Structure and Zeatin Binding of the Peach Allergen Pru p 1

The PR-10 Protein Pru p 1 is an Endonuclease that Preferentially Cleaves Single-Stranded RNA

Pathogenesis-related class 10 (PR-10) proteins play a crucial role in plant defense by acting as ribonucleases. The specific mechanism of action and substrate specificity of these proteins have remained largely unexplored so far. In this study, we elucidate the enzymatic activity of Pru p 1, a PR-10 protein from peach. We demonstrate that this protein catalyzes the endonucleolytic backbone cleavage of RNA substrates into short oligonucleotides. Initial cleavage products, identified through kinetic analysis, can bind again, priming them for further degradation. NMR binding site mapping reveals that the large internal cavity of Pru p 1, which is characteristic for PR-10 proteins, serves as an anchoring site for single-stranded ribonucleotide chains. We propose a structure-based mechanistic model that accounts for the observed cleavage patterns and the inhibitory effect of zeatin, a nucleoside analog, on the ribonuclease activity of Pru p 1.

Precision engineering for localization, validation, and modification of allergenic epitopes

The allergen-IgE interaction is essential for the genesis of allergic responses, yet investigation of the molecular basis of these interactions is in its infancy. Precision engineering has unveiled the molecular features of allergen-antibody interactions at the atomic level. High-resolution technologies, including x-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy, determine allergen-antibody structures. X-ray crystallography of an allergen-antibody complex localizes in detail amino acid residues and interactions that define the epitope-paratope interface. Multiple structures involving murine IgG mAbs have recently been resolved. The number of amino acids forming the epitope broadly correlates with the epitope area. The production of human IgE mAbs from B cells of allergic subjects is an exciting recent development that has for the first time enabled an actual IgE epitope to be defined. The biologic activity of defined IgE epitopes can be validated in vivo in animal models or by measuring mediator release from engineered basophilic cell lines. Finally, gene-editing approaches using the Clustered Regularly Interspaced Short Palindromic Repeats technology to either remove allergen genes or make targeted epitope engineering at the source are on the horizon. This review presents an overview of the identification and validation of allergenic epitopes by precision engineering.

Structural Characterization of Food Allergens by Nuclear Magnetic Resonance Spectroscopy

As allergies, especially those triggered by food, are becoming more and more prevalent, it is of increasing importance to fully understand the structures and dynamic behaviors of allergenic proteins along with their interactions with potential natural ligands. Therefore, we have established a solid routine to achieve structural characterization of food allergens, especially for birch pollen-related cross-reactive proteins from the class 10 of pathogenesis-related proteins (PR-10), by nuclear magnetic resonance (NMR) spectroscopy. Following expression of the desired allergen in Escherichia coli in isotope-labeled minimal media, the three-dimensional solution structures of these proteins can be determined, and insight into ligand binding mechanics and structural dynamic properties are accessible through NMR spin relaxation experiments.

Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen

Allergies related to kiwi consumption have become a growing health concern, with their prevalence on the rise. Many of these allergic reactions are attributed to cross-reactivity, particularly with the major allergen found in birch pollen. This cross-reactivity is associated with proteins belonging to the pathogenesis-related class 10 (PR-10) protein family. In our study, we determined the three-dimensional structures of the two PR-10 proteins in gold and green kiwi fruits, Act c 8 and Act d 8, using nuclear magnetic resonance (NMR) spectroscopy. The structures of both kiwi proteins closely resemble the major birch pollen allergen, Bet v 1, providing a molecular explanation for the observed immunological cross-reactivity between kiwi and birch pollen. Compared to Act d 11, however, a kiwi allergen that shares the same architecture as PR-10 proteins, structural differences are apparent. Moreover, despite both Act c 8 and Act d 8 containing multiple cysteine residues, no disulfide bridges are present within their structures. Instead, all the cysteines are accessible on the protein's surface and exposed to the surrounding solvent, where they are available for reactions with components of the natural food matrix. This structural characteristic sets Act c 8 and Act d 8 apart from other kiwi proteins with a high cysteine content. Furthermore, we demonstrate that pyrogallol, the most abundant phenolic compound found in kiwi, binds into the internal cavities of these two proteins, albeit with low affinity. Our research offers a foundation for further studies aimed at understanding allergic reactions associated with this fruit and exploring how interactions with the natural food matrix might be employed to enhance food safety.

Effect of ultrahigh-pressure treatment on the structure and allergenicity of peach allergenic proteins

Peach is a common plant-derived allergenic food and ultrahigh-pressure treatment is often used in peach products. In our study, an in-depth analysis of the structural and allergenicity changes of peach allergenic proteins after UHP treatment was performed by spectroscopy, mass spectrometry combined with serology and cytology. The results indicated that UHP treatment could reduce the content of peach soluble proteins and cause changes in secondary and tertiary structures. In addition, more hydrophobic residues were exposed and proteins tended to polymerize after UHP-treatment. The results of immunological assays showed that UHP treatment could reduce the IgE binding capacity of peach proteins and affect the ability of basophil degranulation, the upregulation of some cytokines may contribute to the reduction of peach protein allergenicity. Notably, UHP treatment may lead to the masking of some digestion sites in Pru p 3 epitopes, thus impeding human digestion and increasing the potential risk of allergenicity.

2-Hydrazinoterephthalic Acid as a Novel Negative-Ion Matrix-Assisted Laser Desorption/Ionization Matrix for Qualitative and Quantitative Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Analysis of N-Glycans in Peach Allergy Research

Glycans recently attracted considerable attention as the proposal of cross-reactive carbohydrate determinants for food allergy. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is powerful in analyzing biomolecules, while its applications in glycans are still challenging. Herein, a novel reactive matrix-assisted laser desorption/ionization (MALDI) matrix, 2-hydrazinoterephthalic acid, was rationally designed and synthesized. It provides uniform co-crystallization with glycans and only produces deprotonated ions with high intensities in the negative-ion mode. In combination with sinapic acid, a rapid and high-throughput method was established for on-target analysis of glycans with a superior limit of detection at the femtomole level and a good linearity (R² > 0.999). Furthermore, the established method was successfully applied to quantify N-glycans in different cultivars and tissues of peach [Prunus persica (L.) Batsch]. Our work suggests the potential role of N-glycans as biomarkers for food-borne allergy and lays a methodological foundation for the elucidation of the possible relationship between carbohydrate epitopes and food allergy.

The Structural Flexibility of PR-10 Food Allergens

PR-10 proteins constitute a major cause of food allergic reactions. Birch-pollen-related food allergies are triggered by the immunologic cross-reactivity of IgE antibodies with structurally homologous PR-10 proteins that are present in birch pollen and various food sources. While the three-dimensional structures of PR-10 food allergens have been characterized in detail, only a few experimental studies have addressed the structural flexibility of these proteins. In this study, we analyze the millisecond-timescale structural flexibility of thirteen PR-10 proteins from prevalent plant food sources by NMR relaxation-dispersion spectroscopy, in a comparative manner. We show that all the allergens in this study have inherently flexible protein backbones in solution, yet the extent of the structural flexibility appears to be strikingly protein-specific (but not food-source-specific). Above-average flexibility is present in the two short helices, α1 and α2, which form a V-shaped support for the long C-terminal helix α3, and shape the internal ligand-binding cavity, which is characteristic for PR-10 proteins. An in-depth analysis of the NMR relaxation-dispersion data for the PR-10 allergen from peanut reveals the presence of at least two subglobal conformational transitions on the millisecond timescale, which may be related to the release of bound low-molecular-weight ligands from the internal cavity.

Identification of Major B-Cell Linear Epitopes of Peach Allergen Pru p 3 Using Immune Slot-Blot Microarray Assay

Pru p 3, one of the most representative proteins of the lipid transfer proteins (LTPs), is responsible for clinical allergic reactions to food of peach origin. The identification of Pru p 3 epitopes is not comprehensive due to different methods and principles of epitope screening. In addition, evaluation of the stability of the epitopes and the validation of the immunological key amino acids still need further research. Therefore, in the present study, an immune slot-blot microarray assay was performed to screen the epitopes from Pru p 3 overlapping peptide library, and a new epitope (P-1, AA1-16, ITCGQVSSALAPCIPY) was identified and two identified epitopes were deeply investigated (P-2, AA12-27, PCIPYVRGGGAVPPAC; P-3, AA23-38, VPPACCNGIRNVNNLA). The stability of these epitopes was then verified by thermal processing treatment and digestion experiments. Moreover, the key amino acids of the three identified epitopes were obtained by epitope amino acid mutation combined with slot-blot experiments. These findings may contribute to the further understanding of Pru p 3 and the prevention of peach allergy.

Effect of Processing on the Structure and Allergenicity of Peanut Allergen Ara h 2 Roasted in a Matrix

Peanut allergy is the leading pediatric food allergy. Many attempts have been made to reduce its allergenicity by processing. After roasting, Ara h 2 and its derivatives in the matrix were isolated by immunoaffinity chromatography (IAC). The structure and allergenicity of Ara h 2 were analyzed by circular dichroism, mass spectrometry (MS), western blotting, the enzyme-linked immunoassay, and cell modeling. Our results showed that a large portion of Ara h 2 was fragmented and cross-linked. Ara h 2 monomers accounted for only 13% of the total proteins after IAC purification. In addition, the structure of Ara h 2 changed after roasting. In addition to methylation and oxidation modification, the disulfide bonds of Ara h 2 were found to be rearranged after roasting. In the conformational structure of Ara h 2, the content of the α-helix decreased from 27.1 to 21.6% after roasting, while the content of the random coil increased from 29.1 to 34.3%. Six cleavage sites of trypsin were exposed, while three were covered. In terms of allergenicity, most of the cross-linking products were not recognized by patients' sera. Only one faint band around 40 kDa was observed in our blotting. For Ara h 2 monomers, roasting enhanced their IgE binding capacity and ability to stimulate the degranulation of basophils. The potential allergenicity increase of Ara h 2 monomers did not reflect the allergenicity change of Ara h 2 in the matrix due to the amount and property of its derivatives after roasting.

Microscale Thermophoresis Reveals Oxidized Glutathione as High-Affinity Ligand of Mal d 1

Pathogenesis-related (PR)-10 proteins, due to their particular secondary structure, can bind various ligands which could be important for their biological function. Accordingly, the PR-10 protein Mal d 1, the major apple allergen, probably also binds molecules in the hydrophobic cavity of its secondary structure, but it has not yet been investigated in this respect. In this study, various natural products found in apples such as flavonoids, glutathione (GSH), and glutathione disulfide (GSSG) were investigated as possible ligands of Mal d 1 using microscale thermophoresis. Dissociation constants of 16.39 µM, 29.51 µM, 35.79 µM, and 0.157 µM were determined for catechin, quercetin-3-O-rhamnoside, GSH, and GSSG, respectively. Molecular docking was performed to better understand the underlying binding mechanism and revealed hydrophobic interactions that stabilize the ligands within the pocket while hydrophilic interactions determine the binding of both GSH derivatives. The binding of these ligands could be important for the allergenicity of the PR-10 protein and provide further insights into its physiological role.