Effects of peptide length and composition on binding to an empty class I MHC heterodimer.

Class I major histocompatibility complex (MHC) proteins present peptide antigens to T cells during the immune response against viruses. Peptides are loaded into newly synthesized class I heterodimers in the endoplasmic reticulum such that most or all cell surface class I molecules contain peptides derived from endogenous or foreign proteins. We previously reported the assembly of empty heterodimers of the murine class I MHC molecule H-2Kd, from denatured heavy and light chains from which endogenous peptides had been removed [Fahnestock et al. (1992) Science 258, 1658-1662]. Here we measure thermal stability profiles of empty versus peptide-filled molecules and compare the effects of human versus murine light chains on the overall stability of the Kd heterodimer. The majority of empty heterodimers are stable at 37 degrees C regardless of the species of light chain, indicating that our previous report of the unexpectedly high thermal stability was an intrinsic property of the Kd molecule and not due to use of a murine/human chimeric protein. Binding constants are derived for a series of peptides interacting with empty Kd heterodimers. The dissociation constants of four known Kd-restricted peptides range from 2.3 x 10(-7) to 3.4 x 10(-8) M. Using a series of 24 analog peptides, the effects of length and peptide composition on binding affinity of one Kd-restricted peptide are explored, and the results are interpreted with reference to the known three-dimensional structures of class I MHC protein/peptide complexes.