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HLA-DM captures partially empty HLA-DR molecules for catalyzed removal of peptide

Abstract

The mechanisms of HLA-DM-catalyzed peptide exchange remain uncertain. Here we found that all stages of the interaction of HLA-DM with HLA-DR were dependent on the occupancy state of the peptide-binding groove. High-affinity peptides were protected from removal by HLA-DM through two mechanisms: peptide binding induced the dissociation of a long-lived complex of empty HLA-DR and HLA-DM, and high-affinity HLA-DR–peptide complexes bound HLA-DM only very slowly. Nonbinding covalent HLA-DR–peptide complexes were converted into efficient HLA-DM binders after truncation of an N-terminal peptide segment that emptied the P1 pocket and disrupted conserved hydrogen bonds to HLA-DR. HLA-DM thus binds only to HLA-DR conformers in which a critical part of the binding site is already vacant because of spontaneous peptide motion.

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Figure 1: Peptide disrupts the long-lived complex of empty HLA-DR and HLA-DM.
Figure 2: Rate of HLA-DM–HLA-DR complex dissociation is determined by peptide affinity.
Figure 3: High-affinity HLA-DR–peptide complexes interact slowly with HLA-DM.
Figure 4: HLA-DM binds with fast kinetics to HLA-DR–peptide complexes without an engaged peptide N terminus.
Figure 5: Truncated peptides covalently linked through peptide position P3 also bind HLA-DM.
Figure 6: HLA-DRα Trp43 is important for interaction with HLA-DM.
Figure 7: Large energy barrier for the binding of HLA-DR–peptide to HLA-DM.

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Acknowledgements

We thank A. Chakraborty for discussions; H. Ploegh and G. Grotenbreg (Massachusetts Institute of Technology) for the photolabile peptide; J. Fraser (University of Auckland) for human rhinovirus 3C protease; and J. Pyrdol for help with the purification of HLA-DR–peptide complexes. Supported by the National Institutes of Health (R01 AI057493 and NS044914 to K.W.W.) and the Cancer Research Institute (Irvington Institute Fellowship Program, D.A.S.).

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A.-K.A., M.J.C. and K.W.W. conceived of the study, designed experiments and wrote the paper; A.-K.A. generated HLA-DR–peptide complexes and did most of the SPR experiments; M.-S.E.D.S. did a set of SPR experiments with high-affinity HLA-DR–peptide complexes; E.J.S. provided advice for SPR experiments; M.J.C. did most of the FP peptide-binding assays; K.D.F. did mathematical modeling of Biacore data; D.A.S. did functional assays of HLA-DR–peptide complexes; and N.P.S. generated Chinese hamster ovary cell lines producing HLA-DR–CLIP complexes.

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Correspondence to Kai W Wucherpfennig.

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Anders, AK., Call, M., Schulze, MS. et al. HLA-DM captures partially empty HLA-DR molecules for catalyzed removal of peptide. Nat Immunol 12, 54–61 (2011). https://doi.org/10.1038/ni.1967

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