Origin, structure and motifs of naturally processed MHC class II ligands

In the past few years a considerable number of naturally processed MHC class II ligands have been identified and sequenced. Most of them derive from endogenous sources, predominantly from plasma membrane proteins. Generally, they display variability in length but exhibit characteristic patterns of invariant amino acid positions, which reflect the allele-specific binding requirements. As a general feature, class II ligands also often contain a pattern of proline residues interpreted as a ‘processing motif’.