Major linear IgE epitopes of mountain cedar pollen allergen Jun a 1 map to the pectate lyase catalytic site

Identifying Similar Allergens and Potentially Cross-Reacting Areas Using Structural Database of Allergenic Proteins (SDAP) Tools and D-Graph

The Structural Database of Allergenic Proteins (SDAP) provides rapid search tools to identify similarities among allergens, their IgE epitopes, and to determine the potential allergenicity of any novel protein. Many labs have identified IgE-binding proteins and their antibody binding or T cell epitopes using dotspots or microarrays. This chapter describes how to determine the relationship of these proteins and peptides to known allergens using the tools implemented in SDAP. One can also search with these smaller peptide similarity search tool implemented in SDAP to find similar sequences with low property distance (PD) values in the over 1500 sequences of allergens. The sequences can be compared by mapping on the surface of the protein structures provided for nearly all the allergens in SDAP. Once the user has a unique list of similar sequences, they can be graphed in 2D according to interpeptide PD values calculated automatically by the D-graph program. This chapter provides a step-by-step description of how to do this, starting from a protein similar to the Ole e 1 (olive pollen) allergen family.

The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated bioinformatics tools

Background

Allergenic proteins can cause IgE-mediated adverse reactions in sensitized individuals. Although the sequences of many allergenic proteins have been identified, bioinformatics data analysis with advanced computational methods and modeling is needed to identify the basis for IgE binding and cross-reactivity.

Objective

We aim to present the features and use of the updated Structural Database of Allergenic Proteins 2.0 (SDAP 2.0) webserver, a unique, publicly available resource to compare allergens using specially designed computational tools and new high-quality 3-D models for most known allergens.

Methods

Previously developed and novel software tools for identifying cross-reactive allergens using sequence and structure similarity are implemented in SDAP 2.0. A comprehensive set of high-quality 3-D models of most allergens was generated with the state-of-the-art AlphaFold 2 software. A graphics tool enables the interactive visualization of IgE epitopes on experimentally determined and modeled 3-D structures.

Results

A user can search for allergens similar to a given input sequence with the FASTA algorithm or the window-based World Health Organization/International Union of Immunological Societies (WHO/IUIS) guidelines on safety concerns of novel food products. Peptides similar to known IgE epitopes can be identified with the property distance tool and conformational epitopes by the Cross-React method. The updated database contains 1657 manually curated sequences including all allergens from the IUIS database, 334 experimentally determined X-ray or NMR structures, and 1565 3-D models. Each allergen/isoallergen is classified according to its protein family.

Conclusions

SDAP provides access to the steadily increasing information on allergenic structures and epitopes with integrated bioinformatics tools to identify and analyze their similarities. In addition to serving the research and regulatory community, it provides clinicians with tools to identify potential coallergies in a sensitive patient and can help companies to design hypoallergenic foods and immunotherapies.

Safety evaluation of the food enzyme endo-polygalacturonase from the non-genetically modified Aspergillus tubingensis strain MUCL 55013

The food enzyme endo-polygalacturonase ((1→4)-α-d-galacturonan glycanohydrolase (endo-cleaving); EC 3.2.1.15)) is produced with the non-genetically modified Aspergillus tubingensis strain MUCL 55013 by Soufflet Biotechnologies. The food enzyme is free from viable cells of the production organism. It is intended to be used in 10 food manufacturing processes: processing of fruits and vegetables for the production of juices, other fruit and vegetable products, wine, distilled spirits from wine, alcoholic beverages other than grape wine; processing of plant-derived products for the production of refined and unrefined sugar, edible oils from plants, green coffee beans by demucilation, coffee extracts and tea and other herbal and fruit infusions. Since residual amounts of total organic solids (TOS) are removed in three processes, dietary exposure was calculated only for the remaining seven food manufacturing processes. Exposure was estimated to be up to 7.834 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 2,097 mg TOS/kg bw per day, the highest dose tested, resulting in a margin of exposure of at least 268. A search for the similarity of the amino acid sequence of the food enzyme to known allergens found 14 matches, one of which was to a food allergen. The Panel considered that the risk of allergic reactions upon dietary exposure to this food enzyme cannot be excluded, in particular for individuals sensitised to papaya, but that the risk will not exceed that of consumption of papaya. In addition, oral allergy reactions cannot be excluded in pollen-sensitised individuals. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Peptide immunotherapy for aeroallergens

Background: Allergen specific immunotherapy (SIT) has been used for more than a century. Researchers have been working to improve efficacy and reduce the side effects. Objective: We have reviewed the literature about peptides immunotherapy for inhaled allergens. The mechanism of SIT is to induce regulatory T (Treg) cells and to reduce T helper (Th)2 cells to induce class switching from IgE to IgG and induce blocking antibodies to inhibit allergen binding of IgE. Methods: The relevant published literatures on the peptide SIT for aeroallergens have been searched on the medline. Results: Modification of allergens and routes of treatment has been performed. Among them, many researchers were interested in peptide immunotherapy. T-cell epitope peptide has no IgE epitope, that is able to bind IgE, but rather induces Treg and reduces Th2 cells, which was considered an ideal therapy. Results from cellular and animal model studies have been successful. However, in clinical studies, T-cell peptide immunotherapy has failed to show efficacy and caused side effects, because of the high effective rate of placebo and the development of IgE against T-cell epitope peptides. Currently, the modifications of IgE-allergen binding by blocking antibodies are considered for successful allergen immunotherapy. Conclusion: Newly developed hypoallergenic B cell epitope peptides and computational identification methods hold great potential to develop new peptide immunotherapies.

Safety evaluation of a food enzyme containing endo-polygalacturonase and pectin lyase activities from the non-genetically modified Aspergillus tubingensis strain NZYM-PE

The food enzyme with the declared activities endo-polygalacturonase ((1-4)-α-D-galacturonan glycanohydrolase; EC 3.2.1.15) and pectin lyase ((1-4)-6-O-methyl-α-D-galacturonan lyase; EC 4.2.2.10) is produced with the non-genetically modified Aspergillus tubingensis strain NZYM-PE by Novozymes A/S. It is intended to be used in four food manufacturing processes: fruit and vegetable processing for juice production, fruit and vegetable processing for products other than juices, refined olive oil production and wine and wine vinegar production. Since residual amounts of total organic solids (TOS) are removed during production, dietary exposure was not calculated for refined olive oil production. For the remaining three food processes, it was estimated to be up to 0.132 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level (NOAEL) of 1,430 mg TOS/kg bw per day, the highest dose tested, which when compared with the estimated dietary exposure, resulted in a margin of exposure above 10,833. A search for the similarity of the amino acid sequence of the food enzyme to known allergens was made and 13 matches were found, including one food allergen (papaya). The Panel considered that, under the intended conditions of use, the risk of allergic reactions upon dietary exposure to this food enzyme cannot be excluded, in particular for individuals sensitised to papaya, but that the risk will not exceed that of consumption of papaya. In addition, oral allergy reactions cannot be excluded in pollen-sensitised individuals. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Safety evaluation of the food enzyme endo-polygalacturonase from the genetically modified Aspergillus niger strain EPG

The food enzyme endo-polygalacturonase ((1-4)-α-d-galacturonan glycanohydrolase; EC 3.2.1.15) is produced with the genetically modified Aspergillus niger strain EPG by DSM Food Specialties B.V. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and its DNA. It is intended to be used in fruit and vegetable processing for juice production. The dietary exposure to the food enzyme-total organic solids (TOS) was estimated to be up to 0.122 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1,014 mg TOS/kg bw per day, the highest dose tested, which, when compared with the estimated dietary exposure, resulted in a margin of exposure at least 8,311. A search for the similarity of the amino acid sequence of the food enzyme to known allergens was made and 38 matches were found, two of which are food allergens. The Panel considered that, under the intended conditions of use, the risk of allergic reactions upon dietary exposure to this food enzyme cannot be excluded, in particular for individuals sensitised to papaya or maize, but that the risk will not exceed that of consumption of papaya or maize. In addition, oral allergy reactions cannot be excluded in pollen-sensitised individuals. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Safety evaluation of the food enzyme containing endo-polygalacturonase and endo-1,3(4)-β-glucanase from the non-genetically modified Aspergillus fijiensis strain NZYM-RE

The food enzyme has two declared activities, endo-polygalacuronase ((1→4)-α-D-galacturonan glycanohydrolase; EC 3.2.1.15) and endo-1,3(4)-β-glucanase (3-(1→3;1→4)-β-D-glucan 3(4)-glucanohydrolase; EC 3.2.1.6) and is produced with the non-genetically modified Aspergillus fijiensis strain NZYM-RE by Novozymes A/S. The food enzyme was considered free from viable cells of the production organism. It is intended to be used in eight food manufacturing processes, i.e. distilled alcohol production, brewing processes, baking processes, cereal-based processes, wine and wine vinegar production, fruit and vegetable processing for juice production, fruit and vegetable processing for products other than juices and refined olive oil production. Since residual amounts of total organic solids (TOS) are removed during distilled alcohol production and refined olive oil production, dietary exposure was not calculated for these two processes. For the remaining six food manufacturing processes, dietary exposure was estimated to be up to 0.553 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 3,677 mg TOS/kg bw per day, the highest dose tested, resulting in a margin of exposure of at least 6,649. A search for similarity of the amino acid sequence of the food enzyme to known allergens was made and nine matches were found. The Panel considered that, under the intended conditions of use (other than distilled alcohol production), the risk of allergic reactions by dietary exposure to this food enzyme, particularly in individuals suffering from the oral allergy syndrome or sensitised to papaya, cannot be excluded. The Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety evaluation of the food enzyme pectin lyase from the genetically modified Trichoderma reesei strain RF6199

The food enzyme pectin lyase ((1-4)-6-O-methyl-α-D-galacturonan lyase; EC 4.2.2.10) is produced with the genetically modified Trichoderma reesei strain RF6199 by AB Enzymes GmbH. The genetic modifications do not give rise to safety concerns. The food enzyme is considered free from viable cells of the production organism and its DNA. It is intended to be used in six manufacturing processes: fruit and vegetable processing for juice production, fruit and vegetable processing for fruit brandies, fruit and vegetable processing for products other than juices, wine and wine vinegar production, refined and unrefined sugar production and coffee bean demucilation. Foods obtained from fruit processing for fruit brandies and coffee bean demucilation, as well as refined sugars, were excluded from dietary exposure estimation. For the remaining four processes, dietary exposure to the food enzyme-total organic solids (TOS) was estimated to be up to 0.2 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1,000 mg TOS/kg bw per day, the highest dose tested, which, when compared with the estimated dietary exposure, results in a margin of exposure of at least 5,000. A search for the similarity of the amino acid sequence of the food enzyme to known allergens was made and no match was found. The Panel considered that, under the intended conditions of use, the risk of allergic reactions by dietary exposure cannot be excluded, but the likelihood of such reactions is low. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Identification of Potential IgE-Binding Epitopes Contributing to the Cross-Reactivity of the Major Cupressaceae Pectate-Lyase Pollen Allergens (Group 1)

Pectate-lyase allergens, the group 1 of allergens from Cupressaceae pollen, consist of glycoproteins exhibiting an extremely well-conserved three-dimensional structure and sequential IgE-binding epitopes. Up to 10 IgE-binding epitopic regions were identified on the molecular surface, which essentially cluster at both extremities of the long, curved β-prism-shaped allergens. Most of these IgE-binding epitopes possess very similar conformations that provide insight into the IgE-binding cross-reactivity and cross-allergenicity commonly observed among Cupressaceae pollen allergens. Some of these epitopic regions coincide with putative N-glycosylation sites that most probably consist of glycotopes or cross-reactive carbohydrate determinants, recognized by the corresponding IgE antibodies from allergic patients. Pectate-lyase allergens of Cupressaceae pollen offer a nice example of structurally conserved allergens that are widely distributed in closely-related plants (Chamæcyparis, Cryptomeria, Cupressus, Hesperocyparis, Juniperus, Thuja) and responsible for frequent cross-allergenicity.

Safety evaluation of the food enzyme chymosin from the genetically modified Kluyveromyces lactis strain CIN

The food enzyme chymosin (EC 3.4.23.4) is produced with the genetically modified Kluyveromyces lactis strain CIN by DSM Food Specialties B.V. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and its recombinant DNA. It is intended to be used in milk processing for cheese production and for the production of fermented milk products. Dietary exposure was estimated to be up to 0.73 mg total organic solids (TOS)/kg body weight (bw) per day in European populations. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1,000 mg TOS/kg bw per day, the highest dose tested, which when compared with the estimated dietary exposure, results in a margin of exposure of at least 1,300. Similarity of the amino acid sequence of the food enzyme to those of known allergens was searched for and four matches were found. The Panel considered that under the intended conditions of use the risk of allergic sensitisation and elicitation reactions by dietary exposure, although unlikely, cannot be excluded, particularly for individuals sensitised to cedar pollen allergens. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety evaluation of the food enzyme chymosin from the genetically modified Aspergillus niger strain DSM 29546

The food enzyme chymosin (EC 3.4.23.4) is produced with the genetically modified Aspergillus niger strain DSM 29546 by Chr. Hansen. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and its DNA. It is intended to be used in milk processing for cheese production and for the production of fermented milk products. Dietary exposure was estimated to be up to 0.52 mg total organic solids (TOS)/kg body weight (bw) per day in European populations. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 410 mg TOS/kg bw per day, the highest dose tested, which when compared with the estimated dietary exposure, results in a margin of exposure of at least 790. Similarity of the amino acid sequence of the food enzyme to those of known allergens was searched and four matches were found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure, although unlikely, cannot be excluded, particularly for individuals sensitised to cedar pollen allergens. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety evaluation of the food enzyme chymosin from the genetically modified Kluyveromyces lactis strain CHY

The food enzyme chymosin (EC 3.4.23.4) is produced with the genetically modified Kluyveromyces lactis strain CHY by DSM Food Specialties B.V. It is intended to be used in milk processing for cheese production and for production of fermented milk products. Dietary exposure was estimated to be up to 0.69 mg total organic solids (TOS)/kg body weight (bw) per day in European populations. The production strain contains multiple copies of known antimicrobial resistance genes and consequently, it does not fully fulfil the requirements for the qualified presumption of safety (QPS) approach to safety assessment. However, considering the absence of viable cells and DNA from the production organism in the food enzyme, this is not considered to be a risk. As no other concerns arising from the microbial source and its subsequent genetic modification or from the manufacturing process have been identified, the Panel considered that toxicological tests were not needed for the assessment of this food enzyme. Similarity of the amino acid sequence of the food enzyme to those of known allergens was searched and four matches were found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure, although unlikely, cannot be excluded, particularly for individuals sensitised to cedar pollen allergens. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety evaluation of the food enzyme β‐galactosidase from the genetically modified Bacillus licheniformis strain NZYM‐BT

The food enzyme β‐galactosidase (β‐d‐galactoside galactohydrolase; EC 3.2.1.23) is produced with the genetically modified Bacillus licheniformis strain NZYM‐BT by Novozymes A/S. The genetic modifications do not give rise to safety concerns. The production strain has been shown to qualify for the qualified presumption of safety (QPS) status. The food enzyme was considered free from viable cells of the production organism and its DNA. It is intended to be used in milk processing for the hydrolysis of lactose. Based on the assumption that all selected milk and milk products are enzymatically treated, dietary exposure to the food enzyme–total organic solids (TOS) was estimated to be up to 0.34 mg TOS/kg body weight (bw) per day in European populations. Toxicological data were reported and were considered as supporting evidence of the safety of the food enzyme. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by means of a repeated dose 90‐day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 672 mg TOS/kg bw per day, the highest dose tested, which when compared with the estimated dietary exposure, results in a margin of exposure above 1,950. A search for similarity of the amino acid sequence of the food enzyme to known allergens was made and one match was found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded, especially in individuals sensitised to galactosidase or to the matching allergen of pollen from Platanus. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety evaluation of the food enzyme endo‐polygalacturonase from the genetically modified Aspergillus luchuensis strain FLYSC

The food enzyme endo‐polygalacturonase ((1→4)‐α‐d‐galacturonan glycanohydrolase; EC 2.3.1.15), is produced with the genetically modified Aspergillus luchuensis strain FLYSC by Advanced Enzyme Technologies Ltd. The genetic modifications do not give rise to safety concerns. The food enzyme is considered free from viable cells of the production organism and its DNA. The food enzyme is intended to be used in fruit and vegetable processing for juice production. Based on the maximum use level, dietary exposure to the food enzyme–total organic solids (TOS) was estimated to be up to 0.138 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90‐day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 800 mg TOS/kg bw per day, the highest dose tested, which when compared with the estimated dietary exposure, results in a margin of exposure of at least 5,800. A search for similarity of the amino acid sequence of the food enzyme to known allergens was made and six matches were found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded for individuals sensitised to cedar or grass pollen or maize. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Design of peptides with high affinity binding to a monoclonal antibody as a basis for immunotherapy

About half of the US population is sensitized to one or more allergens, as found by a National Health and Nutrition Examination Survey (NHANES). The most common treatment for seasonal allergic responses is the daily use of oral antihistamines, which can control some of the symptoms, but are not effective for nasal congestion, and can be debilitating in many patients. Peptide immunotherapy is a promising new approach to treat allergic airway diseases. The small size of the immunogens cannot lead to an unwanted allergic reaction in sensitized patients, and the production of peptides with sufficient amounts for immunotherapy is time- and cost-effective. However, it is not known what peptides are the most effective for an immunotherapy of allergens. We previously produced a unique monoclonal antibody (mAb) E58, which can inhibit the binding of multiple groups of mAbs and human IgEs from patients affected by the major group 1 allergens of ragweed (Amb a 1) and conifer pollens (Jun a 1, Cup s 1, and Cry j 1). Here, we demonstrated that a combined approach, starting from two linear E58 epitopes of the tree pollen allergen Jun a 1 and the ragweed pollen allergen Amb a 1, and residue modifications suggested by molecular docking calculations and peptide design could identify a large number of high affinity binding peptides. We propose that this combined experimental and computational approach by structural analysis of linear IgE epitopes and peptide design, can lead to potential new candidates for peptide immunotherapy.

Mountain cedar allergy: A review of current available literature

OBJECTIVE

To review the literature related to mountain cedar in terms of allergic disease and societal impact.

DATA SOURCES

English-language articles obtained through PubMed searches with relevance to mountain cedar allergies.

STUDY SELECTIONS

Articles with the following search terms were included: mountain cedar, Juniperus ashei, juniper, allergy, pollen, cedar fever, Jun a 1, and San Antonio.

RESULTS

A total of 61 relevant articles were selected regarding mountain cedar and its distribution, phylogenetics, allergens, potency, cross-reactivity, pollen counting and monitoring, symptoms, diagnosis, treatment, and future research.

CONCLUSION

Mountain cedar remains a major cause of allergic rhinoconjunctivitis in the south central United States during the winter months. Key treatment strategies involve a combination of allergen avoidance, pharmacologic therapy, and subcutaneous immunotherapy. Allergists can help affected patients in their management of "cedar fever."

Genome shuffling for improving the activity of alkaline pectinase in Bacillus subtilis FS105 and its molecular mechanism

Genome shuffling for improving the activity of alkaline pectinase in Bacillus subtilis FS105 and its molecular mechanism were investigated. The fused strain B. subtilis FS105 with the highest activity of alkaline pectinase was obtained after two rounds of genome shuffling. The activity of alkaline pectinase in B. subtilis FS105 was 499 U/ml, which was improved by 1.6 times compared to that in original strain. To elucidate its molecular mechanism, rpsL gene sequences from original and fused strains were cloned and aligned, and the space structure of their coding proteins were also analyzed and compared. The alignment of the rpsL gene sequences indicated that three bases G, G and C were respectively replaced by A, A and G in the positions 52, 408 and 409 after genome shuffling. This resulted in the substitution of two amino acid residues in ribosomal protein S12: D18N and P137A, and therefore improving the biosynthesis of alkaline pectinase. This study lays a foundation for improving the activity of alkaline pectinase by genome shuffling and understanding its molecular mechanism.

Pollen food allergy syndrome to tomato in mountain cedar pollen hypersensitivity

BACKGROUND

Mountain cedar pollen is recognized as a major cause of seasonal hypersensitivity in the US. We describe here that a subgroup of these patients also suffer from pollen food allergy syndrome (PFAS).

OBJECTIVE

We performed this study to determine the frequency of PFAS among patients with mountain cedar hypersensitivity.

METHODS

We performed mail-out/telephone surveys of 800 mountain cedar-sensitive patients in Austin, TX. The subjects for this survey were selected by telephone screening, and skin and serologic testing. We performed immunoblot inhibition assay and mass spectrometry (MS) to identify the allergens that cause PFAS.

RESULTS

Of the 28 patients with suspected food allergies, 15 had clinical manifestations of PFAS. Eleven of them had positive skin tests to tomato, six to banana, and one to apple. The subjects with PFAS have stronger cutaneous and in vitro reactivity to cedar pollen. The intensities of the tomato and banana reactivity were correlated with the cedar reactivity. The results of the ImmunoCAP inhibition experiments demonstrated a strong cross-reactivity between IgE antibodies to cedar pollen and fruits. This suggested that their primary sensitization was to cedar pollen, since absorption with cedar pollen extract strongly inhibited reactivity to each of the fruits, while the absorption with tomato extract did not significantly inhibit IgE binding to cedar extract. We determined that polygalacturonase 2 A (PG2 A) in tomato is the cause of PFAS.

CONCLUSION

This is the first report of a PFAS in patients with mountain cedar pollinosis. Sensitivity to tomato, banana, and apple should be considered in cedar-sensitive patients.

Molecular patterns in the isotype-specific antibody responses to the major cedar aeroallergen Jun a 1

Most studies of the immune responses in allergic rhinitis have focused on IgE antibodies to mixtures of allergenic proteins. Based on our previous studies of the major mountain cedar allergen Jun a 1, we sought to describe a broader assessment of the humoral immune responses to a single, dominant allergen, in three groups of allergic subjects, all of whom had similarly exposures to the whole cedar pollen. The major outcomes of this study was that, with the onset of allergic rhinitis symptoms, and after treatment with immunotherapy, serum IgE and IgG (but not IgA) antibodies to Jun a 1 increased. Interestingly, both IgE and IgG4 antibodies to the Jun a 1 allergen were strongly focused on its conformation epitopes. These IgG antibodies to conformationalstructures may be a useful marker of the therapeutic response to immunotherapy.

Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs

Quantitative guidelines to distinguish allergenic proteins from related, but non-allergenic ones are urgently needed for regulatory agencies, biotech companies and physicians. In a previous study, we found that allergenic proteins populate a relatively small number of protein families, as characterized by the Pfam database. However, these families also contain non-allergenic proteins, meaning that allergenic determinants must lie within more discrete regions of the sequence. Thus, new methods are needed to discriminate allergenic proteins within those families. Physical-Chemical Properties (PCP)-motifs specific for allergens within a Pfam class were determined for 17 highly populated protein domains. A novel scoring method based on PCP-motifs that characterize known allergenic proteins within these families was developed, and validated for those domains. The motif scores distinguished sequences of allergens from a large selection of 80,000 randomly selected non-allergenic sequences. The motif scores for the birch pollen allergen (Bet v 1) family, which also contains related fruit and nut allergens, correlated better than global sequence similarities with clinically observed cross-reactivities among those allergens. Further, we demonstrated that the average scores of allergen specific motifs for allergenic profilins are significantly different from the scores of non-allergenic profilins. Several of the selective motifs coincide with experimentally determined IgE epitopes of allergenic profilins. The motifs also discriminated allergenic pectate lyases, including Jun a 1 from mountain cedar pollen, from similar proteins in the human microbiome, which can be assumed to be non-allergens. The latter lacked key motifs characteristic of the known allergens, some of which correlate with known IgE binding sites.

Preparation and identification of Per a 5 as a novel American cockroach allergen

Glutathione S-transferase (GST) from various arthropods can elicit allergic reactions. In the present study, Per a 5, a GST, was cloned from American cockroach (CR) and expressed in both baculovirus-infected insect cell (iPer a 5) and E. coli expression (bPer a 5) systems. The secondary structures were predicted to be 45.93 and 8.69% of α-helix β-sheets in iPer a 5 and 42.54 and 8.49% of α-helix and β-sheets in bPer a 5, respectively. It is found that 4 out of 16 (25%) sera from American CR allergy patients reacted to both bPer a 9 and iPer a 9 as assessed by ELISA and Western blotting analysis, confirming that Per a 5 is not a major allergen of American CR. Induction of upregulated expression of CD63 and CCR3 on passively sensitized human basophils (sera from American CR allergy patients) by approximately up to 4.5- and 3.2-fold indicates that iPer a 5 and bPer a 5 are functionally active. Recombinant Per a 5 (rPer a 5) should be a useful tool for studying and understanding the role of Per a 5 in CR allergy.

Epitope mapping with membrane-bound synthetic overlapping peptides

Epitope mapping with synthetic overlapping peptides is used for identifying epitopes of monoclonal antibodies (mAbs) and antibodies from patient sera (Midoro-Horiuti et al. Mol Immunol 43:509-518, 2006; Ivanciuc et al. J Agric Food Chem 51:4830-4837, 2003; Midoro-Horiuti et al. Mol Immunol 40:555-562, 2003; Wang et al. J Allergy Clin Immunol 125:695-702, 702.e1-702.e6, 2010). When the mAbs recognize epitopes that are also recognized by patients of interest, they may be useful as surrogates for patient antibodies.

The mountain cedar model in clinical trials of seasonal allergic rhinoconjunctivitis

BACKGROUND

Clinical trials of seasonal allergic rhinoconjunctivitis use the mountain cedar (Juniperus ashei) season as the predominate model.

OBJECTIVE

To evaluate clinical trials of rhinoconjunctivitis using mountain cedar, to present analysis of pollen counts during 18 seasons, and to discuss the model.

METHODS

The medical literature was searched for clinical trials performed using mountain cedar either in or out of season. Pollen counts were recorded and analyzed for the duration of 18 seasons.

RESULTS

Thirty-eight trials were identified. Of these, 1 evaluated onset of allergy, 8 were immunotherapy trials, 28 were pharmaceutical clinical trials, and 1 studied symptoms elicited in a pollen challenge chamber trial. Many generic equivalency trials are unreported. In the 18 years of counts in the Texas Hill Country, a dependable and intense pollen density was present in every season. The combination of dependable seasons without confounding pollens, the large number of allergic patients, and the ability to concentrate resources in one geographic area has made mountain cedar allergy a mainstay for therapeutic trials for allergic rhinoconjunctivitis.

CONCLUSION

Mountain cedar allergy presents a dependable and durable model of allergic rhinoconjunctivitis.

Analysis of conformational and sequential IgE epitopes on the major allergen Cry j 2 of Japanese cedar (Cryptomeria japonica) pollen in humans by using monoclonal antibodies for Cry j 2

PURPOSE

Japanese cedar (Cryptomeria japonica; CJ) pollinosis is a type I allergy induced by CJ pollen, and Cry j 2 is one of the major allergens in this pollen. In a previous study, we analyzed IgE epitopes on Cry j 2 in humans by using synthetic peptides. The main purpose of this study was to identify B-cell epitopes on Cry j 2 in patients with CJ pollinosis by using monoclonal antibodies (mAbs) for Cry j 2.

METHODS

We used ELISA with mAbs for the epitope analysis. Sera samples were collected from 80 patients with CJ pollinosis, and allergenic epitopes for mAbs and human IgE were identified using ELISA with synthetic peptides. The importance of the epitopes for human IgE was analyzed using an inhibition ELISA.

RESULTS

Four independent epitopes (epitope #1, #2, #3, and #4) were identified on Cry j 2 with the use of mAbs. Epitope #3 and #4, corresponding to peptides No. 25 and No. 33, respectively, were newly determined as epitopes for mAbs and human IgE. Inhibition ELISA showed that not only epitope #2 (sequential) but epitope #1 (conformational) may play an important role in the CJ pollinosis.

CONCLUSIONS

Our results revealed 4 epitopes, including two new ones, on Cry j 2. We also found that inhibition ELISA with appropriate mAbs could be a viable method of evaluating the importance of the conformational and sequential epitopes for human IgE. These results are beneficial for the development of safer and more efficient therapeutic strategies for treating CJ pollinosis.

AllerML: markup language for allergens

Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis.

Plant-expressed recombinant mountain cedar allergen Jun a 1 is allergenic and has limited pectate lyase activity

BACKGROUND

Mountain cedar (Juniperus ashei) pollen commonly causes a winter time allergic rhinitis in the central USA. Jun a 1 is the dominant allergenic protein, but biologically active recombinant Jun a 1 has not been successfully expressed, despite numerous attempts with several expression systems.

METHOD

Jun a 1 cDNA was inserted into a tobacco mosaic virus vector and transferred to Agrobacterium tumefaciens. Bacteria were syringe-inoculated into leaves of Nicotiana benthamiana (agroinoculation). The interstitial (apoplastic) fluid containing Jun a 1 was isolated. The recombinant protein was analyzed by SDS-PAGE, N-terminal sequencing and MALDI-TOF to confirm identity. Immunogenicity was examined with IgE from allergic patient's sera, mouse monoclonal anti-Jun a 1 antibodies, IgE-binding inhibition and by degranulation of RBL SX-38 cells sensitized with sera from allergic patients. Pectate lyase activity was assayed by capillary zone electrophoresis and mass spectrometry analysis.

RESULTS

Recombinant Jun a 1 was recovered in good quantity (100 μg/g leaf material), was confirmed as Jun a 1, bound IgE from sera from cedar hypersensitive patients and inhibited IgE binding to native Jun a 1. Jun a 1 mutants were created and their pectate lyase activity quantified. For the first time, Jun a 1 pectate lyase activity was demonstrated, which may explain the necrosis seen on host plants, which was similar to that of control plants expressing banana pectate lyase.

CONCLUSIONS

A means of producing recombinant Jun a 1 is now available for structure/function studies and potentially for diagnostic and therapeutic uses.

Structural analysis of linear and conformational epitopes of allergens

In many countries regulatory agencies have adopted safety guidelines, based on bioinformatics rules from the WHO/FAO and EFSA recommendations, to prevent potentially allergenic novel foods or agricultural products from reaching consumers. We created the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to combine data that had previously been available only as flat files on Web pages or in the literature. SDAP was designed to be user friendly, to be of maximum use to regulatory agencies, clinicians, as well as to scientists interested in assessing the potential allergenic risk of a protein. We developed methods, unique to SDAP, to compare the physicochemical properties of discrete areas of allergenic proteins to known IgE epitopes. We developed a new similarity measure, the property distance (PD) value that can be used to detect related segments in allergens with clinical observed cross-reactivity. We have now expanded this work to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to known IgE epitopes. In complementary work we show how sequence motifs characteristic of allergenic proteins in protein families can be used as fingerprints for allergenicity.

Molecular cloning, recombinant expression, and immunological characterization of a novel allergen from tartary buckwheat

Buckwheat is generally regarded as a nutritionally rich food source. However, earlier studies prove that it also causes allergies to subjects. Allergenic proteins with a strong IgE-binding activity have been identified in common buckwheat (CB) and a 24 kDa allergen (rTBa) in tartary buckwheat (TB). The objective of this research was to clone and express a novel allergen in tartary buckwheat and to evaluate its structure and immunological activity. The 1773 bp full-length cDNA was amplified and cloned from the total RNA of TB by polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE) methods. Its nucleotide sequence had high similarity with legume-like 13S storage protein mRNA in CB. The deduced amino acid sequence included a putative signal peptide and 18 fragments as its epitope sites. The predicted full-length TB allergen sequence was found to have two domains, and the recombinant protein reacted with sera from patients with positive IgE binding to buckwheat and had a lower binding ability than the recombinant TBa and recombinant TBb (C- and N-terminal amino acid sequence of TBt codes for protein). This fact suggests that full-length TB allergen may hydrolyze to two domains in vivo, decreasing the IgE-binding ability.

Characteristic motifs for families of allergenic proteins

The identification of potential allergenic proteins is usually done by scanning a database of allergenic proteins and locating known allergens with a high sequence similarity. However, there is no universally accepted cut-off value for sequence similarity to indicate potential IgE cross-reactivity. Further, overall sequence similarity may be less important than discrete areas of similarity in proteins with homologous structure. To identify such areas, we first classified all allergens and their subdomains in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to their closest protein families as defined in Pfam, and identified conserved physicochemical property motifs characteristic of each group of sequences. Allergens populate only a small subset of all known Pfam families, as all allergenic proteins in SDAP could be grouped to only 130 (of 9318 total) Pfams, and 31 families contain more than four allergens. Conserved physicochemical property motifs for the aligned sequences of the most populated Pfam families were identified with the PCPMer program suite and catalogued in the webserver MotifMate (http://born.utmb.edu/motifmate/summary.php). We also determined specific motifs for allergenic members of a family that could distinguish them from non-allergenic ones. These allergen specific motifs should be most useful in database searches for potential allergens. We found that sequence motifs unique to the allergens in three families (seed storage proteins, Bet v 1, and tropomyosin) overlap with known IgE epitopes, thus providing evidence that our motif based approach can be used to assess the potential allergenicity of novel proteins.

The property distance index PD predicts peptides that cross-react with IgE antibodies

Similarities in the sequence and structure of allergens can explain clinically observed cross-reactivities. Distinguishing sequences that bind IgE in patient sera can be used to identify potentially allergenic protein sequences and aid in the design of hypo-allergenic proteins. The property distance index PD, incorporated in our Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/), may identify potentially cross-reactive segments of proteins, based on their similarity to known IgE epitopes. We sought to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to three linear IgE epitopes of Jun a 1, the dominant allergen from mountain cedar pollen. For each of the three epitopes, 60 peptides were designed with increasing PD values (decreasing physicochemical similarity) to the starting sequence. The peptides synthesized on a derivatized cellulose membrane were probed with sera from patients who were allergic to Jun a 1, and the experimental data were interpreted with a PD classification method. Peptides with low PD values relative to a given epitope were more likely to bind IgE from the sera than were those with PD values larger than 6. Control sequences, with PD values between 18 and 20 to all the three epitopes, did not bind patient IgE, thus validating our procedure for identifying negative control peptides. The PD index is a statistically validated method to detect discrete regions of proteins that have a high probability of cross-reacting with IgE from allergic patients.

Mapping IgE-binding epitopes of Ric c 1 and Ric c 3, allergens from Ricinus communis, by mast cell degranulation assay

Ric c 1 and Ric c 3 are the major castor bean allergens. In order to identify continuous IgE-epitopes in Ric c 1 and Ric c 3, pools of sera from rats immunized with a pool of 2S albumin from these seeds, Ric c 1 and Ric c 3 overlapping synthetic peptides, were used to screen for IgE-binding epitopes. The allergenic properties were monitored by mast cell degranulation assays, histamine quantification and human-IgE binding. Large and small chains isolated from these proteins present allergenic properties. Four continuous epitopes were identified in Ric c 3 and two in Ric c 1. This knowledge may allow the induction of protective antibody responses to antagonize the IgE recognition.

Cross-reactivity of pollen allergens: impact on allergen immunotherapy

OBJECTIVE

To provide guidelines for the rational formulation of allergen immunotherapy extracts based on knowledge of pollen allergen and epitope cross-reactivity.

DATA SOURCES

A PubMed search was performed for articles published from 1966 to 2007 using the keywords pollen, allergen, and cross-reactivity. Older literature was found through cross-referencing of older articles and older reviews on pollen cross-reactivity.

STUDY SELECTION

Articles that dealt with crude pollen extracts and characterized allergens that addressed cross-reactivity were selected for inclusion in this review.

RESULTS

In addition to unique allergens, several families of botanic proteins have similarities that allow them to act as pan-allergens. Although frequently these are minor allergens, in some circumstances they may also be major allergens. Recent studies have investigated nonspecific lipid transfer proteins, calcium-binding proteins, pathogenesis-related protein families, and profilins. Calcium-binding proteins and nonspecific lipid transfer proteins are responsible for pollen-fruit interactions and pollen cross-reactivity. Clarification of pollen allergen enzymatic activity helps explain the ubiquitous nature of these proteins.

CONCLUSION

Characterization of specific pollen allergens and their protein families has provided insight into cross-reactivity. Clarification of these relationships allows for consolidation or substitution in formulation of inhalant extracts.

Bioinformatics approaches to classifying allergens and predicting cross-reactivity

Allergenic proteins from very different environmental sources have similar sequences and structures. This fact may account for multiple allergen syndromes, whereby a myriad of diverse plants and foods may induce a similar IgE-based reaction in certain patients. Identifying the common triggering protein in these sources, in silico, can aid designing individualized therapy for allergen sufferers. This article provides an overview of databases on allergenic proteins, and ways to identify common proteins that may be the cause of multiple allergy syndromes. The major emphasis is on the relational Structural Database of Allergenic Proteins (SDAP []), which includes cross-referenced data on the sequence, structure, and IgE epitopes of over 800 allergenic proteins, coupled with specially developed bioinformatics tools to group all allergens and identify discrete areas that may account for cross-reactivity. SDAP is freely available on the Web to clinicians and patients.

Evaluation of available IgE-binding epitope data and its utility in bioinformatics

This paper reviews the role played by IgE-binding epitopes in eliciting clinical symptoms, the types of IgE-binding epitopes in allergenic proteins, the methods used to identify IgE-binding epitopes, and the availability of IgE-binding epitopes in allergenic sources. Finally, bioinformatics methods to assess protein allergenicity using knowledge of IgE-binding epitopes are discussed.

Cross-reactivity of pollen allergens: recommendations for immunotherapy vaccines

PURPOSE OF REVIEW

This review will summarize recent research on pollen allergen and epitope cross-reactivity. Knowledge of these relationships aids in the rational formulation of allergen immunotherapy vaccines.

RECENT FINDINGS

There has been further clarification of panallergens and their roles as both major and minor allergens. Recent studies have targeted non-specific lipid transfer proteins and calcium-binding proteins (polcalcins), as well as pathogenesis-related protein families and profilins. Polcalcins and non-specific lipid transfer proteins are responsible for pollen-fruit interactions as well as pollen cross-reactivity, in some cases, but not all, accounting for major allergenicity. Delineation of the enzymatic activity of certain allergens explains the ubiquitous nature of these pollen proteins.

SUMMARY

Characterization of specific pollen allergens and their protein families has provided insight into the grounds for cross-reactivity. Continuing clarification of these relationships will allow the substitution and consolidation of inhalant extracts as described in the conclusion.

Major mountain cedar allergen, Jun a 1, contains conformational as well as linear IgE epitopes

We have previously identified four linear IgE epitopes on Jun a 1, the dominant allergen in mountain cedar pollen, and mapped these to the surfaces of a molecular model and to the crystal structure of this glycoprotein. The aim of the present study was to determine if Jun a 1 also displays conformational IgE epitopes. Jun a 1 was denatured by heating at 75 degrees C for 1h, exposure to 6M guanidine or by reductive alkylation in the presence and absence of guanidine. The effects of these manipulations on the binding to IgE from patients with mountain cedar hypersensitivity was evaluated by an ImmunoCAP inhibition assay, using Jun a 1-specific caps. Treatment-associated changes in the 3D-structure were assessed by dynamic light scattering and CD spectroscopy. IgE binding to native Jun a 1 was inhibited 92+/-9% by soluble native protein and 92+/-9% by reduced and alkylated Jun a 1. However, the capacity of Jun a 1 to inhibit the binding of IgE antibodies was significantly diminished upon denaturation by heat, guanidine alone, or reduction and alkylation in guanidine, compared to native Jun a 1. Reductive alkylation treatment under denaturing conditions also increased the Stoke's radius, suggesting that the protein was partially unfolded. Analysis of the circular dichroism (CD) spectra suggested that heating and treatment with guanidine caused a loss of alpha-helical structure. Guanidine also caused an increase in random coil structure. Thus, at least a portion of the anti-Jun a 1 IgE antibodies produced by allergic humans recognize conformational epitopes and it is likely that some of these epitopes reside in alpha-helical structures of Jun a 1.

Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens

Although many sequences and linear IgE epitopes of allergenic proteins have been identified and archived in databases, structural and physicochemical discriminators that define their specific properties are lacking. Current bioinformatics tools for predicting the potential allergenicity of a novel protein use methods that were not designed to compare peptides. Novel tools to determine the quantitative sequence and three-dimensional (3D) relationships between IgE epitopes of major allergens from peanut and other foods have been implemented in the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/). These peptide comparison tools are based on five-dimensional physicochemical property (PCP) vectors. Sequences from SDAP proteins similar in their physicochemical properties to known epitopes of Ara h 1 and Ara h 2 were identified by calculating property distance (PD) values. A 3D model of Ara h 1 was generated to visualize the 3D structure and surface exposure of the epitope regions and peptides with a low PD value to them. Many sequences similar to the known epitopes were identified in related nut allergens, and others were within the sequences of Ara h 1 and Ara h 2. Some of the sequences with low PD values correspond to other known epitopes. Regions with low PD values to one another in Ara h 1 had similar predicted structure, on opposite sides of the internal dimer axis. The PD scale detected epitope pairs that are similar in structure and/or reactivity with patient IgE. The high immunogenicity and IgE reactivity of peanut allergen proteins might be due to the proteins' arrays of similar antigenic regions on opposite sides of a single protein structure.

Identification of human T cell epitopes in Japanese cypress pollen allergen, Cha o 1, elucidates the intrinsic mechanism of cross-allergenicity between Cha o 1 and Cry j 1, the major allergen of Japanese cedar pollen, at the T cell level

BACKGROUND

Pollens from species of Cupressaceae family are one of the most important causes of respiratory allergies worldwide. In Japan, many patients with pollinosis have specific IgE to both pollens of Japanese cypress (Chamaecyparis obtusa) and Japanese cedar (Cryptomeria japonica). The sequences between Cha o 1 and Cry j 1, the major allergens of Japanese cypress and Japanese cedar pollens, respectively, are 80% identical.

OBJECTIVE

This study was undertaken to identify T cell epitopes in Cha o 1, and to elucidate the mechanism of cross-allergenicity between Cha o 1 and Cry j 1, at the T cell level.

METHODS

T cell epitopes in Cha o 1 were identified by the reactivity of T cell lines, generated from 19 patients, to stimulation with overlapping peptides. The subsets of T cell clones specific to rCha o 1 were determined according to their ability to produce IL-4 and IFN-gamma. Peptide specificities of two T cell clones were determined by stimulation with the peptides from Cha o 1 and Cry j 1.

RESULTS

Four dominant and six subdominant T cell epitopes were identified in Cha o 1. While four T cell epitopes, p11-30, p211-230, p251-270 and p331-350, were common to Cha o 1 and Cry j 1, 4 T cell epitopes, p61-80, p71-90, p311-330 and p321-340, were considered to be unique to Cha o 1. The subsets of T cell clones were predominantly of T helper2-type. One T cell clone recognized p16-30, which is common to Cha o 1 and Cry j 1, but another recognized p321-330, which is unique to Cha o 1.

CONCLUSION

Presence of both T cells reactive to T cell epitopes common to Cha o 1 and Cry j 1 and T cells specific to T cell epitopes unique to Cha o 1 in patients with pollinosis contributes to prolonged symptoms after the cedar pollen season in March and the following cypress pollen season in April.

Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein

Although Alzheimer's Abeta peptide has been shown to form beta-sheet structure, a high-resolution molecular structure is still unavailable to date. A search for a sequence neighbor using Abeta(10-42) as the query in the Protein Data-Bank (PDB) revealed that an RNA binding protein, AF-Sm1 from Archaeoglobus fulgidus (PDB entry: 1i4k chain Z), shared 36% identical residues. Using AF-Sm1 as a template, we built a molecular model of Abeta(10-42) by applying comparative modeling methods. The model of Abeta(10-42) contains an antiparallel beta-sheet formed by residues 16-23 and 32-41. Hydrophobic surface constituted by residues 17-20 (LVFF) separates distinctly charged regions. Residues that interact with RNA in the AF-Sm1 crystal structure were found to be conserved in Abeta. Using a native gel we demonstrate for the first time that RNA can interact with Abeta and selectively retard the formation of fibrils or higher-order oligomers. We hypothesize that in a similar fashion to AF-Sm1, RNA interacts with Abeta in the beta-hairpin (beta-turn-beta) structure and prevents fibril formation.

Structural basis for epitope sharing between group 1 allergens of cedar pollen

The group 1 allergens are a major cause of cedar pollen hypersensitivity in several geographic areas. Allergens from several taxa have been shown to cross-react. The goal of these studies was to compare the structural features of the shared and unique epitopes of the group 1 allergen from mountain cedar (Jun a 1) and Japanese cedar (Cry j 1). An array of overlapping peptides from the sequence of Jun a 1 and a panel of monoclonal anti-Cry j 1 antibodies were used to identify the IgE epitopes recognized by cedar-sensitive patients from Texas and Japan. IgE from Japanese patients reacted with peptides representing one of the two linear epitopes within the highly conserved beta-helical core structure and both epitopes within less ordered loops and turns near the N- and C-termini of Jun a 1. A three-dimensional (3D) model of the Cry j 1, based on the crystal structure of Jun a 1, indicated a similar surface exposure for the four described epitopes of Jun a 1 and the homologous regions of Cry j 1. The monoclonal antibodies identified another shared epitope, which is most likely conformational and a unique Cry j 1 epitope that may be the previously recognized glycopeptide IgE epitope. Defining the structural basis for shared and unique epitopes will help to identify critical features of IgE epitopes that can be used to develop mimotopes or identify allergen homologues for vaccine development.

Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core

Pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the Northern Hemisphere. We report the first crystal structure of a cedar allergen, Jun a 1, from the pollen of the mountain cedar Juniperus ashei (Cupressaceae). The core of the structure consists primarily of a parallel beta-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms. Four IgE epitopes mapped to the surface of the protein are accessible to the solvent. The conserved vWiDH sequence is covered by the first 30 residues of the N terminus. The potential reactive arginine, analogous to the pectin/pectate lyase reaction site, is accessible to the solvent, but the substrate binding groove is blocked by a histidine-aspartate salt bridge, a glutamine, and an alpha-helix, all of which are unique to Jun a 1. These observations suggest that steric hindrance in Jun a 1 precludes enzyme activity. The overall results suggest that it is the structure of Jun a 1 that makes it a potent allergen.

Cross-reactivity of pollen allergens

Pollen cross-allergenicity has practical implications on the management of inhalant allergy, in both evaluation and therapy, especially with allergen vaccine immunotherapy. The study of cross-reactivity among pollen allergens has expanded beyond investigation of crude extracts to the characterization and cloning of numerous pollen proteins. In this review, the interrelationships between these pollen allergens in the context of botanical systematics are examined, to provide a framework for cross-reactivity understanding. Recommendations for choices in evaluation and therapy are given.

Refolding of the Cupressus arizonica major pollen allergen Cup a1.02 overexpressed in Escherichia coli

The cDNA encoding an isoform of the cypress major pollen allergen, Cup a1.02, has been cloned and expressed in Escherichia coli as a N-terminal 6x His-tagged protein. To increase recovery, Cup a1.02 was expressed at high levels exploiting the T5 strong promoter and led to accumulate as inclusion bodies. The insoluble purified aggregates were solubilized in 6 M guanidine hydrochloride, immobilized using nickel-chelating affinity chromatography, and successfully refolded by controlled removal of the chaotropic reagent. Enhanced protein refolding was observed by reducing the protein concentration at 0.6-0.8 mg/ml. SDS-PAGE and gel filtration chromatography indicated an apparent molecular mass of approximately 40 kDa and the occurrence of the protein as monomers. The reconstituted fusion protein displayed the same immunological properties of the native Cup a1.02 protein as proven by IgE immunoreactivity. Immunoblotting, ELISA, and histamine release test showed that the tag did not preclude the protein functionality hence validating its correct three-dimensional folding. The protein fold was also assessed by CD spectroscopy and deconvolution of the spectrum allowed to estimate the secondary structure as a prevalence of beta structures (higher than 60%) and a small contribution from alpha helices (less than 12%). The reported procedure has proven to be useful for the production of multi-milligrams of recombinant Cup a1.02 allergen suitable for structural biology studies and for the molecular and functional characterization of the IgE binding sites.