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Large-scale characterization of peptide-MHC binding landscapes with structural simulations

Class I major histocompatibility complex proteins play a critical role in the adaptive immune system by binding to peptides derived from cytosolic proteins and presenting them on the cell surface for surveillance by T cells. The varied peptide binding specificity of these highly polymorphic molecules has important consequences for vaccine design, transplantation, autoimmunity, and cancer development. Here, we describe a molecular modeling study of MHC-peptide interactions that integrates sampling techniques from protein–protein docking, loop modeling, de novo structure prediction, and protein design in order to construct atomically detailed peptide binding landscapes for a diverse set of MHC proteins. Specificity profiles derived from these landscapes recover key features of experimental binding profiles and can be used to predict peptide binding with reasonable accuracy. Family wide comparison of the predicted binding landscapes recapitulates previously reported patterns of specificity divergence and peptide-repertoire diversity while providing a structural basis for observed specificity patterns. The size and sequence diversity of these structure-based binding landscapes enable us to identify subtle patterns of covariation between peptide sequence positions; analysis of the associated structural models suggests physical interactions that may mediate these sequence correlations.