Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding

TAP-independent induction of N-myristoylated lipopeptide-specific CTLs in transgenic mice expressing the rhesus MHC class I allomorph, Mamu-B*098

A novel subset of classical major histocompatibility complex class I molecules has recently been identified in rhesus monkeys that mediates the presentation of N-myristoylated lipopeptides, rather than conventional peptides, to CD8+ cytotoxic T lymphocytes (CTLs). For example, the rhesus Mamu-B*098 allomorph binds an N-terminal 5-mer fragment (C14 fatty acid-Gly-Gly-Ala-Ile-Ser; C14nef5) derived from the N-myristoylated SIV Nef protein and activates C14nef5-specific CTLs. Additionally, a transporter for antigen presentation (TAP)-independent cell-surface expression was observed for Mamu-B*098 in the in vitro transfection experiments, leading us to hypothesize that TAP-independent pathways may exist for CTL activation. To address this directly, we generated transgenic mice expressing Mamu-B*098 and analyzed its function under TAP-deficient conditions. We first confirmed that its expression level was unchanged on the surface of TAP-deficient cells compared with that of TAP-sufficient cells. Second, the CD8+ T cell population, but not the CD4+ T cell population, increased in TAP knockout (KO) mice as a result of the acquisition of Mamu-B*098 expression. Third, C14nef5-specific, Mamu-B*098-restricted CD8+ T cells were readily inducible in Mamu-B*098 transgenic/TAP KO but not in nontransgenic/TAP KO mice. Finally, the CD8+ T cells expressed cytolytic granule contents and functioned as CTLs. These findings provide evidence that in addition to conventional peptide-specific CTL responses that require TAP, an alternative TAP-independent pathway for CTL activation exists in primates. This novel pathway may be valuable when TAP is targeted by pathogenic viruses for immune evasion. We propose that the established concept of major histocompatibility complex class I biology may require modifications to incorporate TAP-independent pathways of lipopeptide-specific CTL responses.

Micropolymorphism outside the peptide-binding groove of human leukocyte antigen (HLA)-C*14 modulates structural stability and shapes immune responses

Micropolymorphisms in human leukocyte antigen class I (HLA-I) molecules critically influence antigen presentation and immune recognition. Most studies have focused on variations within the peptide-binding groove (PBG), neglecting the potential impact of residues located outside this region. HLA-C*14:02 and HLA-C*14:03 differ only at position 21 (R21 and H21, respectively), which is situated outside the PBG, yet these two allotypes exhibit distinct clinical associations with HIV control in the context of KIR2DL2, an inhibitory killer cell immunoglobulin-like receptor that modulates natural killer (NK) cell activity. Here, we investigated the molecular mechanisms by which the R21H micropolymorphism shapes immune responses. Structural and biochemical analyses revealed that position 21 indirectly regulates the conformation of the B pocket within the PBG, significantly affecting HLA-C*14 stability and altering the composition of its peptide repertoire, while preserving core peptide motifs and recognition by KIR2DL2. Notably, the R21H variation is evolutionarily conserved across various HLA-I molecules and exhibits similar interactions with neighboring residues, suggesting a broadly conserved role in structural stability and immune regulation. These findings suggest that the stability differences between HLA-C*14 allotypes may influence their differential clinical associations, highlighting the previously underappreciated role of micropolymorphisms outside the PBG in modulating immune responses.

Antigen presentation of post-translationally modified peptides in major histocompatibility complexes

T cells of the adaptive immune system recognize pathogens and malignantly transformed cells through a process called antigen presentation. During this process, peptides are displayed on major histocompatibility complex (MHC) class I and II molecules. Self-reactive T cells are typically removed or suppressed during T-cell development and through peripheral tolerance mechanisms, ensuring that only T cells recognizing peptides that are either absent or present in low abundance under normal conditions remain. This selective process allows T cells to respond to peptides derived from foreign proteins while ignoring those from self-proteins. However, T cells can also respond to peptides derived from proteins that have undergone post-translational modifications (PTMs). Over 200 different PTMs have been described, and while they are essential for protein function, localization and stability, their dysregulation is often associated with disease conditions. PTMs can affect the proteolytic processing of proteins and prevent MHC binding, thereby changing the repertoire of peptides presented on MHC molecules. However, it is also increasingly evident that many peptides presented on MHC molecules carry PTMs, which can alter their immunogenicity. As a result, the presentation of post-translationally modified peptides by MHC molecules plays a significant role in various diseases, as well as autoimmune disorders and allergies. This review will provide an overview of the impact of PTMs on antigen presentation and their implications for immune recognition and disease.

Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules

Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).