Ion selectivity strategies of sodium channel selectivity filters

Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies

Epilepsy is a severe, relapsing, and multifactorial neurological disorder. Studies regarding the accurate diagnosis, prognosis, and in-depth pathogenesis are crucial for the precise and effective treatment of epilepsy. The pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression, protein expression, ion channel activity, energy metabolites, and gut microbiota composition. Satisfactory results are lacking for conventional treatments for epilepsy. Surgical resection of lesions, drug therapy, and non-drug interventions are mainly used in clinical practice to treat pain associated with epilepsy. Non-pharmacological treatments, such as a ketogenic diet, gene therapy for nerve regeneration, and neural regulation, are currently areas of research focus. This review provides a comprehensive overview of the pathogenesis, diagnostic methods, and treatments of epilepsy. It also elaborates on the theoretical basis, treatment modes, and effects of invasive nerve stimulation in neurotherapy, including percutaneous vagus nerve stimulation, deep brain electrical stimulation, repetitive nerve electrical stimulation, in addition to non-invasive transcranial magnetic stimulation and transcranial direct current stimulation. Numerous studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic seizures. Additionally, many new technologies for the diagnosis and treatment of epilepsy are being explored. However, current research is mainly focused on analyzing patients' clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level, which has led to a lack of consensus regarding the mechanisms related to the disease.

An all-atom model of the human cardiac sodium channel in a lipid bilayer

Voltage-gated sodium channels (NaV) are complex macromolecular proteins that are responsible for the initial upstroke of an action potential in excitable cells. Appropriate function is necessary for many physiological processes such as heartbeat, voluntary muscle contraction, nerve conduction, and neurological function. Dysfunction can have life-threatening consequences. During the past decade, there have been significant advancements with ion channel structural characterization by CryoEM, yet descriptions of cytosolic components are often lacking. Many investigations have biophysically characterized reconstituted cytosolic components and their interactions. However, extrapolating the structural alterations and allosteric communication within an intact ion channel can be challenging. To address this, we have developed an all-atom model of the human cardiac sodium channel (NaV1.5) in a lipid bilayer with explicit salt and water. Our simulations contain descriptions of cytosolic components that are poorly predicted by AlphaFold and lacking in many CryoEM structures. Leveraging the latest advancements of the Amber force fields (ff19sb and Lipid21) and water model (OPC), our simulations improved protein backbone torsion angles and generated structural information across time (four independent one-microsecond simulations). Our analysis provided descriptions of lipid and solvent contacts and insight into the C-Terminal Domain - inactivation gate and inactivation gate - latch receptor interactions.

A unimolecular artificial cation channel based on cascaded hydrated acid groups

A cation channel possessing cascaded hydrated acid groups has been successfully constructed using pillar[5]arene integrated with dual cyclodextrins. As a proof-of-concept, the secondary side of cyclodextrin substituted by 24 -CO2H groups presents high coordination sites, which helps hydrated cations to quickly dehydrate and accelerates efficient cation transport (Rb+ > Cs+ > K+ > Na+ > Li+). Notably, benefitted by the protonation and deprotonation of -CO2H groups, ion permeation activity of the channel molecules under acidic condition (pH = 6.0) is 2.8 times higher than that under alkaline conditions (pH = 8.0), exhibiting pH-modulated property and promising potential in building intelligent artificial ion channels with customized features.

A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5

A key capability of ion channels is the facilitation of selective permeation of certain ionic species across cellular membranes at high rates. Due to their physiological significance, ion channels are of great pharmaceutical interest as drug targets. The polymodal signal-detecting transient receptor potential (TRP) superfamily of ion channels forms a particularly promising group of drug targets. While most members of this family permeate a broad range of cations including Ca2+, TRPM4 and TRPM5 are unique due to their strong monovalent selectivity and impermeability for divalent cations. Here, we investigated the mechanistic basis for their unique monovalent selectivity by in silico electrophysiology simulations of TRPM5. Our simulations reveal an unusual mechanism of cation selectivity, which is underpinned by the function of the central channel cavity alongside the selectivity filter. Our results suggest that a subtle hydrophobic barrier at the cavity entrance ("hydrophobic funnel") enables monovalent but not divalent cations to pass and occupy the cavity at physiologically relevant membrane voltages. Monovalent cations then permeate efficiently by a cooperative, distant knock-on mechanism between two binding regions in the extracellular pore vestibule and the central cavity. By contrast, divalent cations do not enter or interact favorably with the channel cavity due to its raised hydrophobicity. Hydrophilic mutations in the transition zone between the selectivity filter and the central channel cavity abolish the barrier for divalent cations, enabling both monovalent and divalent cations to traverse TRPM5.

A Bioinspired Membrane with Ultrahigh Li+/Na+ and Li+/K+ Separations Enables Direct Lithium Extraction from Brine

Membranes with precise Li+/Na+ and Li+/K+ separations are imperative for lithium extraction from brine to address the lithium supply shortage. However, achieving this goal remains a daunting challenge due to the similar valence, chemical properties, and subtle atomic-scale distinctions among these monovalent cations. Herein, inspired by the strict size-sieving effect of biological ion channels, a membrane is presented based on nonporous crystalline materials featuring structurally rigid, dimensionally confined, and long-range ordered ion channels that exclusively permeate naked Li+ but block Na+ and K+. This naked-Li+-sieving behavior not only enables unprecedented Li+/Na+ and Li+/K+ selectivities up to 2707.4 and 5109.8, respectively, even surpassing the state-of-the-art membranes by at least two orders of magnitude, but also demonstrates impressive Li+/Mg2+ and Li+/Ca2+ separation capabilities. Moreover, this bioinspired membrane has to be utilized for creating a one-step lithium extraction strategy from natural brines rich in Na+, K+, and Mg2+ without utilizing chemicals or creating solid waste, and it simultaneously produces hydrogen. This research has proposed a new type of ion-sieving membrane and also provides an envisioning of the design paradigm and development of advanced membranes, ion separation, and lithium extraction.

Honeybee CaV4 has distinct permeation, inactivation, and pharmacology from homologous NaV channels

DSC1, a Drosophila channel with sequence similarity to the voltage-gated sodium channel (NaV), was identified over 20 years ago. This channel was suspected to function as a non-specific cation channel with the ability to facilitate the permeation of calcium ions (Ca2+). A honeybee channel homologous to DSC1 was recently cloned and shown to exhibit strict selectivity for Ca2+, while excluding sodium ions (Na+), thus defining a new family of Ca2+ channels, known as CaV4. In this study, we characterize CaV4, showing that it exhibits an unprecedented type of inactivation, which depends on both an IFM motif and on the permeating divalent cation, like NaV and CaV1 channels, respectively. CaV4 displays a specific pharmacology with an unusual response to the alkaloid veratrine. It also possesses an inactivation mechanism that uses the same structural domains as NaV but permeates Ca2+ ions instead. This distinctive feature may provide valuable insights into how voltage- and calcium-dependent modulation of voltage-gated Ca2+ and Na+ channels occur under conditions involving local changes in intracellular calcium concentrations. Our study underscores the unique profile of CaV4 and defines this channel as a novel class of voltage-gated Ca2+ channels.

Carbonic Anhydrases: Different Active Sites, Same Metal Selectivity Rules

Carbonic anhydrases are mononuclear metalloenzymes catalyzing the reversible hydration of carbon dioxide in organisms belonging to all three domains of life. Although the mechanism of the catalytic reaction is similar, different families of carbonic anhydrases do not have a common ancestor nor do they exhibit significant resemblance in the amino acid sequence or the structure and composition of the metal-binding sites. Little is known about the physical principles determining the metal affinity and selectivity of the catalytic centers, and how well the native metal is protected from being dislodged by other metal species from the local environment. Here, we endeavor to shed light on these issues by studying (via a combination of density functional theory calculations and polarizable continuum model computations) the thermodynamic outcome of the competition between the native metal cation and its noncognate competitor in various metal-binding sites. Typical representatives of the competing cations from the cellular environments of the respective classes of carbonic anhydrases are considered. The calculations reveal how the Gibbs energy of the metal competition changes when varying the metal type, structure, composition, and solvent exposure of the active center. Physical principles governing metal competition in different carbonic anhydrase metal-binding sites are delineated.

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

Highly Selective Lithium Transport through Crown Ether Pillared Angstrom Channels

Biological ion channels use the synergistic effects of various strategies to realize highly selective ion sieving. For example, potassium channels use functional groups and angstrom-sized pores to discriminate rival ions and enrich target ions. Inspired by this, we constructed a layered crystal pillared by crown ether that incorporates these strategies to realize high Li+ selectivity. The pillared channels and crown ether have an angstrom-scale size. The crown ether specifically allows the low-barrier transport of Li+ . The channels attract and enrich Li+ ions by up to orders of magnitude. As a result, our material sieves Li+ out of various common ions such as Na+ , K+ , Ca2+ , Mg2+ and Al3+ . Moreover, by spontaneously enriching Li+ ions, it realizes an effective Li+ /Na+ selectivity of 1422 in artificial seawater where the Li+ concentration is merely 25 μM. We expect this work to spark technologies for the extraction of lithium and other dilute metal ions.

Crystalline porous organic salts

Crystalline porous organic salts (CPOSs), formed by the self-assembly of organic acids and organic bases through ionic bonding, possess definite structures and permanent porosity and have rapidly emerged as an important class of porous organic materials in recent years. By rationally designing and controlling tectons, acidity/basicity (pKa), and topology, stable CPOSs with permanent porosity can be efficiently constructed. The characteristics of ionic bonds, charge-separated highly polar nano-confined channels, and permanent porosity endow CPOSs with unique physicochemical properties, offering extensive research opportunities for exploring their functionalities and application scenarios. In this review, we systematically summarize the latest progress in CPOS research, describe the synthetic strategies for synthesizing CPOSs, delineate their structural characteristics, and highlight the differences between CPOSs and hydrogen-bonded organic frameworks (HOFs). Furthermore, we provide an overview of the potential applications of CPOSs in areas such as negative linear compression (NLC), proton conduction, rapid transport of CO2, selective and rapid transport of K+ ions, atmospheric water harvesting (AWH), gas sorption, molecular rotors, fluorescence modulation, room-temperature phosphorescence (RTP) and catalysis. Finally, the challenges and future perspectives of CPOSs are presented.

Artificial Sodium Channels for Enhanced Osmotic Energy Harvesting

Inspired by the ion channels of electric eels, we can use biomimetic nanofluidic materials to harvest the osmotic power released by mixing seawater and river water. While biological ion channels have both cation/anion and inter-cation selectivity, previous nanofluidic materials neglected the latter. As a result, NaCl solutions were generally used to simulate river water, ignoring the fact that the dominating cation in river water is typically Ca2+. In this work, we show that the different ionic compositions of seawater and river water can be exploited to improve osmotic power density by employing biomimetic sodium selective materials. Inspired by a range of properties of biological sodium channels, we constructed artificial sodium channels with zeolitic imidazolate framework-65 crystals, which selectively transport Na+ but almost completely block Ca2+. Resultantly, the effective concentration gradient of seawater/river water is dramatically increased by preventing the major cations in the river water from participating in the ion diffusion. As a result, the osmotic power density can be increased by more than 1 order of magnitude. These results should open new avenues to develop high-performance osmotic generators and may advance other applications based on biomimetic ion channels such as neuromorphic information processing.

Metal-Organic Framework Sub-Nanochannels Formed inside Solid-State Nanopore with Proton Ultra-High Selectivity

Metal-Organic frameworks (MOFs) have the advantages of high porosity, angstrom-scale pore size, and unique structure. In this work, a kind of MOFs, UiO-66 and its derivatives (including aminated UiO-66-(NH2 )2 and sulfonated UiO-66-(NH-SAG)2 ), were constructed on the inner surface of solid-state nanopores for ultra-selective proton transport. UiO-66 and UiO-66-(NH2 )2 nanocrystal particles were in-situ grown at the orifice of glass nanopores firstly, which were used to investigate the ionic current responses in LiCl and HCl solutions when the monovalent anions (Cl- ) were unchanged. Compared with UiO-66-modifed nanopores, the aminated MOFs modification (UiO-66-(NH2 )2 ) can improve the proton selectivity obviously. However, when the UiO-66-(NH-SAG)2 nanopore is prepared by further post-modification with sulfo-acetic acid, lithium ions can hardly pass through the channel, and the interaction between protons and sulfonic acid groups can promote the transport of protons, thus achieving ultra-high selectivity to protons. This work provides a new way to achieve sub-nanochannels with high selectivity, which can widely be used in ion separation, sensing and energy conversion.

A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels

The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.

Historical Perspective of the Characterization of Conotoxins Targeting Voltage-Gated Sodium Channels

Marine toxins have potent actions on diverse sodium ion channels regulated by transmembrane voltage (voltage-gated ion channels) or by neurotransmitters (nicotinic acetylcholine receptor channels). Studies of these toxins have focused on varied aspects of venom peptides ranging from evolutionary relationships of predator and prey, biological actions on excitable tissues, potential application as pharmacological intervention in disease therapy, and as part of multiple experimental approaches towards an understanding of the atomistic characterization of ion channel structure. This review examines the historical perspective of the study of conotoxin peptides active on sodium channels gated by transmembrane voltage, which has led to recent advances in ion channel research made possible with the exploitation of the diversity of these marine toxins.

Lanthanides as Calcium Mimetic Species in Calcium-Signaling/Buffering Proteins: The Effect of Lanthanide Type on the Ca2+/Ln3+ Competition

Lanthanides, the 14 4f-block elements plus Lanthanum, have been extensively used to study the structure and biochemical properties of metalloproteins. The characteristics of lanthanides within the lanthanide series are similar, but not identical. The present research offers a systematic investigation of the ability of the entire Ln3+ series to substitute for Ca2+ in biological systems. A well-calibrated DFT/PCM protocol is employed in studying the factors that control the metal selectivity in biological systems by modeling typical calcium signaling/buffering binding sites and elucidating the thermodynamic outcome of the competition between the “alien” La3+/Ln3+ and “native” Ca2+, and La3+ − Ln3+ within the lanthanide series. The calculations performed reveal that the major determinant of the Ca2+/Ln3+ selectivity in calcium proteins is the net charge of the calcium binding pocket; the more negative the charge, the higher the competitiveness of the trivalent Ln3+ with respect to its Ca2+ contender. Solvent exposure of the binding site also influences the process; buried active centers with net charge of −4 or −3 are characterized by higher Ln3+ over Ca2+ selectivity, whereas it is the opposite for sites with overall charge of −1. Within the series, the competition between La3+ and its fellow lanthanides is determined by the balance between two competing effects: electronic (favoring heavier lanthanides) and solvation (generally favoring the lighter lanthanides).

An artificial sodium-selective subnanochannel

Single-ion selectivity with high precision has long been pursued for fundamental bioinspired engineering and applications such as in ion separation and energy conversion. However, it remains a challenge to develop artificial ion channels to achieve single-ion selectivity comparable to their biological analogs, especially for high Na⁺/K⁺ selectivity. Here, we report an artificial sodium channel by subnanoconfinement of 4'-aminobenzo-15-crown-5 ethers (15C5s) into ~6-Å-sized metal-organic framework subnanochannel (MOFSNC). The resulting 15C5-MOFSNC shows an unprecedented Na⁺/K⁺ selectivity of tens to 10² and Na⁺/Li⁺ selectivity of 10³ under multicomponent permeation conditions, comparable to biological sodium channels. A co-ion-responsive single-file transport mechanism in 15C-MOFSNC is proposed for the preferential transport of Na⁺ over K⁺ due to the synergetic effects of size exclusion, charge selectivity, local hydrophobicity, and preferential binding with functional groups. This study provides an alternative strategy for developing potential single-ion selective channels and membranes for many applications.

Holo-chromodulin: competition between the native Cr3+ and other biogenic cations (Fe3+, Fe2+, Mg2+, and Zn2+) for the binding sites

Chromodulin is an oligopeptide that has an essential role for the flawless functioning of insulin. Although the precise sequence of the constituent amino acid residues and the 3D structure of the molecule has not yet been deciphered, it is known that chromodulin contains only four amino acids in the ratio of Glu-: Gly: Cys: Asp- = 4: 2: 2: 2. An indispensable part for the integrity of the molecule in its active (holo-) form are four chromium cations (hence the name) in the oxidation state of 3+, positioned in two metal binding sites containing one and three Cr3+ ions. Experimental works provide some hints/clues concerning the structure of the metal centers, although their exact composition, type, and arrangement of metal ligating entities remain enigmatic. In the current study, we endeavor to unveil possible structure(s) of the Cr3+ loaded binding sites by strictly following the evidence provided by the experimental data. Well-calibrated in silico methodology for optimization and evaluation of Gibbs free energies is applied and gives strong premises for reliably deciphering the composition/structure of chromodulin metal binding sites. Additional computations reveal the advantage of choosing Cr3+ over other tri- (Fe3+) and divalent (Fe2+, Mg2+, and Zn2+) biogenic ions for securing maximum stability of the metal-occupied binding sites.

From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic

The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi-targeting strategy against SARS-CoV-2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+-sites in several SARS-CoV-2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+-bound, can be targeted using the same Zn-ejector drug (disulfiram/ebselen), which enables the use of broad-spectrum anti-virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn-ejector drug combined with other broad-spectrum anti-viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisStructure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Density Functional Theory.

"Virtual patch clamp analysis" for predicting the functional significance of pathogenic variants in sodium channels

OBJECTIVE

Opening of voltage-gated sodium channels is crucial for neuronal depolarization. Proper channel opening and influx of Na⁺ through the ion pore, is dependent upon binding of Na⁺ ion to a specific amino-acid motif (DEKA) within the pore. In this study we used molecular dynamic simulations, an advanced bioinformatic tool, to research the dysfunction caused by pathogenic variants in SCN1a, SCN2a and SCN8a genes.

METHOD

Molecular dynamic simulations were performed in six patients: three patients with Dravet syndrome (p.Gly177Ala,p.Ser259Arg and p.Met1267Ile, SCN1a), two patients with early onset drug resistant epilepsy(p.Ala263Val, SCN2a and p.Ile251Arg, SCN8a), and a patient with autism (p.Thr155Ala, SCN2a). After predicting the 3D-structure of mutated proteins by homology modeling, time dependent molecular dynamic simulations were performed, using the Schrödinger algorithm. The opening of the sodium channel, including the detachment of the sodium ion to the DEKA motif and pore diameter were assessed. Results were compared to the existent patch clamp analysis in four patients, and consistency with clinical phenotype was noted.

RESULTS

The Na⁺ ion remained attached to DEKA filter longer when compared to wild type in the p.Gly177Ala, p.Ser259Arg,SCN1a, and p.Thr155Ala, SCN2a variants, consistent with loss-of-function. In contrast, it detached quicker from DEKA than wild type in the p.Ala263Val,SCN2a variant, consistent with gain-of-function. In the p.Met1267Ile,SCN1a variant, detachment from DEKA was quicker, but pore diameter decreased, suggesting partial loss-of-function. In the p.Leu251Arg,SCN8a variant, the pore remained opened longer when compared to wild type, consistent with a gain-of-function. The molecular dynamic simulation results were consistent with the existing patch-clamp analysis studies, as well as the clinical phenotype.

SIGNIFICANCE

Molecular dynamic simulation can be useful in predicting pathogenicity of variants and the disease phenotype, and selecting targeted treatment based on channel dysfunction. Further development of these bioinformatic tools may lead to "virtual patch-clamp analysis".

Single ion free energy calculation in ASIC1: the importance of the HG loop

Acid Sensing Ion Channels (ASICs) are one of the most studied channels of the Epithelial Sodium Channel/Degenerin (ENaC/DEG) superfamily. They are responsible for excitatory responses following acidification of the extracellular medium and are involved in several important physiological roles. The ASIC1 subunit can form a functional homotrimeric channel and its structure is currently the most characterised of the whole ENaC/DEG family. Here we computed the free energy profiles for single ion permeation in two different structures of ASIC1 using both Na⁺ and Cl^- as permeating ions. The first structure is the open structure of the channel from the PDB entry 4NTW, and the second structure is the closed structure with the re-entrant loop which contains the highly conserved 'HG' motif form PDB entry 6VTK. Both structures show cation selective free energy profiles, however the profiles of the permeating Na⁺ differ significantly between the two structures. Indeed, whereas there is only a small energetically favorable (-0.5 kcal mol^-1) location for Na⁺ in the open channel (4NTW) near the end of the pore, we observed a clear ion binding site (-7.8 kcal mol^-1) located in between the 'GAS' belt and the 'HG' loop for the channel containing the re-entrant loop (6VTK). Knowing that the 'GAS' motif was determined as the selectivity filter, our results support previous observations while addressing the importance of the 'HG' motif for the interactions between the pore and the permeating cations.

The Ionic Composition and Chemistry of Nanopore-Confined Solutions

There is increasing interest in understanding the properties of solutions confined within nanotubes and synthetic or biological nanopores. How the ionic content of a nanopore-confined solution differs from that of a contacting bulk salt solution is of particular importance, for example, to water desalinization, industrial electrolysis, and all living systems. This paper explores ionic content, ionic interactions, and ion-transport properties of solutions confined within the 10 nm diameter pores of a synthetic polymer membrane. The membrane has a fixed negative pore-wall and surface charge due to ionizable carbonate groups. As a result, under some conditions, the nanopore-confined solution contains only cations and no anions or salt present in a contacting solution, ideal cation permselectivity. This anion- and salt-rejecting ability varies greatly with the cation of the salt, a result that is in contradiction to the prevailing model for permselectivity in nanopores. The extant model fails because it does not account for specific chemical interactions between the cation and the carbonate groups. The nature of these ion-selective interactions is discussed here.

Cellular and behavioral effects of altered NaV1.2 sodium channel ion permeability in Scn2aK1422E mice

Genetic variants in SCN2A, encoding the Na_V1.2 voltage-gated sodium channel, are associated with a range of neurodevelopmental disorders with overlapping phenotypes. Some variants fit into a framework wherein gain-of-function missense variants that increase neuronal excitability lead to developmental and epileptic encephalopathy, while loss-of-function variants that reduce neuronal excitability lead to intellectual disability and/or autism spectrum disorder (ASD) with or without co-morbid seizures. One unique case less easily classified using this framework is the de novo missense variant SCN2A-p.K1422E, associated with infant-onset developmental delay, infantile spasms and features of ASD. Prior structure–function studies demonstrated that K1422E substitution alters ion selectivity of Na_V1.2, conferring Ca²⁺ permeability, lowering overall conductance and conferring resistance to tetrodotoxin (TTX). Based on heterologous expression of K1422E, we developed a compartmental neuron model incorporating variant channels that predicted reductions in peak action potential (AP) speed. We generated Scn2a^K1422E mice and characterized effects on neurons and neurological/neurobehavioral phenotypes. Cultured cortical neurons from heterozygous Scn2a^K1422E/+ mice exhibited lower current density with a TTX-resistant component and reversal potential consistent with mixed ion permeation. Recordings from Scn2a^K1442E/+ cortical slices demonstrated impaired AP initiation and larger Ca²⁺ transients at the axon initial segment during the rising phase of the AP, suggesting complex effects on channel function. Scn2a^K1422E/+ mice exhibited rare spontaneous seizures, interictal electroencephalogram abnormalities, altered induced seizure thresholds, reduced anxiety-like behavior and alterations in olfactory-guided social behavior. Overall, Scn2a^K1422E/+ mice present with phenotypes similar yet distinct from other Scn2a models, consistent with complex effects of K1422E on Na_V1.2 channel function.

Ultrafast rectifying counter-directional transport of proton and metal ions in metal-organic framework-based nanochannels

Bioinspired control of ion transport at the subnanoscale has become a major focus in the fields of nanofluidics and membrane separation. It is fundamentally important to achieve rectifying ion-specific transport in artificial ion channels, but it remains a challenge. Here, we report a previously unidentified metal-organic framework nanochannel (MOF NC) nanofluidic system to achieve unidirectional ultrafast counter-directional transport of alkaline metal ions and proton. This highly effective ion-specific rectifying transport behavior is attributed to two distinct mechanisms for metal ions and proton, elucidated by theoretical simulations. Notably, the MOF NC exhibits ultrafast proton conduction stemming from ultrahigh proton mobility, i.e., 11.3 × 10^-7 m² /V·s, and low energy barrier of 0.075 eV in MIL-53-COOH subnanochannels. Furthermore, the MOF NC shows excellent osmotic power-harvesting performance in reverse electrodialysis. This work expects to inspire further research into multifunctional biomimetic ion channels for advanced nanofluidics, biomimetics, and separation applications.

Interactions between Artificial Channel Protein, Water Molecules, and Ions Based on Theoretical Approaches

Contemporary techniques of molecular modeling allow for rational design of several specific classes of artificial proteins. Transmembrane channels are among these classes. A recent successful synthesis of self-assembling, highly symmetrical 12- or 16-helix channels by David Baker’s group prompted us to study interactions between one of these proteins, TMHC6, and low-molecular-weight components of the environment: water molecules and ions. To examine protein stability in a polar environment, molecular dynamics (MD) with classical force fields of the AMBER family was employed. Further characteristics of the chosen interactions were obtained using interaction energy calculations with usage of partially polarizable GFN-FF force field of Spicher and Grimme, symmetry-adapted perturbation theory (SAPT) and atoms in molecules (AIM) approaches for models of residues from the channel entry, crucial for interactions with water molecules and ions. The comparison of the interaction energy values between the gas phase and solvent reaction field gives the quantitative estimation of the strength of the interactions. The energy decomposition via the SAPT method showed that the electrostatics forces play a dominant role in the substructure stabilization. An application of the AIM theory enabled a description of the intermolecular hydrogen bonds and other noncovalent interactions.

Nomogram to predict 3-month unfavorable outcome after thrombectomy for stroke

Background

Mechanical thrombectomy (MT) is an effective treatment for large-vessel occlusion in acute ischemic stroke, however, only some revascularized patients have a good prognosis. For stroke patients undergoing MT, predicting the risk of unfavorable outcomes and adjusting the treatment strategies accordingly can greatly improve prognosis. Therefore, we aimed to develop and validate a nomogram that can predict 3-month unfavorable outcomes for individual stroke patient treated with MT.

Methods

We analyzed 258 patients with acute ischemic stroke who underwent MT from January 2018 to February 2021. The primary outcome was a 3-month unfavorable outcome, assessed using the modified Rankin Scale (mRS), 3–6. A nomogram was generated based on a multivariable logistic model. We used the area under the receiver-operating characteristic curve to evaluate the discriminative performance and used the calibration curve and Spiegelhalter’s Z-test to assess the calibration performance of the risk prediction model.

Results

In our visual nomogram, gender (odds ratio [OR], 3.40; 95%CI, 1.54–7.54), collateral circulation (OR, 0.46; 95%CI, 0.28–0.76), postoperative mTICI (OR, 0.06; 95%CI, 0.01–0.50), stroke-associated pneumonia (OR, 5.76; 95%CI, 2.79–11.87), preoperative Na (OR, 0.82; 95%CI, 0.72–0.92) and creatinine (OR, 1.02; 95%CI, 1.01–1.03) remained independent predictors of 3-month unfavorable outcomes in stroke patients treated with MT. The area under the nomogram curve was 0.8791 with good calibration performance (P = 0.873 for the Spiegelhalter’s Z-test).

Conclusions

A novel nomogram consisting of gender, collateral circulation, postoperative mTICI, stroke-associated pneumonia, preoperative Na and creatinine can predict the 3-month unfavorable outcomes in stroke patients treated with MT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12883-022-02633-1.

Molecular basis of multistep voltage activation in plant two-pore channel 1

Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.

A DFT/PCM Study on the Affinity of Salinomycin to Bind Monovalent Metal Cations

The affinity of the polyether ionophore salinomycin to bind IA/IB metal ions was accessed using the Gibbs free energy of the competition reaction between SalNa (taken as a reference) and its rival ions: [M+-solution] + [SalNa] → [SalM] + [Na+-solution] (M = Li, K, Rb, Cs, Cu, Ag, Au). The DFT/PCM computations revealed that the ionic radius, charge density and accepting ability of the competing metal cations, as well as the dielectric properties of the solvent, have an influence upon the selectivity of salinomycin. The optimized structures of the monovalent metal complexes demonstrate the flexibility of the ionophore, allowing the coordination of one or two water ligands in SalM-W1 and SalM-W2, respectively. The metal cations are responsible for the inner coordination sphere geometry, with coordination numbers spread between 2 (Au+), 4 (Li+ and Cu+), 5/6 (Na+, K+, Ag+), 6/7 (Rb+) and 7/8 (Cs+). The metals' affinity to salinomycin in low-polarity media follows the order of Li+ > Cu+ > Na+ > K+ > Au+ > Ag+ > Rb+ > Cs+, whereas some derangement takes place in high-dielectric environment: Li+ ≥ Na+ > K+ > Cu+ > Au+ > Ag+ > Rb+ > Cs+.

Processed Food and Atopic Dermatitis: A Pooled Analysis of Three Cross-Sectional Studies in Chinese Adults

Objective: The effect of processed foods on atopic dermatitis (AD) in adults is unclear. This study was to evaluate the association between processed foods and AD in the Chinese adult population.

Design: This study included three population-based cross-sectional studies using cluster sampling by villages, institutions, or factories. Participants underwent dermatological examinations by certificated dermatologists and a food frequency questionnaire survey. A spot urine sample was collected to estimate the daily sodium intake. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were presented as the effect size.

Setting: Shiyan city of Hubei province, and Huayuan, Shimen, Hengyang, Zhuzhou, and Changsha of Hunan province.

Participants: Automobile manufacture workers from Shiyan of Hubei province, and rural residents and civil servants from Hunan.

Results: A total of 15,062 participants, including 3,781 rural residents, 5,111 civil servants, and 6,170 workers, completed all evaluations. Compared to those hardly consumed pickles, consumption of pickles 1–3 times per week was significantly associated with AD (aOR: 1.35; 95% CI: 1.06–1.70). The intake of processed meats 1–3 times per month (aOR: 1.29; 95% CI: 1.05–1.58) and 1–3 times per week (aOR: 1.44; 95% CI: 1.11–1.87) were associated with AD dose-dependently when compared with those who rarely ate processed meats. Compared with non-consumers, the consumption of any processed foods 1–3 times per week (aOR: 1.39; 95% CI: 1.08–1.80) and ≥4 times per week (aOR: 1.41; 95% CI: 1.05–1.89) showed increased risks of AD. A positive association of estimated sodium intake with AD was also observed.

Conclusion: Intake of processed foods is associated with AD in Chinese adults.

The Ionic Selectivity of Lysenin Channels in Open and Sub-Conducting States

The electrochemical gradients established across cell membranes are paramount for the execution of biological functions. Besides ion channels, other transporters, such as exogenous pore-forming toxins, may present ionic selectivity upon reconstitution in natural and artificial lipid membranes and contribute to the electrochemical gradients. In this context, we utilized electrophysiology approaches to assess the ionic selectivity of the pore-forming toxin lysenin reconstituted in planar bilayer lipid membranes. The membrane voltages were determined from the reversal potentials recorded upon channel exposure to asymmetrical ionic conditions, and the permeability ratios were calculated from the fit with the Goldman-Hodgkin-Katz equation. Our work shows that lysenin channels are ion-selective and the determined permeability coefficients are cation and anion-species dependent. We also exploited the unique property of lysenin channels to transition to a stable sub-conducting state upon exposure to calcium ions and assessed their subsequent change in ionic selectivity. The observed loss of selectivity was implemented in an electrical model describing the dependency of reversal potentials on calcium concentration. In conclusion, our work demonstrates that this pore-forming toxin presents ionic selectivity but this is adjusted by the particular conduction state of the channels.

Selective Fluoride Transport in Subnanometer TiO2 Pores

Synthesizing nanopores which mimic the functionality of ion-selective biological channels has been a challenging yet promising approach to advance technologies for precise ion-ion separations. Inspired by the facilitated fluoride (F^-) permeation in the biological fluoride channel, we designed a highly fluoride-selective TiO₂ film using the atomic layer deposition (ALD) technique. The subnanometer voids within the fabricated TiO₂ film (4 Å < d < 12 Å, with two distinct peaks at 5.5 and 6.5 Å), created by the hindered diffusion of ALD precursors (d = 7 Å), resulted in more than eight times faster permeation of sodium fluoride compared to other sodium halides. We show that the specific Ti-F interactions compensate for the energy penalty of F^- dehydration during the partitioning of F^- ions into the pore and allow for an intrapore accumulation of F^- ions. Concomitantly, the accumulation of F^- ions on the pore walls also enhances the transport of sodium (Na⁺) cations due to electrostatic interactions. Molecular dynamics simulations probing the ion concentration and mobility within the TiO₂ pore further support our proposed mechanisms for the selective F^- transport and enhanced Na⁺ permeation in the TiO₂ film. Overall, our work provides insights toward the design of ion-selective nanopores using the ALD technique.

Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis

The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.

Neuromorphic van der Waals crystals for substantial energy generation

Controlling ion transport in nanofluidics is fundamental to water purification, bio-sensing, energy storage, energy conversion, and numerous other applications. For any of these, it is essential to design nanofluidic channels that are stable in the liquid phase and enable specific ions to pass. A human neuron is one such system, where electrical signals are transmitted by cation transport for high-speed communication related to neuromorphic computing. Here, we present a concept of neuro-inspired energy harvesting that uses confined van der Waals crystal and demonstrate a method to maximise the ion diffusion flux to generate an electromotive force. The confined nanochannel is robust in liquids as in neuron cells, enabling steady-state ion diffusion for hundred of hours and exhibiting ion selectivity of 95.8%, energy conversion efficiency of 41.4%, and power density of 5.26 W/m². This fundamental understanding and rational design strategy can enable previously unrealisable applications of passive-type large-scale power generation.

Competition between abiogenic and biogenic metal cations in biological systems: Mechanisms of gallium's anticancer and antibacterial effect

Metal cations are key players in a plethora of essential biological processes. Over the course of evolution specific biological functions have been bestowed upon two dozen of (biogenic) metal species, some of the most frequently found being sodium, potassium, magnesium, calcium, zinc, manganese, iron, and copper. On the other hand, there is a group of less studied abiogenic metals like lithium, strontium and gallium that possess not known functions in living organisms, but, by mimicking the native ions and/or competing with them for binding to key metalloenzymes, may exert beneficial effect on humans in particular medical conditions. This review summarizes and critically examines the mechanisms of gallium's therapeutic action in anticancer and antibacterial therapies by exploiting the tools of molecular modeling and experimental biochemistry. These approaches allow for identifying key factors for Ga³⁺ beneficial effect such as the electrostatic interactions with the protein ligands, substrates or bacterial siderophores, intramolecular hydrogen bond formation, and pH and dielectric properties of the medium. Several intriguing questions concerning the gallium competition with the native ferric ion have found their answers.

Variable patterns of mutation density among NaV1.1, NaV1.2 and NaV1.6 point to channel-specific functional differences associated with childhood epilepsy

Variants implicated in childhood epilepsy have been identified in all four voltage-gated sodium channels that initiate action potentials in the central nervous system. Previous research has focused on the functional effects of particular variants within the most studied of these channels (Na_V1.1, Na_V1.2 and Na_V1.6); however, there have been few comparative studies across channels to infer the impact of mutations in patients with epilepsy. Here we compare patterns of variation in patient and public databases to test the hypothesis that regions of known functional significance within voltage-gated sodium (Na_V) channels have an increased burden of deleterious variants. We assessed mutational burden in different regions of the Na_v channels by (1) performing Fisher exact tests on odds ratios to infer excess variants in domains, segments, and loops of each channel in patient databases versus public “control” databases, and (2) comparing the cumulative distribution of variant sites along DNA sequences of each gene in patient and public databases (i.e., independent of protein structure). Patient variant density was concordant among channels in regions known to play a role in channel function, with statistically significant higher patient variant density in S4-S6 and DIII-DIV and an excess of public variants in SI-S3, DI-DII, DII-DIII. On the other hand, channel-specific patterns of patient burden were found in the Na_V1.6 inactivation gate and Na_V1.1 S5-S6 linkers, while Na_V1.2 and Na_V1.6 S4-S5 linkers and S5 segments shared patient variant patterns that contrasted with those in Na_V1.1. These different patterns may reflect different roles played by the Na_V1.6 inactivation gate in action potential propagation, and by Na_V1.1 S5-S6 linkers in loss of function and haploinsufficiency. Interestingly, Na_V1.2 and Na_V1.6 both lack amino acid substitutions over significantly long stretches in both the patient and public databases suggesting that new mutations in these regions may cause embryonic lethality or a non-epileptic disease phenotype.

Semipermeable Mixed Phospholipid-Fatty Acid Membranes Exhibit K+/Na+ Selectivity in the Absence of Proteins

Two important ions, K⁺ and Na⁺, are unequally distributed across the contemporary phospholipid-based cell membrane because modern cells evolved a series of sophisticated protein channels and pumps to maintain ion gradients. The earliest life-like entities or protocells did not possess either ion-tight membranes or ion pumps, which would result in the equilibration of the intra-protocellular K⁺/Na⁺ ratio with that in the external environment. Here, we show that the most primitive protocell membranes composed of fatty acids, that were initially leaky, would eventually become less ion permeable as their membranes evolved towards having increasing phospholipid contents. Furthermore, these mixed fatty acid-phospholipid membranes selectively retain K⁺ but allow the passage of Na⁺ out of the cell. The K⁺/Na⁺ selectivity of these mixed fatty acid-phospholipid semipermeable membranes suggests that protocells at intermediate stages of evolution could have acquired electrochemical K⁺/Na⁺ ion gradients in the absence of any macromolecular transport machinery or pumps, thus potentially facilitating rudimentary protometabolism.

Factors governing the competition between group IA and IB cations for monensin A: a DFT/PCM study

The results obtained suggest that the metal selectivity of monensin can be modulated by changing the solvents used.

How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins

The results obtained reveal that applying mechanical forces with a given strength and directionality can modulate the metal affinity and selectivity of metal binding sites in metalloproteins.

Free and Bound Therapeutic Lithium in Brain Signaling

Lithium, a first-line therapy for bipolar disorder, is effective in preventing suicide and new depressive/manic episodes. Yet, how this beguilingly simple monocation with only two electrons could yield such profound therapeutic effects remains unclear. An in-depth understanding of lithium's mechanisms of actions would help one to develop better treatments limiting its adverse side effects and repurpose lithium for treating traumatic brain injury and chronic neurodegenerative diseases. In this Account, we begin with a comparison of the physicochemical properties of Li⁺ and its key native rivals, Na⁺ and Mg²⁺, to provide physical grounds for their competition in protein binding sites. Next, we review the abnormal signaling pathways and proteins found in bipolar patients, who generally have abnormally high intracellular Na⁺ and Ca²⁺ concentrations, high G-protein levels, and hyperactive phosphatidylinositol signaling and glycogen synthase kinase-3β (GSK3β) activity. We briefly summarize experimental findings on how lithium, at therapeutic doses, modulates these abnormal signaling pathways and proteins. Following this survey, we address the following aspects of lithium's therapeutic actions: (1) Can Li⁺ displace Na⁺ from the allosteric Na⁺-binding sites in neurotransmitter transporters and G-protein coupled receptors (GPCRs); if so, how would this affect the host protein's function? (2) Why are certain Mg²⁺-dependent enzymes targeted by Li⁺? (3) How does Li⁺ binding to Mg²⁺-bound ATP/GTP (denoted as NTP) in solution affect the cofactor's conformation and subsequent recognition by the host protein? (4) How do NTP-Mg-Li complexes modulate the properties of the respective cellular receptors and signal-transducing proteins? We show that Li⁺ may displace Na⁺ from allosteric Na⁺-binding sites in certain GPCRs and stabilize inactive conformations, preventing these receptors from relaying signal to the respective G-proteins. It may also displace Mg²⁺ in enzymes containing highly cationic Mg²⁺-binding sites such as GSK3β, but not in enzymes containing Mg²⁺-binding sites with low or zero charge. We further show that Li⁺ binding to Mg²⁺-NTP in water does not alter the NTP conformation, which is locked by all three phosphates binding to Mg²⁺. However, bound lithium in the form of [NTP-Mg-Li]^2- dianions can activate or inhibit the host protein depending on the NTP-binding pocket's shape, which determines the metal-binding mode: The ATP-binding pocket's shape in the P2X receptor is complementary to the native ATP-Mg solution conformation and nicely fits [ATP-Mg-Li]^2-. However, since the ATP βγ phosphates bind Li⁺, bimetallic [ATP-Mg-Li]^2- may be more resistant to hydrolysis than the native cofactor, enabling ATP to reside longer in the binding site and elicit a prolonged P2X response. In contrast, the elongated GTP-binding pockets in G-proteins allow only two GTP phosphates to bind Mg²⁺, so the GTP conformation is no longer "triply-locked". Consequently, Li⁺ binding to GTP-Mg can significantly alter the native cofactor's structure, lowering the activated G-protein level, thus attenuating hyperactive G-protein-mediated signaling in bipolar patients. In summary, we have presented a larger "connected" picture of lithium's diverse effects based on its competition as a free monocation with native cations or as a phosphate-bound polyanionic complex modulating the host protein function.

The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems

Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.

Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel

Bacterial and human voltage-gated sodium channels (Navs) exhibit similar cation selectivity, despite their distinct EEEE and DEKA selectivity filter signature sequences. Recent high-resolution structures for bacterial Navs have allowed us to learn about ion conduction mechanisms in these simpler homo-tetrameric channels, but our understanding of the function of their mammalian counterparts remains limited. To probe these conduction mechanisms, a model of the human Nav1.2 channel has been constructed by grafting residues of its selectivity filter and external vestibular region onto the bacterial NavRh channel with atomic-resolution structure. Multi-μs fully atomistic simulations capture long time-scale ion and protein movements associated with the permeation of Na+ and K+ ions, and their differences. We observe a Na+ ion knock-on conduction mechanism facilitated by low energy multi-carboxylate/multi-Na+ complexes, akin to the bacterial channels. These complexes involve both the DEKA and vestibular EEDD rings, acting to draw multiple Na+ into the selectivity filter and promote permeation. When the DEKA ring lysine is protonated, we observe that its ammonium group is actively participating in Na+ permeation, presuming the role of another ion. It participates in the formation of a stable complex involving carboxylates that collectively bind both Na+ and the Lys ammonium group in a high-field strength site, permitting pass-by translocation of Na+. In contrast, multiple K+ ion complexes with the DEKA and EEDD rings are disfavored by up to 8.3 kcal/mol, with the K+-lysine-carboxylate complex non-existent. As a result, lysine acts as an electrostatic plug that partially blocks the flow of K+ ions, which must instead wait for isomerization of lysine downward to clear the path for K+ passage. These distinct mechanisms give us insight into the nature of ion conduction and selectivity in human Nav channels, while uncovering high field strength carboxylate binding complexes that define the more general phenomenon of Na+-selective ion transport in nature.

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade

Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer. Our model was comprehensively validated by using reported mutagenesis data, comparisons with previous models, and binding to a panel of known hNav1.5 blockers. The relatively long classical MD simulation was sufficient to observe a natural sodium permeation event across the channel's selectivity filters to reach the channel's central cavity, together with the identification of a unique role of the lysine residue. Electrostatic potential calculations revealed the existence of two potential binding sites for the sodium ion at the outer selectivity filters. To obtain further mechanistic insight into the permeation event from the central cavity to the intracellular region of the channel, we further employed "state-of-the-art" steered molecular dynamics (SMD) simulations. Our SMD simulations revealed two different pathways through which a sodium ion can be expelled from the channel. Further, the SMD simulations identified the key residues that are likely to control these processes. Finally, we discuss the potential binding modes of a panel of known hNav1.5 blockers to our structural model of hNav1.5. We believe that the data presented here will enhance our understanding of the structure-property relationships of the hNav1.5 ion channel and the underlying molecular mechanisms in sodium ion permeation and drug interactions. The results presented here could be useful for designing safer drugs that do not block the hNav1.5 channel.

From direct to indirect lithium targets: a comprehensive review of omics data

Metal ions are critical to a wide range of biological processes.