Peptide variants reveal how antibodies recognize major histocompatibility complex class I

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Abstract
The T cell receptor (TcR) on CD8+ T lymphocytes recognizes a complex which consists of a major histocompatibility complex (MHC) heavy chain, β2‐microglobulin (β2M), and peptide on the surface of antigen‐presenting cells. Mutational analyses have suggested that the TcR recognizes both the αl and α2 domains of the heavy chain as well as the peptide. In light of this, it is of interest to know to what extent the heavy chain domains take on distinct conformations when bound to individual peptides. It has recently been shown that antibodies which recognize the Kb MHC complex are sensitive to which peptides are bound in the groove. We have extended this analysis to include eight Kb‐specific antibodies, seven of which are peptide sensitive. These antibodies, all of which are allo‐antibodies, recognize Kb‐bearing cells which, it is now appreciated, have a highly heterogeneous mix of self peptides presented in their grooves. We show that these self peptides also can affect antibody binding. It has been suggested that peptides alter the conformation of the αl and α2 domains of the heavy chain and that this in turn affects the recognition of Kb by antibody. An alternative hypothesis is that solvent‐exposed peptide side chains may prevent the antibody from binding the complex. Using a panel of 128 single‐amino acid variants of a Kb‐binding antigenic peptide from ovalbumin we show that for most Kb‐specific antibodies, the second idea is more likely. Those variants which prevent antibody binding are at solvent exposed positions, and in general, the bulkier the side chain, the greater the inhibition of antibody binding. However, in the case of two antibodies, 100.30 and 34.4.20, the peptide residues which affect antibody recognition are buried, suggesting that these antibodies see an alternate conformation of the peptide/MHC complex.