Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region
Fig 4
Interactions of the TCR-CD3 with lipid headgroups.
(A) Normalized number of contacts of each full-length TCR-CD3 subunit with lipid headgroups. The normalization (N) is done by dividing the number of lipid contacts of each residue (n1) by the number of the specific lipid in the bilayer (n2) and by the number of simulation frames (n3) i.e. N = n1/n2/n3. Interactions of each TCR-CD3 subunit with anionic lipids are shown on the right whereas those with neutral lipids are shown on the left. The scale of non-anionic interactions was magnified 10 times (scale: 0 to 0.1) for clarity. The ITAMs (red lines) of ζ and all CD3 subunits, the BRS motifs (blue lines) of CD3ε and ζ subunits, and poly-proline motifs (black lines) of the CD3ε subunits are also indicated. (B) Contacts of the TCR-CD3 with each lipid headgroup type are normalized separately on a scale of 0 to 1 and mapped as a colour gradient (blue: low, green: medium, red: high) on the TCR-CD3 structure extracted from the end of a simulation.