INTERACTIONS AMONG POLYMORPHIC AND CONSERVED RESIDUES IN MHC CLASS-II PROTEINS AFFECT MHC-PEPTIDE CONFORMATION AND T-CELL RECOGNITION

The structural basis for MHC-restricted T cell recognition of the N-terminal peptide of myelin basic protein (MBP Ac1-11) presented by two mouse class II alleles, A(k) and A(u), was examined, focusing on the roles of A(beta) chain polymorphic residues 38(beta) (in the beta sheet) and 61(beta)(in the alpha helix) in controlling the responses of panels of A(k)- and A(u)-restricted T cell hybridomas. Despite the conservative nature of the substitutions at 38(beta) (k = Val, u = Leu) and 61(beta) (k = Trp, u = Tyr), transfectants expressing A(k) or A(u) proteins carrying allelic substitutions at 38(beta) and/or 61(beta) gave dramatically reduced T cell responses. The modest reduction in peptide binding detected using a biotinylated MBP peptide analog appear insufficient to explain the reduced responses, suggesting that changes at 38,61(beta) create conformational changes in the MHC-peptide complex. The impact of allelic substitutions at 38,61(beta) on T cell responses is also modulated by other residues differing between A(k) and A(u). To explore the structural basis for these phenomena, protein models were developed of the A(k), A(u) and 38,61(beta) mutant proteins using self-consistent ensemble optimization methodologies. Substitutions of the alternative allelic residue at 38(beta) and/or 61(beta), which are in van der Waals contact, change the configuration of this region of the peptide-binding groove, and potentially might affect the conformation of the bound peptide and its hydrogen-bonding to residue 61(beta). The models predict that this region of the groove is markedly altered by allelic differences at A(beta) residue 9(beta) (k = His, u = Val) which determine the position of the side-chain of Tyr30(beta), adjacent to residues 38(beta) and 61(beta). Thus, interactions among polymorphic and conserved residues control the antigen presentations functions of MHC class II proteins.