ANALYSIS OF NATURALLY PROCESSED PEPTIDES ELUTED FROM HLA-DRB1-ASTERISK-0402 AND HLA-DRB1-ASTERISK-0404

Understanding the structural features of naturally processed peptides found within the major histocompatibility complex (MHC) class II pepti de binding groove from disease-associated MHC molecules may provide in sights into the nature of potential disease-related antigens, Class II MHC/peptide complexes were purified by immunoaffinity from transforme d B cell lines homozygous for DRB10404 (an allele associated with rhe umatoid arthritis) and 0402 (a closely related allele not associated with this disease). Peptides were eluted at acidic pH, fractionated by reversed phase HPLC, and analyzed by capillary electrophoresis. Those fractions containing a single dominant peptide were sequenced by auto mated Edman degradation and tandem mass spectrometry, The predominant peptide species identified came from non-polymorphic regions of the HL A class I molecules expressed by each cell line, Peptides from DRB104 04 were found to be nested clusters derived from positions 26-43 of th e HLA-B and -C alpha-chain, DRB10402 contained as the predominant pep tide species a nested cluster from positions 129-145 of the HLA-B alph a-chain. The primary structure of the class I derived peptides was con sistent with that seen by peptides exhibiting promiscuous DR binding b ehavior, Processing of MHC-derived peptides by MHC class II molecules is a common occurrence in the transformed B cell lines analyzed. (C) 1 996 Wiley-Liss, Inc.