Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes

Numan Oezguen, Bin Zhou, Surendra S. Negi, Ovidiu Ivanciuc, Catherine H. Schein, Gilles Labesse, Werner Braun

Research output: Contribution to journalArticlepeer-review

49 Scopus citations

Abstract

Similarities in sequences and 3D structures of allergenic proteins provide vital clues to identify clinically relevant immunoglobulin E (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.

Original languageEnglish (US)
Pages (from-to)3740-3747
Number of pages8
JournalMolecular Immunology
Volume45
Issue number14
DOIs
StatePublished - Aug 2008

Keywords

  • Allergens
  • Linear epitopes
  • SDAP
  • Structural database

ASJC Scopus subject areas

  • Immunology
  • Molecular Biology

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