Kinetics of registry selection of chimeric peptides binding to MHC II

Major histocompatability complex type II proteins (MHC II) are alphabeta-heterodimeric glycoproteins that present peptides to the T cell receptor (TCR) of CD4(+) T-cells. This presentation may result in activation of these T-cells, depending on the nature of the peptide. Peptides interact specifically with MHC II with nine peptide amino acid positions, and the corresponding MHC II pocket positions are usually labeled P1-P9. However, the length of peptides binding to MHC II may be greater than nine amino acids, and therefore these peptides may potentially bind to the MHC II in more than one registry. To investigate the mechanism by which a long peptide binds to I-E(k), a murine MHC II, a chimeric peptide with two nonoverlapping registries, f-IAYLKQATKQLRMATPLLMR was designed. The IAYLKQATK peptide segment is based on moth cytochrome c 95-103 (MCC 95-103), and the QLRMATPLLMR segment is based on murine Ii CLIP 89-99 M90L (Ii CLIP 89-99 M90L). This chimeric peptide forms two isomeric complexes. The MCC and Ii CLIP registries dissociate from I-E(k) with t(1/2) values of >>800 and 4.94 h, respectively. The registry composition of this MHC II/chimeric peptide complex was found to change as a function of time in approaching thermodynamic equilibrium: the results are consistent with a kinetic model that involves no intramolecular isomer interconversion. The model depicts uncorrelated binding to the MHC II determined by relative association rates to the two registries. This is followed by dissociation and subsequent rebinding, leading ultimately to a preponderance of the most stable complex. Similar results were obtained at pH 5.3. The behavior of this chimeric peptide approximates the binding of a 1:1 solution mixture of two peptides to MHC II, where the more stable complex is selected over time. We have also found that a chimeric peptide and a human MHC II, HLA-DR40401, form isomers with relative association rates to DR0401 at pH 5.3 of 15% for one isomer and 85% for the second isomer.