopt stabilized β-sheet conformations consistent with simulated structures. Replacement of the peptide side-chain Cys-Cys disulfide by a lactam cross-link enhanced the broad-spectrum antibacterial activity compared to the parent peptide and exhibited greater propensity to induce proinflammatory activity in macrophages. The combination of molecular simulations and conformational and biological analyses of the synthetic peptides provides a useful paradigm for the rational design of therapeutically active peptides with constrained β-sheet structures.

Genetic background of walking ability and its relationship with leg defects, mortality, and performance traits in turkeys (Meleagris gallopavo)

This study aimed to explore the genetic basis of walking ability and potentially related performance traits in turkey purebred populations. Phenotypic, pedigree, and genomic datasets from 2 turkey lines hatched between 2010 and 2023 were included in the study. Walking ability data, defined based on a scoring system ranging from 1 (worst) to 6 (best), were collected on 192,019 animals of a female line and 235,461 animals of a male line. Genomic information was obtained for 46,427 turkeys (22,302 from a female line and 24,125 from a male line) using a 65K single nucleotide polymorphism (SNP) panel. Variance components and heritability for walking ability were estimated. Furthermore, genetic and phenotypic correlations among walking ability, mortality and disorders, and performance traits were calculated. A genome-wide association study (GWAS) was also conducted to identify SNPs associated with walking ability. Walking ability is moderately heritable (0.23 ± 0.01) in both turkey lines. The genetic correlations between walking ability and the other evaluated traits ranged from -0.02 to -0.78, with leg defects exhibiting the strongest negative correlation with walking ability. In the female line, 31 SNPs were associated with walking ability and overlapped with 116 genes. These positional genes are linked to 6 gene ontology (GO) terms. Notably, genes such as CSRP2, DDX1, RHBDL1, SEZ6L, and CTSK are involved in growth, development, locomotion, and bone disorders. GO terms, including fibronectin binding (GO:0001968), peptide cross-linking (GO:0018149), and catabolic process (GO:0009057), are directly linked with mobility. In the male line, 66 markers associated with walking ability were identified and overlapped with 281 genes. These genes are linked to 12 GO terms. Genes such as RB1CC1, TNNI1, MSTN, FN1, SIK3, PADI2, ERBB4, B3GNT2, and BACE1 are associated with cell growth, myostatin development, and disorders. GO terms in the male line are predominantly related to lipid metabolism. In conclusion, walking ability is moderately heritable in both populations. Furthermore, walking ability can be enhanced through targeted genetic selection, emphasizing its relevance to both animal welfare and productivity.

A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.

Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.

Probing Protein Structural Changes in Alzheimer's Disease via Quantitative Cross-linking Mass Spectrometry.

Alzheimer's disease (AD) is a progressive neurological disorder featuring abnormal protein aggregation in the brain, including the pathological hallmarks of amyloid plaques and hyperphosphorylated tau. Despite extensive research efforts, understanding the molecular intricacies driving AD development remains a formidable challenge. This study focuses on identifying key protein conformational changes associated with the progression of AD. To achieve this, we employed quantitative cross-linking mass spectrometry (XL-MS) to elucidate conformational changes in the protein networks in cerebrospinal fluid (CSF). By using isotopically labeled cross-linkers BS3d0 and BS3d4, we reveal a dynamic shift in protein interaction networks during AD progression. Our comprehensive analysis highlights distinct alterations in protein-protein interactions within mild cognitive impairment (MCI) states. This study accentuates the potential of cross-linked peptides as indicators of AD-related conformational changes, including previously unreported site-specific binding between α-1-antitrypsin (A1AT) and complement component 3 (CO3). Furthermore, this work enables detailed structural characterization of apolipoprotein E (ApoE) and reveals modifications within its helical domains, suggesting their involvement in MCI pathogenesis. The quantitative approach provides insights into site-specific interactions and changes in the abundance of cross-linked peptides, offering an improved understanding of the intricate protein-protein interactions underlying AD progression. These findings lay a foundation for the development of potential diagnostic or therapeutic strategies aimed at mitigating the negative impact of AD.

Production of novel mung bean peptides-based zinc supplement: Process optimization, chelation mechanism, and stability assessment in vitro

To realize the add value of protein resources from mung bean processing by-products, mung bean peptides-zinc chelate (MBP-Zn), a novel zinc supplement, was synthesized in the present study. Under the optimized process conditions (MBP concentration of 6%, pH 5.0, mass ratio of MBP to zinc salt of 2:1, temperature of 60 °C and time of 80 min), the zinc chelation rate of MBP-Zn reached up to 98.15%. Integrating the results of Fourier transform infrared spectroscopy and amino acid profiles, it is inferred that zinc ions may bind to MBP via carboxy oxygen, amino nitrogen, and sulfhydryl sulfur atoms. The incorporation of zinc ions dramatically changed the structure of the chelate, as evidenced by the blue shift and attenuation of the original UV and fluorescence spectra. The morphological analysis revealed that Zn2+ induced cross-linking of peptides, forming enlarged nanoparticles that fragmented the original smooth surface of MBP. Surprisingly, the superior stability of MBP-Zn over the conventional zinc supplement ZnSO4 was confirmed, regardless of pH and temperature variations, or simulated gastrointestinal digestion circumstances. These findings pave the way for the large-scale production of mung bean peptide-based zinc supplements as nutraceuticals in the food industry.