REACTIONS OF PEPTIDES WITH CLASS-II PROTEINS OF THE MAJOR HISTOCOMPATIBILITY COMPLEX

The kinetics of the reactions of peptides with class II proteins of th e major histocompatibility complex (MHC) are simulated so as to includ e the spontaneous inactivation of peptide-free MHC proteins. These sim ulations include the kinetics of loss of endogenous peptides normally present in preparations of these proteins and, in some cases, the form ation of kinetic intermediates in the binding of added peptides to pep tide-free proteins. In these reactions the amount of complex between t he MHC protein and added peptide does not represent an equilibrium sta te of the system but rather a quasistationary concentration that is th e result of a competition between peptide binding and inactivation of the peptide-free protein. It is shown that in spite of these complex k inetics. Scatchard plots of simulated binding data are frequently line ar, as observed experimentally. However, the ''equilibrium constants'' derived from the slopes of such plots bear no simple relationship to the true equilibrium constants for the reactions.