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Bioinformatics Advance Access originally published online on October 4, 2005
Bioinformatics 2005 21(23):4201-4204; 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{at}oxfordjournals.org

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

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

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

*To whom correspondence should be addressed at Division of Immunology, Queen's Medical Centre, Nottingham NG7 2UH, UK

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.

Contact: farouk.shakib{at}nottingham.ac.uk

Supplementary Information: http://www.nottingham.ac.uk/immunology/research/BI

Received on July 11, 2005; revised on September 28, 2005; accepted on September 28, 2005

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