Figure 2.

Differences in the Average Number of Contacts Formed during pHLA Engagement of WT TCRs versus aeTCRs

(A) Difference (Δ) in the number of contacts between WT TCRs and aeTCRs segregated by contact type analyzed using crystal structures. Boxplots represent median (middle line), interquartile ranges Q1 (box lower) and Q3 (box upper), Q1-1.5∗IQR (lower whisker), and Q3+1.5∗IQR (upper whisker). Individual scatter points of each TCR are overlaid and colored by the TCR-pHLA system-indicated inset. vdW, van der Waals (≤4.0 Å); HBs, hydrogen bonds (≤3.4 Å); SBs, salt bridges (≤3.4 Å). (B) Difference in the number of contacts between WT and aeTCRs from crystal structures segregated by contacts to HLA or peptide atoms or both (total). (C) Surface plots of the pHLA (peptide atoms shown as spheres) with each structure color mapped according the average number of vdWs contacts formed between the given residue and the TCR during the course of MD simulations. Color mapping was performed from white (no contacts) through yellow and orange to red (highest number of contacts observed for each of the pairs of TCR-pHLAs studied). All pHLA structures are shown in the same orientation, such that the peptide N terminus is left, and the C terminus is right. TCR residues contributing substantially to new contacts are labeled in black and indicated with black lines. Corresponding peptide or HLA residues are labeled in light blue. For brevity, only one 1G4 aeTCR is shown; all others are shown in Figure S2. Note that (A) and (B) were generated from crystal structure analysis, while (C) was generated from MD simulation data.