Characteristic Motifs for Families of Allergenic Proteins

Overview

Journal Mol Immunol

Specialties Allergy & Immunology
Molecular Biology

Date 2008 Oct 28

PMID 18951633

Citations 28

Authors

Ovidiu Ivanciuc

Tzintzuni Garcia

Miguel Torres

Catherine H Schein

Werner Braun

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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

Negi S, Schein C, Braun W J Allergy Clin Immunol Glob. 2023; 2(4):100162.

PMID: 37781674 PMC: 10509899. DOI: 10.1016/j.jacig.2023.100162.

Still SDAPing Along: 20 Years of the Structural Database of Allergenic Proteins.

Schein C, Negi S, Braun W Front Allergy. 2022; 3:863172.

PMID: 35386653 PMC: 8974667. DOI: 10.3389/falgy.2022.863172.

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

Negi S, Goldblum R, Braun W, Midoro-Horiuti T Peptides. 2021; 145:170628.

PMID: 34411692 PMC: 8484066. DOI: 10.1016/j.peptides.2021.170628.

Nutritional, functional, and allergenic properties of silkworm pupae.

Wu X, He K, Cirkovic Velickovic T, Liu Z Food Sci Nutr. 2021; 9(8):4655-4665.

PMID: 34401111 PMC: 8358373. DOI: 10.1002/fsn3.2428.

DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors.

Braun B, Schein C, Braun W Bioinform Biol Insights. 2021; 15:11779322211020316.

PMID: 34163149 PMC: 8188974. DOI: 10.1177/11779322211020316.

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