Inhibition of class II MHC-peptide complex formation by protease inhibitors

Studies on the kinetics of antigenic peptide binding to major histocompatibility complex class II molecules have been used extensively to probe major histocompatibility complex (MHC) structure as well as to investigate the molecular mechanism of peptide recognition. Previous experiments have frequently been carried out in the presence of a cocktail of protease inhibitors to inhibit the proteolysis of MHC heterodimers. By using high performance size exclusion chromatography to measure fluorescent peptide binding to MHC protein, we have found that the addition of a commonly used mixture of protease inhibitors leads to a significant reduction in peptide binding to the class II heterodimer.