ABSTRACT Anion channels, active transporters, and lipid scramblases are central players in human physiology. These integral membrane proteins play key roles in physiology where they control a panoply of processes, ranging from epithelial salt reabsorption and neuromuscular excitability to blood coagulation, membrane fusion and repair. My long-term objective is to understand the molecular mechanisms of gating and regulation of two families of membrane transport proteins, the voltage-gated CLCs and the Ca2+-activated TMEM16s. An unexpectedly shared property of CLCs and TMEM16s is that they display remarkable functional diversity within conserved structural frameworks. Whereas both families were originally identified as chloride channels, subsequent work revealed that many CLCs are H+-coupled active transporters and most TMEM16s are dual-function phospholipid scramblases and non-selective ion channels. Missense mutations that cause dysfunction in members of both families cause inheritable disorders of bone, kidney, brain, and muscle. Thus, CLCs and TMEM16s are priority targets for the development of pharmacological tools to treat these disorders. However, a lack of understanding of how CLCs and TMEM16s function at the atomic level significantly hinders the development of such tools. For example, the rational design of compounds to treat these disorders is hampered by the lack of structural information on the specific conformations stabilized by the gain or loss of function mutations. The overarching goal of our proposal is to understand at the atomic level how CLCs and TMEM16s are regulated by physiological stimuli and to elucidate how disease-causing mutations alter their structure-function relationships. To this end, we will focus on the CLC-1 channel which is mutated in myotonia congenita, a rare muscle disorder, and on the TMEM16E scramblase, which is mutated in limb girdle muscular dystrophy and in gnathodiaphyseal dysplasia, a rare bone disorder. The limited unde