Mapping the peptide binding groove of MHC class I

An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule. This novel approach allows us to examine the binding properties of diverse peptides. The unique stability of our MHC class I even enables us to determine the binding affinity of complexes, which are suboptimally loaded with truncated or charge-reduced peptides. Notably, a unique erucamide adduct decouples affinity analysis from peptide identity alleviating issues usually attributed to clustering during electrospray ionization. We discovered that two anchor positions at the binding surface between MHC and peptide can be stabilized independently and further identify the contribution of other peptidic amino acids on the binding. We propose this as an alternative, likely universally applicable method to artificial prediction tools to estimate the binding strength of peptides to MHC class I complexes quickly and efficiently. This newly described MHC class I-peptide binding affinity quantitation represents a much needed orthogonal, independent approach to existing computational affinity predictions and has the potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy. ### Competing Interest Statement The authors have declared no competing interest. * AUC : area under the curve β2m : beta-2 microglobulin CID : collision-induced dissociation dsA2 : disulfide-stabilized HLA-A*02:01 dsMHC : disulfide-stabilized MHC class I molecules ESI : electrospray ionization hc : heavy chain iDSF : isothermal analysis of nanoscale differential scanning fluorimetry ISD : in-source dissociation K d,iDSF : dissociation constant determined by iDSF K d,low & K d,high : dissociation constant determined by native MS K d,th : dissociation constant predicted by NetMHC MHC : major histocompatibility complex MS : mass spectrometry nDSF : nanoscale differential scanning fluorimetry PDB : protein Data Bank pMHC : peptide/MHC class I complex SEC : size-exclusion chromatography.