Proteins function as molecular machines, facilitating various cellular activities. In the dynamic cellular environment, proteins interact with binding partners to catalyze reactions, transduce signals, or serve as scaffolds. Over the past two decades, advances in structural biology have expanded the tools available for protein structure determination, enabling visualization of ever more complex states at the molecular level. Cryogenic electron microscopy (Cryo-EM) has emerged as a powerful technique, providing high-resolution structures for proteins that are otherwise challenging to study, such as those with disordered regions and post-translational modifications or that function through oligomerization. During my Ph.D. research in the Cerione and Crane labs, I utilized Cryo-EM and other biophysical methods to investigate proteins involved in cancer and circadian rhythms. My research focused on elucidating the mechanisms by which these proteins function through allosteric conformational changes. In the Cerione lab, I studied glutaminase, a key metabolic enzyme implicated in cancer progression and considered a potential drug target. My findings revealed that glutaminase activity is coupled to filament formation, with two flexible regions: the activation loop and lid loop, forming a substrate lock that optimally positions the substrate for enzymatic activity. In the Crane lab, I investigated circadian clock proteins that regulate universal rhythms in animals, plants, and fungi. I resolved the first structure of a cryptochrome photoreceptor bound to its target, which elucidated regulation of the downstream circadian clock repressor Timeless. Additionally, I deciphered how a post-translationally modified and disordered region of Timeless regulates its nuclear entry. Overall my work reveals how coupled conformational changes in protein complexes propagate to regulate enzymatic activity and signal transduction.