Kinetics of peptide binding to the class II MHC protein I-E

Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an exte nded type II polyproline-like conformation and present them for immune reco gnition. Because empty MHC is unstable, measurement of the rate of the seco nd-order reaction between peptide and MHC is challenging. In this report, w e use dissociation of a pre-bound peptide to generate the active, peptide-r eceptive form of the empty class II MHC molecule I-E-k. This allows us to m easure directly the rate of reaction between active, empty I-E-k and a set of peptides that vary in structure. We find that all peptides studied, desp ite having highly variable dissociation rates, bind with similar associatio n rate constants, Thus, the rate-limiting step in peptide binding is minima lly sensitive to peptide side-chain structure. An interesting complication to this simple model is that a single peptide can sometimes bind to I-Ek in two kinetically distinguishable conformations, with the stable peptide-MHC complex isomer forming much more slowly than the less-stable one. This dem onstrates that an additional free-energy barrier limits the formation of ce rtain specific MHC-peptide complex conformations.