Model for the Peptide-Free Conformation of Class II MHC Proteins
Figure 4
Binding of peptide-loaded and peptide-free DR1 to conformationally sensitive probes.
(A–C) SEC3 binding to immobilized bio_DR. A) SPR using peptide-loaded DR1. B) SPR using peptide-free DR1. Residuals shown below SPR traces C) Equilibrium RU values vs. DR concentration, open circles, peptide-free DR1, closed triangles, peptide-loaded DR1. (D–F) DR1 binding to immobilized MEM264. D) SPR using peptide-loaded DR1. E) SPR using peptide-free DR1. F) ELISA of MEM264 binding empty, open circles, and loaded, closed triangles, DR1. (G–I) DR1 binding to immobilized LB3.1. G) SPR using peptide-loaded DR1. (H) SPR using peptide-free DR1.Residuals shown below. (I) ELISA of immobilized LB3.1 binding to peptide-free (open circles) and peptide-loaded (closed triangles) DR1. (J–K) Comparison of experimental to model data. J, Ribbon diagram of the peptide-binding site of DR1, colored by peptide-free to peptide-loaded Cα distances at the end of the dynamics runs. Larger distances shown in darker red. K, same view but colored to indicate sites of conformational probe interaction. The yellow region represents DR1 residues that interact with the superantigen SEC3, magenta resides that interact with the conformationally sensitive antibody LB3.1, and blue residues in the peptide-free protein that interact with the antibody MEM264 specific for the peptide-free protein.