Atom-level mechanism of tapasin-independent peptide editing by Major Histocompatibility Complex class I molecules

Peptide binding to major histocompatibility complex class I molecules (MHC-I) and their presentation to cytotoxic immune cells is a keystone of the adaptive immune system. The selection of MHC-I bound peptides is facilitated by the chaperone tapasin, which allows MHC-I to iteratively sample peptides until they are loaded with optimal binding peptides, known as peptide editing. However, some MHC-I allotypes can select high affinity binding peptides independently of tapasin, and the molecular mechanism(s) for such peptide editing are unknown. Here, we used enhanced sampling molecular dynamics simulations of peptide-deficient MHC-I to investigate tapasin-independent peptide editing. Our simulations revealed transient disruption of hydrogen bonds between MHC-I and the peptide backbone could allow for peptide editing, a process we term "active displacement". Destabilisation of interactions with the peptide backbone, necessitates sequence-specific sidechain interactions to maintain peptide binding. Our active displacement model predicts surface expression levels for multiple MHC-I allotypes and accounts for the presentation of an immunogenic mutant KRAS-G12D neoepitope by HLA-C*08:02, but not by closely related HLA-C*05:01. Together our data provide a molecular mechanism for tapasin-independent MHC-I peptide editing, influencing the surface immunopeptidome and anti-tumour immunity. Significance StatementMajor histocompatibility complex class I molecules (MHC-I) bind and present peptides to specialised killer cells of the immune system. These immune cells can unleash their cytotoxic effector functions if they recognise the peptide-MHC-I complex. Which peptides are presented by MHC-I is therefore highly important. Peptide selection is usually assisted by the tapasin protein, although some MHC-I molecules can select peptides independently of tapasin, but it is not known how this occurs. Here, we provide an atomistic description of the tapasin-independent peptide selection mechanism. Our mechanism applies to multiple MHC-I allotypes and illustrates how an immunogenic peptide is presented by one MHC-I molecule, but not by another closely related molecule. This new insight provides a rational basis for therapeutic treatments.