Based on the crystal structure of HLA-A2.1 and the recognition of a panel of mutant HLA-A2.1 molecules by a large number of alloreactive cytotoxic T lymphocyte clones, a model to explain alloreactivity is described. In this model recognition of an allogeneic major histocompatibility complex molecule by a self-restricted T-cell receptor occurs as the result ofaccommodation by the receptor ofa few amino acid differences in the major histocompatibility complex moleculei.e., cross-recognition. Alloreactivity is the result of the presence in the foreign antigen binding site of the allogeneic major histocompatibility complex molecule of unusual self-peptides, reactivity to which could not have been eliminated by negative thymic selection.Class I major histocompatibility complex (MHC) molecules (HLA molecules in man) were originally identified as the target structures responsible for the humoral (alloantibody) and cellular (alloreactive cytotoxic T lymphocyte) responses generated during the rejection of transplanted foreign tissue (1). However, the central role of these highly polymorphic cellsurface glycoproteins is to serve as restricting elements in the recognition by T cells of virus-infected, chemically modified, or neoplastic cells (2-5). The regions in contact between the molecules involved in the recognition process (T-cell receptor, class I MHC molecule, peptide, and accessory molecules) are not yet precisely described, and the nature and and biophysical characteristics of these interactions (6) remain to be determined. Identification of specific residues on class I MHC molecules involved in the recognition by human cytotoxic T lymphocytes (CTL) has been facilitated over the last few years by the structural characterization of natural HLA variants initially distinguished by cytotoxicity assays (7) and/or isoelectric focusing (8). In population studies, sequence comparison of these otherwise serologically similar HLA molecules (9), exon shuffling (10,11), and site-directed mutagenesis (12)(13)(14)(15) have all highlighted the importance of polymorphic residues in the a1 and/or a2 domains of the HLA molecule in the recognition process. Moreover, the class I MHC molecules were shown to present peptides derived from processed antigens to the receptor of cytotoxic T cells (16, 17). Elucidation ofthe crystal structure ofHLA-A2 revealed a platform ofeight antiparallel (3 strands topped by two a-helices (18,19). A prominent groove between the helices was identified as the site for binding of foreign peptides.In the present study, site-directed mutagenesis of HLA-A2