Thesis advisor: Evan R. Kantrowitz / The regulatory mechanism of allostery is exhibited by certain proteins such as Escherichia coli aspartate transcarbamoylase (ATCase), and is defined as the change in shape and activity (of enzymes) resulting from the binding of particular molecules at locations distant from the active site. This particular enzyme and the property of allostery in general have been investigated for several decades, yet the molecular mechanisms underlying allosteric regulation remain unclear. Therefore in this thesis we have attempted via several biophysical methods, along with the tools of molecular biology and biochemistry, to correlate the changes in allosteric structure with presence of the allosteric effectors and enzymatic activity. We created a double mutant version of ATCase, in which the only native cysteine residue in the catalytic chain was mutated to alanine and another alanine on a loop was mutated to cysteine, in order to lock the enzyme into the R allosteric state by disulfide bonds. This disulfide locked R state exhibited no regulation by the allosteric effectors ATP and CTP and lost all cooperativity for aspartate, and then regained those regulatory properties after the disulfide links were severed by addition of a reducing agent. This double mutant was then chemically modified by covalent attachment of a fluorescent probe. The T and R allosteric states of this fluorophore-labeled enzyme had dramatically different fluorescence emission spectra, providing a highly sensitive tool for testing the effects of the allosteric effectors on the allosteric state. The changes in the fluorescence spectra, and hence quaternary structure, matched the changes in activity after addition of ATP or CTP. This fluorophore labeled enzyme was also encapsulated within a solgel, changing the time scale of the allosteric transition from milliseconds to several hours. The fluorophore labels allowed monitoring the allosteric state within the sol-gel, and the physically trapped T and R states both showed no regulation by the allosteric effectors ATP and CTP, and no cooperativity for aspartate. The trapped T state had low-affinity for aspartate and low activity, and the trapped R state had high-affinity for aspartate and high activity. Timeresolved small-angle x-ray scattering (TR-SAXS) was used to determine the kinetics of the allosteric transition, and to monitor the structure of the enzyme in real time after the addition of substrates and allosteric effectors. These TR-SAXS studies demonstrated a correlation between the presence of the allosteric effectors, the quaternary allosteric state, and activity, suggesting like the previous studies in this thesis that the behavior of ATCase is well explained by the twostate model. However, the effector ATP appeared to destabilize the T state and CTP to destabilize the R state, suggesting a different allosteric molecular mechanism than that of the two-state model. This thesis demonstrates the validity of many of the concepts of the two-state model, while suggesting minor modifications to that elegantly simple model in order to conform with the complex structure and function of ATCase. / Thesis (PhD) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.