The cation selectivity filter of the bacterial sodium channel, NaChBac

Bottom-up design of calcium channels from defined selectivity filter geometry

Native ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices1,2. Protein design has been harnessed to generate pore-containing transmembrane proteins, but the capability to design ion selectivity based on the interactions between ions and selectivity filter residues, a crucial feature of native ion channels3, has been constrained by the lack of methods to place the metal-coordinating residues with atomic-level precision. Here we describe a bottom-up RFdiffusion-based approach to construct Ca2+ channels from defined selectivity filter residue geometries, and use this approach to design symmetric oligomeric channels with Ca2+ selectivity filters having different coordination numbers and different geometries at the entrance of a wide pore buttressed by multiple transmembrane helices. The designed channel proteins assemble into homogenous pore-containing particles, and for both tetrameric and hexameric ion-coordinating configurations, patch-clamp experiments show that the designed channels have higher conductances for Ca2+ than for Na+ and other divalent ions (Sr2+ and Mg2+). Cryo-electron microscopy indicates that the design method has high accuracy: the structure of the hexameric Ca2+ channel is nearly identical to the design model. Our bottom-up design approach now enables the testing of hypotheses relating filter geometry to ion selectivity by direct construction, and provides a roadmap for creating selective ion channels for a wide range of applications.

The chemistry of electrical signaling in sodium channels from bacteria and beyond

Electrical signaling is essential for all fast processes in biology, but its molecular mechanisms have been uncertain. This review article focuses on studies of bacterial sodium channels in order to home in on the essential molecular and chemical mechanisms underlying transmembrane ion conductance and voltage-dependent gating without the overlay of complex protein interactions and regulatory mechanisms in mammalian sodium channels. This minimalist approach has yielded a nearly complete picture of sodium channel function at the atomic level that are mostly conserved in mammalian sodium channels, including sodium selectivity and conductance, voltage sensing and activation, electromechanical coupling to pore opening and closing, slow inactivation, and pathogenic dysfunction in a debilitating channelopathy. Future studies of nature's simplest sodium channels may continue to yield key insights into the fundamental molecular and chemical principles of their function and further elucidate the chemical basis of electrical signaling.

A governance of ion selectivity based on the occupancy of the "beacon" in one- and four-domain calcium and sodium channels

One of nature's exceptions was discovered when a Cav3 T-type channel was observed to switch phenotype from a calcium channel into a sodium channel by neutralizing an aspartate residue in the high field strength (HFS) +1 position within the ion selectivity filter. The HFS+1 site is dubbed a "beacon" for its location at the entryway just above the constricted, minimum radius of the HFS site's electronegative ring. A classification is proposed based on the occupancy of the HFS+1 "beacon" which correlates with the calcium- or sodium-selectivity phenotype. If the beacon is a glycine, or neutral, non-glycine residue, then the cation channel is calcium-selective or sodium-permeable, respectively (Class I). Occupancy of a beacon aspartate are calcium-selective channels (Class II) or possessing a strong calcium block (Class III). A residue lacking in position of the sequence alignment for the beacon are sodium channels (Class IV). The extent to which animal channels are sodium-selective is dictated in the occupancy of the HFS site with a lysine residue (Class III/IV). Governance involving the beacon solves the quandary the HFS site as a basis for ion selectivity, where an electronegative ring of glutamates at the HFS site generates a sodium-selective channel in one-domain channels but generates a calcium-selective channel in four-domain channels. Discovery of a splice variant in an exceptional channel revealed nature's exploits, highlighting the "beacon" as a principal determinant for calcium and sodium selectivity, encompassing known ion channels composed of one and four domains, from bacteria to animals.

Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin

The sodium channel Na_V1.6 is widely expressed in neurons of the central and peripheral nervous systems, which plays a critical role in regulating neuronal excitability. Dysfunction of Na_V1.6 has been linked to epileptic encephalopathy, intellectual disability and movement disorders. Here we present cryo-EM structures of human Na_V1.6/β1/β2 alone and complexed with a guanidinium neurotoxin 4,9-anhydro-tetrodotoxin (4,9-ah-TTX), revealing molecular mechanism of Na_V1.6 inhibition by the blocker. The apo-form structure reveals two potential Na⁺ binding sites within the selectivity filter, suggesting a possible mechanism for Na⁺ selectivity and conductance. In the 4,9-ah-TTX bound structure, 4,9-ah-TTX binds to a pocket similar to the tetrodotoxin (TTX) binding site, which occupies the Na⁺ binding sites and completely blocks the channel. Molecular dynamics simulation results show that subtle conformational differences in the selectivity filter affect the affinity of TTX analogues. Taken together, our results provide important insights into Na_V1.6 structure, ion conductance, and inhibition.

Switchable Na+ and K+ selectivity in an amino acid functionalized 2D covalent organic framework membrane

Biological cell membranes can efficiently switch Na⁺/K⁺ selectivity in response to external stimuli, but achieving analogous functions in a single artificial membrane is challenging. Here, we report highly crystalline covalent organic framework (COF) membranes with well-defined nanochannels and coordinative sites (i. e., amino acid) that act as ion-selective switches to manipulate Na⁺ and K⁺ transport. The ion selectivity of the COF membrane is dynamic and can be switched between K⁺-selective and Na⁺-selective in a single membrane by applying a pH stimulus. The experimental results combined with molecular dynamics simulations reveal that the switchable Na⁺/K⁺ selectivity originates from the differentiated coordination interactions between ions and amino acids. Benefiting from the switchable Na⁺/K⁺ selectivity, we further demonstrate the membrane potential switches by varying electrolyte pH, miming the membrane polarity reversal during neural signal transduction in vivo, suggesting the great potential of these membranes for in vitro biomimetic applications.

Structural Advances in Voltage-Gated Sodium Channels

Voltage-gated sodium (Na_V) channels are responsible for the rapid rising-phase of action potentials in excitable cells. Over 1,000 mutations in Na_V channels are associated with human diseases including epilepsy, periodic paralysis, arrhythmias and pain disorders. Natural toxins and clinically-used small-molecule drugs bind to Na_V channels and modulate their functions. Recent advances from cryo-electron microscopy (cryo-EM) structures of Na_V channels reveal invaluable insights into the architecture, activation, fast inactivation, electromechanical coupling, ligand modulation and pharmacology of eukaryotic Na_V channels. These structural analyses not only demonstrate molecular mechanisms for Na_V channel structure and function, but also provide atomic level templates for rational development of potential subtype-selective therapeutics. In this review, we summarize recent structural advances of eukaryotic Na_V channels, highlighting the structural features of eukaryotic Na_V channels as well as distinct modulation mechanisms by a wide range of modulators from natural toxins to synthetic small-molecules.

The insights into calcium ion selectivity provided by ancestral prokaryotic ion channels

Prokaryotic channels play an important role in the structural biology of ion channels. At the end of the 20^th century, the first structure of a prokaryotic ion channel was revealed. Subsequently, the reporting of structures of various prokaryotic ion channels have provided fundamental insights into the structure of ion channels of higher organisms. Voltage-dependent Ca²⁺ channels (Cavs) are indispensable for coupling action potentials with Ca²⁺ signaling. Similar to other proteins, Cavs were predicted to have a prokaryotic counterpart; however, it has taken more than 20 years for one to be identified. The homotetrameric channel obtained from Meiothermus ruber generates the calcium ion specific current, so it is named as CavMr. Its selectivity filter contains a smaller number of negatively charged residues than mutant Cavs generated from other prokaryotic channels. CavMr belonged to a different cluster of phylogenetic trees than canonical prokaryotic cation channels. The glycine residue of the CavMr selectivity filter is a determinant for calcium selectivity. This glycine residue is conserved among eukaryotic Cavs, suggesting that there is a universal mechanism for calcium selectivity. A family of homotetrameric channels has also been identified from eukaryotic unicellular algae, and the investigation of these channels can help to understand the mechanism for ion selection that is conserved from prokaryotes to eukaryotes.

An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine

Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.

Artificial sodium-selective ionic device based on crown-ether crystals with subnanometer pores

Biological sodium channels ferry sodium ions across the lipid membrane while rejecting potassium ions and other metal ions. Realizing such ion selectivity in an artificial solid-state ionic device will enable new separation technologies but remains highly challenging. In this work, we report an artificial sodium-selective ionic device, built on synthesized porous crown-ether crystals which consist of densely packed 0.26-nm-wide pores. The Na⁺ selectivity of the artificial sodium-selective ionic device reached 15 against K⁺, which is comparable to the biological counterpart, 523 against Ca^2 +, which is nearly two orders of magnitude higher than the biological one, and 1128 against Mg^2 +. The selectivity may arise from the size effect and molecular recognition effect. This work may contribute to the understanding of the structure-performance relationship of ion selective nanopores.

In vitro discovery of novel prokaryotic ion channel candidates for antiarrhythmic gene therapy

Sudden cardiac death continues to have a devastating impact on public health prompting the continued efforts to develop more effective therapies for cardiac arrhythmias. Among different approaches to normalize function of ion channels and prevent arrhythmogenic remodeling of tissue substrate, cardiac cell and gene therapies are emerging as promising strategies to restore and maintain normal heart rhythm. Specifically, the ability to genetically enhance electrical excitability of diseased hearts through voltage-gated sodium channel (VGSC) gene transfer could improve velocity of action potential conduction and act to stop reentrant circuits underlying sustained arrhythmias. For this purpose, prokaryotic VGSC genes are promising therapeutic candidates due to their small size (<1kb) and potential to be effectively packaged in adeno-associated viral (AAV) vectors and delivered to cardiomyocytes for stable, long-term expression. This article describes a versatile method to discover and characterize novel prokaryotic ion channels for use in gene and cell therapies for heart disease including cardiac arrhythmias. Detailed protocols are provided for: (1) identification of potential ion channel candidates from large genomic databases, (2) candidate screening and characterization using site-directed mutagenesis and engineered human excitable cell system and, (3) candidate validation using electrophysiological techniques and an in vitro model of impaired cardiac impulse conduction.

Brevetoxin and Conotoxin Interactions with Single-Domain Voltage-Gated Sodium Channels from a Diatom and Coccolithophore

The recently characterized single-domain voltage-gated ion channels from eukaryotic protists (EukCats) provide an array of novel channel proteins upon which to test the pharmacology of both clinically and environmentally relevant marine toxins. Here, we examined the effects of the hydrophilic µ-CTx PIIIA and the lipophilic brevetoxins PbTx-2 and PbTx-3 on heterologously expressed EukCat ion channels from a marine diatom and coccolithophore. Surprisingly, none of the toxins inhibited the peak currents evoked by the two EukCats tested. The lack of homology in the outer pore elements of the channel may disrupt the binding of µ-CTx PIIIA, while major structural differences between mammalian sodium channels and the C-terminal domains of the EukCats may diminish interactions with the brevetoxins. However, all three toxins produced significant negative shifts in the voltage dependence of activation and steady state inactivation, suggesting alternative and state-dependent binding conformations that potentially lead to changes in the excitability of the phytoplankton themselves.

Application of a Statistical and Linear Response Theory to Multi-Ion Na+ Conduction in NaChBac

Biological ion channels are fundamental to maintaining life. In this manuscript we apply our recently developed statistical and linear response theory to investigate Na+ conduction through the prokaryotic Na+ channel NaChBac. This work is extended theoretically by the derivation of ionic conductivity and current in an electrochemical gradient, thus enabling us to compare to a range of whole-cell data sets performed on this channel. Furthermore, we also compare the magnitudes of the currents and populations at each binding site to previously published single-channel recordings and molecular dynamics simulations respectively. In doing so, we find excellent agreement between theory and data, with predicted energy barriers at each of the four binding sites of ∼4,2.9,3.6, and 4kT.

Are antibacterial effects of non-antibiotic drugs random or purposeful because of a common evolutionary origin of bacterial and mammalian targets?

Purpose

Advances in structural biology, genetics, bioinformatics, etc. resulted in the availability of an enormous pool of information enabling the analysis of the ancestry of pro- and eukaryotic genes and proteins.

Methods

This review summarizes findings of structural and/or functional homologies of pro- and eukaryotic enzymes catalysing analogous biological reactions because of their highly conserved active centres so that non-antibiotics interacted with bacterial targets.

Results

Protease inhibitors such as staurosporine or camostat inhibited bacterial serine/threonine or serine/tyrosine protein kinases, serine/threonine phosphatases, and serine/threonine kinases, to which penicillin-binding-proteins are linked, so that these drugs synergized with β-lactams, reverted aminoglycoside-resistance and attenuated bacterial virulence. Calcium antagonists such as nitrendipine or verapamil blocked not only prokaryotic ion channels but interacted with negatively charged bacterial cell membranes thus disrupting membrane energetics and inducing membrane stress response resulting in inhibition of P-glycoprotein such as bacterial pumps thus improving anti-mycobacterial activities of rifampicin, tetracycline, fluoroquinolones, bedaquilin and imipenem-activity against Acinetobacter spp. Ciclosporine and tacrolimus attenuated bacterial virulence. ACE-inhibitors like captopril interacted with metallo-β-lactamases thus reverting carbapenem-resistance; prokaryotic carbonic anhydrases were inhibited as well resulting in growth impairment. In general, non-antibiotics exerted weak antibacterial activities on their own but synergized with antibiotics, and/or reverted resistance and/or attenuated virulence.

Conclusions

Data summarized in this review support the theory that prokaryotic proteins represent targets for non-antibiotics because of a common evolutionary origin of bacterial- and mammalian targets resulting in highly conserved active centres of both, pro- and eukaryotic proteins with which the non-antibiotics interact and exert antibacterial actions.

Changes in Ion Selectivity Following the Asymmetrical Addition of Charge to the Selectivity Filter of Bacterial Sodium Channels

Voltage-gated sodium channels (NaVs) play fundamental roles in eukaryotes, but their exceptional size hinders their structural resolution. Bacterial NaVs are simplified homologues of their eukaryotic counterparts, but their use as models of eukaryotic Na⁺ channels is limited by their homotetrameric structure at odds with the asymmetric Selectivity Filter (SF) of eukaryotic NaVs. This work aims at mimicking the SF of eukaryotic NaVs by engineering radial asymmetry into the SF of bacterial channels. This goal was pursued with two approaches: the co-expression of different monomers of the NaChBac bacterial channel to induce the random assembly of heterotetramers, and the concatenation of four bacterial monomers to form a concatemer that can be targeted by site-specific mutagenesis. Patch-clamp measurements and Molecular Dynamics simulations showed that an additional gating charge in the SF leads to a significant increase in Na⁺ and a modest increase in the Ca²⁺ conductance in the NavMs concatemer in agreement with the behavior of the population of random heterotetramers with the highest proportion of channels with charge -5e. We thus showed that charge, despite being important, is not the only determinant of conduction and selectivity, and we created new tools extending the use of bacterial channels as models of eukaryotic counterparts.

A Novel Single-Domain Na+-Selective Voltage-Gated Channel in Photosynthetic Eukaryotes

The evolution of Na⁺-selective four-domain voltage-gated channels (4D-Na_vs) in animals allowed rapid Na⁺-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signaling. While bacteria encode single-domain Na⁺-selective voltage-gated channels (BacNa_v), they typically exhibit much slower kinetics than 4D-Na_vs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na⁺-selective signaling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus flytrap (Dionaea muscipula) where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na⁺-selective, single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores, Emiliania huxleyi and Scyphosphaera apsteinii The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and isoform-specific sensitivity to the highly selective 4D-Na_v blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na⁺-based signaling in eukaryotes is not restricted to animals or to the presence of 4D-Na_vs. The EukCatB channels therefore represent an independent evolution of fast Na⁺-based electrical signaling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae.

Canales de calcio como blanco de interés farmacológico

Los canales de calcio son proteínas de membrana que constituyen la vía más importante para el ingreso del ion calcio (Ca2+) a la célula. Al abrirse, permiten el ingreso selectivo del ion, iniciando una variedad de procesos como contracción muscular, secreción endocrina y liberación de neurotransmisores, entre otros. Estas proteínas se agrupan en tres categorías de acuerdo con sus propiedades estructurales y funcionales: (i) Canales de Ca2+ operados por interacción receptor-ligando (ROCC), (ii) Canales activados por parámetros físicos (Transient Receptor Potencial, TRP) y (iii) Canales de Calcio dependientes de voltaje (VDCCs), siendo estos últimos los más estudiados debido a su presencia en células excitables. Dada la importancia de Ca2+ en la fisiología celular, los canales de Ca2+ constituyen un punto de acción farmacológica importante para múltiples tratamientos y, por tanto, son objeto de estudio para el desarrollo de nuevos fármacos. El objetivo de esta revisión es explicar la importancia de los canales de Ca2+ desde una proyección farmacológica, a partir de la exploración documental de artículos publicados hasta la fecha teniendo en cuenta temas relacionados con la estructura de los canales Ca2+, sus propiedades biofísicas, localización celular, funcionamiento y su interacción farmacológica.

Ionic Coulomb blockade and the determinants of selectivity in the NaChBac bacterial sodium channel

Mutation-induced transformations of conductivity and selectivity in NaChBac bacterial channels are studied experimentally and interpreted within the framework of ionic Coulomb blockade (ICB), while also taking account of resonant quantised dehydration (QD) and site protonation. Site-directed mutagenesis and whole-cell patch-clamp experiments are used to investigate how the fixed charge Q_f at the selectivity filter (SF) affects both valence selectivity and same-charge selectivity. The new ICB/QD model predicts that increasing ∣Q_f∣ should lead to a shift in selectivity sequences toward larger ion sizes, in agreement with the present experiments and with earlier work. Comparison of the model with experimental data leads to the introduction of an effective charge Q_f^∗ at the SF, which was found to differ between Aspartate and Glutamate charged rings, and also to depend on position within the SF. It is suggested that protonation of the residues within the restricted space of the SF is important in significantly reducing the effective charge of the EEEE ring. Values of Q_f^∗ derived from experiments on divalent blockade agree well with expectations based on the ICB/QD model and have led to the first demonstration of ICB oscillations in Ca²⁺ conduction as a function of the fixed charge. Preliminary studies of the dependence of Ca²⁺ conduction on pH are qualitatively consistent with the predictions of the model.

A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence

Voltage-dependent Ca²⁺ channels (Cavs) are indispensable for coupling action potentials with Ca²⁺ signaling in living organisms. The structure of Cavs is similar to that of voltage-dependent Na⁺ channels (Navs). It is known that prokaryotic Navs can obtain Ca²⁺ selectivity by negative charge mutations of the selectivity filter, but native prokaryotic Cavs had not yet been identified. We report the first identification of a native prokaryotic Cav, CavMr, whose selectivity filter contains a smaller number of negatively charged residues than that of artificial prokaryotic Cavs. A relative mutant whose selectivity filter was replaced with that of CavMr exhibits high Ca²⁺ selectivity. Mutational analyses revealed that the glycine residue of the CavMr selectivity filter is a determinant for Ca²⁺ selectivity. This glycine residue is well conserved among subdomains I and III of eukaryotic Cavs. These findings provide new insight into the Ca²⁺ selectivity mechanism that is conserved from prokaryotes to eukaryotes.

Electrical signals in the brain and muscles allow animals – including humans – to think, make memories and move around. Cells generate these signals by enabling charged particles known as ions to pass through the physical barrier that surrounds all cells, the cell membrane, at certain times and in certain locations.

The ions pass through pores made by various channel proteins, which generally have so-called “selectivity filters” that only allow particular types of ions to fit through. For example, the selectivity filters of a family of channels in mammals known as the Cavs only allow calcium ions to pass through. Another family of ion channels in mammals are similar in structure to the Cavs but their selectivity filters only allow sodium ions to pass through instead of calcium ions.

Ion channels are found in all living cells including in bacteria. It is thought that the Cavs and sodium-selective channels may have both evolved from Cav-like channels in an ancient lifeform that was the common ancestor of modern bacteria and animals. Previous studies in bacteria found that modifying the selectivity filters of some sodium-selective channels known as BacNavs allowed calcium ions to pass through the mutant channels instead of sodium ions. However, no Cav channels had been identified in bacteria so far, representing a missing link in the evolutionary history of ion channels.

Shimomura et al. have now found a Cav-like channel in a bacterium known as Meiothermus ruber. Like all proteins, ion channels are made from amino acids and comparing the selectivity filter of the M. ruber Cav with those of mammalian Cavs and the calcium-selective BacNav mutants from previous studies revealed one amino acid that plays a particularly important role. This amino acid is a glycine that helps select which ions may pass through the pore and is also present in the selectivity filters of many Cavs in mammals.

Together these findings suggest that the Cav channel from M. ruber is similar to the mammal Cav channels and may more closely resemble the Cav-like channels thought to have existed in the common ancestor of bacteria and animals. Since other channel proteins from bacteria are useful genetic tools for studies in human and other animal cells, the Cav channel from M. ruber has the potential to be used to stimulate calcium signaling in experiments.

Structure and Pharmacology of Voltage-Gated Sodium and Calcium Channels

Voltage-gated sodium and calcium channels are evolutionarily related transmembrane signaling proteins that initiate action potentials, neurotransmission, excitation-contraction coupling, and other physiological processes. Genetic or acquired dysfunction of these proteins causes numerous diseases, termed channelopathies, and sodium and calcium channels are the molecular targets for several major classes of drugs. Recent advances in the structural biology of these proteins using X-ray crystallography and cryo-electron microscopy have given new insights into the molecular basis for their function and pharmacology. Here we review this recent literature and integrate findings on sodium and calcium channels to reveal the structural basis for their voltage-dependent activation, fast and slow inactivation, ion conductance and selectivity, and complex pharmacology at the atomic level. We conclude with the theme that new understanding of the diseases and therapeutics of these channels will be derived from application of the emerging structural principles from these recent structural analyses.

Resonance-driven ion transport and selectivity in prokaryotic ion channels

Ion channels exhibit a remarkably high accuracy in selecting uniquely its associated type of ion. The mechanisms behind ion selectivity are not well understood. Current explanations build mainly on molecular biology and bioinformatics. Here we propose a simple physical model for ion selectivity based on the driven damped harmonic oscillator (DDHO). The driving force for this oscillator is provided by self-organizing harmonic turbulent structures in the dehydrating ionic flow through the ion channel, namely, oscillating pressure waves in one dimension, and toroidal vortices in two and three dimensions. Density fluctuations caused by these turbulences efficiently transmit their energy to aqua ions that resonate with the driving frequency. Consequently, these release their hydration shell and exit the ion channel as free ions. Existing modeling frameworks do not express the required complex spatiotemporal dynamics, hence we introduce a macroscopic continuum model for ionic dehydration and transport, based on the hydrodynamics of a dissipative ionic flow through an ion channel, subject to electrostatic and amphiphilic interactions. This model combines three classical physical fields: Navier-Stokes equations from hydrodynamics, Gauss's law from Maxwell theory, and the convection-diffusion equation from continuum physics. Numerical experiments with mixtures of chemical species of ions in various degrees of hydration indeed reveal the emergence of strong oscillations in the ionic flow that are instrumental in the efficient dehydration and cause a strong ionic jet into the cell. As such, they provide a powerful engine for the DDHO mechanism. Theoretical predictions of the modeling framework match significantly with empirical patch-clamp data. The DDHO standard response curve defines a unique resonance frequency that depends on the mass and charge of the ion. In this way, the driving oscillations act as a selection mechanism that filters out one specific ion. Application of the DDHO model to real ion data shows that this mechanism indeed clearly distinguishes between chemical species and between aqua and bare ions with a large Mahalanobis distance and high oscillator quality. The DDHO framework helps to understand how SNP mutations can cause severe genetic pathologies as they destroy the geometry of the channel and so alter the resonance peaks of the required ion type.

Bases of Bacterial Sodium Channel Selectivity Among Organic Cations

Hille's (1971) seminal study of organic cation selectivity of eukaryotic voltage-gated sodium channels showed a sharp size cut-off for ion permeation, such that no ion possessing a methyl group was permeant. Using the prokaryotic channel, NaChBac, we found some similarity and two peculiar differences in the selectivity profiles for small polyatomic cations. First, we identified a diverse group of minimally permeant cations for wildtype NaChBac, ranging in sizes from ammonium to guanidinium and tetramethylammonium; and second, for both ammonium and hydrazinium, the charge-conserving selectivity filter mutation (E191D) yielded substantial increases in relative permeability (PX/PNa). The relative permeabilities varied inversely with relative Kd calculated from 1D Potential of Mean Force profiles (PMFs) for the single cations traversing the channel. Several of the cations bound more strongly than Na+, and hence appear to act as blockers, as well as charge carriers. Consistent with experimental observations, the E191D mutation had little impact on Na+ binding to the selectivity filter, but disrupted the binding of ammonium and hydrazinium, consequently facilitating ion permeation across the NaChBac-like filter. We concluded that for prokaryotic sodium channels, a fine balance among filter size, binding affinity, occupancy, and flexibility seems to contribute to observed functional differences.

Alternative Mechanisms for Fast Na+/Ca2+ Signaling in Eukaryotes via a Novel Class of Single-Domain Voltage-Gated Channels

Rapid Na⁺/Ca²⁺-based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na⁺/Ca²⁺ channels (4D-Ca_vs/Na_vs). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca_v/Na_vs [5, 6, 7]. Because these lineages appear to lack rapid Na⁺/Ca²⁺-based action potentials, 4D-Ca_v/Na_vs are generally considered necessary for fast Na⁺/Ca²⁺-based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8, 9, 10]. We previously demonstrated that certain diatom genomes encode 4D-Ca_v/Na_vs [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na⁺ channels (BacNa_vs) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na⁺- and Ca²⁺-permeable channels, with rapid kinetics resembling metazoan 4D-Ca_vs/Na_vs. In Phaeodactylum tricornutum, which lacks 4D-Ca_v/Na_vs, EukCatAs underpin voltage-activated Ca²⁺ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na⁺/Ca²⁺ signaling in eukaryotes and may functionally replace 4D-Ca_vs/Na_vs in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans.

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Novel class of single-domain, voltage-gated channels (EukCatAs) identified in diatoms

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EukCatAs are fast voltage-gated Na⁺- and Ca²⁺-permeable channels

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EukCatAs underpin voltage-activated Ca²⁺ signaling and membrane excitability

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EukCatAs may have functionally replaced 4D-Ca_v/Na_v channels in pennate diatoms

Different roles for aspartates and glutamates for cation permeation in bacterial sodium channels

A key driving force for ion channel selectivity is represented by the negative charge of the Selectivity Filter carried by aspartate (D) and glutamate (E) residues. However, the structural effects and specific properties of D and E residues have not been extensively studied. In order to investigate this issue we studied the mutants of NaChBac channel with all possible combinations of D and E in the charged rings in position 191 and 192. Electrophysiological measurements showed significant Ca²⁺ currents only when position 191 was occupied by E. Equilibrium Molecular Dynamics simulations revealed the existence of two binding sites, corresponding to the charged rings and another one, more internal, at the level of L190. The simulations showed that the ion in the innermost site can interact with the residue in position 191 only when this is glutamate. Based on the MD simulations, we suggest that a D in position 191 leads to a high affinity Ca²⁺ block site resulting from a significant drop in the free energy of binding for an ion moving between the binding sites; in contrast, the free energy change is more gradual when an E residue occupies position 191, resulting in Ca²⁺ permeability. This scenario is consistent with the model of ion channel selectivity through stepwise changes in binding affinity proposed by Dang and McCleskey. Our study also highlights the importance of the structure of the selectivity filter which should contribute to the development of more detailed physical models for ion channel selectivity.

Eukaryotic Voltage-Gated Sodium Channels: On Their Origins, Asymmetries, Losses, Diversification and Adaptations

The appearance of voltage-gated, sodium-selective channels with rapid gating kinetics was a limiting factor in the evolution of nervous systems. Two rounds of domain duplications generated a common 24 transmembrane segment (4 × 6 TM) template that is shared amongst voltage-gated sodium (Na_v1 and Na_v2) and calcium channels (Ca_v1, Ca_v2, and Ca_v3) and leak channel (NALCN) plus homologs from yeast, different single-cell protists (heterokont and unikont) and algae (green and brown). A shared architecture in 4 × 6 TM channels include an asymmetrical arrangement of extended extracellular L5/L6 turrets containing a 4-0-2-2 pattern of cysteines, glycosylated residues, a universally short III-IV cytoplasmic linker and often a recognizable, C-terminal PDZ binding motif. Six intron splice junctions are conserved in the first domain, including a rare U12-type of the minor spliceosome provides support for a shared heritage for sodium and calcium channels, and a separate lineage for NALCN. The asymmetrically arranged pores of 4x6 TM channels allows for a changeable ion selectivity by means of a single lysine residue change in the high field strength site of the ion selectivity filter in Domains II or III. Multicellularity and the appearance of systems was an impetus for Na_v1 channels to adapt to sodium ion selectivity and fast ion gating. A non-selective, and slowly gating Na_v2 channel homolog in single cell eukaryotes, predate the diversification of Na_v1 channels from a basal homolog in a common ancestor to extant cnidarians to the nine vertebrate Na_v1.x channel genes plus Nax. A close kinship between Na_v2 and Na_v1 homologs is evident in the sharing of most (twenty) intron splice junctions. Different metazoan groups have lost their Na_v1 channel genes altogether, while vertebrates rapidly expanded their gene numbers. The expansion in vertebrate Na_v1 channel genes fills unique functional niches and generates overlapping properties contributing to redundancies. Specific nervous system adaptations include cytoplasmic linkers with phosphorylation sites and tethered elements to protein assemblies in First Initial Segments and nodes of Ranvier. Analogous accessory beta subunit appeared alongside Na_v1 channels within different animal sub-phyla. Na_v1 channels contribute to pace-making as persistent or resurgent currents, the former which is widespread across animals, while the latter is a likely vertebrate adaptation.

Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel

Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the presence of a novel motif consisting of an extensive network of salt bridges involving residues in the voltage sensor, S4-S5 linker, pore, and C-terminal domains. This motif has been proposed to be responsible for maintaining an open conformation that enables ion translocation through the channel. In this study, we have used long-time molecular dynamics calculations without artificial restraints to demonstrate that the interaction network of full-length NavMs indeed prevents a rapid collapse and closure of the gate, in marked difference to earlier studies of the pore-only construct in which the gate had to be restrained to remain open. Interestingly, a frequently discussed "hydrophobic gating" mechanism at nanoscopic level is also observed in our simulations, in which the discontinuous water wire close to the gate region leads to an energetic barrier for ion conduction. In addition, we demonstrate the effects of in silico mutations of several of the key residues in the motif on the open channel's stability and functioning, correlating them with existing functional studies on this channel and homologous disease-associated mutations in human sodium channels; we also examine the effects of truncating/removing the voltage sensor and C-terminal domains in maintaining an open gate.

Structural and Functional Analysis of Sodium Channels Viewed from an Evolutionary Perspective

Voltage-gated sodium channels initiate and propagate action potentials in excitable cells. They respond to membrane depolarization through opening, followed by fast inactivation that terminates the sodium current. This ON-OFF behavior of voltage-gated sodium channels underlays the coding of information and its transmission from one location in the nervous system to another. In this review, we explore and compare structural and functional data from prokaryotic and eukaryotic channels to infer the effects of evolution on sodium channel structure and function.

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.

Comparison of permeation mechanisms in sodium-selective ion channels

Voltage-gated sodium channels are the molecular components of electrical signaling in the body, yet the molecular origins of Na⁺-selective transport remain obscured by diverse protein chemistries within this family of ion channels. In particular, bacterial and mammalian sodium channels are known to exhibit similar relative ion permeabilities for Na⁺ over K⁺ ions, despite their distinct signature EEEE and DEKA sequences. Atomic-level molecular dynamics simulations using high-resolution bacterial channel structures and mammalian channel models have begun to describe how these sequences lead to analogous high field strength ion binding sites that drive Na⁺ conduction. Similar complexes have also been identified in unrelated acid sensing ion channels involving glutamate and aspartate side chains that control their selectivity. These studies suggest the possibility of a common origin for Na⁺ selective binding and transport.

Cross-kingdom auxiliary subunit modulation of a voltage-gated sodium channel

Voltage-gated, sodium ion-selective channels (NaV) generate electrical signals contributing to the upstroke of the action potential in animals. NaVs are also found in bacteria and are members of a larger family of tetrameric voltage-gated channels that includes CaVs, KVs, and NaVs. Prokaryotic NaVs likely emerged from a homotetrameric Ca2+-selective voltage-gated progenerator, and later developed Na+ selectivity independently. The NaV signaling complex in eukaryotes contains auxiliary proteins, termed beta (β) subunits, which are potent modulators of the expression profiles and voltage-gated properties of the NaV pore, but it is unknown whether they can functionally interact with prokaryotic NaV channels. Herein, we report that the eukaryotic NaVβ1-subunit isoform interacts with and enhances the surface expression as well as the voltage-dependent gating properties of the bacterial NaV, NaChBac in Xenopus oocytes. A phylogenetic analysis of the β-subunit gene family proteins confirms that these proteins appeared roughly 420 million years ago and that they have no clear homologues in bacterial phyla. However, a comparison between eukaryotic and bacterial NaV structures highlighted the presence of a conserved fold, which could support interactions with the β-subunit. Our electrophysiological, biochemical, structural, and bioinformatics results suggests that the prerequisites for β-subunit regulation are an evolutionarily stable and intrinsic property of some voltage-gated channels.

Interaction of a dinoflagellate neurotoxin with voltage-activated ion channels in a marine diatom

Background

The potent neurotoxins produced by the harmful algal bloom species Karenia brevis are activators of sodium voltage-gated channels (VGC) in animals, resulting in altered channel kinetics and membrane hyperexcitability. Recent biophysical and genomic evidence supports widespread presence of homologous sodium (Na⁺) and calcium (Ca²⁺) permeable VGCs in unicellular algae, including marine phytoplankton. We therefore hypothesized that VGCs of these phytoplankton may be an allelopathic target for waterborne neurotoxins produced by K. brevis blooms that could lead to ion channel dysfunction and disruption of signaling in a similar manner to animal Na⁺ VGCs.

Methods

We examined the interaction of brevetoxin-3 (PbTx-3), a K. brevis neurotoxin, with the Na⁺/Ca²⁺ VGC of the non-toxic diatom Odontella sinensis using electrophysiology. Single electrode current- and voltage- clamp recordings from O. sinensis in the presence of PbTx-3 were used to examine the toxin’s effect on voltage gated Na⁺/Ca²⁺ currents. In silico analysis was used to identify the putative PbTx binding site in the diatoms. We identified Na⁺/Ca²⁺ VCG homologs from the transcriptomes and genomes of 12 diatoms, including three transcripts from O. sinensis and aligned them with site-5 of Na⁺ VGCs, previously identified as the PbTx binding site in animals.

Results

Up to 1 µM PbTx had no effect on diatom resting membrane potential or membrane excitability. The kinetics of fast inward Na⁺/Ca²⁺ currents that underlie diatom action potentials were also unaffected. However, the peak inward current was inhibited by 33%, delayed outward current was inhibited by 25%, and reversal potential of the currents shifted positive, indicating a change in permeability of the underlying channels. Sequence analysis showed a lack of conservation of the PbTx binding site in diatom VGC homologs, many of which share molecular features more similar to single-domain bacterial Na⁺/Ca²⁺ VGCs than the 4-domain eukaryote channels.

Discussion

Although membrane excitability and the kinetics of action potential currents were unaffected, the permeation of the channels underlying the diatom action potential was significantly altered in the presence of PbTx-3. However, at environmentally relevant concentrations the effects of PbTx- on diatom voltage activated currents and interference of cell signaling through this pathway may be limited. The relative insensitivity of phytoplankton VGCs may be due to divergence of site-5 (the putative PbTx binding site), and in some cases, such as O. sinensis, resistance to toxin effects may be because of evolutionary loss of the 4-domain eukaryote channel, while retaining a single domain bacterial-like VGC that can substitute in the generation of fast action potentials.

Npas4 Is a Critical Regulator of Learning-Induced Plasticity at Mossy Fiber-CA3 Synapses during Contextual Memory Formation

Synaptic connections between hippocampal mossy fibers (MFs) and CA3 pyramidal neurons are essential for contextual memory encoding, but the molecular mechanisms regulating MF-CA3 synapses during memory formation and the exact nature of this regulation are poorly understood. Here we report that the activity-dependent transcription factor Npas4 selectively regulates the structure and strength of MF-CA3 synapses by restricting the number of their functional synaptic contacts without affecting the other synaptic inputs onto CA3 pyramidal neurons. Using an activity-dependent reporter, we identified CA3 pyramidal cells that were activated by contextual learning and found that MF inputs on these cells were selectively strengthened. Deletion of Npas4 prevented both contextual memory formation and this learning-induced synaptic modification. We further show that Npas4 regulates MF-CA3 synapses by controlling the expression of the polo-like kinase Plk2. Thus, Npas4 is a critical regulator of experience-dependent, structural, and functional plasticity at MF-CA3 synapses during contextual memory formation.

On the selectivity of the NaChBac channel: an integrated computational and experimental analysis of sodium and calcium permeation

Ion channel selectivity is essential for their function, yet the molecular basis of a channel's ability to select between ions is still rather controversial. In this work, using a combination of molecular dynamics simulations and electrophysiological current measurements we analyze the ability of the NaChBac channel to discriminate between calcium and sodium. Our simulations show that a single calcium ion can access the Selectivity Filter (SF) interacting so strongly with the glutamate ring so as to remain blocked inside. This is consistent with the tiny calcium currents recorded in our patch-clamp experiments. Two reasons explain this scenario. The first is the higher free energy of ion/SF binding of Ca²⁺ with respect to Na⁺. The second is the strong electrostatic repulsion exerted by the resident ion that turns back a second potentially incoming Ca²⁺, preventing the knock-on permeation mechanism. Finally, we analyzed the possibility of the Anomalous Mole Fraction Effect (AMFE), i.e. the ability of micromolar Ca²⁺ concentrations to block Na⁺ currents. Current measurements in Na⁺/Ca²⁺ mixed solutions excluded the AMFE, in agreement with metadynamics simulations showing the ability of a sodium ion to by-pass and partially displace the resident calcium. Our work supports a new scenario for Na⁺/Ca²⁺ selectivity in the bacterial sodium channel, challenging the traditional notion of an exclusion mechanism strictly confining Ca²⁺ ions outside the channel.

Evolutionary History of Voltage-Gated Sodium Channels

Every cell within living organisms actively maintains an intracellular Na⁺ concentration that is 10-12 times lower than the extracellular concentration. The cells then utilize this transmembrane Na⁺ concentration gradient as a driving force to produce electrical signals, sometimes in the form of action potentials. The protein family comprising voltage-gated sodium channels (Na_Vs) is essential for such signaling and enables cells to change their status in a regenerative manner and to rapidly communicate with one another. Na_Vs were first predicted in squid and were later identified through molecular biology in the electric eel. Since then, these proteins have been discovered in organisms ranging from bacteria to humans. Recent research has succeeded in decoding the amino acid sequences of a wide variety of Na_V family members, as well as the three-dimensional structures of some. These studies and others have uncovered several of the major steps in the functional and structural transition of Na_V proteins that has occurred along the course of the evolutionary history of organisms. Here we present an overview of the molecular evolutionary innovations that established present-day Na_V α subunits and discuss their contribution to the evolutionary changes in animal bodies.

The chemical basis for electrical signaling

Electrical signals generated by minute currents of ions moving across cell membranes are central to all rapid processes in biology. Initiation and propagation of electrical signals requires voltage-gated sodium (Na_V) and calcium (Ca_V) channels. These channels contain a tetramer of membrane-bound subunits or domains comprising a voltage sensor and a pore module. Voltage-dependent activation occurs as membrane depolarization drives outward movements of positive gating changes in the voltage sensor via a sliding-helix mechanism, which leads to a conformational change in the pore module that opens its intracellular activation gate. A unique negatively charged site in the selectivity filter conducts hydrated Na⁺ or Ca²⁺ rapidly and selectively. Ion conductance is terminated by voltage-dependent inactivation, which causes asymmetric pore collapse. This Review focuses on recent advances in structure and function of Na_V and Ca_V channels that expand our current understanding of the chemical basis for electrical signaling mechanisms conserved from bacteria to humans.

Isoflurane modulates activation and inactivation gating of the prokaryotic Na+ channel NaChBac

The pharmacological effects of inhaled anesthetics on ion channel function are poorly understood. Sand et al. analyze macroscopic gating of the prokaryotic voltage-gated sodium channel, NaChBac, using a six-state kinetic scheme and demonstrate that isoflurane modulates microscopic gating properties.

Voltage-gated Na⁺ channels (Na_v) have emerged as important presynaptic targets for volatile anesthetic (VA) effects on synaptic transmission. However, the detailed biophysical mechanisms by which VAs modulate Na_v function remain unclear. VAs alter macroscopic activation and inactivation of the prokaryotic Na⁺ channel, NaChBac, which provides a useful structural and functional model of mammalian Na_v. Here, we study the effects of the common general anesthetic isoflurane on NaChBac function by analyzing macroscopic Na⁺ currents (I_Na) in wild-type (WT) channels and mutants with impaired (G229A) or enhanced (G219A) inactivation. We use a previously described six-state Markov model to analyze empirical WT and mutant NaChBac channel gating data. The model reproduces the mean empirical gating manifest in I_Na time courses and optimally estimates microscopic rate constants, valences (z), and fractional electrical distances (x) of forward and backward transitions. The model also reproduces gating observed for all three channels in the absence or presence of isoflurane, providing further validation. We show using this model that isoflurane increases forward activation and inactivation rate constants at 0 mV, which are associated with estimated chemical free energy changes of approximately −0.2 and −0.7 kcal/mol, respectively. Activation is voltage dependent (z ≈ 2e₀, x ≈ 0.3), inactivation shows little voltage dependence, and isoflurane has no significant effect on either. Forward inactivation rate constants are more than 20-fold greater than backward rate constants in the absence or presence of isoflurane. These results indicate that isoflurane modulates NaChBac gating primarily by increasing forward activation and inactivation rate constants. These findings support accumulating evidence for multiple sites of anesthetic interaction with the channel.

Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution

Voltage-gated sodium (Na_v) channels are responsible for the initiation and propagation of action potentials. They are associated with a variety of channelopathies and are targeted by multiple pharmaceutical drugs and natural toxins. Here, we report the cryogenic electron microscopy structure of a putative Na_v channel from American cockroach (designated Na_vPaS) at 3.8 angstrom resolution. The voltage-sensing domains (VSDs) of the four repeats exhibit distinct conformations. The entrance to the asymmetric selectivity filter vestibule is guarded by heavily glycosylated and disulfide bond-stabilized extracellular loops. On the cytoplasmic side, a conserved amino-terminal domain is placed below VSD_I, and a carboxy-terminal domain binds to the III-IV linker. The structure of Na_vPaS establishes an important foundation for understanding function and disease mechanism of Na_v and related voltage-gated calcium channels.

Sodium Binding Sites and Permeation Mechanism in the NaChBac Channel: A Molecular Dynamics Study

NaChBac was the first discovered bacterial sodium voltage-dependent channel, yet computational studies are still limited due to the lack of a crystal structure. In this work, a pore-only construct built using the NavMs template was investigated using unbiased molecular dynamics and metadynamics. The potential of mean force (PMF) from the unbiased run features four minima, three of which correspond to sites IN, CEN, and HFS discovered in NavAb. During the run, the selectivity filter (SF) is spontaneously occupied by two ions, and frequent access of a third one is often observed. In the innermost sites IN and CEN, Na⁺ is fully hydrated by six water molecules and occupies an on-axis position. In site HFS sodium interacts with a glutamate and a serine from the same subunit and is forced to adopt an off-axis placement. Metadynamics simulations biasing one and two ions show an energy barrier in the SF that prevents single-ion permeation. An analysis of the permeation mechanism was performed both computing minimum energy paths in the axial-axial PMF and through a combination of Markov state modeling and transition path theory. Both approaches reveal a knock-on mechanism involving at least two but possibly three ions. The currents predicted from the unbiased simulation using linear response theory are in excellent agreement with single-channel patch-clamp recordings.

Voltage-gated sodium channels viewed through a structural biology lens

Voltage-gated sodium (Nav) channels initiate and propagate action potentials in excitable cells, and are frequently dysregulated or mutated in human disease. Despite decades of intense physiological and biophysical research, eukaryotic Nav channels have so far eluded high-resolution structure determination because of their biochemical complexity. Recently, simpler bacterial voltage-gated sodium (BacNav) channels have provided templates to understand the structural basis of voltage-dependent activation, inactivation, ion selectivity, and drug block in eukaryotic Nav and related voltage-gated calcium (Cav) channels. Further breakthroughs employing BacNav channels have also enabled visualization of bound small molecule modulators that can guide the rational design of next generation therapeutics. This review will highlight the emerging structural biology of BacNav channels and its contribution to our understanding of the gating, ion selectivity, and pharmacological regulation of eukaryotic Nav (and Cav) channels.

Engineering prokaryotic channels for control of mammalian tissue excitability

The ability to directly enhance electrical excitability of human cells is hampered by the lack of methods to efficiently overexpress large mammalian voltage-gated sodium channels (VGSC). Here we describe the use of small prokaryotic sodium channels (BacNa_v) to create de novo excitable human tissues and augment impaired action potential conduction in vitro. Lentiviral co-expression of specific BacNa_v orthologues, an inward-rectifying potassium channel, and connexin-43 in primary human fibroblasts from the heart, skin or brain yields actively conducting cells with customizable electrophysiological phenotypes. Engineered fibroblasts ('E-Fibs') retain stable functional properties following extensive subculture or differentiation into myofibroblasts and rescue conduction slowing in an in vitro model of cardiac interstitial fibrosis. Co-expression of engineered BacNa_v with endogenous mammalian VGSCs enhances action potential conduction and prevents conduction failure during depolarization by elevated extracellular K⁺, decoupling or ischaemia. These studies establish the utility of engineered BacNa_v channels for induction, control and recovery of mammalian tissue excitability.

Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels

This chapter describes the adaptive features found in voltage-gated sodium channels (NaVs) of prokaryotes and eukaryotes. These two families are distinct, having diverged early in evolutionary history but maintain a surprising degree of convergence in function. While prokaryotic NaVs are required for growth and motility, eukaryotic NaVs selectively conduct fast electrical currents for short- and long-range signaling across cell membranes in mammalian organs. Current interest in prokaryotic NaVs is stoked by their resolved high-resolution structures and functional features which are reminiscent of eukaryotic NaVs. In this chapter, comparisons between eukaryotic and prokaryotic NaVs are made to highlight the shared and unique aspects of ion selectivity, voltage sensitivity, and pharmacology. Examples of prokaryotic and eukaryotic NaV convergent evolution will be discussed within the context of their structural features.

Lysine and the Na+/K+ Selectivity in Mammalian Voltage-Gated Sodium Channels

Voltage-gated sodium (Na_v) channels are critical in the generation and transmission of neuronal signals in mammals. The crystal structures of several prokaryotic Na_v channels determined in recent years inspire the mechanistic studies on their selection upon the permeable cations (especially between Na⁺ and K⁺ ions), a property that is proposed to be mainly determined by residues in the selectivity filter. However, the mechanism of cation selection in mammalian Na_v channels lacks direct explanation at atomic level due to the difference in amino acid sequences between mammalian and prokaryotic Na_v homologues, especially at the constriction site where the DEKA motif has been identified to determine the Na⁺/K⁺ selectivity in mammalian Na_v channels but is completely absent in the prokaryotic counterparts. Among the DEKA residues, Lys is of the most importance since its mutation to Arg abolishes the Na⁺/K⁺ selectivity. In this work, we modeled the pore domain of mammalian Na_v channels by mutating the four residues at the constriction site of a prokaryotic Na_v channel (Na_vRh) to DEKA, and then mechanistically investigated the contribution of Lys in cation selection using molecular dynamics simulations. The DERA mutant was generated as a comparison to understand the loss of ion selectivity caused by the K-to-R mutation. Simulations and free energy calculations on the mutants indicate that Lys facilitates Na⁺/K⁺ selection by electrostatically repelling the cation to a highly Na⁺-selective location sandwiched by the carboxylate groups of Asp and Glu at the constriction site. In contrast, the electrostatic repulsion is substantially weakened when Lys is mutated to Arg, because of two intrinsic properties of the Arg side chain: the planar geometric design and the sparse charge distribution of the guanidine group.

Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures

Sodium channels are chief proteins involved in electrical signaling in the nervous system, enabling critical functions like heartbeat and brain activity. New high-resolution X-ray structures for bacterial sodium channels have created an opportunity to see how these proteins operate at the molecular level. An important challenge to overcome is establishing relationships between the structures and functions of mammalian and bacterial channels. Bacterial sodium channels are known to exhibit the main structural features of their mammalian counterparts, as well as several key functional characteristics, including selective ion conduction, voltage-dependent gating, pore-based inactivation and modulation by local anesthetic, antiarrhythmic and antiepileptic drugs. Simulations have begun to shed light on each of these features in the past few years. Despite deviations in selectivity signatures for bacterial and mammalian channels, simulations have uncovered the nature of the multiion conduction mechanism associated with Na(+) binding to a high-field strength site established by charged glutamate side chains. Simulations demonstrated a surprising level of flexibility of the protein, showing that these side chains are active participants in the permeation process. They have also uncovered changes in protein structure, leading to asymmetrical collapses of the activation gate that have been proposed to correspond to inactivated structures. These observations offer the potential to examine the mechanisms of state-dependent drug activity, focusing on pore-blocking and pore-based slow inactivation in bacterial channels, without the complexities of inactivation on multiple timescales seen in eukaryotic channels. Simulations have provided molecular views of the interactions of drugs, consistent with sites predicted in mammalian channels, as well as a wealth of other sites as potential new drug targets. In this chapter, we survey the new insights into sodium channel function that have emerged from studies of simpler bacterial channels, which provide an excellent learning platform, and promising avenues for mechanistic discovery and pharmacological development.

Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations

The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs.

Molecular basis of ion permeability in a voltage-gated sodium channel

Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na⁺ ≈ Li⁺ ≫ K⁺, Ca²⁺, Mg²⁺) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.