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

Abstract

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.

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Fig. 1: Heavy and light chain dynamics of free pMHC-I.
Fig. 2: NMR characterization of the 87 kDa pMHC-I–TAPBPR complex.
Fig. 3: Modulation of dynamics in MHC-I–TAPBPR complexes.
Fig. 4: Recognition of different peptide probes by the MHC-I–TAPBPR complex.
Fig. 5: TAPBPR-mediated loading of isotopically labeled peptides.
Fig. 6: Molecular mechanism of chaperone-assisted peptide exchange.

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Acknowledgements

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.

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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.

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Correspondence to Nikolaos G. Sgourakis.

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McShan, A.C., Natarajan, K., Kumirov, V.K. et al. Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle. Nat Chem Biol 14, 811–820 (2018). https://doi.org/10.1038/s41589-018-0096-2

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