key: cord-0304127-sxmmxn6f
authors: Liu, Yang; San, Dan; Yin, Lei
title: Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection
date: 2021-06-07
journal: bioRxiv
DOI: 10.1101/2021.06.06.447276
sha: 0678b2f1503d34f05e45eef768d4e26ff22b1e31
doc_id: 304127
cord_uid: sxmmxn6f

Although both HLA B*81:01 and HLA B*42:01 are members of the B7 supertype and can present many of the same HIV-1 epitopes, the identification of a dual-reactive T-cell phenotype was unexpected, since structural data suggested that TL9 peptide binds to each allele in a distinct conformation. How the dual-reactive TCR recognizes these radically distinct p-MHC surfaces is revealed by our structural study, that the introduction of TCR T18A induces a molecular switch of the TL9 peptide in B4201 to approach its conformation in B8101. Most importantly, unique docking of CDR3β towards MHC but not peptide ligand strengthens the peptide tolerance of T18A, extends the ability of TCR to adapt mutations. Moreover, the high affinity of dual-reactive TCR for WT and escape mutant TL9 highlights the functional advantage of the alloreactive phenotype.

cell phenotype was unexpected, since structural data suggested that TL9 peptide binds 27 to each allele in a distinct conformation. How the dual-reactive TCR recognizes these 28 radically distinct p-MHC surfaces is revealed by our structural study, that the 29 introduction of TCR T18A induces a molecular switch of the TL9 peptide in B4201 to 30 approach its conformation in B8101. Most importantly, unique docking of CDR3β 31 towards MHC but not peptide ligand strengthens the peptide tolerance of T18A, 32 extends the ability of TCR to adapt mutations. Moreover, the high affinity of dual-33 reactive TCR for WT and escape mutant TL9 highlights the functional advantage of the 34 alloreactive phenotype. 37 Antigen-specific T cell immunity is a fundamental 'law' of immunology, that is, T cell 38 responses are highly specific and are developmentally restricted to the recognition of confronted with the CD8 + T cell response targeting the same epitope but restricted by 80 different HLA molecules. At a population level, this may result in differential HLA-81 associated viral replication capacity and disease prognosis (Carlson et al., 2012) . 82 In this study, we investigate the mechanism of the high-affinity CD8 + T cell 83 response to immunodominant HIV-1 epitope Gag-TL9 by first reporting its TCR-pHLA 84 ternary-complex structure. In addition, the cross-restriction structure of the same TCR To critically examine why T18A TCR can creatively bind to distinct antigen-presenting 107 surfaces in different HLA contexts, we determined the structure of T18A and 108 TPQDLNTML in the B*81:01 and B*42:01 complexes. The statistics of the crystals were 109 described in table S1, and the structures of the ternary complexes were shown ( Figure   110 1A, C). The T18A TCR combines pMHC in a traditional diagonal manner, with a total 111 6 buried surface area (Lesk and Chothia, 1987) The online version of this article includes the following source data for figure 1: 150 Table S1 . Data collection and refinement statistics of TCR-peptide-HLA complexes. 151 Table S2 . and B4201 presentation upon TCR binding were shown and compared ( Fig 1K) . The register change of TL9 peptide seems due to TCR binding make its conformation closer to its 176 pressed into the bind groove for about 5 Å, the solvent exposed P7T is also press to the bind groove 181 for 4.3 Å. The buried residue P6N shifts upwards by 8.2 Å and contact to the CDR2β of T18A. 182

The online version of this article includes the following source data for figure 2: 183 Under the B*42:01 restriction, the electron density showed that the central part 186 of TPQDLNTML had a 'conformational switch' compared to its conformation in the free 187 pMHC (Fig.2D) . The side chain of leucine at P5 (P5L) turned down with a movement of 188 about 5.2 Å, and its peptide backbone was pressed toward the antigen-binding cleft. 189 At the same time, anchor residue P6N was flipping by 112°, becoming solvent exposed 190 and was involved in CDR2β interactions. On the contrary, solvent exposed P7T shifted interaction between Jα and Vα strands was intact, but they were separated at the 302 second glycine of the FGXG motif in a similar pattern, although different TRAV 303 sequences were used. Conformational changes in the Vα core made it possible for the 304 same TCR to cross-recognize multiple distinct MHCs (Fig. 5C ). 305 The direct consequence of this conformational change was to enlarge the distance 306 between Jα and Vα, which finally led to the perturbation of the Vα domain including 307 CDR1 and CDR2 loops, which swang away from the Vβ domain (Fig. 5D ). We 308 superimposed T18A (TRAV26-1/ TRBV12-3) and 1E6 TCR (TRAV12-3/TRBV12-4) to 309 compare the effect of "opened" or "closed" Jα-Vα interactions on the entire TCR (Table S4 ). In all of these, CDR3β interacts with peptide and MHC ligands, 381 most mainly focused on the peptide. However, CDR3β of T18A was unique, which was 382 far away from the peptide but formed rigidly interaction with MHC ligand. This 383 remarkably rare characteristic of T18A extended its tolerance to mutated peptides and 384 might be related to the delayed viral escape in the clinic. Fig.S6 ). 431 Although the B*81:01-derived, mono-reactive T11A also had a strong affinity for wild-432 type TL9 (Kd≈4.9μM), its ability to bind mutated TL9 was weaker than that of T18A, 433 such that only one significant binding is confirmed against TL9 mutants. On the other 434 hand, B*42:01-derived, mono-reactive TCR T7A showed no obvious response to either 435 wild-type or mutated TL9, as also evidenced by the native-PAGE results (Fig.S5) 602 We thank the staff of the Shanghai Synchrotron Radiation Facility (beamline BL19U1). 603 We sincerely pay tribute to the people who have strived in the forefront of fighting 604 against the HIV-1 pandemic and who studied this virus around the world. Table S1 . Data collection and refinement statistics of TCR-peptide-HLA-B structures. Figure S1 . T18A engagement does not change the conformation of TL9 peptide restricted by B8101. (a) The structure of TL9 before TCR involvement is colored in magenta; The conformation of TL9 after TCR binding is colored in orange. Table S3 . HLA-associated variation in TL9-Gag from studies in last decade.

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