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Proteasome plays an essential role not only in continual turnover of intracellular proteins but also in antigen processing, generating peptides which can be presented on MHC I molecules and recognized by cytotoxic T-lymphocytes. Recently we have shown that myelin basic protein (MBP), one of major autoantigenes in multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), is degraded by 26S proteasome ubiquitin-independently. As proteasomal degradation of MBP is not controlled by ubiquitylation system, rate of MBP degradation and composition of the resulting peptide pool is dependent mainly on the protesome substrate specificity. b1ihigh immunoproteasome, which is upregulated in the brain of SJL mice with EAE, generates increased amount of MBP83–90 peptide epitope (ENPVVHFF). This peptide can be presented on mouse MHC I molecules of H2-Kk and H2-Ks haplotypes and induces cytotoxic CD8+ T cells to target oligodendrocytes ex vivo. Inhibition of immunoproteasome activity, inhibition of MBP deimination, or increase of MBP expression level can affect the oligodendrocytes’ susceptibility to cytotoxic T-cells-mediated damage.