Specificity of peptide binding to class I

Class I molecules must be able to bind peptides with a variety of sequences. Thus, the binding must lack the exquisite specificity of antibodies. At the same time we know from biochemical binding experiments that binding is limited. These molecules utilize specific interactions with specific amino acids called anchor residues, as well as contacts with other atoms in the peptide. The anchor residues differ among the different K/D/L proteins, both in the position of interaction of the peptide and in the amino acid in the anchor position. For example Kk binds glutamic acid at position 2 and isoleucine at position 8, while Kd binds tyrosine at position 2 and leucine at position 9. Thus different K alleles will bind different sets of peptides, as will different D and L alleles. This maximizes the possibility that any virus will have at least one peptide that can be productively presented to the immune system.

The class lb molecules appear to have distinct binding characteristics. For example, the iVl locus products bind peptides with N-formyl methionine as the N-terminus, suggesting a role in the presentation of peptides derived from intracellular bacteria. Some

CD1 proteins may present nonpeptide epitopes derived from cell membranes and cell walls of Mycobacteria to y8 T cells. The specificity of other class lb molecules is unknown.

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