title: Peptide length significantly influences in vitro affinity for MHC class II molecules.
abstract: BACKGROUND
  Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules.
  
  
  RESULTS
  By analysing 1279 peptide elongation events covering 19 distinct HLA alleles it was observed that, in general, peptide elongation resulted in increased MHC class II molecule affinity. It was also possible to determine an optimal peptide length for MHC class II affinity of approximately 18-20 amino acids; elongation of peptides beyond this length resulted in a null or negative effect on affinity.
  
  
  CONCLUSIONS
  The observed relationship between peptide length and MHC class II affinity has significant implications for the design of vaccines and the study of the epitopic basis of immunological disease.
authors.affiliation: Department of Immunology and Institute of Molecular Medicine, St James's Hospital and Trinity College Dublin, Ireland. obrien.cathal@gmail.com
authors.forename: Cathal
authors.initials: C
authors.lastname: O'Brien
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
authors.forename: Conleth
authors.initials: C
authors.lastname: Feighery