A post-translational modification of nuclear proteins, N-G,N-G-dimethyl-Arg, found in a natural HLA class I peptide ligand

Presentation of peptides derived from endogenous proteins by class I major histocompatibility complex molecules is essential both for immunological se lf-tolerance and induction of cytotoxic T-cell responses against intracellu lar parasites. Despite frequent and diverse post-translational modification of eukaryotic cell proteins, very few class I-bound peptides with post-tra nslationally modified residues are known. Here we describe a natural dodeca mer ligand of HLA-B39 (B*3910) derived from an RNA-binding nucleoprotein th at carried N-G,N-G-dimethyl-Arg. Although common among RNA-binding proteins , this modification was not previously known among natural class I ligands. The sequence of this peptide was determined by Edman degradation and elect rospray ion trap mass spectrometry. The fragmentation pattern of the dimeth yl-Arg side chain observed with this latter technique allowed us to unambig uously assign the isomeric form of the modified residue. The post-translati onally modified ligand was a prominent component (1-2%) of the B*3910-bound peptide repertoire. The dimethyl-Arg residue was located in a central posi tion of the peptide, amenable to interacting with T-cell receptors, and mos t other residues in the middle region of the peptide were Gly. These struct ural features strongly suggest that the post-translationally modified resid ue may have a major influence on the antigenic properties of this natural l igand.