Peptide Ligands of MHC Class I Molecules

Strategies for the determination of natural T-cell epitopes include mostly the identification of epitopes from source proteins by molecular genetic techniques. Truncation mutants of the original genes were analyzed in bioassays and further characterized with overlapping peptides [29]. Alternatively, natural T-cell epitopes are eluted from cell lines that restrict the T-cell response. The eluted peptides are purified and sequenced by Ed-man degradation [30]. 

These approaches are time-consuming and limited by the amount of biological materials. A fast method to define recognition patterns of MHC molecules has been introduced by screening synthetic combinatorial peptide libraries [31]. 

The synthetic generation of millions of peptides can supplement the search for natural epitopes. Synthetic, as well as natural, epitopes can be modified to obtain potential drugs with patient specific properties [32]. 

The rules for peptide selection by MHC class I molecules were defined by the characterization of peptide mixtures extracted from class I complexes [33], and furthermore, by the effects of collections of different peptides on binding to MHC molecules and by the response of cytotoxic T cells on these presented peptides [34]. Crystal structure analyses of defined MHC-peptide and MHC-peptide-T-cell receptor (TCR) complexes [35-38] gave detailed information on the molecular interaction between peptides and MHC proteins. MHC class I ligands are mainly octa- or nonapeptides and obey allele-specific sequence motifs carrying prominent anchor residues [24], The peptide-binding groove offers specific pockets to interact with these anchor residues [35]. 

Prominent primary anchor residues in anchor positions determined by pool sequencing (e.g., positions 5 and 8 for H-2Kb, positions 2 and 8 for H-2Ld) were ascertained by screening octapeptide libraries [39], Unfavorable effects on binding can be induced also by amino acids in non anchor positions. Conformational analysis of several individual peptides bound to MHC class I molecules showed that the position of the peptide backbone in the binding groove, as well as the orientation of side chains in other sequence positions, is influenced by individual amino acid side chains [36]. These interactions strongly determine the accessibility of the peptide on the MHC 1 surface and thus the response of the CTL effector cells. Anchor residues promote efficient binding to MHC 1, but notably suppress the CTL response to the complex peptide libraries [39]. 

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