Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination

Adil Doganay Duru; Renhua Sun; Eva B. Allerbring; Jesseka Chadderton; Nadir Kadri; Xiao Han; Hannes Uchtenhagen; Chaithanya Madhurantakam; Sara Pellegrino; Tatyana Sandalova; Per-Åke Nygren; Stephen J. Turner; Adnane Achour

TCR-210 unbound pMHC (Fig. 4, Fig. S8 ). The side chain of p4Y, essential for recognition by P14 [4, 33, 211 34], rotates down following P14 binding to both H-2D b /gp33 and H-2D b /V3P (Fig. 4A-B) . A 212 similar rotation was also observed for residue p4F in H-2D b /PF upon binding to P14 (Fig. 4C) . 213 The side chain of p6F in gp33 is also affected upon binding to P14 (Fig. 4A) . Interestingly, the 214 p3P modification resulted in a similar conformation for p6F in both H-2D b /V3P and H-2D b /PF 215 prior to binding to P14 ( Fig. 1D and Fig. 4) . Furthermore, the side chain of residue p1K in H-216 2D b /gp33 also moves towards the N-terminal of the peptide binding cleft following P14 binding 217 (Fig. 4A) , taking an identical conformation as in both p3P-substituted peptides (Fig. 4D) . The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint 12 P14 docking, p3V in gp33 extends 1.2 Å deeper into the D-pocket of H-2D b , combined with a 180° 222 rotation (Fig. 4A) . In contrast to gp33, the p2-p4 section is more constrained in both V3P and PF, 223 following TCR binding (Fig. 4B, 4C ). However, it should be noted that the final conformations of 224 all three peptides in the ternary complexes is nearly identical (Fig. 4D ). In conclusion, residues 1 225 and 6 in p3P-APLs take the same conformations prior to TCR binding as found in the ternary 226 complexes, potentially enabling a more favorable surface for P14 TCR binding. Furthermore, p1K in gp33 also takes a different conformation upon binding to P14, bending 239 backwards towards the H-2D b residues R62 and E163, which conformations are affected (Fig. 4A , 240 5A). Here again, the side chain of p1K takes exactly this conformation in both V3P and PF already 241 before TCR binding (Fig. 4, 5) . Altogether, p1K, P6F and heavy chain residues R62, H155 and 242 E163 have already adopted in the unbound V3P and PF complexes similar conformations to those 243 observed in all three ternary structures (Fig. 4, 5) . Thus, the p3P substitution potentially facilitates 244 TCR recognition by positioning specific key peptide and MHC residues prior to the formation of 245 . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint 13 the ternary complexes. This is well in line with our SPR and ITC results, which indicate that the 246 energy required for P14 recognition of V3P is reduced compared to gp33 (Table 1, Fig. S1 ). The results presented within this study indicate in our opinion that i) docking of P14 to p3P-331 modified peptides is facilitated since the conformations of key residues in both peptide and heavy 332 chain are already optimal prior to TCR binding (ready-to-go conformation); ii) consequently, the 333 energetic costs for TCR recognition should be reduced since there is no need for any major 334 movement in the rigidified epitope besides the conformational change for residue p4Y. As The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint