Solution mapping of MHC-I:TCR interactions using a minimalistic protein system

Abstract

Recognition of epitopic peptide antigens presented on class I major histocompatibility complex (MHC-I) proteins by T cell receptors (TCRs) forms the cornerstone of immune surveillance, leading to a plethora of adaptive immune responses. Characterization of TCR:peptide/MHC-I interactions is critical for understanding immune recognition, and developing immunotherapies, but the large variation in docking orientations of TCRs on their peptide/MHC-I targets challenges structural modeling. NMR spectroscopy could potentially resolve this ambiguity, but the large size of the TCR:peptide/MHC-I complex limits data quality. Here, we demonstrate that a designed MHC-I protein, SMART A*02:01, enables facile solution mapping of MHC-I:TCR interactions at scale. Our approach can be combined with computational modeling and structure-guided engineering to aid the development of TCR-based therapeutics.

Keywords: HLA; T cell receptor; computational protein design; human leukocyte antigen; peptide antigen.

Fig. 1.

NMR chemical shifts highlight structural adaptations in the SMART A*02:01 peptide binding groove upon binding to different antigens. (A) CSPs plotted as a color gradient (white → red) on a Robetta (32) model of SMART A*02:01. Missing assignments are plotted as black spheres. (B) Overlay of native HLA-A*02:01/β₂m/TAX9 (PDB ID 1hhk, wheat) and HLA-A*02:01/β₂m/NYESO (1s9w, pink) crystal structures, with residues undergoing strong CSPs shown as sticks. Peptides are colored darker for clarity (TAX9 in brown, NYESO in dark pink).

Fig. 2.

Solution mapping the docking orientation of the A6c134 TCR on SMART A*02:01/TAX9. CSPs plotted as a color gradient (white → red) and exchange broadened sites (colored purple) on a Robetta (32) model of SMART A*02:01, including both the (A) side and (B) top views. Residues with missing assignment sites are plotted as black spheres. An overlay of the A6c134:A*02:01/TAX9 structure is included for reference (PDB ID 4ftv, teal). Note that CDR1β only makes contact with the TAX9 peptide, and CDR2β does not interact with the pMHC at all (33). (C and D) Close-up views of residues with strong CSPs. (E) Overlay of native HLA-A*02:01/β₂m/TAX9 (1hhk, wheat) and HLA-A*02:01/β₂m/TAX9:A6c134 (4ftv, teal) crystal structures, highlighting a conformational shift at the α_2-1 helix. TAX9 is colored differently in apo (brown) and bound (yellow) structures for clarity.