The molecular basis of antigen presentation.

We have used a multifactorial approach to investigate the relationship between the structure of class II major histocompatibility complex (MHC)-encoded cell surface molecules (Ia) and the recognition of Ia-bound peptide antigens by clonally distributed alpha beta heterodimeric T cell receptors (TCR). Four distinct parameters of Ia structure-function--1) control of Ia assembly and transport to the surface membrane; 2) serological reactivity with panels of monoclonal antibodies; 3) ability to present peptide antigens to T cells for functional activation; and 4) differential peptide binding independent of the TCR--have been measured. This has allowed assignment of allelically polymorphic subregions or individual residues to locations in a model class II molecular structure and attribution to these subregions and residues of specific functions such as control of alpha beta chain interaction and protein folding, antigenic peptide binding, or TCR binding. The results of these analyses have provided an internally consistent picture of the class II molecule that fits well with a hypothetical model for Ia derived by analogy from the recently solved HLA class I crystal structure. They have also given us the first clear definition of specific peptide binding residues within the general peptide binding region of Ia and have revealed an unexpected asymmetry in the structure-function relationships of the putative alpha and beta chain helical regions. Overall, the results of these studies indicate the critical importance of multi-parameter analysis in creating useful molecular models using non-chemical techniques. They also suggest that hypotheses about TCR-Ia interaction may have to take into account a significant asymmetry in the function of the two major polymorphic regions of histocompatibility molecules.