X‐Ray Single Molecule Tracking Reveal Motions of Peptides in the Binding Groove of MHC II Regulated by DM

Abstract

Class II MHC can take loosely bound peptides conformations, which generated in the recycling endosomes or cell surface, that are recognized by autoimmune T cells. DM converts loosely bound complexes to tightly bound complexes; crystal structure advocated that DM bound form of MHC II generate novel threshold for peptide binding by creating a hydrogen bond inside the binding groove, that form loosely bound intermediate peptides complex. We used soluble I‐Ak and two peptides that differ in their length as a model system to detect such floating peptides. Fluorescein quenching study provided remarkable difference; fluorescein on the peptides gave about twice a strength signal with DM than without DM, suggests peptides floating half way from MHC II. Diffracted X‐ray tracking (DXT) that monitors real‐time motion of individual peptides/MHC in solution at micro‐second level, revealed that motions of peptides inside binding groove divided into two groups without DM. Addition of DM shifted the slow velocity peak to the fast one. Thus, we successfully detected the DM mediated loosely bound peptides intermediate by two distinct methods. We suggest that measuring the motion of peptide at micro‐second level presents new parameters for both peptide/MHC complex and DM function.