Human invariant natural killer T (NKT) cell TCRs bind to CD1d via an ''invariant'' Va24-Ja18 chain (iNKTa) paired to semi-invariant Vb11 chains (iNKTb). Single-amino acid variations at position 93 (p93) of iNKTa, immediately upstream of the ''invariant'' CDR3a region, have been reported in a substantial proportion of human iNKT-cell clones (4-30%). Although p93, a serine in most human iNKT-cell TCRs, makes no contact with CD1d, it could affect CD1d binding by altering the conformation of the crucial CDR3a loop. By generating recombinant refolded iNKT-cell TCRs, we show that natural single-nucleotide variations in iNKTa, translating to serine, threonine, asparagine or isoleucine at p93, exert a powerful effect on CD1d binding, with up to 28-fold differences in affinity between these variants. This effect was observed with CD1d loaded with either the artificial a-galactosylceramide antigens KRN7000 or OCH, or the endogenous glycolipid b-galactosylceramide, and its importance for autoreactive recognition of endogenous lipids was demonstrated by the binding of variant iNKT-cell TCR tetramers to cell surface expressed CD1d. The serine-containing variant showed the strongest CD1d binding, offering an explanation for its predominance in vivo. Complementary molecular dynamics modeling studies were consistent with an impact of p93 on the conformation of the CDR3a loop.Key words: CD1d . iNKT cells . Molecular modeling . Surface plasmon resonance . TCR
IntroductionInvariant natural killer T (iNKT) lymphocytes are a versatile and potent subset of T cells which play important roles in both host defense and tolerance. In contrast to conventional T cells, they recognize the non-polymorphic lipid-antigen-presenting molecule CD1d via highly conserved TCRs. In fact, all iNKT-cell TCRs use an ''invariant'' TCRa chain (iNKTa), Va24-Ja18 in humans, Va14-Ja18 in mice, paired to ''semi-invariant'' TCRb chains (iNKTb), which in humans solely utilize Vb11 rearranged with diverse TCR Ã These authors contributed equally to this work.
248Jb segments. For all iNKT-cell TCRs, binding to CD1d is primarily mediated by the Va-Ja rearranged ''invariant'' CDR3a loop as well as the two germline-encoded CDR1a and CDR2b loops [1,2]. In addition, we have recently shown that the only variable region of human iNKT-cell TCRs, i.e. the CDR3b loop, strongly modulates the affinity to CD1d [3].Human iNKT-cell clones with single-amino acid variations in the ''invariant'' Va24-Ja18 iNKTa chain have been previously identified [4,5], and a recent study found that 4-30% of human iNKT-cell clones carried such variations [4]. However, the effect of these variations on iNKT-cell TCR binding to CD1d has not been examined. All of the described variations to date are located immediately upstream of the CDR3a loop region and most of these involve residue 93 (p93). The most commonly used amino acid at this position is serine (Ser93), which is encoded for by the germline sequence of human Va24S1 (AE00521.1), but other identified natural variations at this position inclu...