Identification of MHC class II binding peptides: microarray and soluble MHC class II molecules

CD4+ T-helper cells recognize antigenic peptides presented by MHC class II molecules. The binding of the nominal peptide to the MHC class II allele is dependent on the amino acid sequence of the peptide as well as on amino acid (aa) residues in the peptide binding groove of the MHC class II allele. MHC class II alleles can either be associated with protection or susceptibility to disease (coined as "MHC class II-associated diseases"). A detailed knowledge about the nature, composition, and biochemical interaction of peptides with MHC class II molecules aids to link individual peptide species with MHC class II presentation and ultimately with CD4+ T-cell recognition. Several methods have been described to identify potential MHC class II candidate binding peptides. We present here a high content screening for MHC class II (HLA-DR) binding to a peptide library in a chip-format. Binding of soluble MHC class II molecules to individual peptides can be visualized using an anti-DR directed monoclonal antibody (mAb). Positive events (MHC class II/peptide complexes) are normalized and available for pattern analysis.