A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T-cell receptors exhibiting different levels of cross-reactivity

Abstract

T-cell receptors (TCRs) can productively interact with many different peptides bound within the MHC binding groove. This property varies with the level of cross-reactivity of TCRs; some TCRs are particularly hyper cross-reactive while others exhibit greater specificity. To elucidate the mechanism behind these differences, we studied five TCRs in complex with the same class II MHC (1A^b )-peptide (3K), that are known to exhibit different levels of cross-reactivity. Although these complexes have similar binding affinities, the interface areas between the TCR and the peptide-MHC (pMHC) differ significantly. We investigated static and dynamic structural features of the TCR-pMHC complexes and of TCRs in a free state, as well as the relationship between binding affinity and interface area. It was found that the TCRs known to exhibit lower levels of cross-reactivity bound to pMHC using an induced-fitting mechanism, forming large and tight interfaces rich in specific hydrogen bonds. In contrast, TCRs known to exhibit high levels of cross-reactivity used a more rigid binding mechanism where non-specific π-interactions involving the bulky Trp residue in CDR3β dominated. As entropy loss upon binding in these highly degenerate and rigid TCRs is smaller than that in less degenerate TCRs, they can better tolerate changes in residues distal from the major contacts with MHC-bound peptide. Hence, our dynamics study revealed that differences in the peptide recognition mechanisms by TCRs appear to correlate with the levels of T-cell cross-reactivity.

Keywords: CH-π interactions; binding affinity-interface area relationship; cross-reactive T-cell receptor recognition; fragment molecular orbital method; molecular dynamics simulation.

Figure 1

Interface areas in 31 class II MHC–peptide–T‐cell receptor (TCR) complexes. The black and grey solid lines and black dotted line indicate interface areas between TCR and peptide–MHC (pMHC), TCR and MHC, and TCR and peptide, respectively. Protein Data Bank (PDB) IDs of the complexes arranged in the order of interface size are shown on the horizontal axis. The binding affinity data are shown below the PDB IDs, if available in the primary citations. The complexes that according to the primary citations contain self‐peptides are marked with open black circles.

Figure 2

T‐cell receptor (TCR) regions interacting with peptide–MHC (pMHC). (a–e) MHC and peptide‐binding footprints on TCR surface in B3K506, 14.C6, J809.B5, 2W20 and YAe62, respectively, in the crystal structure (upper figures) and the MD snapshot at 200 ns (lower figures). From left to right, the binding footprints of peptide, MHC and pMHC, respectively, are shown in purple. CDR regions are defined based on the IMGT 3D structure‐DB 39 and Dunbrack definition,40 as summarized in Table 2 for CDR3 loops, and shown in Figure 3. CDR1α–3α and CDR1β–3β are coloured cyan, orange, green, blue, pink and yellow, respectively. [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 3

Fluctuations of T‐cell receptor (TCR) residues in the free and complex states. (a–e) The root‐mean‐square (RMS) fluctuations of the CDR residues in B3K506, 14.C6, J809.B5, 2W20 and YAe62, respectively, are shown. The fluctuations were calculated applying Eq. (1) to the molecular dynamics (MD) snapshots from 20 to 200 ns. The black and grey lines indicate the fluctuations in the free TCR and complex states, respectively.