TCR RECOGNITION OF THE MHC-PEPTIDE DIMER - STRUCTURAL-PROPERTIES OF ATERNARY COMPLEX

We have developed a method that utilizes site-specific mutation data, sequence analysis, immunological data and free-energy minimization, to determine structural features of the ternary complex formed by the T- cell receptor (TcR) and the class I major histocompatibility complex ( MHC) molecule bound by peptide. The analysis focuses on the mouse Kd M HC system, for which a large set of clones with sequenced T-cell recep tors is available for specific peptides. The general philosophy is to reduce the uncertainties and computation time in a free-energy minimiz ation procedure by identifying and imposing experimental constraints. In addition to assessing compatibility with various kinds of immunolog ical data, we are particularly interested in differentiating the struc tural features peculiar to this particular system from generic feature s, and in ascertaining the robustness of the structure; i.e. determini ng, in so far as possible, the variations in the structure that leave its compatibility with experiment unaltered from those that do not. Th is last is equivalent to recognizing that certain features of the mode l are presented with a reasonable degree of confidence, while others r emain highly tentative. The central conclusion in the former category is a placement of the TcR on the Kd peptide complex, which has its bet a(2), beta(3) and alpha(3) loops (i.e. the second and third complement arity-determining region of the TcR beta chain, and the third compleme ntarity-determining region of the alpha chain) covering the peptide; t he a, and at loops covering the MHC alpha(1) helix; the alpha(1) loop interacting with residues on the MHC beta sheet; and the beta 1 and (p art of) the beta 2 loops covering the alpha 2 MHC helix. More specific ally, our findings include the following. (1) A highly conserved histi dine residue in the first complementarity-determining region of the Tc R beta chain (beta:CDR1) points outward and interacts with highly cons erved side-chains on the MHC alpha(2) helix. (2) The amino-terminal po rtion of the beta(2) loop interacts with the carboxyl portion of the p eptide. A particularly important interaction is K4 of the loop interac ting with E8 of the peptide. (3) Charged side-chains of the 11-residue TcR alpha(2) loop interact with conserved charged side-chains at posi tions 44, 58, 61 and 68 on the MHC. (4) The TcR beta(3) loop interacts with the amino-terminal part of the peptide, up through position 4. ( 5) the TcR alpha(3) loop interacts with the central portion of the pep tide and stacks against the beta(2) loop. (6) Because of the interacti on between the beta(2) loop and the peptide, and stacking of beta(2) O n alpha(3), alpha(3) gene and V-beta gene selection can be correlated. (7) Using the topology of the recently solved TcR oc chain we predict that the alpha(2) loop interacts with the loop on the MHC beta sheet floor, which encompasses residues 42 to 44. (C) 1996 Academic Press Li mited