Investigation of the Differential Dynamics of T Cell Receptors and Their Ligands: The Role of Dynamics in Immunological Recognition

One of the primary functions of the cell mediated immune response is the recognition and elimination of infected or damaged cells. This process is facilitated through the interactions between the T lymphocyte cell surface receptor, or T-cell receptor, and a major histocompatibility complex, or MHC, presenting a peptide on the surface of antigen presenting cells. If the affinity between these two molecules is strong enough, the T-cell will become activated and mount an immune response against the antigen presenting cell. Amazingly, while a single TCR can recognize over a million peptide-MHC ligands, it is still able to discriminate between peptides sourced from normal and aberrant expression. Through the study of crystal structures, this specificity and cross reactivity has been attributed to a structural and chemical homology between the TCR and the peptide-MHC. While the structural and chemical compatibility between the TCR and peptideMHC is essential for conducive interactions, these two things alone neglect to account for the inherent dynamics of these molecules. Conformational diversity, and by association protein dynamics, has been observed for all three components of this interaction; the TCR, peptide and MHC. The magnitude of protein motion, however, is not conserved for any one of these molecules. As such, it stands to reason that differential dynamics for any of these molecules can have a direct impact on the recognition of a peptide-MHC by a TCR. To that end, in this dissertation I address the differential dynamics of these molecules. Through the use of molecular dynamics simulations, I decomposed differences in protein motion for all components in the TCR/peptide-MHC complex. Through critical analysis of these simulations, I was able to identify key differences in dynamics for each of the three proteins involved. I was able to correlate these differential dynamics to differences in mechanisms of cross reactivity, specificity and immunogenicity. While much is left to be done, the data presented herein demonstrate the clear role that differential dynamics play in immunological recognition.