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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Lanzavecchia, A., Reid, P.A. & Watts, C. Irreversible association of peptides with class II MHC molecules in living cells. Nature 357, 249–252 (1992).
Jensen, P.E. Long-lived complexes between peptide and class II major histocompatibility complex are formed at low pH with no requirement for pH neutralization. J. Exp. Med. 176, 793–798 (1992).
Stern, L.J. et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368, 215–221 (1994).
Brown, J.H. et al. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364, 33–39 (1993).
Germain, R.N. & Rinker, A.G. Jr. Peptide binding inhibits protein aggregation of invariant-chain free class II dimers and promotes surface expression of occupied molecules. Nature 363, 725–728 (1993).
Rabinowitz, J.D. et al. Formation of a highly peptide-receptive state of class II MHC. Immunity 9, 699–709 (1998).
Roche, P.A. & Cresswell, P. Invariant chain association with HLA-DR molecules inhibits immunogenic peptide binding. Nature 345, 615–618 (1990).
Riberdy, J.M., Newcomb, J.R., Surman, M.J., Barbosa, J.A. & Cresswell, P. HLA-DR molecules from an antigen-processing mutant cell line are associated with invariant chain peptides. Nature 360, 474–477 (1992).
Morris, P. et al. An essential role for HLA-DM in antigen presentation by class II major histocompatibility molecules. Nature 368, 551–554 (1994).
Stebbins, C.C., Loss, G.E. Jr ., Elias, C.G., Chervonsky, A. & Sant, A.J. The requirement for DM in class II-restricted antigen presentation and SDS-stable dimer formation is allele and species dependent. J. Exp. Med. 181, 223–234 (1995).
Sloan, V.S. et al. Mediation by HLA-DM of dissociation of peptides from HLA-DR. Nature 375, 802–806 (1995).
Denzin, L.K. & Cresswell, P. HLA-DM induces CLIP dissociation from MHC class II αβ dimers and facilitates peptide loading. Cell 82, 155–165 (1995).
Sherman, M.A., Weber, D.A. & Jensen, P.E. DM enhances peptide binding to class II MHC by release of invariant chain-derived peptide. Immunity 3, 197–205 (1995).
Nanda, N.K. & Sant, A.J. DM determines the cryptic and immunodominant fate of T cell epitopes. J. Exp. Med. 192, 781–788 (2000).
Katz, J.F., Stebbins, C., Appella, E. & Sant, A.J. Invariant chain and DM edit self-peptide presentation by major histocompatibility complex (MHC) class II molecules. J. Exp. Med. 184, 1747–1753 (1996).
Lich, J.D., Jayne, J.A., Zhou, D., Elliott, J.F. & Blum, J.S. Editing of an immunodominant epitope of glutamate decarboxylase by HLA-DM. J. Immunol. 171, 853–859 (2003).
Lovitch, S.B., Petzold, S.J. & Unanue, E.R. Cutting edge: H-2DM is responsible for the large differences in presentation among peptides selected by I-Ak during antigen processing. J. Immunol. 171, 2183–2186 (2003).
Pathak, S.S., Lich, J.D. & Blum, J.S. Cutting edge: editing of recycling class II:peptide complexes by HLA-DM. J. Immunol. 167, 632–635 (2001).
Lazarski, C.A. et al. The kinetic stability of MHC class II:peptide complexes is a key parameter that dictates immunodominance. Immunity 23, 29–40 (2005).
Lazarski, C.A., Chaves, F.A. & Sant, A.J. The impact of DM on MHC class II-restricted antigen presentation can be altered by manipulation of MHC-peptide kinetic stability. J. Exp. Med. 203, 1319–1328 (2006).
Denzin, L.K., Hammond, C. & Cresswell, P. HLA-DM interactions with intermediates in HLA-DR maturation and a role for HLA-DM in stabilizing empty HLA-DR molecules. J. Exp. Med. 184, 2153–2165 (1996).
Kropshofer, H., Arndt, S.O., Moldenhauer, G., Hammerling, G.J. & Vogt, A.B. HLA-DM acts as a molecular chaperone and rescues empty HLA-DR molecules at lysosomal pH. Immunity 6, 293–302 (1997).
Grotenbreg, G.M. et al. Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association. J. Biol. Chem. 282, 21425–21436 (2007).
Mosyak, L., Zaller, D.M. & Wiley, D.C. The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation. Immunity 9, 377–383 (1998).
Fremont, D.H., Crawford, F., Marrack, P., Hendrickson, W.A. & Kappler, J. Crystal structure of mouse H2-M. Immunity 9, 385–393 (1998).
Doebele, R.C., Busch, R., Scott, H.M., Pashine, A. & Mellins, E.D. Determination of the HLA-DM interaction site on HLA-DR molecules. Immunity 13, 517–527 (2000).
Pashine, A. et al. Interaction of HLA-DR with an acidic face of HLA-DM disrupts sequence-dependent interactions with peptides. Immunity 19, 183–192 (2003).
Stratikos, E., Mosyak, L., Zaller, D.M. & Wiley, D.C. Identification of the lateral interaction surfaces of human histocompatibility leukocyte antigen (HLA)-DM with HLA-DR1 by formation of tethered complexes that present enhanced HLA-DM catalysis. J. Exp. Med. 196, 173–183 (2002).
Weber, D.A., Evavold, B.D. & Jensen, P.E. Enhanced dissociation of HLA-DR-bound peptides in the presence of HLA-DM. Science 274, 618–620 (1996).
Belmares, M.P., Busch, R., Wucherpfennig, K.W., McConnell, H.M. & Mellins, E.D. Structural factors contributing to DM susceptibility of MHC class II/peptide complexes. J. Immunol. 169, 5109–5117 (2002).
Narayan, K. et al. HLA-DM targets the hydrogen bond between the histidine at position β81 and peptide to dissociate HLA-DR–peptide complexes. Nat. Immunol. 8, 92–100 (2007).
Zhou, Z., Callaway, K.A., Weber, D.A. & Jensen, P.E. Cutting edge: HLA-DM functions through a mechanism that does not require specific conserved hydrogen bonds in class II MHC-peptide complexes. J. Immunol. 183, 4187–4191 (2009).
Ferrante, A. & Gorski, J. Cutting edge: HLA-DM-mediated peptide exchange functions normally on MHC class II-peptide complexes that have been weakened by elimination of a conserved hydrogen bond. J. Immunol. 184, 1153–1158 (2010).
Stratikos, E., Wiley, D.C. & Stern, L.J. Enhanced catalytic action of HLA-DM on the exchange of peptides lacking backbone hydrogen bonds between their N-terminal region and the MHC class II α-chain. J. Immunol. 172, 1109–1117 (2004).
Zarutskie, J.A. et al. A conformational change in the human major histocompatibility complex protein HLA-DR1 induced by peptide binding. Biochemistry 38, 5878–5887 (1999).
Weber, D.A., Dao, C.T., Jun, J., Wigal, J.L. & Jensen, P.E. Transmembrane domain-mediated colocalization of HLA-DM and HLA-DR is required for optimal HLA-DM catalytic activity. J. Immunol. 167, 5167–5174 (2001).
Chicz, R.M. et al. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature 358, 764–768 (1992).
Kropshofer, H. et al. Editing of the HLA-DR-peptide repertoire by HLA-DM. EMBO J. 15, 6144–6154 (1996).
Vogt, A.B., Kropshofer, H., Moldenhauer, G. & Hammerling, G.J. Kinetic analysis of peptide loading onto HLA-DR molecules mediated by HLA-DM. Proc. Natl. Acad. Sci. USA 93, 9724–9729 (1996).
Jardetzky, T.S. et al. Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 9, 1797–1803 (1990).
McFarland, B.J., Katz, J.F., Beeson, C. & Sant, A.J. Energetic asymmetry among hydrogen bonds in MHC class II*peptide complexes. Proc. Natl. Acad. Sci. USA 98, 9231–9236 (2001).
Reay, P.A., Wettstein, D.A. & Davis, M.M. pH dependence and exchange of high and low responder peptides binding to a class II MHC molecule. EMBO J. 11, 2829–2839 (1992).
Sanderson, F., Thomas, C., Neefjes, J. & Trowsdale, J. Association between HLA-DM and HLA-DR in vivo. Immunity 4, 87–96 (1996).
Chou, C.L. & Sadegh-Nasseri, S. HLA-DM recognizes the flexible conformation of major histocompatibility complex class II. J. Exp. Med. 192, 1697–1706 (2000).
Painter, C.A., Cruz, A., Lopez, G.E., Stern, L.J. & Zavala-Ruiz, Z. Model for the peptide-free conformation of class II MHC proteins. PLoS One 3, e2403 (2008).
Patil, N.S. et al. Rheumatoid arthritis (RA)-associated HLA-DR alleles form less stable complexes with class II-associated invariant chain peptide than non-RA-associated HLA-DR alleles. J. Immunol. 167, 7157–7168 (2001).
Nicholson, M.J. et al. Small molecules that enhance the catalytic efficiency of HLA-DM. J. Immunol. 176, 4208–4220 (2006).
Day, C.L. et al. Ex vivo analysis of human memory CD4 T cells specific for hepatitis C virus using MHC class II tetramers. J. Clin. Invest. 112, 831–842 (2003).
Call, M.J. et al. In vivo enhancement of peptide display by MHC class II molecules with small molecule catalysts of peptide exchange. J. Immunol. 182, 6342–6352 (2009).
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.).
Author information
Authors and Affiliations
Contributions
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.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–10 (PDF 986 kb)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ni.1967
This article is cited by
-
MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Nature Chemical Biology (2023)
-
Hypoxia-induced shift in the phenotype of proteasome from 26S toward immunoproteasome triggers loss of immunoprivilege of mesenchymal stem cells
Cell Death & Disease (2020)
-
Synergy between B cell receptor/antigen uptake and MHCII peptide editing relies on HLA-DO tuning
Scientific Reports (2019)
-
Class II MHC antigen processing in immune tolerance and inflammation
Immunogenetics (2019)
-
What to do with HLA-DO/H-2O two decades later?
Immunogenetics (2019)