Article | Published:

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle

Nature Chemical Biologyvolume 14pages811820 (2018) | Download Citation


Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from $8.99

All prices are NET prices.

Additional information

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Neefjes, J., Jongsma, M. L. M., Paul, P. & Bakke, O. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat. Rev. Immunol. 11, 823–836 (2011).

  2. 2.

    Rock, K. L., Reits, E. & Neefjes, J. Present Yourself! By MHC Class I and MHC Class II Molecules. Trends Immunol. 37, 724–737 (2016).

  3. 3.

    Wearsch, P. A. & Cresswell, P. Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer. Nat. Immunol. 8, 873–881 (2007).

  4. 4.

    Barnden, M. J., Purcell, A. W., Gorman, J. J. & McCluskey, J. Tapasin-mediated retention and optimization of peptide ligands during the assembly of class I molecules. J. Immunol. 165, 322–330 (2000).

  5. 5.

    Hermann, C. et al. TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst. eLife 4, e09617 (2015).

  6. 6.

    Morozov, G. I. et al. Interaction of TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing. Proc. Natl. Acad. Sci. USA 113, E1006–E1015 (2016).

  7. 7.

    Paul, S. et al. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. J. Immunol. 191, 5831–5839 (2013).

  8. 8.

    Shionoya, Y. et al. Loss of tapasin in human lung and colon cancer cells and escape from tumor-associated antigen-specific CTL recognition. OncoImmunology 6, e1274476 (2017).

  9. 9.

    Chen, Q.-R., Hu, Y., Yan, C., Buetow, K. & Meerzaman, D. Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival. PLoS One 9, e105393 (2014).

  10. 10.

    Park, B. et al. Human cytomegalovirus inhibits tapasin-dependent peptide loading and optimization of the MHC class I peptide cargo for immune evasion. Immunity 20, 71–85 (2004).

  11. 11.

    Montserrat, V., Galocha, B., Marcilla, M., Vázquez, M. & López de Castro, J. A. HLA-B*2704, an allotype associated with ankylosing spondylitis, is critically dependent on transporter associated with antigen processing and relatively independent of tapasin and immunoproteasome for maturation, surface expression, and T cell recognition: relationship to B*2705 and B*2706. J. Immunol. 177, 7015–7023 (2006).

  12. 12.

    Lee, J. H. et al. Further examination of the candidate genes in chromosome 12p13 locus for late-onset Alzheimer disease. Neurogenetics 9, 127–138 (2008).

  13. 13.

    Thomas, C. & Tampé, R. Proofreading of peptide-MHC complexes through dynamic multivalent interactions. Front. Immunol. 8, 65 (2017).

  14. 14.

    van Hateren, A., Bailey, A. & Elliott, T. Recent advances in major histocompatibility complex (MHC) class I antigen presentation: plastic MHC molecules and TAPBPR-mediated quality control. F1000Res. 6, 158 (2017).

  15. 15.

    Neerincx, A. & Boyle, L. H. Properties of the tapasin homologue TAPBPR. Curr. Opin. Immunol. 46, 97–102 (2017).

  16. 16.

    Boyle, L. H. et al. Tapasin-related protein TAPBPR is an additional component of the MHC class I presentation pathway. Proc. Natl. Acad. Sci. USA 110, 3465–3470 (2013).

  17. 17.

    Hermann, C., Strittmatter, L. M., Deane, J. E. & Boyle, L. H. The binding of TAPBPR and Tapasin to MHC class I is mutually exclusive. J. Immunol. 191, 5743–5750 (2013).

  18. 18.

    Neerincx, A. et al. TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway. eLife 6, e23049 (2017).

  19. 19.

    Thomas, C. & Tampé, R. Structure of the TAPBPR–MHC I complex defines the mechanism of peptide loading and editing. Science 358, 1060–1064 (2017).

  20. 20.

    Jiang, J. et al. Crystal structure of a TAPBPR–MHC-I complex reveals the mechanism of peptide editing in antigen presentation. Science 358, 1064–1068 (2017).

  21. 21.

    Wieczorek, M. et al. Major histocompatibility complex (MHC) class I and MHC class II proteins: conformational plasticity in antigen presentation. Front. Immunol. 8, 292 (2017).

  22. 22.

    Ayres, C. M., Corcelli, S. A. & Baker, B. M. Peptide and peptide-dependent motions in MHC proteins: immunological implications and biophysical underpinnings. Front. Immunol. 8, 935 (2017).

  23. 23.

    Blees, A. et al. Structure of the human MHC-I peptide-loading complex. Nature 551, 525–528 (2017).

  24. 24.

    Tugarinov, V., Kanelis, V. & Kay, L. E. Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat. Protoc. 1, 749–754 (2006).

  25. 25.

    Pedersen, L. O. et al. The interaction of β 2-microglobulin (β 2m) with mouse class I major histocompatibility antigens and its ability to support peptide binding. A comparison of human and mouse β 2m. Eur. J. Immunol. 25, 1609–1616 (1995).

  26. 26.

    Lakomek, N.-A., Ying, J. & Bax, A. Measurement of 15N relaxation rates in perdeuterated proteins by TROSY-based methods. J. Biomol. NMR 53, 209–221 (2012).

  27. 27.

    Korzhnev, D. M., Kloiber, K. & Kay, L. E. Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application. J. Am. Chem. Soc. 126, 7320–7329 (2004).

  28. 28.

    Wearsch, P. A. et al. Major histocompatibility complex class I molecules expressed with monoglucosylated N-linked glycans bind calreticulin independently of their assembly status. J. Biol. Chem. 279, 25112–25121 (2004).

  29. 29.

    Ryan, S. O. & Cobb, B. A. Roles for major histocompatibility complex glycosylation in immune function. Semin. Immunopathol. 34, 425–441 (2012).

  30. 30.

    Kovrigin, E. L. NMR line shapes and multi-state binding equilibria. J. Biomol. NMR 53, 257–270 (2012).

  31. 31.

    Rodenko, B. et al. Generation of peptide-MHC class I complexes through UV-mediated ligand exchange. Nat. Protoc. 1, 1120–1132 (2006).

  32. 32.

    Chen, M. & Bouvier, M. Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J. 26, 1681–1690 (2007).

  33. 33.

    van Hateren, A. et al. A mechanistic basis for the co-evolution of chicken tapasin and major histocompatibility complex class I (MHC I) proteins. J. Biol. Chem. 288, 32797–32808 (2013).

  34. 34.

    Latham, M. P., Zimmermann, G. R. & Pardi, A. NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. J. Am. Chem. Soc. 131, 5052–5053 (2009).

  35. 35.

    Hein, Z. et al. Peptide-independent stabilization of MHC class I molecules breaches cellular quality control. J. Cell Sci. 127, 2885–2897 (2014).

  36. 36.

    Pos, W. et al. Crystal structure of the HLA-DM-HLA-DR1 complex defines mechanisms for rapid peptide selection. Cell 151, 1557–1568 (2012).

  37. 37.

    Kurimoto, E. et al. Structural and functional mosaic nature of MHC class I molecules in their peptide-free form. Mol. Immunol. 55, 393–399 (2013).

  38. 38.

    Beerbaum, M. et al. NMR spectroscopy reveals unexpected structural variation at the protein-protein interface in MHC class I molecules. J. Biomol. NMR 57, 167–178 (2013).

  39. 39.

    Yanaka, S. et al. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. J. Biol. Chem. 289, 24680–24690 (2014).

  40. 40.

    Hateren, Avan et al. Direct evidence for conformational dynamics in major histocompatibility complex class I molecules. J. Biol. Chem. 292, 20255–20269 (2017).

  41. 41.

    Hee, C.-S. et al. Dynamics of free versus complexed β2-microglobulin and the evolution of interfaces in MHC class I molecules. Immunogenetics 65, 157–172 (2013).

  42. 42.

    Bailey, A. et al. Selector function of MHC I molecules is determined by protein plasticity. Sci. Rep. 5, 14928 (2015).

  43. 43.

    Sieker, F., Springer, S. & Zacharias, M. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Protein Sci. 16, 299–308 (2007).

  44. 44.

    Fisette, O., Wingbermühle, S., Tampé, R. & Schäfer, L. V. Molecular mechanism of peptide editing in the tapasin-MHC I complex. Sci. Rep. 6, 19085 (2016).

  45. 45.

    Abualrous, E. T. et al. The carboxy terminus of the ligand peptide determines the stability of the MHC class I molecule H-2Kb: a combined molecular dynamics and experimental study. PLoS One 10, e0135421 (2015).

  46. 46.

    Li, H., Natarajan, K., Malchiodi, E. L., Margulies, D. H. & Mariuzza, R. A. Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120. J. Mol. Biol. 283, 179–191 (1998).

  47. 47.

    Natarajan, K. et al. An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role. Nat. Commun. 8, 15260 (2017).

  48. 48.

    Rossi, P., Xia, Y., Khanra, N., Veglia, G. & Kalodimos, C. G. 15N and 13C- SOFAST-HMQC editing enhances 3D-NOESY sensitivity in highly deuterated, selectively [1H,13C]-labeled proteins. J. Biomol. NMR 66, 259–271 (2016).

  49. 49.

    Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

  50. 50.

    Lee, W., Tonelli, M. & Markley, J. L. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31, 1325–1327 (2015).

  51. 51.

    Kleckner, I. R. & Foster, M. P. GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data. J. Biomol. NMR 52, 11–22 (2012).

  52. 52.

    Waudby, C. A., Ramos, A., Cabrita, L. D. & Christodoulou, J. Two-dimensional NMR lineshape analysis. Sci. Rep. 6, 24826 (2016).

Download references


The authors would like to acknowledge G. Morozov and A. Bax for helpful discussions, J. Ying and V. Tugarinov for assistance with recording NMR relaxation data, and C. Waudby for help with NMR line shape fitting in TITAN. MHC-I constructs for protein expression were generously provided by D. Long of the NIH Tetramer Core Facility. E.L.K. was supported by the Regular Research Grant 2016 from Committee on Research (COR), Marquette University. This research was supported by the Intramural research program of the NIAID, NIH, a K-22 Career Development and an R35 Outstanding Investigator Award to N.G.S. through NIAID(AI2573-01) and NIGMS(1R35GM125034-01), and by the Office of the Director, NIH, under High End Instrumentation (HIE) Grant S10OD018455, which funded the 800 MHz NMR spectrometer at UCSC.

Author information


  1. Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA

    • Andrew C. McShan
    • , Vlad K. Kumirov
    • , David Flores-Solis
    • , Mareike Badstübner
    • , Jugmohit S. Toor
    • , Clive R. Bagshaw
    •  & Nikolaos G. Sgourakis
  2. Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA

    • Kannan Natarajan
    • , Jiansheng Jiang
    •  & David H. Margulies
  3. Department of Chemistry, Marquette University, Milwaukee, WI, USA

    • Evgenii L. Kovrigin


  1. Search for Andrew C. McShan in:

  2. Search for Kannan Natarajan in:

  3. Search for Vlad K. Kumirov in:

  4. Search for David Flores-Solis in:

  5. Search for Jiansheng Jiang in:

  6. Search for Mareike Badstübner in:

  7. Search for Jugmohit S. Toor in:

  8. Search for Clive R. Bagshaw in:

  9. Search for Evgenii L. Kovrigin in:

  10. Search for David H. Margulies in:

  11. Search for Nikolaos G. Sgourakis in:


A.C.M., K.N., D.H.M. and N.G.S. designed the research, interpreted data and wrote the manuscript. K.N. performed SPR experiments. A.C.M performed differential scanning fluorimetry experiments. J.S.T. performed fluorescence anisotropy experiments with analysis performed by C.R.B. A.C.M., K.N. and M.B. generated constructs, performed protein expression and purification. A.C.M. and D.F.-S. prepared and purified isotopically labeled peptides. A.C.M., V.K.K., D.F.-S. and N.G.S. acquired and analyzed NMR data. A.C.M. and E.L.K. performed NMR line shape analysis. A.C.M. and D.F.-S. performed and analyzed MD simulations. J.J. provided X-ray structures of the RGPGC–H2-Dd S73C–β2m and RGPGC–H2-Dd S73C–β2m–TAPBPR. K.N., J.J., and D.H.M. conceived and validated the disulfide-linked covalent constructs and their binding behavior.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Nikolaos G. Sgourakis.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Table 1–4, Supplementary Figures 1–21

  2. Reporting Summary

About this article

Publication history