Table II. APQPAPENAY peptide contacts with HLA-B*3501 and HLA-B*3508 MHC residue Type of bond 08/01 Peptide residue P1 AlaO AlaN Ala P2 ProO Pro P3 GlnN GlnO 1 GlnN 2 GlnO 1 GlnO Gln Gln P4 P5 P6 P7 Pro Pro Ala Pro P8 P9 P GluN GluO GluO 1 GluO 1 GluO 1 GluO 1 GluO 1 GluO 1 GluO 2 GluO 2 GluO 2 Glu AsnN AsnO AsnO Asn Asn AlaO Ala TyrN TyrO TyrOXT TyrO Tyr 1256 Tyr 159O Tyr 171O , Tyr 7O Met 5, Tyr 7, Tyr 159, Trp 167, Tyr 171 Arg 62N , Arg 62N 2 Tyr 7, Tyr 9, Asn 63, Phe 67, Tyr 99, Tyr 159 Tyr 99O P7 GluO 2 P4 ProO Arg156N 1 Asn 70N 2, Tyr 9O , P7 GluO 2 Tyr 159, Tyr 99, Ile 66 Arg 156, Gln 155 Tyr 159 Ile 66, Leu 163 Ile 66 Thr 69 Asn 70O 1, Thr 73O 1, P7 GluO Thr73O 1 Arg 97N 1 Tyr 74O P8 AsnO Arg 97N 1 Arg 97N 2 Arg 156N 2 Arg 97N 2 Arg 97N 1 Arg 156N 2, N 1 Thr 73, Tyr 74, Asn 70, Tyr 9, Arg 97 Arg 156N 1, N 2 Arg 97N 1 Arg 97N 2 Trp 147, Lys 146, Ala 150 Val 152 Trp 147N 1 Thr 73, Ser 77, Glu 76, Trp 147, Lys 146 Ser 77O Lys 146N , Asn 80O 1 Thr 143O 1, Tyr 84O Ser 116O Ser 77, Thr 143, Leu 81, Trp 147, Tyr 74, Tyr 123, Ser 116, Ile 95, Arg 97, Lys 146, Tyr 84, Asn 80 H bond H bond v.d.w. water mediated v.d.w. H bond water mediated water mediated H bond water mediated v.d.w. v.d.w. v.d.w. v.d.w. v.d.w. v.d.w. water mediated water mediated salt bridge H bond water mediated water mediated salt bridge salt bridge salt bridge salt bridge salt bridge v.d.w. water mediated water mediated water mediated v.d.w. v.d.w. H bond v.d.w. H bond H bond H bond H bond v.d.w. 01 08 08(1) 08 01 08 08 01 08 08 08(2) 08(1) 08(2) 08(1) 08 01 08 Figure 7. The impact of single amino acid substitutions within the APQP peptide on CTL recognition and HLA-B*3508 binding. The APQP-specific CTL clones SB8 (A), SB16 (B), and SB12 (C) were tested for recognition of a panel of altered peptide ligands into which single amino acid substitutions were introduced (E/T ratio 2:1). A range of peptide concentrations were used in these chromium release assays, and the con- centration required for half-maximum lysis was calculated from this dose- response data. (D) MHC–peptide binding assays were also conducted by testing each peptide at a range of concentrations for its ability to stabilize HLA-B*3508 expression on the surface of the antigen-processing mutant T2 cell line. The concentration of peptide required for half-maximum HLA-B*3508 stabilization was calculated. Peptides that were well recognized by a CTL clone were not tested (NT) for MHC binding. were tested for their ability to tolerate single amino acid sub- stitutions throughout the length of the peptide (Fig. 7, A–C). To aid with interpretation of this data, peptide–MHC binding assays were also performed on selected peptides that were not well recognized by any of the CTL clones. These binding assays measured stabilization of HLA-B*3508 mole- cules on the surface of the T2.B*3508 cell line after exoge- nous peptide addition, and the concentration of peptide re- quired for half-maximum stabilization of HLA-B*3508 was then calculated (Fig. 7 D). Considering that the primary an- chor residues at P2 and P10 were maintained within all the THE INFLUENCE OF PEPTIDE CONFORMATION ON A CYTOTOXIC T CELL RESPONSE | Tynan et al.