title: Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: an in silico analysis.
abstract: BACKGROUND
  The body of sequence and structural information on allergens and the sequence analysis of whole plant genomes are facilitating the application of bioinformatic approaches to identifying and defining plant allergens.
  
  
  OBJECTIVE
  An in silico approach was used to quantify the distribution of plant food allergen sequences across protein families and to develop and apply a novel means of assessing conserved surface features important for IgE cross-reactivity.
  
  
  METHODS
  Plant food allergen sequences were classified into Pfam families on the basis of sequence homology. Contact surface areas of selected proteins were calculated with MOLMOL by using a 1.4-A probe, corrected by removing contributions from IgE inaccessible main chains and side chains forming the ligand binding sites.
  
  
  RESULTS
  A set of 129 food allergen sequences were classified into only 20 of 3849 possible Pfam families, with 4 families accounting for more than 65% of food allergens. Structural bioinformatic analysis of conserved exterior main chains and amino acid side chains in cross-reactive homologues of Bet v 1 and nonspecific lipid transfer proteins showed higher levels of similarity than shown by simple sequence comparisons. Thus, 75% of the Mal d 1 surface is likely to bind anti-Bet v 1 antibodies, compared with a sequence identity of approximately 56%.
  
  
  CONCLUSIONS
  Most plant food allergens belong to only 4 structural families, indicating that conserved structures and biological activities may play a role in determining or promoting allergenic properties. Structural bioinformatic analysis shows that conservation of 3-dimensional structure should be included in any assessment of potential IgE cross-reactivity in, for example, novel proteins.
authors.affiliation: Institute of Food Research, Norwich, Cambridge, United Kingdom.
authors.forename: John A
authors.initials: JA
authors.lastname: Jenkins
authors.forename: Sam
authors.initials: S
authors.lastname: Griffiths-Jones
authors.forename: Peter R
authors.initials: PR
authors.lastname: Shewry
authors.forename: Heimo
authors.initials: H
authors.lastname: Breiteneder
authors.forename: E N Clare
authors.initials: EN
authors.lastname: Mills
mesh_terms: D000485:Allergens / Q000737:chemistry / Q000145:classification* / Q000276:immunology; D000906:Antibodies / Q000276:immunology; D000918:Antibody Specificity; D003429:Cross Reactions; D030562:Databases, Protein; D005502:Food; D018745:Genome, Plant; D007073:Immunoglobulin E / Q000276:immunology; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification* / Q000276:immunology; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein
chemical_list: D000485:Allergens; D000906:Antibodies; D010940:Plant Proteins; D007073:Immunoglobulin E