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Prediction of IgE-binding epitopes by means of allergen surface comparison and correlation to cross-reactivity  Fabio Dall'Antonia, PhD, Anna Gieras,

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Presentation on theme: "Prediction of IgE-binding epitopes by means of allergen surface comparison and correlation to cross-reactivity  Fabio Dall'Antonia, PhD, Anna Gieras,"— Presentation transcript:

1 Prediction of IgE-binding epitopes by means of allergen surface comparison and correlation to cross-reactivity  Fabio Dall'Antonia, PhD, Anna Gieras, PhD, Siva Charan Devanaboyina, PhD, Rudolf Valenta, MD, Walter Keller, PhD  Journal of Allergy and Clinical Immunology  Volume 128, Issue 4, Pages e8 (October 2011) DOI: /j.jaci Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

2 Fig 1 Exemplary windows of the SPADE graphic user interface and its PyMol interface. A, Main window with its protein comparison input fields on the left. B, Bar graph window for the display of pairwise comparison results, with aligned sequences on top. C, Input window for the epitope prediction. Available pairwise comparisons are listed on the left. CR values can be assigned by using the sliders. D, A reference allergen surface with mapped Δ-sim from −100 to 100 colored red through white to blue. E, Text output with predicted epitope residues listed. F, The according display of predicted epitopes on the target surface. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

3 Fig 2 Assessment of the SPADE epitope prediction for bBLG. A, Projection of relevant residues onto the bBLG surface. Correctly predicted IgE-binding residues are colored magenta, missing residues are colored blue, and falsely predicted residues (of the first SPADE patch) are colored red. B, SPADE relocalization performance in comparison with 5 other programs. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

4 Fig 3 Surface similarity analysis for 2 target allergens. A, Similarity at 15 IgE-binding residues of bBLG with respect to 3 homologs compared. B, Similarity at 17 IgG-binding residues of Bet v 1a with respect to 6 homologs compared. C, As for Fig 3, B, looking at 9 IgE-binding residues predicted by using SPADE. In all graphs, the x-axes denote the involved residues. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

5 Fig 4 Binding of serum IgE to Bet v 1a and 10 homologs. Co, Negative control (BSA). Serum IgE reactivities to recombinant Bet v 1a and Bet v 1−homologous proteins (y-axis) are shown as OD values (x-axis) in the form of box-and-whisker plots. Boxes show medians and quartiles, and whiskers display maximum and minimum values within 1.5× interquartile distances from the medians. Extreme values are shown as asterisks. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

6 Fig 5 The Bet v 1 epitope prediction compared with experimentally studied peptides. A, Outcome of the standard method (patches colored magenta) compared with the localization of peptides 5 (yellow) and 6 (blue). B, Outcome of the isoform-based “negative definition” variant (magenta) compared with the localization of peptides 3 (green), 5 (yellow), and 6 (blue). I, Prediction; II, experiment (both in cartoon style with residues labeled); III, consensus surface (the actual consensus area is colored deep purple). Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

7 Fig E1 Determinants of surface similarity. Correlation between comparison parameters visualized and quantified by using the linear (Pearson) correlation coefficient. A, Correlation of similarity scores to PAM250 scores. B, Correlation of similarity scores to α-carbon distances after global superimposition. In both cases the same set of pairwise comparison data was used. Each data point corresponds to 1 amino acid residue. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

8 Fig E2 Effect of the surface similarity threshold on the patch localization. A, Sample case bBLG. B, Sample case Bet v 1. Numbers of filtered amino acid residues and the major patch size are plotted on different y-axes. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

9 Fig E3 Phl p 2 IgE epitopes predicted by using SPADE. A, The amino acid residues belonging to the predicted epitope 1 are depicted as labeled side-chain stick models. B, The IgE-binding residues of the experimental epitope in the Phl p 2–IgE complex structure (as depicted by Padavattan et alE15) are here mapped to the unbound Phl p 2 structure. Model orientation and representation are as for Fig E1, A. C, The agreement of prediction and experiment mapped to the Phl p 2 surface. The overlap region is colored orange, the falsely predicted region is colored yellow, and the nonpredicted epitope region is colored blue. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

10 Fig E4 The SPADE performance in comparison with other prediction tools. A, left, SPADE similarity scores and sequence conservation table for the 21 target residues involved in the experimental IgE epitope. Residues included in the SPADE prediction after filtering at 60% are indicated by orange bars. P94 is preselected but spatially isolated and thus not included. Right, Prediction hits for the 5 programs compared and the correlation to solvent accessibility of the respective target residues. F68 is buried in the unbound structure used for all predictions but exposed in the complex structure. Different match symbols and black labels are used for directly IgE-binding residues. B, Prediction sensitivity and specificity values (x-axis and y-axis, respectively) of the 5 programs compared. Journal of Allergy and Clinical Immunology  , e8DOI: ( /j.jaci ) Copyright © 2011 American Academy of Allergy, Asthma & Immunology Terms and Conditions

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