Peptide-SLA anchor residue preferences and proposed binding motifs for SLA-1*14:02 and SLA-2*11:04.

(A) SLA-1*14:02 restricted, nucleoprotein peptide specific CD8 clones grown from Babraham pig 650 were used to define the peptide binding motif for SLA-1*14:02. Clone KT4.650 (left axis) recognizes index peptide DFEREGYSL and clone KLT.650 (right axis) index peptide EFEDLTFLA. Each of the proteogenic amino acids residues was tested at positions 2 (upper graph) and 9 (lower graph) by substitution of the index peptides. For example: DFEREGYSL index peptide and anchor 2 variants: DA/C/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y/EREGYSL (each residue in bold tested in turn). The corresponding clone was used in peptide titration assays and ELISAs were performed to determine MIP-1β release, with data displayed for 10⁻⁷ M peptide. The limit of maximal detection of MIP-1β release was ~10 ng/mL, data below 0.5 ng/mL has been omitted for clarity, and mean + SEM shown. (B) As for (A), but using the SLA-1*11:04 restricted, nucleoprotein peptide specific clones KT22.625 (left axis, index peptide NGKWMRELI) and Bab.625 (right axis, index peptide IAYERMCNI) grown from Babraham pig 625 to define the peptide binding motif for SLA-2*11:04. Data displayed for 10⁻⁸ M peptide. (C) Binding pocket composition and proposed binding motif for SLA-1*14:02 and SLA-2*11:04 determined from the data in panels A and B. SLA-1*14:02 (green) with EFEDLTFLA (orange sticks) and SLA-2*11:04 (yellow) with IAYERMCNI (cyan sticks). Double conformers have been removed for visual clarity. B pocket is shown in red and the F pocket in pink.