TCR Scanning of Peptide/MHC through Complementary Matching of Receptor and Ligand Molecular Flexibility

Abstract

Although conformational changes in TCRs and pMHC molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. Here we used NMR to study TCR-pMHC binding, examining recognition of the QL9/H-2Ld complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR-pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR-pMHC complex. Determination of conformational exchange kinetics revealed that the motions of CDR3β and QL9 are closely matched. The matching of conformational exchange in the free proteins and its persistence in the complex enhances the thermodynamic and kinetic stability of the TCR-pMHC complex and provides a mechanism for facile binding. We thus propose that matching of structural fluctuations is a component of how TCRs scan amongst potential ligands for those that can bind with sufficient stability to enable T cell signaling.

CD1b-restricted GEM T cell responses are modulated byMycobacterium tuberculosismycolic acid meromycolate chains

“…Our findings suggest a mechanism for TCR-ligand interaction, which may also be generalizable for ligand recognition by CD1c and CD1d molecules. It may also contribute to the fine-tuning of classical peptide-MHC recognition by TCR (42).…”

How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

“…Contacts between TCR and MHC were identified using ContPro (54), the PyMOL script DistancesRH, and Accelrys Discovery Studio 4.1, using a 4.5-Å distance cutoff. We used this more liberal cutoff distance (compared with the more common 4 Å) to better account for coordinate error and the nonstatic nature of the protein interfaces (55,56). TCR-pMHC complexes were superimposed by the PyMOL pair fit function, fitting the α carbon of residues 1-180 of the MHC protein.…”

A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR

“…Toward this end, we prepared samples of the mini-H2-L d construct refolded in vitro with two different peptides. In particular, we used the QL9 peptide (21) (also employed previously to study binding to the 2C TCR (13,16,17)) and a high affinity NIH self-peptide. Although initially, both samples gave well dispersed two-dimensional TROSY spectra, each indicative of a properly conformed peptide⅐ MHC-I complex, the sample prepared with QL9 deteriorated within 1 week at 25°C.…”

“…Subsequent structural characterization showed that this molecule preserves the binding epitopes for T cell recognition in their native orientation, as indicated by co-crystal structures of several peptide⅐MHC-I/TCR complexes (15). More recently, solution NMR studies of the 2C/mini-H2-L d system explored recognition dynamics at the MHC-I/TCR interface (16,17).…”