Advertisement

An Alignment-Independent Platform for Allergenicity Prediction

  • Ivan DimitrovEmail author
  • Irini Doytchinova
Protocol
  • 113 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2131)

Abstract

A great number of novel proteins have been generated from new sources and genetically modified foods during the last decade. As the allergenicity of these proteins is of particular importance for their safe usage, fast and reliable screening strategies for allergenicity assessment are required. The WHO/FAO guidance directs to structural similarities between the novel proteins and known allergens detected by sequence alignment. However, the allergic response involves conformational IgE epitopes that are undetectable by sequence alignment. Here, we present a protocol for allergenicity prediction based on a platform of three alignment-independent servers developed in our lab: AllerTOP v.1, AllerTOP v.2, and AllergenFP. The servers use similar datasets but different chemical descriptors and methods to derive models for allergenicity prediction. The platform is freely accessible and user-friendly. The protocol is demonstrated stepwise on a randomly chosen query protein.

Key words

Allergenicity Allergenicity prediction Physicochemical properties of amino acids Alignment-independent methods 

Notes

Acknowledgments

This work has been accomplished with the financial support by the Grant No BG05M2OP001-1.001-0003, financed by the Science and Education for Smart Growth Operational Program (2014-2020), and co-financed by the European Union through the European structural and investment funds.

References

  1. 1.
    FAO/WHO (2009) Foods derived from modern biotechnology (annex: assessment of possible allergenicity, Codex Alimentarius—joint FAO/WHO food standards), 2nd edn. WHO, GenevaGoogle Scholar
  2. 2.
    Dimitrov I, Flower DR, Doytchinova I (2013) AllerTOP—a server for in silico prediction of allergens. BMC Bioinformatics 14(Suppl.6):S4CrossRefGoogle Scholar
  3. 3.
    Dimitrov I, Bangov I, Flower DR, Doytchinova I (2014) AllerTOP v.2—a server for in silico prediction of allergens. J Mol Model 20:2278CrossRefGoogle Scholar
  4. 4.
    Dimitrov I, Naneva L, Bangov I, Doytchinova I (2014) AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics 30:846–851CrossRefGoogle Scholar
  5. 5.
    Hellberg S, Sjöström M, Skagerberg B, Wold S (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30:1126–1135CrossRefGoogle Scholar
  6. 6.
    Wold S, Jonsson J, Sjöström M, Sandberg M, Rännar S (1993) DNA and peptide sequences and chemical processes multivariately modelled by principal components analysis and partial least squares projections to latent structures. Anal Chim Acta 277:239–253CrossRefGoogle Scholar
  7. 7.
    Venkatarajan MS, Braun W (2001) New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. J Mol Model 7:445–453CrossRefGoogle Scholar
  8. 8.
    Tanimoto TT (1958) An elementary mathematical theory of classification and prediction. IBM Research Yorktown Heights, New YorkGoogle Scholar
  9. 9.
    Franz-Oberdorf K, Eberlein B, Edelmann K, Hücherig S, Besbes F, Darsow U, Ring J, Schwab W (2016) Fra a 1.02 is the most potent isoform of the bet v 1-like allergen in strawberry fruit. J Agric Food Chem 64:3688–3696CrossRefGoogle Scholar
  10. 10.
    Gao ZS, van de Weg WE, Schaart JG, Schouten HJ, Tran DH, Kodde LP, van der Meer IM, van der Geest AHM, Kodde J, Breiteneder H, Hoffmann-Sommergruber K, Bosch D, Gilissen LJWJ (2005) Genomic cloning and linkage mapping of the mal d 1 (PR-10) gene family in apple (Malus domestica). Theor Appl Genet 111:171–183CrossRefGoogle Scholar
  11. 11.
    Hsieh LS, Moos M, Lin Y (1995) Characterization of apple 18 and 31 kd allergens by microsequencing and evaluation of their content during storage and ripening. J Allergy Clin Immunol 96:960–970CrossRefGoogle Scholar
  12. 12.
    Scheurer S, Pastorello EA, Wangorsch A, Kästner M, Haustein D, Vieths S (2001) Recombinant allergens Pru av 1 and Pru av 4 and a newly identified lipid transfer protein in the in vitro diagnosis of cherry allergy. J Allergy Clin Immunol 107:724–731CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Faculty of PharmacyMedical University of SofiaSofiaBulgaria

Personalised recommendations