Sequencedependent MHC peptide binding

The sequence-independent network of hydrogen bonds between conserved MHC residues and the peptide main-chain gives rise to a broad, but not unlimited, peptide-binding capacity. Indeed, most natural peptide sequences lack the characteristics necessary to bind to MHC molecules, because peptide main-chain interactions are not the only mode of MHC binding. Some of the peptide side-chains contact residues within the MHC cleft and increase the overall binding affinity and specificity of the associated peptides (anchor residues); others interfere with residues of the MHC cleft and reduce binding (inhibitory residues). These sequence-dependent interactions are due to the irregular surface of the MHC cleft. MHC side-chains protrude into the cleft and form pockets or ridges, resulting in strong preferences for interaction with particular amino acid side-chains (Figure 1).

Notably, most pockets in the MHC groove are

Table 1 MHC motifs

MHC molecules Peptide positions
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