Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which articular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing ‘agretopes'. Here we set out a new means of evaluating the TCR faces of viral peptides in addition to their agretopes, integrating evaluations of both sides of the ternary complex in a single analysis.
He, Lu; De Groot, Anne S.; Gutierrez, Andres H.; Martin, William D.; Moise, Lenny; and Bailey-Kellogg, Chris, "Integrated Assessment of Predicted MHC Binding and Cross-Conservation with Self Reveals Patterns of Viral Camouflage" (2014). Open Dartmouth: Faculty Open Access Articles. 566.