  T cells orchestrate adaptive immune responses upon activation. T cell
activation requires sufficiently strong binding of T cell receptors on their
surface to short peptides derived from foreign proteins bound to protein
products of the major histocompatibility (MHC) gene products, which are
displayed on the surface of antigen presenting cells. T cells can also interact
with peptide-MHC complexes, where the peptide is derived from host (self)
proteins. A diverse repertoire of relatively self-tolerant T cell receptors is
selected in the thymus. We study a model, computationally and analytically, to
describe how thymic selection shapes the repertoire of T cell receptors, such
that T cell receptor recognition of pathogenic peptides is both specific and
degenerate. We also discuss the escape probability of autoimmune T cells from
the thymus.
