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

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Food Allergens

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2717))

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Abstract

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.

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References

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Acknowledgments

SDAP was originally designed and compiled by Dr. Ovidiu Ivanciuc and Prof. Werner Braun (WB) and is now maintained by Surendra S. Negi. Allergen 3D-models were originally generated by Numan S. Oezguen and Trevor D. Power and are currently being updated by Dr. Negi. The PD search began with work of Venkatarajan A. Mathura. The D-graph program was written by Benjamin A. Braun, PhD, with physics advice from Werner Braun and validated for use with allergen and virus sequences by CHS. SDAP was originally funded by a Research Development Grant (#2535-01) from the John Sealy Memorial Endowment Fund for Biomedical Research and grants from the US-Food and Drug Administration (FD-U-002249) and the Texas Higher Education Coordinating Board (ATP grant 004952-0036-2003) to Werner Braun. Our work with allergenic proteins and SDAP upkeep has been supported by grants from the U.S. Environmental Protection Agency under STAR Research Assistance Agreements (RD- 833137, RD-834823-01 to Werner Braun, RE-83406601 to CHS), the US Department of Agriculture (ARS 58-6435-9-40 to CHS) and the National Institute of Health (R01 AI 064913 to Werner Braun, 1R01AI165866-01 to Stephen Dreskin; subcontract to CHS). Funding for this chapter was provided by the Margaret Maccallum Gage and Tracy Davis Gage Professorship in Biochemistry and Allergies to Werner Braun. We thank all these funders and our collaborators over the more than 20 years of SDAP’s online presence. We also thank those who have used its data and tools in their research and regulatory matters.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch, Galveston, TX, USA

    Catherine H. Schein

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  1. Catherine H. Schein
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Correspondence to Catherine H. Schein .

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Editors and Affiliations

  1. Department of Allergy, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain

    Beatriz Cabanillas

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Schein, C.H. (2024). Identifying Similar Allergens and Potentially Cross-Reacting Areas Using Structural Database of Allergenic Proteins (SDAP) Tools and D-Graph. In: Cabanillas, B. (eds) Food Allergens. Methods in Molecular Biology, vol 2717. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3453-0_18

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  • DOI: https://doi.org/10.1007/978-1-0716-3453-0_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3452-3

  • Online ISBN: 978-1-0716-3453-0

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