PAS proteins: Study and application of signaling mechanisms

ABSTRACT For cells to detect and respond to changing environmental conditions within and around them, they rely on proteins to sense these changes and initiate appropriate biological responses. Several classes of ligand- regulated protein/protein interaction domains participate in these processes, making it important to have mechanistic insights into their signaling processes to understand both normal function and dysfunction in disease. Additionally, the ability to switch such protein/protein interactions by small molecules has made these domains particularly useful for therapeutic and biotechnology applications. Here we focus on obtaining such mechanistic information for proteins with PAS (Period-ARNT-Singleminded) domains, found in tens of thousands of proteins throughout all three kingdoms of life, where they control the activity of over 20 enzymatic and non-enzymatic effector domains. These processes are regulated by different stimuli in different members of the family, harnessing changes in the occupancy or configuration of bound cofactors to “switch” activity on and off. Some aspects of these triggers are understood in some PAS domains, such as in the subset known as LOV (Light-Oxygen-Voltage) photosensory domains, where blue light illumination drives the specific photochemical formation of protein/flavin adducts which allosterically controls protein conformation around the chromophore. Despite the need to understand these signaling processes for fundamental and applied reasons, several knowledge gaps remain limiting our ability to do so. To address these limitations, we propose a combination of structural, biophysical, and biochemical studies to tackle outstanding issues in the field, probing topics like the structural and dynamic changes associated with activation, the generality of signaling processes among related receptors, and correlations between in vitro and cellular activities. We will do so by a pursuing a strategy based on comparative studies across a group of PAS-containing proteins, including ones newly-identified by computational or experimental methods as likely to have new ligand specificities and regulatory modes. We anticipate that the findings of the proposed research will answer long-standing questions in several areas of protein allostery and biological control, while generating tools to answer pursue new topics in cellular and in vitro biochemistry.