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Selective recognition and transport of Na + and Ca 2+ ions by sodium-calcium exchanger (NCX) proteins is a primary prerequisite for Ca 2+ signaling and homeostasis. Twelve ion-coordinating residues are highly conserved among NCXs, and distinct NCX orthologs contain two or three carboxylates, while sharing a common ion-exchange stoichiometry (3Na + :1Ca 2+ ). How these structural differences affect the ion-binding affinity, selectivity, and transport rates remains unclear. Here, the mutational effects of three carboxylates (E54, E213, and D240) were analyzed on the ion-exchange rates in the archaeal NCX from Methanococcus jannaschii and ion-induced structure-affinity changes were monitored by attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR). The D240N mutation elevated the ion-transport rates by twofold to threefold, meaning that the deprotonation of D240 is not essential for transport catalysis. In contrast, mutating E54 or E213 to A, D, N, or Q dramatically decreased the ion-transport rates. ATR-FTIR revealed high- and low-affinity binding of Na + or Ca 2+ with E54 and E213, but not with D240. These findings reveal distinct structure-affinity states at specific ion-binding sites in the inward-facing (IF) and outward-facing orientation. Collectively, two multidentate carboxylate counterparts (E54 and E213) play a critical role in determining the ion coordination/transport in prokaryotic and eukaryotic NCXs, whereas the ortholog substitutions in prokaryotes (aspartate) and eukaryotes (asparagine) at the 240 position affect the ion-transport rates differently (k cat ), probably due to the structural differences in the transition state., (© 2020 Federation of European Biochemical Societies.)

Na + /Ca 2+ exchanger (NCX) proteins operate through the alternating access mechanism, where the ion-binding pocket is exposed in succession either to the extracellular or the intracellular face of the membrane. The archaeal NCX_Mj ( Methanococcus jannaschii NCX) system was used to resolve the backbone dynamics in the inward-facing (IF) and outward-facing (OF) states by analyzing purified preparations of apo- and ion-bound forms of NCX_Mj-WT and its mutant, NCX_Mj-5L6-8. First, the exposure of extracellular and cytosolic vestibules to the bulk phase was evaluated as the reactivity of single cysteine mutants to a fluorescent probe, verifying that NCX_Mj-WT and NCX_Mj-5L6-8 preferentially adopt the OF and IF states, respectively. Next, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) was employed to analyze the backbone dynamics profiles in proteins, preferentially adopting the OF (WT) and IF (5L6-8) states either in the presence or absence of ions. Characteristic differences in the backbone dynamics were identified between apo NCX_Mj-WT and NCX_Mj-5L6-8, thereby underscoring specific conformational patterns owned by the OF and IF states. Saturating concentrations of Na + or Ca 2+ specifically modify HDX patterns, revealing that the ion-bound/occluded states are much more stable (rigid) in the OF than in the IF state. Conformational differences observed in the ion-occluded OF and IF states can account for diversifying the ion-release dynamics and apparent affinity ( K m ) at opposite sides of the membrane, where specific structure-dynamic elements can effectively match the rates of bidirectional ion movements at physiological ion concentrations., (© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.)

In analogy with many other proteins, Na(+)/Ca(2+) exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na(+)/Ca(2+) exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na(+)or Ca(2+) binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct "noncatalytic" residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins.

Magnesium ion channels and transporters regulate the cellular concentrations of Mg(2+), which must be tightly controlled as imbalances have been associated with diseases such as osteoporosis, diabetes, and high blood pressure in humans. The channels and transporters allow the "native" Mg(2+) to be transported against a high background concentration of its major competitor, Ca(2+). Their selectivity filters (the narrowest part of the open pore) control metal ion selectivity. As the structures of Mg(2+) channels in an open conformation with bound Mg(2+) have not yet been solved, the key determinants of Mg(2+)/Ca(2+) selectivity in Mg(2+) ion channels remain elusive. Here, using density functional theory combined with continuum dielectric methods, we evaluated how the competition between Mg(2+) and Ca(2+) in model selectivity filters depends on the degree of metal hydration, which correlates with the pore size/rigidity as well as the composition and solvent accessibility of the selectivity filter. The key determinant of the selectivity for Mg(2+) over Ca(2+) in the Mg(2+) channel selectivity filter is a pore that is sufficiently large to accommodate hexahydrated Mg ions. In such wide pores, the hexahydrated metal ions interact indirectly with the protein ligands, hence metal desolvation and ligand-ligand steric repulsion become less important than Mg(2+)-water-protein interactions. These wide pores are Mg(2+)-selective because compared to Ca(2+) or Na(+) and K(+) monocations, Mg(2+) better polarizes the bound water molecules resulting in stronger Mg(2+)-water-protein interactions. Although both tetrameric and pentameric filters with pores that can accommodate hexahydrated metal ions could select Mg(2+) over Ca(2+), a bilayered pentameric filter lined with a ring of amides and a ring of carboxylates seems to best discriminate the "native" Mg(2+) from its key rival, Ca(2+). Our results are consistent with available experimental data and help to elucidate the selectivity filters in the Mg(2+)-selective TRPM6 and CorA channels.