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The biochemical characterization of antigen degradation is an important basis for a better understanding of both the immune response and autoimmune diseases mediated by MHC class II molecules. In this study we used high-performance liquid chromatography and mass spectrometry to analyze the processing of myelin basic protein (MBP), a potential autoantigen implicated in the pathogenesis of multiple sclerosis. We resolved the kinetics of MBP processing by lysosomal extracts or purified endocytic proteases, identified the major cleavage sites during this process and assigned them to the activity of proteolytic enzymes. Proteolytic processing of MBP is mostly guided along the hydrophobic regions of the protein. It is initiated by two proteolytic steps (after N(92) and S(110)) that are performed by an asparagine-specific endopeptidase (AEP) and by cathepsin (Cat) S, respectively. The resulting processing intermediates are converted into more than 60 different species of 20-40-mers due to the activity of endopeptidases including CatS, D and L. The fragments thus generated are subsequently degraded by C- or N-terminal trimming. Strikingly, the initial cleavages during MBP processing affect two immunodominant regions of the potential autoantigen [MBP(85-99) and MBP(111-129)] in an inverse manner. CatS directly generates the N terminus of the epitope MBP(111-129) in large quantities during the initial phase of processing, which might explain the immunogenicity of this region in spite of its relatively poor binding to HLA-DR4. In contrast, the dominant cleavage by AEP mediates the destruction of MBP(85-99) unless the epitope is protected, e.g. by binding to HLA-DR. Our results thus characterize the proteolytic events during processing of MBP on a molecular level and suggest a biochemical basis for the immunogenicity of the immunodominant epitopes, which could serve as a guideline for future therapeutic strategies.