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

Calcium ion-triggered liquid-liquid phase separation of silk fibroin and spinning through acidification and shear stress

Many studies try to comprehend and replicate the natural silk spinning process due to its energy-efficient and eco-friendly process. In contrast to spider silk, the mechanisms of how silkworm silk fibroin (SF) undergoes liquid-liquid phase separation (LLPS) concerning the various environmental factors in the silk glands or how the SF coacervates transform into fibers remain unexplored. Here, we show that calcium ions, among the most abundant metal ions inside the silk glands, induce LLPS of SF under macromolecular crowded conditions by increasing both hydrophobic and electrostatic interactions between SF. Furthermore, SF coacervates assemble and further develop into fibrils under acidification and shear force. Finally, we prepare SF fiber using a pultrusion-based dry spinning, mirroring the natural silk spinning system. Unlike previous artificial spinning methods requiring concentrated solutions or harsh solvents, our process uses a less concentrated aqueous SF solution and minimal shear force, offering a biomimetic approach to fiber production.

19F-NMR Probing of Ion-Induced Conformational Changes in Detergent-Solubilized and Nanodisc-Reconstituted NCX_Mj

Consecutive interactions of 3Na+ or 1Ca2+ with the Na+/Ca2+ exchanger (NCX) result in an alternative exposure (access) of the cytosolic and extracellular vestibules to opposite sides of the membrane, where ion-induced transitions between the outward-facing (OF) and inward-facing (IF) conformational states drive a transport cycle. Here, we investigate sub-state populations of apo and ion-bound species in the OF and IF states by analyzing detergent-solubilized and nanodisc-reconstituted preparations of NCX_Mj with 19F-NMR. The 19F probe was covalently attached to the cysteine residues at entry locations of the cytosolic and extracellular vestibules. Multiple sub-states of apo and ion-bound species were observed in nanodisc-reconstituted (but not in detergent-solubilized) NCX_Mj, meaning that the lipid-membrane environment preconditions multiple sub-state populations toward the OF/IF swapping. Most importantly, ion-induced sub-state redistributions occur within each major (OF or IF) state, where sub-state interconversions may precondition the OF/IF swapping. In contrast with large changes in population redistributions, the sum of sub-state populations within each inherent state (OF or IF) remains nearly unchanged upon ion addition. The present findings allow the further elucidation of structure-dynamic modules underlying ion-induced conformational changes that determine a functional asymmetry of ion access/translocation at opposite sides of the membrane and ion transport rates concurring physiological demands.

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.

Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1

Na+/Ca2+ exchangers (NCX) transport Ca2+ in or out of cells in exchange for Na+. They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca2+ homeostasis. Although extensively studied, little is known about the global structural arrangement of eukaryotic NCXs and the structural mechanisms underlying their regulation by various cellular cues including cytosolic Na+ and Ca2+. Here we present the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange function and its modulation by cytosolic Ca2+ and Na+. We demonstrate that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca2+], a TM-associated four-stranded β-hub mediates a tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange function. Ca2+ binding to the cytosolic second Ca2+-binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the current NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins.

Specific zinc binding to heliorhodopsin

Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to animal and microbial rhodopsins. The slow photocycle of HeRs suggests a light-sensor function, although the actual function remains unknown. Although HeRs exhibit no specific binding of monovalent cations or anions, recent ATR-FTIR spectroscopy studies have demonstrated the binding of Zn²⁺ to HeR from Thermoplasmatales archaeon (TaHeR) and 48C12. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn²⁺-binding, suggesting a possible modification of the HeR function by Zn²⁺. The present study shows that Zn²⁺-binding lowers the thermal stability of TaHeR, and slows back proton transfer to the retinal Schiff base (M decay) during its photocycle. Zn²⁺-binding was similarly observed for a TaHeR opsin that lacks the retinal chromophore. We then studied the Zn²⁺-binding site by means of the ATR-FTIR spectroscopy of site-directed mutants. Among five and four mutants of His and Asp/Glu, respectively, only E150Q exhibited a completely different spectral feature of the α-helix (amide-I) in ATR-FTIR spectroscopy, suggesting that E150 is responsible for Zn²⁺-binding. Molecular dynamics (MD) simulations built a coordination structure of Zn²⁺-bound TaHeR, where E150 and protein bound water molecules participate in direct coordination. It was concluded that the specific binding site of Zn²⁺ is located at the cytoplasmic side of TaHeR, and that Zn²⁺-binding affects the structure and structural dynamics, possibly modifying the unknown function of TaHeR.

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.

Conformational transition induced in the aspartate:alanine antiporter by L-Ala binding

An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate^1-:alanine⁰ exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of L-aspartate (-Asp) and L-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of L-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of L-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of L-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (L-Ala or L-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of L-Ala differed from that in the presence of L-Asp. From these results, we concluded that L-Ala binding yields a conformation different from the apo or L-Asp binding conformations.

Lockdown of mitochondrial Ca2+ extrusion and subsequent resveratrol treatment kill HeLa cells by Ca2+ overload

Anticancer effect of resveratrol and the role of sodium/lithium/calcium exchanger in context with calcium ions are studied in human cervical cancer cell line. This therapeutic approach using siNCLX mediated gene silencing and drug therapy with resveratrol indicates the disruption of calcium homeostasis, increase in caspase (-3, 8, 9) mRNA expressions and DNA damage leading to apoptotic cell death. Monitoring the intracellular Ca2+ changes using fluo-4AM indicates highest rise in [Ca2+] level in sodium/lithium/calcium exchanger silenced group with five different stages, that is distinguishable based on the fluorescence intensity. In resveratrol treated and siNCLX + resveratrol treated groups no such cell staging differences were observed, despite uniform Ca2+ rise followed by decrease in the intensity. Integrating RNAi gene silencing of sodium/lithium/calcium exchanger with resveratrol can form the most interesting, efficient and promising therapeutic strategy in the treatment of cancer.

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.

Pyrroloquinoline quinone can prevent chronic heart failure by regulating mitochondrial function

Background

Myocardial mitochondrial dysfunction is the leading cause of chronic heart failure (CHF). Increased reactive oxygen species (ROS) levels, disruption of mitochondrial biogenesis and mitochondrial Ca²⁺([Ca²⁺]m) homeostasis and reduction of the mitochondrial membrane potential (ΔΨm) cause myocardial mitochondrial dysfunction. Therefore, treating CHF by targeting mitochondrial function is a focus of current research. For the first time, this study investigated the effects of the strong antioxidant pyrroloquinoline quinone (PQQ) on mitochondrial function in a cardiac pressure overload model, and the mechanism by which PQQ regulates [Ca²⁺]m homeostasis was explored in depth.

Methods

After transaortic constriction (TAC), normal saline and PQQ (0.4, 2 and 10 mg/kg) were administered intragastrically to Sprague Dawley (SD) rats for 12 weeks. In vitro, neonatal rat left ventricle myocytes (NRVMs) were pretreated with 200 nm angiotensin II (Ang II) with or without PQQ (1, 10 and 100 μM). Rat heart remodelling was verified by assessment of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) levels (qRT-PCR), cell surface area (wheat germ agglutinin (WGA) staining in vivo and α-actin in vitro) and echocardiography. Myocardial mitochondrial morphology was assessed by transmission electron microscopy. Western blotting was used to assess mitochondrial biogenesis [peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) and transcription factor A, mitochondrial (TFAM)]. The ΔΨm was determined by tetraethyl benzimidazolyl carbocyanine iodide (JC-1) staining and flow cytometry, and ROS levels were measured by dichloro-dihydro-fluorescein diacetate (DCFH-DA) and MitoSOX Red staining. [Ca²⁺]m was measured by isolating rat mitochondria, and mitochondrial Ca²⁺ channel proteins [the mitochondrial Na⁺/Ca²⁺ exchanger (NCLX) and mitochondrial Ca²⁺ uniporter (MCU)] were detected by Western blot.

Results

In vivo and in vitro, PQQ pretreatment improved pressure overload-induced cardiac remodelling and cell hypertrophy, thus preventing the occurrence of CHF. PQQ also prevented mitochondrial morphology damage and reduced the PGC-1α and TFAM downregulation caused by TAC or Ang II. In addition, in NRVMs treated with Ang II + PQQ, PQQ regulated ROS levels and increased the ΔΨm. PQQ also regulated [Ca²⁺]m homeostasis and prohibited [Ca²⁺]m overloading by increasing NCLX expression.

Conclusions

These results show that PQQ can prevent [Ca²⁺]m overload by increasing NCLX expression and thereby reducing ROS production and protecting the ΔΨm. At the same time, PQQ can increase PGC-1α and TFAM expression to regulate mitochondrial biogenesis. These factors can prevent mitochondrial dysfunction, thereby reducing cardiac damage caused by pressure overload and preventing the occurrence of CHF.