Na⁺/H⁺ exchangers play a vital role in maintaining intracellular pH balance, sodium (Na⁺) reabsorption, and cellular volume homeostasis. In this thesis, I explore four distinct exchangers to unravel common mechanistic themes and unique regulatory adaptations found in bacterial and eukaryotic systems. In the first paper, we investigate the bacterial exchanger. KefC, demonstrating its remarkable K+ selectivity attributed to conserved binding residues. We further reveal that its activity is modulated by C-terminal RCK domains, which detach upon binding of glutathione adduct under electrophilic stress, thereby facilitating cytosolic acidification. Papers II and III uncover that specific lipid interactions are crucial for the stability and function of the eukaryotic endosomal exchangers NHE9 and NHE6. These interactions stabilize the proteins in their homodimeric form, which is essential for effective endosomal pH regulation. Any mislocalization of NHE9 and NHE6 can disrupt dimerization, resulting in a loss of activity and impaired cellular homeostasis. Additionally, our structural studies of NHA2 in complex with a Fab fragment and the inhibitor phloretin provide insights into the molecular mechanisms behind its therapeutic potential. These findings clarify NHA2’s crucial role in insulin secretion, electrolyte balance, and blood pressure regulation, thus paving the way for targeted drug development. Overall, the goals of my thesis emphasize the central role of lipid interactions and structural adaptations in regulating ion exchanger function.

The strict exchange of Na⁺ for H⁺ ions across cell membranes is a reaction carried out in almost every cell. Na⁺/H⁺ exchangers that perform this task are physiological homodimers, and whilst the ion transporting domain is highly conserved, their dimerization differs. The Na⁺/H⁺ exchanger NhaA from Escherichia coli has a weak dimerization interface mediated by a β-hairpin domain and with dimer retention dependent on cardiolipin. Similarly, organellar Na⁺/H⁺ exchangers NHE6, NHE7 and NHE9 also contain β-hairpin domains and recent analysis of Equus caballus NHE9 indicated PIP₂ lipids could bind at the dimer interface. However, structural validation of the predicted lipid-mediated oligomerization has been lacking. Here, we report cryo-EM structures of E. coli NhaA and E. caballus NHE9 in complex with cardiolipin and phosphatidylinositol-3,5-bisphosphate PI(3,5)P₂ lipids binding at their respective dimer interfaces. We further show how the endosomal specific PI(3,5)P₂ lipid stabilizes the NHE9 homodimer and enhances transport activity. Indeed, we show that NHE9 is active in endosomes, but not at the plasma membrane where the PI(3,5)P₂ lipid is absent. Thus, specific lipids can regulate Na⁺/H⁺ exchange activity by stabilizing dimerization in response to either cell specific cues or upon trafficking to their correct membrane location.

The sodium/proton exchanger NHA2, also known as SLC9B2, is important for insulin secretion, renal blood pressure regulation, and electrolyte retention. Recent structures of bison NHA2 has revealed its unique 14-transmembrane helix architecture, which is different from SLC9A/NHE members made up from 13-TM helices. Sodium/proton exchangers are functional homodimers, and the additional N-terminal helix in NHA2 was found to alter homodimer assembly. Here, we present the cryo-electron microscopy structures of apo human NHA2 in complex with a Fab fragment and also with the inhibitor phloretin bound at 2.8 and 2.9 Å resolution, respectively. We show how phosphatidic acid (PA) lipids bind to the homodimer interface of NHA2 on the extracellular side, which we propose has a regulatory role linked to cell volume regulation. The ion binding site of human NHA2 has a salt bridge interaction between the ion binding aspartate D278 and R432, an interaction previously broken in the bison NHA2 structure, and these differences suggest a possible ion coupling mechanism. Lastly, the human NHA2 structure in complex with phloretin offers a template for structure-guided drug design, potentially leading to the development of more selective and potent NHA2 inhibitors.

Intracellular potassium (K⁺) homeostasis is fundamental to cell viability. In addition to channels, K⁺ levels are maintained by various ion transporters. One major family is the proton-driven K⁺ efflux transporters, which in gram-negative bacteria is important for detoxification and in plants is critical for efficient photosynthesis and growth. Despite their importance, the structure and molecular basis for K⁺-selectivity is poorly understood. Here, we report ~3.1 Å resolution cryo-EM structures of the Escherichia coli glutathione (GSH)-gated K⁺ efflux transporter KefC in complex with AMP, AMP/GSH and an ion-binding variant. KefC forms a homodimer similar to the inward-facing conformation of Na⁺/H⁺ antiporter NapA. By structural assignment of a coordinated K⁺ ion, MD simulations, and SSM-based electrophysiology, we demonstrate how ion-binding in KefC is adapted for binding a dehydrated K⁺ ion. KefC harbors C-terminal regulator of K⁺ conductance (RCK) domains, as present in some bacterial K⁺-ion channels. The domain-swapped helices in the RCK domains bind AMP and GSH and they inhibit transport by directly interacting with the ion-transporter module. Taken together, we propose that KefC is activated by detachment of the RCK domains and that ion selectivity exploits the biophysical properties likewise adapted by K⁺-ion-channels.