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Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity

Nature Immunology volume 17, pages 87–94 (2016)Cite this article

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Abstract

The T cell antigen receptor (TCR)–peptide–major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.

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Figure 1: TCR selections of a circularly permuted yeast-displayed H-2Ld library.
Figure 2: Signaling properties of 42F3 TCR–reactive peptide antigens.
Figure 3: Peptide specificity of the 42F3 TCR.
Figure 4: A Vα3 germline motif anchors two TCR-pMHC docking geometries.

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Acknowledgements

We thank S. O'Herrin (Ben May Institute for Cancer Research) for the 58α−/β− cell line; J.M. Connolly (Washington University School of Medicine) for the LM1.8-H-2LdW97R cell line; and N. Goriatcheva, E. Özkan, D.Wittrup, E. Newell, N. Jarvik and M. McLaughlin for discussions. Supported by the Canadian Institutes of Health Research (J.J.A.), the National Science Foundation (M.E.B.), the US National Institutes of Health (AI103867, AI045757 and AI057229 to K.C.G., and GM55767 to D.M.K.), the Jordan family, and the Howard Hughes Medical Institute (K.C.G.). Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract number DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the Department of Energy Office of Biological and Environmental Research and by the US National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393).

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Author notes

  1. Jarrett J Adams, Samanthi Narayanan and Michael E Birnbaum: These authors contributed equally to this work.

Authors and Affiliations

  1. and Departments of Molecular and Cellular Physiology, Howard Hughes Medical Institute, and Structural Biology, Program in Immunology, Stanford University School of Medicine, Stanford, California, USA

    Jarrett J Adams, Michael E Birnbaum, Marvin H Gee, Leah V Sibener & K Christopher Garcia

  2. Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Terrence Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada

    Jarrett J Adams & Sachdev S Sidhu

  3. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

    Samanthi Narayanan & David M Kranz

  4. Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA

    Sydney J Blevins & Brian M Baker

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Contributions

J.J.A., S.N., M.E.B., D.M.K. and K.C.G. conceived of the project; J.J.A., S.N., and M.E.B. performed experiments and analyzed data; and all authors interpreted data, developed the concepts in the manuscript, and wrote and edited the manuscript.

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Correspondence to K Christopher Garcia.

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Integrated supplementary information

Supplementary Figure 1 Evolution of a second-generation H-2Ld scaffold.

(a) The protein architecture of the single chain m31r-CP template used for error prone PCR. (b) The enrichment of gain-of-function mutations in yeast scaffolds, during rounds of selections using TCR-tetramers. (c) The gain-of-function mutations that provided the brightest 2C-tetramer and 42F3-tetramer staining on the clonal yeast population m31r-CP-E3. Inset is the zoomed in depiction of the peptide linker-MHC-junctions and proximal selected mutations (sticks). (d) Mutations in the m31s-W167A used to display the C-terminally linked peptide libraries. (e) Staining of 96 clonal yeast populations isolated from the final round of selection for the 42F3 TCR. (f) The unique peptide sequences selected by 42F3 TCR observed in the sequencing sample. The P2 and P9 positions with restricted diversity are highlighted in black and blue respectively, and positions fully diversified are highlighted in red.

Supplementary Figure 2 Peptide dose response for the activation of 42F3 T cells.

Peptide dose response of IL-2 release for 42F3 T cells, separated into ‘full agonist’ (a) and ‘partial agonist’ (b) groups. Data is represented as mean ± s.e.m., n=2 of technical replicates.

Supplementary Figure 3 Binding kinetics of 42F3 TCR–agonistic peptide–MHC.

(a) The surface plasmon traces and steady-state fits (inset) for agonist peptide-MHC binding to the 42F3 TCR analyte. (b) The surface plasmon traces and kinetic fits for agonist peptide-MHC binding 42F3 TCR. (c) A kinetic summary for each peptide-MHC-TCR complex.

Supplementary Figure 4 Structures of 42F3 TCR–agonistic peptides.

(a) The overall structure of the 42F3 complex recognizing second-generation synthetic peptides presented by mini-H-2Ld. (b) The 2Fo-Fc map of peptides (yellow sticks) in electron density (blue mesh) contoured for 1-1.5σ. (c) The overall structure of the 42F3 complex recognizing first-generation synthetic peptides presented by mini-H-2Ld. (d) The 2Fo-Fc map of peptides (yellow sticks) in electron density (blue mesh) is contoured for 1-1.5σ.

Supplementary Figure 5 The conserved germline contacts of the 42F3 TCR to the MHC.

(a) Structures of the Vα3.3 contacts to the α2 domain of H-2Ld for five second-generation agonist complexes. (b) Structures of the Vβ8.3 contacts to the α1 domain of H-2Ld for five second-generation agonist complexes. The MHC is colored green, Vα is colored red, and the Vβ is colored blue. Contact residues are depicted as sticks where dashed lines represent hydrogen bonds.

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Adams, J., Narayanan, S., Birnbaum, M. et al. Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat Immunol 17, 87–94 (2016). https://doi.org/10.1038/ni.3310

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