Binding of viral antigens to major histocompatibility complex class I H-2D(b) molecules is controlled by dominant negative elements at peptide non-anchor residues - Implications for peptide selection and presentation

Binding of viral antigens to major histocompatibility complex (MHC) class I molecules is a critical step in the activation process of CD8(+) cytotoxic T lymphocytes, In this study, we investigated the impact of structural factors at non-anchor residues in peptide-MHC interaction using the model of lymphocytic choriomeningitis virus (LCMV) infection of its natural host, the mouse, Altering viral genes by making reassortants, recombinants, and using synthetic peptides, CD8(+) cytotoxic T lymphocytes were shown to recognize only three H-2D(b)-restricted epitopes, GP amino acids 33-41/43, GP 276-286, and NP 396-404, However, LCMV NP and GP proteins contain 31 other peptides bearing the H-2D(b) motif, These 34 LCMV peptides and 11 other known H2-D-b-restricted peptides were synthesized and examined for MHC binding properties, Despite the presence of the H-2D(b) binding motif, the majority of LCMV peptides showed weak or no affinity for H-2D(b), We observed that dominant negative structural elements located at non-anchor positions played a crucial role in peptide-MHC interaction, By comparative sequence analysis of strong versus non-binders and using molecular modeling, we delineated these negative elements and evaluated their impact on peptide-MHC interaction, Our findings were validated by showing that a single mutation of a favorable non-anchor residue in the sequence of known viral epitopes for a negative element resulted in dramatic reduction of antigen presentation properties, while conversely, substitution of one negative for a positive element in the sequence of a non-binder conferred to the peptide an ability to now bind to MHC molecules.