Fig. 2.

Summary of sequence and thermodynamic data for the self-peptides with reactivity toward the AND, 5C.C7, and OT-I TCRs. (A) Amino acid sequences of a subset of the known I-E^k-bound self-peptides⁴¹ and H-2K^b-bound self-peptides (Ref. 37; the Cappa1 peptide was originally described in Ref. 36). I-E^k-binding peptides are shown in their predicted I-E^k-binding register; MHC pocket residues are highlighted.^42,43 The peptides’ reactivity toward the indicated TCR was measured by CD69 upregulation of DP thymocytes bearing that TCR toward the indicated peptide presented by APCs or platebound I-E^k.^39,40 For OT-I, reactivity was measured in terms of CD4 CD8 coreceptor downregulation, or dulling.³⁷ The ability of these peptides to positively select T cells bearing the indicated TCR was assessed: for AND, in reaggregate thymus cultures with the ANV41.2 cTEC cell line as APCs; for 5C.C7, in 5C.C7 Ii^−/− fetal thymus organ cultures (FTOCs); and for OT-I, in OT-I TAP^−/− FTOCs. (B) A summary of affinities of the OT-I TCR for different peptide–H-2K^b and a schematic of the relation between affinity and selection outcome. Positive selection data for E1 (EIINFEKL) and R4 (SIIRFEKL) are from Ref. 44, positive selection data for the self-peptides are from Ref. 37. Affinity measurements are from Ref. 38 except for ☼ (Ref. 28), at 25 °C, and ‡ (Ref. 32), also at 25 °C.