Atomistic TCR-pMHC interactions bias CD8 memory fate within a single antigen-specific repertoire

Memory CD8 T cells provide durable protection against recurrent infection and cancer, but how individual TCR clonotypes contribute to distinct memory fates remains enigmatic. Here, we analyzed 242 murine CD8 TCRαβ clonotypes specific for an influenza NP_366-374/H-2D^b ligand (pMHC) by integrating single-cell transcriptomics and paired TCR sequencing with force-dependent biophysics, structural analysis, and in vivo retrogenic validation. Within this shared antigenic and inflammatory setting, clonotype identity was associated with central memory, effector memory, or bipolar transcriptional outcomes. Structural and biophysical analyses of representative TCRs revealed differences in Vα-centric versus Vβ-centric pMHC engagement and in atomistic contacts that are consistent with altered force transmission through the TCR. These interaction modes correlated with CD3ζ phosphorylation, memory transcriptional programs, clonal expansion, and heterosubtypic crossreactivity. Thus, TCR clonotypes appear to encode not only antigen specificity but also differing propensities for memory differentiation, supporting a model in which TCR-pMHC mechanochemistry contributes to CD8 memory fate.