Structure of allergens and structure based epitope predictions (original) (raw)
Related papers
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces
Bioinformatics and Biology Insights, 2010
Recent progress in the biochemical classification and structural determination of allergens and allergen-antibody complexes has enhanced our understanding of the molecular determinants of allergenicity. Databases of allergens and their epitopes have facilitated the clustering of allergens according to their sequences and, more recently, their structures. Groups of similar sequences are identified for allergenic proteins from diverse sources, and all allergens are classified into a limited number of protein structural families. A gallery of experimental structures selected from the protein classes with the largest number of allergens demonstrate the structural diversity of the allergen universe. Further comparison of these structures and identification of areas that are different from innocuous proteins within the same protein family can be used to identify features specific to known allergens. Experimental and computational results related to the determination of IgE binding surfaces and methods to define allergen-specific motifs are highlighted.
MOLECULAR IMMUNOLOGY, 2008
Similarities in sequences and 3D structures of allergenic proteins provide vital clues to identify clinically relevant IgE cross-reactivities. However, experimental 3D structures are available in the Protein Data Bank for only 5% (45/829) of all allergens catalogued in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP). Here, an automated procedure was used to prepare 3D-models of all allergens where there was no experimentally determined 3D structure or high identity (95%) to another protein of known 3D structure. After a final selection by quality criteria, 433 reliable 3D models were retained and are available from our SDAP Website. The new 3D models extensively enhance our knowledge of allergen structures. As an example of their use, experimentally derived "continuous IgE epitopes" were mapped on 3 experimentally determined structures and 13 of our 3D-models of allergenic proteins. Large portions of these continuous sequences are not entirely on the surface and therefore cannot interact with IgE or other proteins. Only the surface exposed residues are constituents of "conformational IgE epitopes" which are not in all cases continuous in sequence. The surface exposed parts of the experimental determined continuous IgE epitopes showed a distinct statistical distribution as compared to their presence in typical protein-protein interfaces. The amino acids Ala, Ser, Asn, Gly and particularly Lys have a high propensity to occur in IgE binding sites. The 3D-models will facilitate further analysis of the common properties of IgE binding sites of allergenic proteins.
Enlarging the Toolbox for Allergen Epitope Definition with an Allergen-Type Model Protein
PLoS ONE, 2014
Background: Birch pollen-allergic subjects produce polyclonal cross-reactive IgE antibodies that mediate pollen-associated food allergies. The major allergen Bet v 1 and its homologs in plant foods bind IgE in their native protein conformation. Information on location, number and clinical relevance of IgE epitopes is limited. We addressed the use of an allergenrelated protein model to identify amino acids critical for IgE binding of PR-10 allergens.
Objectives: The identification of B-cell epitopes is a challenging approach to explore the antigen-antibody interactions for diagnosis and therapy of hypersensitivity reaction. In our present study, an in-silico approach is used to investigate the interaction of pollen allergen EXPB1 (Zea m 1), pollen allergen from maize with IgE molecules of human. Material and Methods: Paratope of human immunoglobulin E is identified using site-specific proABC predictor method. Phylogenetic analysis of Zea m 1 reveals that 13 pollen allergens from different grasses, maize, timothy grass, velvet grass, Bermuda grass, canary grass, rice and perennial rye grass are close homologs to our query allergen EXPB1. Among them Phl p 1 pollen allergen from Phleum pratense is identified with 60% identity with Zea m 1. Experimental B cell epitopes of Phl p 1 are known and we have verified those epitopes with PIPER, molecular docking software. Thus, interacting amino acids present both in epitopes and paratopes are visualized and confirmed with predicted paratopes. For all homologous allergens, the interacting amino acids i.e. epitopes and paratopes have been identified using the two docking programs, DOT and ZDOCK. Results and Conclusions: Negative binding energies of all pollen allergens with immunoglobulin E confirm their allergenicity. Thus, all allergens become cross reactive with maize allergen. The multiple sequence alignment for all homologous sequences reveals that the positions of antigenic peptide of Zea m 1 sequence are well conserved in its homologs and responsible for cross-reactivity. This cross-reactivity identification will help us to identify the immunotheraputics e.g. vaccine designing for these β expansin family protein allergens during pollinosis. Kumar et al., 2015[6]in their in-silico work, have mapped sequential and conformational B-cell epitopes from the crystal structure of LipL32, the most abundant surfaceassociated protein of Leptospira and identified the order of antigenicity of four B cell epitopes. Radauer et al. [7]
Interfaces between allergen structure and diagnosis: know your epitopes
Current allergy and asthma reports, 2015
Allergy diagnosis is based on the patient's clinical history and can be strengthened by tests that confirm the origin of sensitization. In the past 25 years, these tests have evolved from the exclusive in vivo or in vitro use of allergen extracts, to complementary molecular-based diagnostics that rely on in vitro measurements of IgE reactivity to individual allergens. For this to occur, an increase in our understanding of the molecular structure of allergens, largely due to the development of technologies such as molecular cloning and expression of recombinant allergens, X-ray crystallography, or nuclear magnetic resonance (NMR), has been essential. New in vitro microarray or multiplex systems are now available to measure IgE against a selected panel of purified natural or recombinant allergens. The determination of the three-dimensional structure of allergens has facilitated detailed molecular studies, including the analysis of antigenic determinants for diagnostic purposes.
Journal of Chromatography B: Biomedical Sciences and Applications, 2001
For the understanding of the relationship between protein structure and allergenicity, it is important to identify allergenic epitopes. Two methods to characterize primarily linear epitopes are compared using the major allergen from brown shrimp (Penaeus aztecus), Pen a 1, as an example. A recombinant peptide library was constructed and synthetic, overlapping peptides, spanning the entire Pen a 1 molecule, were synthesized and tested for specific IgE reactivity. Both methods identified IgE-binding of Pen a 1, however, the SPOTs procedure resulted in the identification of more epitopes of the major shrimp allergen Pen a 1 than the usage of the recombinant peptide library. For detection of specific IgE antibodies, the usage 125 of I-labeled detection antibody seems to be superior over enzyme-labeled anti IgE antibodies. The regeneration of SPOTs membranes is possible, but it is prudent to test regenerated membranes for residual activity. If a given food allergen contains significant linear epitopes, which seems to be true for stable major allergens such as those of peanut and shrimp the SPOTs system may be more advantageous than the use of recombinant peptides libraries. However, if allergens are studied that contain more conformational epitopes, recombinant peptide libraries may help to identify the relevant epitopes. It has to be emphasized that no system for epitope identification will detect all epitopes and that the relevance of identified epitopes has to be confirmed with other methods such as inhibition studies, crystallographic analysis or the immunological evaluation of modified whole allergens.
Characteristic motifs for families of allergenic proteins
Molecular Immunology, 2009
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 Motif-Mate (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.
Structural biology of allergens
Current Allergy and Asthma Reports, 2005
Major allergens may have special aerobiological properties and allergenic structures. It would also be instructive to consider the properties of non-allergens and non-allergenic responses.
Structure, 2008
Blo t 5 is the major allergen from Blomia tropicalis mites and shows strong IgE reactivity with up to 90% of asthmatic and rhinitis patients' sera. The NMR solution structure of Blo t 5 comprises three long a helices, forming a coiled-coil, triple-helical bundle with a left-handed twist. TROSY-NMR experiments were used to study Blo t 5 interaction with the Fab 0 of a specific monoclonal antibody, mAb 4A7. The mAb epitope comprises two closely spaced surfaces, I and II, connected by a sharp turn and bearing critical residues Asn46 and Lys47 on one surface, and Lys54 and Arg57 on the other. This discontinuous epitope overlaps with the human IgE epitope(s) of Blo t 5. Epitope surface II is further predicted to undergo conformational exchange in the millisecond to microsecond range. The results presented are critical for the design of a hypoallergenic Blo t 5 for efficacious immunotherapy of allergic diseases.
Mapping of conformational IgE epitopes of food allergens
Allergy, 2018
Food allergies reduce the quality of life of affected individuals and may result in anaphylaxis or even death. Allergen-specific immunotherapy (AIT) is based on vaccination with the disease-causing allergens. However, the administration of food allergens can produce severe side effects. Engineered food allergens with altered IgE