NATURALLY PROCESSED PEPTIDES FROM RHEUMATOID-ARTHRITIS ASSOCIATED ANDNONASSOCIATED HLA-DR ALLELES

Naturally processed peptides from immunoaffinity-purified HLA-DRB1040 1, -DRB10404 (rheumatoid arthritis (RA)-associated), and -DRB1*0402 ( non-RA-associated) molecules were analyzed by capillary liquid chromat ography and mass spectrometry, The molecular weights observed for more than 60 eluted peptides from each HLA-DR protein ranged from 788 to 3 535 atomic mass units, corresponding to peptides 7 to 32 amino acids i n length, Sequencing of more than 60 of the abundant peptides revealed nested sets of peptides that were derived from only 12 different prot eins, The majority of these proteins were membrane-associated (HLA cla ss I, class II, and Ig molecules), Synthetic peptides, corresponding t o endogenous peptide sequences, bound with high affinity (5 to 80 nM) to the HLA-DR molecules from which they were eluted, In addition, most were promiscuous binding peptides in that they also bound to other HL A-DR molecules, Truncations of eluted peptide sequences and alanine sc anning mutational analysis of a Mycobacterium leprae peptide were used to identify the peptide residues involved in binding to DRB10404 and DRB10402 molecules. Furthermore, an invariant chain peptide was elut ed from the DRB10402 molecules but not from the RA-associated molecul es, The lack of invariant chain peptides from DRB10401 and DRB1*0404 molecules may contribute to the loading of autoantigen peptides into t hese molecules and to their association with disease.