MHC molecules are peptide receptors of peculiar specificity (Falk et al. 1991; for review, see Rammensee et al. 1993). Each MHC allelic product has its individual peptide specificity, summarized as a peptide motif that is characterized by the position and occupancy of anchor residues whose side chains protrude into complementary pockets inside the peptide-accomodating groove of the respective MHC molecule. Many class I molecules, in addition, show a preferential peptide length. The most convenient way to obtain information on the peptide motif of a given MHC molecule is to elute its natural ligands, and to sequence them as a pool (Falk et al. 1991). Conserved positions, or anchor positions, will stand out as dominant sequencing signals.
A more laborious way is to isolate and to sequence a number of individual peptide ligands, to align their sequences, and to analyze whether any position is outstanding by virtue of its being frequently occupied by the same or similar residues (Jardetzky et al. 1991).
Here we describe the peptide motifs of HLA-B35 and -B 37, both obtained by pool sequencing (Falk et al. 1991). The B'3501 as well as the B'3701 gene were transfected into mouse P815 cells (Nelson et al. 1991; D. Schendel, unpublished observation). Transfectants were grown to high numbers in roller bottle tissue culture and the human class I molecules were precipitated from detergent lysates of the cells, using PA2.6 antibodies specific for HLA-A, -B, and -C (Parham and Bodmer 1978). Peptides were dissociated from the precipitate by treatment with TFA, and the peptide-containing supernatant was separated by reversed phase high pressure liquid chromotography (HPLC;Falk et al. 1991). The fractions known from previous experience to contain natural MHC ligands were pooled and