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Structural insights into the Natural Killer T cell receptor specificity and CD1d-glycolipid recognition

posted on 09.02.2017, 05:21 authored by Wun, Kwok Soon
Natural Killer T (NKT) cells play an important role in the immune system as demonstrated by their involvement in tumour surveillance, infection and inflammation. Unlike conventional T cells that recognises peptide antigens when presented by the Major Histocompatibility Complex (pMHC), NKT cells recognise glycolipids, presented by a MHC class I-like molecule (CD1d-α-GalCer) to invoke an immune response. Human semi-invariant NKT cells are unique as the majority of them express a T cell receptor (TCR) bearing an invariant α-chain and restricted β-chain repertoire (Vα24-Jα18;Vβ 11). The mouse orthologue also expresses an invariant α-chain (Vα14-Jα18) but a slightly more diverse β-chain repertoire (Vβ2, Vβ7 and Vβ8.2), where Vβ8.2 is most commonly expressed. The crystal structures of the human NKT TCR-CD1d-α-GalCer and mouse orthologue complexes have provided structural insights into how the NKT TCR can recognise a lipid antigen. While it is clear that the NKT TCR docks CD1d-α-GalCer in a different conformation compared to the TCR-pMHC complexes, there was no clear information on the energetic footprint of the NKT TCR's recognition of CD1d-α-GalCer and also how the NKT TCR can differentiate between closely related α-GalCer analogues to induce a biased cytokine response. In this study, an alanine scanning mutagenesis experiment carried out on the human NKT TCR (Vα24-Jα18;Vβ11) and CD1d, as well as the use of α-GalCer analogues, demonstrated that the Jα18-encoded CDR3α loop and Vβ11-encoded CDR2β loop of the NKT TCR play a crucial role in maintaining its interactions with CD1d-α-GalCer. The minimal usage of only six residues, which are also evolutionary conserved in the mouse NKT TCR (Vα14-Jα18;Vβ8.2), explains the semi-invariant nature of the NKT TCR as well as the basis of NKT cell cross-species reactivity. Furthermore, the interactions these residues made are localised directly above the F′ pocket of CD1d, distal from the galactosyl head group of α-GalCer. The use of α-GalCer analogues that contains glycosyl head group modifications, further demonstrated the lesser energetic contribution the NKT TCR CDR1α loop plays in its interactions with the sugar head group of α-GalCer. In contrast, the NKT TCR CDR3α loop, which makes interactions with α-GalCer as well as CD1d, was determined to be the key CDR loop that is energetically important in glycolipid recognition. NKT cells can differentiate between α-GalCer analogues with small modifications on their glycosyl head group to stimulate a biased T helper (Th) cytokine response. Therefore, the ability of how the mouse Vβ8.2 NKT TCR is able to distinguish between different α-GalCer analogues was further investigated through a combination of biophysical, structural and functional experiments. These data had provided further insight into how NKT cells can recognise and differentiate between structurally similar variants of α-GalCer, also referred to as Altered Glycolipid Ligands (AGLs). The crystal structures of all five NKT TCR-CD1d-AGL complexes revealed minimal structural differences. Variations in terms of affinity and kinetics of the NKT TCR engagement onto CD1d-AGLs as well as differences in cellular responses between AGLs were observed. Modifications on the glycosyl head group of the AGLs, directly impacted NKT cell activation as well as the affinity and t1/2 of the NKT TCR recognition. Furthermore, for these glycosyl head group modified AGLs, ligand potency, as determined by the amount of cytokines produced by the NKT cells, was directly affected by the t1/2 of the NKT TCR-CD1d-AGL interaction. In addition, modifications on the acyl chain of the AGLs do not affect the NKT TCR interaction but reduced NKT cell proliferation. This indicated an alternative antigen processing and presentation pathway for these AGLs by CD1d. On the other hand, truncation of the sphingosine chain resulted in a reduction of NKT TCR affinity resulting in an induced-fit mechanism by the NKT TCR. Collectively, the minimal binding requirements of CD1d restriction as well as the molecular basis of NKT fine specificity in CD1d-AGLs recognition were elucidated.


Principal supervisor

Jamie Rossjohn

Year of Award


Department, School or Centre

Biochemistry and Molecular Biology

Campus location



Doctor of Philosophy

Degree Type



Faculty of Medicine Nursing and Health Sciences