The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3:1 stoichiometry

Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity

Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.

Neuronal and astrocyte NCX isoform/splice variants: How do they participate in Na+ and Ca2+ signalling?

NCX1, NCX2, and NCX3 gene isoforms and their splice variants are characteristically expressed in different regions of the brain. The tissue-specific splice variants of NCX1-3 isoforms show specific expression profiles in neurons and astrocytes, whereas the relevant NCX isoform/splice variants exhibit diverse allosteric modes of Na+- and Ca2+-dependent regulation. In general, overexpression of NCX1-3 genes leads to neuroprotective effects, whereas their ablation gains the opposite results. At this end, the partial contributions of NCX isoform/splice variants to neuroprotective effects remain unresolved. The glutamate-dependent Na+ entry generates Na+ transients (in response to neuronal cell activities), whereas the Na+-driven Ca2+ entry (through the reverse NCX mode) raises Ca2+ transients. This special mode of signal coupling translates Na+ transients into the Ca2+ signals while being a part of synaptic neurotransmission. This mechanism is of general interest since disease-related conditions (ischemia, metabolic stress, and stroke among many others) trigger Na+ and Ca2+ overload with deadly outcomes of downstream apoptosis and excitotoxicity. The recently discovered mechanisms of NCX allosteric regulation indicate that some NCX variants might play a critical role in the dynamic coupling of Na+-driven Ca2+ entry. In contrast, the others are less important or even could be dangerous under altered conditions (e.g., metabolic stress). This working hypothesis can be tested by applying advanced experimental approaches and highly focused computational simulations. This may allow the development of structure-based blockers/activators that can selectively modulate predefined NCX variants to lessen the life-threatening outcomes of excitotoxicity, ischemia, apoptosis, metabolic deprivation, brain injury, and stroke.

Ca2+ efflux facilitated by co-transport of inorganic phosphate anion in the H+/Ca2+ antiporter YfkE

Ca²⁺ is an important signaling messenger. In microorganisms, fungi, and plants, H⁺/Ca²⁺ antiporters (CAX) are known to play key roles in the homeostasis of intracellular Ca²⁺ by catalyzing its efflux across the cell membrane. Here, we reveal that the bacterial CAX homolog YfkE transports Ca²⁺ in two distinct modes: a low-flux H⁺/Ca²⁺ exchange mode and a high-flux mode in which Ca²⁺ and phosphate ions are co-transported (1:1) in exchange for H⁺. Coupling with phosphate greatly accelerates the Ca²⁺ efflux activity of YfkE. Our studies reveal that Ca²⁺ and phosphate bind to adjacent sites in a central translocation pathway and lead to mechanistic insights that explain how this CAX alters its conserved alpha-repeat motifs to adopt phosphate as a specific "transport chaperon" for Ca²⁺ translocation. This finding uncovers a co-transport mechanism within the CAX family that indicates this class of proteins contributes to the cellular homeostasis of both Ca²⁺ and phosphate.

Structure-Based Function and Regulation of NCX Variants: Updates and Challenges

The plasma-membrane homeostasis Na⁺/Ca²⁺ exchangers (NCXs) mediate Ca²⁺ extrusion/entry to dynamically shape Ca²⁺ signaling/in biological systems ranging from bacteria to humans. The NCX gene orthologs, isoforms, and their splice variants are expressed in a tissue-specific manner and exhibit nearly 10⁴-fold differences in the transport rates and regulatory specificities to match the cell-specific requirements. Selective pharmacological targeting of NCX variants could benefit many clinical applications, although this intervention remains challenging, mainly because a full-size structure of eukaryotic NCX is unavailable. The crystal structure of the archaeal NCX_Mj, in conjunction with biophysical, computational, and functional analyses, provided a breakthrough in resolving the ion transport mechanisms. However, NCX_Mj (whose size is nearly three times smaller than that of mammalian NCXs) cannot serve as a structure-dynamic model for imitating high transport rates and regulatory modules possessed by eukaryotic NCXs. The crystal structures of isolated regulatory domains (obtained from eukaryotic NCXs) and their biophysical analyses by SAXS, NMR, FRET, and HDX-MS approaches revealed structure-based variances of regulatory modules. Despite these achievements, it remains unclear how multi-domain interactions can decode and integrate diverse allosteric signals, thereby yielding distinct regulatory outcomes in a given ortholog/isoform/splice variant. This article summarizes the relevant issues from the perspective of future developments.

Exploring the Li+ transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX

The plasma membrane (NCX) and mitochondrial (NCLX) Na⁺/Ca²⁺ exchangers are structurally related proteins, although they operate under strictly different ionic conditions and membrane potentials. In contrast with NCX, NCLX can transport either Li⁺ or Na⁺ in exchange for Ca²⁺. Whereas the crystal structure of the archaeal NCX (NCX_Mj) describes the binding sites for alternative binding of 3Na⁺ or 1Ca²⁺, these features remain elusive for NCLX due to the lack of structural information. To elucidate the ion-binding features of mitochondrial NCLX, we analyzed here the Li⁺-transporting NCLX_Mj mutant, produced by replacing the ion-coordinating residues in the archaeal NCX (NCX_Mj) to match the ion-coordinating residues of human NCLX. The NCLX_Mj-mediated Na⁺/Ca²⁺ or Li⁺/Ca²⁺ exchange rates are insensitive to varying voltage, consistent with an electroneutral ion exchange. Molecular dynamics (MD) simulations revealed that NCLX_Mj contains two novel Li⁺ binding sites with four ion-coordinating residues, derived from the three Na⁺ binding sites of NCX_Mj. The ion-coordination modes, observed in the MD simulations, were further supported by two-dimensional infrared (2D IR) spectroscopy and by testing the mutational effects on the ion fluxes. Collectively, our results revealed a structural basis for Li⁺ binding and electroneutral transport (2Na⁺/Li⁺:1Ca²⁺) by NCLX_Mj, meaning that the NCLX-mediated electroneutral transport may predefine mitochondrial Ca²⁺ and Na⁺ signaling to modulate cellular functions.

Understanding Mechanisms of Secondary Active Transport by Analyzing the Effects of Mutations and Stoichiometry

Biological cells frequently exhibit a so-called secondary active transport by moving various species across their membranes. In this mode of transport, an energetically favorable transmembrane gradient of one type of molecule is used to drive another type of molecule in the energetically unfavorable direction against their gradient. Although it is well established that conformational transitions play a critical role in functioning of transporters, the molecular details of underlying mechanisms remain not well understood. Here, we utilize a recently developed theoretical method to understand better the microscopic picture of secondary active transport. Specifically, we evaluate how mutations in different parts of transporters affect their dynamic properties. In addition, we present a possible explanation on existence of different stoichiometries in the secondary active transport. Our theoretical analysis clarifies several important aspects of complex biological transport phenomena.

Assembly and Functional Role of PACE Transporter PA2880 from Pseudomonas aeruginosa

The recently identified proteobacterial antimicrobial compound efflux (PACE) transporters are multidrug transporters energized by the electrochemical gradient of protons. Here, we present the results of phylogenetic and functional studies on the PACE family transporter PA2880 from Pseudomonas aeruginosa. A phylogenetic analysis of the PACE family revealed that PA2880 and AceI from Acinetobacter baumannii are classified into evolutionarily distinct clades, although they both transport chlorhexidine. We demonstrate that PA2880 mainly exists as a dimer in solution, which is independent of pH, and its dimeric state is essential for its proper function. Electrogenicity studies revealed that the chlorhexidine/H+ antiport process is electrogenic. The function of several highly conserved residues was investigated. These findings provide further insights into the functional features of PACE family transporters, facilitating studies on their transport mechanisms. IMPORTANCE Pseudomonas aeruginosa is a pathogen that causes hospital-acquired (nosocomial) infections, such as ventilator-associated pneumonia and sepsis syndromes. Chlorhexidine diacetate is a disinfectant used for bacterial control in various environments potentially harboring P. aeruginosa. Therefore, investigation of the mechanism of the efflux of chlorhexidine mediated by PA2880, a PACE family transporter from P. aeruginosa, is of significance to combat bacterial infections. This study improves our understanding of the transport mechanism of PACE family transporters and will facilitate the effective utilization of chlorhexidine for P. aeruginosa control.

Characteristic attributes limiting the transport rates in NCX orthologs

The Na^+/Ca²⁺ exchangers (NCXs) modulate the Ca2+ signaling and homeostasis in health and disease. The transport cycle turnover rates (kcat) and the kcat/Km values of eukaryotic NCXs are ~10⁴-times higher than those of prokaryotic NCXs. Three ion-coordinating residues (out of twelve) differ between eukaryotic NCXs and NCX_Mj. The replacement of three ion-coordinating residues in NCX_Mj does not increase kcat, probably due to the structural rigidity of NCX_Mj. Phospholipids and cholesterol increase (up to 10-fold) the transport rates in the cardiac NCX1.1, but not in NCX_Mj. A lipid environment can partially contribute to the huge kinetic variances among NCXs.

The Cardiac Na+ -Ca2+ Exchanger: From Structure to Function

Ca²⁺ homeostasis is essential for cell function and survival. As such, the cytosolic Ca²⁺ concentration is tightly controlled by a wide number of specialized Ca²⁺ handling proteins. One among them is the Na⁺ -Ca²⁺ exchanger (NCX), a ubiquitous plasma membrane transporter that exploits the electrochemical gradient of Na⁺ to drive Ca²⁺ out of the cell, against its concentration gradient. In this critical role, this secondary transporter guides vital physiological processes such as Ca²⁺ homeostasis, muscle contraction, bone formation, and memory to name a few. Herein, we review the progress made in recent years about the structure of the mammalian NCX and how it relates to function. Particular emphasis will be given to the mammalian cardiac isoform, NCX1.1, due to the extensive studies conducted on this protein. Given the degree of conservation among the eukaryotic exchangers, the information highlighted herein will provide a foundation for our understanding of this transporter family. We will discuss gene structure, alternative splicing, topology, regulatory mechanisms, and NCX's functional role on cardiac physiology. Throughout this article, we will attempt to highlight important milestones in the field and controversial topics where future studies are required. © 2021 American Physiological Society. Compr Physiol 12:1-37, 2021.

Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes

The cytosolic pH decline from 7.2 to 6.9 results in 90% inactivation of mammalian Na⁺/Ca²⁺ exchangers (NCXs) due to protons interactions with regulatory and transport domains ("proton block"). Remarkably, the pH titration curves of mammalian and prokaryotic NCXs significantly differ, even after excluding the allosteric effects through regulatory domains. This is fascinating since "only" three (out of twelve) ion-coordinating residues (T50S, E213D, and D240N) differ between the archaeal NCX_Mj and mammalian NCXs although they contain either three or two carboxylates, respectively. To resolve the underlying mechanisms of pH-dependent regulation, the ion-coordinating residues of NCX_Mj were mutated to imitate the ion ligation arrays of mammalian NCXs; the mutational effects were tested on the ion binding/transport by using ion-flux assays and two-dimensional infrared (2D IR) spectroscopy. Our analyses revealed that two deprotonated carboxylates ligate 3Na⁺ or 1Ca²⁺ in NCX prototypes with three or two carboxylates. The Na⁺/Ca²⁺ exchange rates of NCX_Mj reach saturation at pH 5.0, whereas the Na⁺/Ca²⁺ exchange rates of the cardiac NCX1.1 gradually increase even at alkaline pHs. The T50S replacement in NCX_Mj "recapitulates" the pH titration curves of mammalian NCX by instigating an alkaline shift. Proteolytic shaving of regulatory CBD domains activates NCX1.1, although the normalized pH-titration curves are comparable in trypsin treated and untreated NCX1.1. Thus, the T50S-dependent alkaline shift sets a dynamic range for "proton block" function at physiological pH, whereas the CBDs (and other regulatory modes) modulate incremental changes in the transport rates rather than affect the shape of pH dependent curves.

The Archaeal Na+/Ca2+ Exchanger (NCX_Mj) as a Model of Ion Transport for the Superfamily of Ca2+/CA Antiporters

The superfamily of Calcium/Cation (Ca²⁺/CA) antiporters extrude Ca²⁺ from the cytosol or subcellular compartments in exchange with Na⁺, K⁺, H⁺, Li⁺, or Mg²⁺ and thereby provide a key mechanism for Ca²⁺ signaling and ion homeostasis in biological systems ranging from bacteria to humans. The structure-dynamic determinants of ion selectivity and transport rates remain unclear, although this is of primary physiological significance. Despite wide variances in the ion selectivity and transport rates, the Ca²⁺/CA proteins share structural motifs, although it remains unclear how the ion recognition/binding is coupled to the ion translocation events. Here, the archaeal Na⁺/Ca²⁺ exchanger (NCX_Mj) is considered as a structure-based model that can help to resolve the ion transport mechanisms by using X-ray, HDX-MS, ATR-FTIR, and computational approaches in conjunction with functional analyses of mutants. Accumulating data reveal that the local backbone dynamics at ion-coordinating residues is characteristically constrained in apo NCX_Mj, which may predefine the affinity and stability of ion-bound species in the ground and transition states. The 3Na⁺ or 1Ca²⁺ binding to respective sites of NCX_Mj rigidify the backbone dynamics at specific segments, where the ion-dependent compression of the ion-permeating four-helix bundle (TM2, TM3, TM7, and TM8) induces the sliding of the two-helix cluster (TM1/TM6) on the protein surface to switch the OF (outward-facing) and IF (inward-facing) conformations. Taking into account the common structural elements shared by Ca²⁺/CAs, NCX_Mj may serve as a model for studying the structure-dynamic and functional determinants of ion-coupled alternating access, transport catalysis, and ion selectivity in Ca²⁺/CA proteins.

Elucidating the Mechanism Behind Sodium-Coupled Neurotransmitter Transporters by Reconstitution

Sodium-coupled neurotransmitter transporters play a fundamental role in the termination of synaptic neurotransmission, which makes them a major drug target. The reconstitution of these secondary active transporters into liposomes has shed light on their molecular transport mechanisms. From the earliest days of the reconstitution technique up to today's single-molecule studies, insights from live functioning transporters have been indispensable for our understanding of their physiological impact. The two classes of sodium-coupled neurotransmitter transporters, the neurotransmitter: sodium symporters and the excitatory amino acid transporters, have vastly different molecular structures, but complementary proteoliposome studies have sought to unravel their ion-dependence and transport kinetics. Furthermore, reconstitution experiments have been used on both protein classes to investigate the role of e.g. the lipid environment, of posttranslational modifications, and of specific amino acid residues in transport. Techniques that allow the detection of transport at a single-vesicle resolution have been developed, and single-molecule studies have started to reveal single transporter kinetics, which will expand our understanding of how transport across the membrane is facilitated at protein level. Here, we review a selection of the results and applications where the reconstitution of the two classes of neurotransmitter transporters has been instrumental.

On the Role of a Conserved Methionine in the Na+-Coupling Mechanism of a Neurotransmitter Transporter Homolog

Excitatory amino acid transporters (EAAT) play a key role in glutamatergic synaptic communication. Driven by transmembrane cation gradients, these transporters catalyze the reuptake of glutamate from the synaptic cleft once this neurotransmitter has been utilized for signaling. Two decades ago, pioneering studies in the Kanner lab identified a conserved methionine within the transmembrane domain as key for substrate turnover rate and specificity; later structural work, particularly for the prokaryotic homologs Glt_Ph and Glt_Tk, revealed that this methionine is involved in the coordination of one of the three Na⁺ ions that are co-transported with the substrate. Albeit extremely atypical, the existence of this interaction is consistent with biophysical analyses of Glt_Ph showing that mutations of this methionine diminish the binding cooperativity between substrates and Na⁺. It has been unclear, however, whether this intriguing methionine influences the thermodynamics of the transport reaction, i.e., its substrate:ion stoichiometry, or whether it simply fosters a specific kinetics in the binding reaction, which, while influential for the turnover rate, do not fundamentally explain the ion-coupling mechanism of this class of transporters. Here, studies of Glt_Tk using experimental and computational methods independently arrive at the conclusion that the latter hypothesis is the most plausible, and lay the groundwork for future efforts to uncover the underlying mechanism.

Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na+ in ion-coupled drug efflux

In both prokaryotes and eukaryotes, multidrug and toxic-compound extrusion (MATE) transporters catalyze the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are secondary-active antiporters, i.e., their drug-efflux activity is coupled to, and powered by, the uptake of ions down a preexisting transmembrane electrochemical gradient. Key aspects of this mechanism, however, remain to be delineated, such as its ion specificity and stoichiometry. We previously revealed the existence of a Na⁺-binding site in a MATE transporter from Pyroccocus furiosus (PfMATE) and hypothesized that this site might be broadly conserved among prokaryotic MATEs. Here, we evaluate this hypothesis by analyzing VcmN and ClbM, which along with PfMATE are the only three prokaryotic MATEs whose molecular structures have been determined at atomic resolution, i.e. better than 3 Å. Reinterpretation of existing crystallographic data and molecular dynamics simulations indeed reveal an occupied Na⁺-binding site in the N-terminal lobe of both structures, analogous to that identified in PfMATE. We likewise find this site to be strongly selective against K⁺, suggesting it is mechanistically significant. Consistent with these computational results, DEER spectroscopy measurements for multiple doubly-spin-labeled VcmN constructs demonstrate Na⁺-dependent changes in protein conformation. The existence of this binding site in three MATE orthologs implicates Na⁺ in the ion-coupled drug-efflux mechanisms of this class of transporters. These results also imply that observations of H⁺-dependent activity likely stem either from a site elsewhere in the structure, or from H⁺ displacing Na⁺ under certain laboratory conditions, as has been noted for other Na⁺-driven transport systems.

Hydration Mimicry by Membrane Ion Channels

Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.

Structure-affinity insights into the Na+ and Ca2+ interactions with multiple sites of a sodium-calcium exchanger

Selective recognition and transport of Na⁺ and Ca²⁺ ions by sodium-calcium exchanger (NCX) proteins is a primary prerequisite for Ca²⁺ 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⁺ :1Ca²⁺ ). 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 Ca²⁺ 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.

A K+/Na+ co-binding state: Simultaneous versus competitive binding of K+ and Na+ to glutamate transporters

Plasma membrane-associated glutamate transporters play a key role in signaling by the major excitatory neurotransmitter glutamate. Uphill glutamate uptake into cells is energetically driven by coupling to co-transport of three Na⁺ ions. In exchange, one K⁺ ion is counter-transported. Currently accepted transport mechanisms assume that Na⁺ and K⁺ effects are exclusive, resulting from competition of these cations at the binding level. Here, we used electrophysiological analysis to test the effects of K⁺ and Na⁺ on neuronal glutamate transporter excitatory amino acid carrier 1 (EAAC1; the rat homologue of human excitatory amino acid transporter 3 (EAAT3)). Unexpectedly, extracellular K⁺ application to EAAC1 induced anion current, but only in the presence of Na⁺ This result could be explained with a K⁺/Na⁺ co-binding state in which the two cations simultaneously bind to the transporter. We obtained further evidence for this co-binding state, and its anion conductance, by analyzing transient currents when Na⁺ was exchanged for K⁺ and effects of the [K⁺]/[Na⁺] ratio on glutamate affinity. Interestingly, we observed the K⁺/Na⁺ co-binding state not only in EAAC1 but also in the subtypes EAAT1 and -2, which, unlike EAAC1, conducted anions in response to K⁺ only. We incorporated these experimental findings in a revised transport mechanism, including the K⁺/Na⁺ co-binding state and the ability of K⁺ to activate anion current. Overall, these results suggest that differentiation between Na⁺ and K⁺ does not occur at the binding level but is conferred by coupling of cation binding to conformational changes. These findings have implications also for other exchangers.

Binding and transport of D-aspartate by the glutamate transporter homolog GltTk

Mammalian glutamate transporters are crucial players in neuronal communication as they perform neurotransmitter reuptake from the synaptic cleft. Besides L-glutamate and L-aspartate, they also recognize D-aspartate, which might participate in mammalian neurotransmission and/or neuromodulation. Much of the mechanistic insight in glutamate transport comes from studies of the archeal homologs Glt_Ph from Pyrococcus horikoshii and Glt_Tk from Thermococcus kodakarensis. Here, we show that Glt_Tk transports D-aspartate with identical Na⁺: substrate coupling stoichiometry as L-aspartate, and that the affinities (K_d and K_m) for the two substrates are similar. We determined a crystal structure of Glt_Tk with bound D-aspartate at 2.8 Å resolution. Comparison of the L- and D-aspartate bound Glt_Tk structures revealed that D-aspartate is accommodated with only minor rearrangements in the structure of the binding site. The structure explains how the geometrically different molecules L- and D-aspartate are recognized and transported by the protein in the same way.

Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger

Prokaryotic and eukaryotic Na+/Ca2+ exchangers (NCX) control Ca2+ homeostasis. NCX orthologs exhibit up to 104-fold differences in their turnover rates (kcat), whereas the ratios between the cytosolic (cyt) and extracellular (ext) Km values (Kint = KmCyt/KmExt) are highly asymmetric and alike (Kint ≤ 0.1) among NCXs. The structural determinants controlling a huge divergence in kcat at comparable Kint remain unclear, although 11 (out of 12) ion-coordinating residues are highly conserved among NCXs. The crystal structure of the archaeal NCX (NCX_Mj) was explored for testing the mutational effects of pore-allied and loop residues on kcat and Kint. Among 55 tested residues, 26 mutations affect either kcat or Kint, where two major groups can be distinguished. The first group of mutations (14 residues) affect kcat rather than Kint. The majority of these residues (10 out of 14) are located within the extracellular vestibule near the pore center. The second group of mutations (12 residues) affect Kint rather than kcat, whereas the majority of residues (9 out 12) are randomly dispersed within the extracellular vestibule. In conjunction with computational modeling-simulations and hydrogen-deuterium exchange mass-spectrometry (HDX-MS), the present mutational analysis highlights structural elements that differentially govern the intrinsic asymmetry and transport rates. The key residues, located at specific segments, can affect the characteristic features of local backbone dynamics and thus, the conformational flexibility of ion-transporting helices contributing to critical conformational transitions. The underlying mechanisms might have a physiological relevance for matching the response modes of NCX variants to cell-specific Ca2+ and Na+ signaling.

Carriers, exchangers, and cotransporters in the first 100 years of the Journal of General Physiology

Jennings reviews the many contributions of JGP articles to our current understanding of solute transporter mechanisms.

Transporters, pumps, and channels are proteins that catalyze the movement of solutes across membranes. The single-solute carriers, coupled exchangers, and coupled cotransporters that are collectively known as transporters are distinct from conductive ion channels, water channels, and ATP-hydrolyzing pumps. The main conceptual framework for studying transporter mechanisms is the alternating access model, which comprises substrate binding and release events on each side of the permeability barrier and translocation events involving conformational changes between inward-facing and outward-facing conformational states. In 1948, the Journal of General Physiology began to publish work that focused on the erythrocyte glucose transporter—the first transporter to be characterized kinetically—followed by articles on the rates, stoichiometries, asymmetries, voltage dependences, and regulation of coupled exchangers and cotransporters beginning in the 1960s. After the dawn of cDNA cloning and sequencing in the 1980s, heterologous expression systems and site-directed mutagenesis allowed identification of the functional roles of specific amino acid residues. In the past two decades, structures of transport proteins have made it possible to propose specific models for transporter function at the molecular level. Here, we review the contribution of JGP articles to our current understanding of solute transporter mechanisms. Whether the topic has been kinetics, energetics, regulation, mutagenesis, or structure-based modeling, a common feature of these articles has been a quantitative, mechanistic approach, leading to lasting insights into the functions of transporters.