The immune system is precisely tuned to rapidly respond to external pathogens which it must selectively distinguish from self-elements. This balance is finely calibrated on many levels- from the cellular localization of immune receptors and the role of accessory proteins in orchestrating an immune signaling complex to the interplay between immune regulation and other cellular processes such as metabolism and ion flux. When this balance is disrupted, the phenotypic result is often disease, including autoimmune inflammation and susceptibility to infection. A molecular level understanding of the interplay between proteins in the immune system and the molecules they sense and process is fundamental in understanding the immune system. This enables a better diagnosis of disease and provides the basis for the rational design of targeted therapeutics.

This work is a molecular level study of the immune proteins Toll-Like Receptor 9 (TLR9), High Mobility Group Box 1 Protein (HMGB1), and Fatty Acid Metabolism-Immunity Nexus (FAMIN). These proteins sense and manipulate specific nucleotide ligands. Techniques from solution biophysics and structural biology were used to provide insight into the forces that govern these interactions. A thorough theoretical equilibrium binding model for TLR9 sensing of ssDNA oligonucleotides is presented and substantiated with quantitative experimental evidence that constrains the binding parameters. The accessory protein HMGB1 is shown to act indirectly in TLR9 signaling, instead of by enhancing the affinity of the ligand. Finally, a biophysical characterization of FAMIN is presented, and the catalytic mechanism by which FAMIN acts as an enzyme in purine metabolism is elucidated through comparative structural biology.