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Bioinformatics Advance Access published online on October 4, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti700
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 11, 2005
Accepted September 28, 2005

Discovery note

An attempt to define allergen-specific molecular surface features: a bioinformatic approach

Ruta Furmonaviciene 1, Brian J. Sutton 2, Fabian Glaser 3, Charlie A. Laughton 4, Nick Jones 5, Herb F. Sewell 1, and Farouk Shakib 1*

1 Allergy Research Group, Institute of Infection, Immunity and Inflammation, The University of Nottingham, Nottingham, United Kingdom
2 The Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
3 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
4 Molecular Recognition Group, School of Pharmacy, The University of Nottingham, Nottingham, United Kingdom
5 Division of Otorhinolaryngology, School of Medical and Surgical Sciences, The University of Nottingham, Nottingham, United Kingdom

* To whom correspondence should be addressed.
Farouk Shakib, E-mail: farouk.shakib{at}nottingham.ac.uk


  Abstract

Allergens are proteins that elicit T helper lymphocyte type 2 (Th2) responses culminating in IgE antibody production and allergic disease. However, we have no answer to the fundamental question of why certain proteins are allergens, while others are not. We hypothesized that analysis of the surface of diverse allergens may reveal common structural features which might enable them to be recognized as Th2-inducing antigens by cells of the innate immune system. We have therefore used the ConSurf server to search for allergen-specific motifs. This has enabled us to identify residue conservation patterns in the homologues of Ara t 8 (plant profilin), Act c 1 (actinidin), Bet v 1 (plant pathogenesis-related protein) and Ves v 5 (venom allergen). The results demonstrate the presence of allergen-specific patches consisting of an unusually high proportion of surface-exposed hydrophobic residues. The patches that have been identified may represent molecular patterns recognizable by cells of the innate immune system.


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