Srivastava et al. define a new and improved way to predict immunoprotective cancer neoepitopes based in part on the difference in MHC-binding scores between the mutant epitope and its wild-type counterpart. Remarkably, all neoepitopes that elicited tumor regression bound to class I MHC molecules with very low affinity.

No abstract

Background: Peptide modulation of MHC flexibility can affect recognition by immune receptors. Results: Different peptides alter the flexibility of the MHC protein at sites around the peptide-binding groove. Conclusion: Peptide modulation of MHC flexibility is not limited to specific peptides or isolated regions. Significance: Peptide modulation of MHC flexibility indicates an extension of antigenicity from the peptide to the MHC.

T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible. These include MHC protein motions, or dynamics, which are believed to influence interactions with a variety of MHC-binding proteins, including not only TCRs, but other activating and inhibitory receptors as well as components of the peptide loading machinery. Here, we investigated the mechanisms by which peptides tune the dynamics of the common class I MHC protein HLA-A2. By examining more than 50 lengthy molecular dynamics simulations of HLA-A2 presenting different peptides, we identified regions susceptible to dynamic tuning, including regions in the peptide binding domain as well as the distal α3 domain. Further analyses of the simulations illuminated mechanisms by which the influences of different peptides are communicated throughout the protein, and involve regions of the peptide binding groove, the β 2 -microglobulin subunit, and the α3 domain. Overall, our results demonstrate that the class I MHC protein is a highly tunable peptide sensor whose physical properties vary considerably with bound peptide. Our data provides insight into the underlying principles and suggest a role for dynamically driven allostery in the immunological function of MHC proteins.