HLA-A26 subtype A pockets accommodate acidic N-termini of ligands

The peptide motifs of HLA-A*2601. HLA-A*2602, and HLA-A*2603 molecules were determined by pool sequencing of natural ligand mixtures using established methods (Falk et al, 1991). HLA molecules were immunoprecipitated from CIR cells transfected with the respective genes using W6/32 antibodies (Barnstable et al. 1978), followed by elution of ligands with 0.1% trifluoroacetic acid, Peptide fractionation was performed by reversed phase HPLC on a mu RPC C2/C18, 2.1x100mm column (Pharmacia, Uppsala, Sweden) using the SMART System (Pharmacia). Distinct peaks were sequenced directly and the peptide-containing fractions were pooled (dominant peaks were omitted) and sequenced by Edman degradation on a sequencer model 494 A (Applied Biosystems, Weiterstadt, Germany). Evaluation of pool sequencing data was performed formed as described (Falk et al. 1991; Stevanovic 1997).