The CLC (“Chloride Channel”) family encompasses two major ion-transport mechanisms: half of CLC homologs are electrodiffusive ion channels, and half are secondary active transporters that stoichiometrically exchange Cl– for H+. The occurrence of two mechanisms in one family suggests they operate by variations on a common theme. Indeed, experimental results support the hypothesis that CLC channels are “broken” transporters, in which tight coordination between inner and outer gates is lost. Thus, subtle differences in protein conformational dynamics and ion binding—and the interactions between them—can produce two different types of ion transport behavior in proteins with the same secondary structure. Understanding the molecular basis of these differences will inform our understanding of both CLC channels and transporters. As secondary active transporters, CLC transporters harness energy stored in one ion’s electrochemical gradient (Cl– or H+) to pump the other ion against its gradient. This occurs through tight coupling of protein conformational changes to ion binding and transport events. To develop a fully integrated structural description of ion coupling in the CLC transport mechanism, this project will combine complementary cutting-edge approaches, including cryo-electron microscopy to determine high-resolution structures, double electron-electron resonance spectroscopy to monitor the conformational state of the transporter under different conditions and with different mutations, MD simulations to determine hydration pathways under various conditions, and quantitative functional assays to connect structural dynamics to function.