Structural insights into the recognition of CD1d-restricted self antigens by the natural killer T-cell T-cell antigen receptor

This thesis investigates the molecular mechanisms of self-recognition by the Natural Killer T cell (NKT cell) T cell antigen Receptor (TCR). A number of crystal structures of complexes comprising an “autoreactive” NKT TCR bound to CD1d presenting a range of different host antigens have been elucidated in this work. With respect to the TCR used in these studies, the NKT TCR autoreactivity is driven by a hydrophobic region of the β-chain (the CDR3β loop) which comprises a “di-leucine motif”. This motif interacts with a hydrophobic patch of the CD1d α2 helix, and it appears that this interaction is the primary mechanism behind the autoreactivity of this NKT TCR. Accordingly, this data supports a general mechanism that the NKT TCRs develop "autoreactivity" by possessing CDR3β sequences that can interact CD1d directly over a particular threshold, in a ligand independent manner. Of course, the NKT TCRs are not completely ligand independent, and it is presented herein that some lipid antigens (e.g., GD3) will disrupt the ability, via steric hindrance, for the TCR to bind to dock onto CD1d. Further, this thesis discloses the mechanism with respect to how a special group of lipid antigens, which feature β-linked carbohydrate headgroups, are recognized. The “β-linked” headgroups of these antigens naturally protrude directly out from the CD1d antigen binding grove when not bound to the NKT TCR, and accordingly, it was unknown how this antigen conformation would allow for NKT TCR recognition. Through the elucidation of complex crystal structures, it is observed that upon TCR engagement the β-linked antigen headgroup is pushed down flat against the CD1d α2 helix, which allows sufficient space for the TCR to dock.