A method to quantify binding of unlabeled peptides to class I MHC molecules and detect their allele specificity.

A general method has been developed for measuring the stabilization of class I MHC molecules in extracts of the mutant cell lines .174/T2 and RMA-S. 35S-Met-labeled class I molecules which have been stabilized by peptides in vitro are immunoprecipitated with conformation dependent monoclonal antibodies and electrophoresed on polyacrylamide gels. The heavy and light chains are excised from the dried gel and quantified on a flat bed scintillation counter. The stabilizing effect of peptides on class I molecules in vitro correlates well with peptide binding measured by direct methods and can be therefore used to assess peptide binding affinity. We show that a peptide from HIV-1 gag (which has a high affinity for Db) is a CTL epitope restricted through Db, and also use the assay to analyse the effects of amino acid substitution on peptide affinity. In addition, the effect of a given peptide on a class I molecule within a mixture of human class I molecules can be distinguished by immunoprecipitation with the monomorphic antibody W6/32 and separation by 1-D isoelectric focussing. The technique therefore requires neither labeled peptide ligands nor allele-specific antibodies. It can be used to identify the peptide ligand of any human class I molecule, and gives a measure of peptide binding affinity. The technique should be of value in identifying epitopes recognized by CTL since we have found that these tend to bind with the highest affinities.