Ion-triggered selectivity in bacterial sodium channels

Ion channel selectivity through ion-modulated changes of selectivity filter pKa values

In bacterial voltage-gated sodium channels, the passage of ions through the pore is controlled by a selectivity filter (SF) composed of four glutamate residues. The mechanism of selectivity has been the subject of intense research, with suggested mechanisms based on steric effects, and ion-triggered conformational change. Here, we propose an alternative mechanism based on ion-triggered shifts in pKa values of SF glutamates. We study the NavMs channel for which the open channel structure is available. Our free-energy calculations based on molecular dynamics simulations suggest that pKa values of the four glutamates are higher in solution of K+ ions than in solution of Na+ ions. Higher pKa in the presence of K+ stems primarily from the higher population of dunked conformations of the protonated Glu sidechain, which exhibit a higher pKa shift. Since pKa values are close to the physiological pH, this results in predominant population of the fully deprotonated state of glutamates in Na+ solution, while protonated states are predominantly populated in K+ solution. Through molecular dynamics simulations we calculate that the deprotonated state is the most conductive, the singly protonated state is less conductive, and the doubly protonated state has significantly reduced conductance. Thus, we propose that a significant component of selectivity is achieved through ion-triggered shifts in the protonation state, which favors more conductive states for Na+ ions and less conductive states for K+ ions. This mechanism also suggests a strong pH dependence of selectivity, which has been experimentally observed in structurally similar NaChBac channels.

Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels

The recent determination of cryo-EM structures of voltage-gated sodium (Na_v) channels has revealed many details of these proteins. However, knowledge of ionic permeation through the Na_v pore remains limited. In this work, we performed atomistic molecular dynamics (MD) simulations to study the structural features of various neuronal Na_v channels based on homology modeling of the cryo-EM structure of the human Na_v1.4 channel and, in addition, on the recently resolved configuration for Na_v1.2. In particular, single Na⁺ permeation events during standard MD runs suggest that the ion resides in the inner part of the Na_v selectivity filter (SF). On-the-fly free energy parametrization (OTFP) temperature-accelerated molecular dynamics (TAMD) was also used to calculate two-dimensional free energy surfaces (FESs) related to single/double Na⁺ translocation through the SF of the homology-based Na_v1.2 model and the cryo-EM Na_v1.2 structure, with different realizations of the DEKA filter domain. These additional simulations revealed distinct mechanisms for single and double Na⁺ permeation through the wild-type SF, which has a charged lysine in the DEKA ring. Moreover, the configurations of the ions in the SF corresponding to the metastable states of the FESs are specific for each SF motif. Overall, the description of these mechanisms gives us new insights into ion conduction in human Na_v cryo-EM-based and cryo-EM configurations that could advance understanding of these systems and how they differ from potassium and bacterial Na_v channels.

Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel

The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca²⁺. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca²⁺ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca²⁺ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca²⁺ plays a pivotal role.

When Is a Potassium Channel Not a Potassium Channel?

Ever since they were first observed in Purkinje fibers of the heart, funny channels have had close connections to potassium channels. Indeed, funny channels were initially thought to produce a potassium current in the heart called I _K2. However, funny channels are completely unlike potassium channels in ways that make their contributions to the physiology of cells unique. An important difference is the greater ability for sodium to permeate funny channels. Although it does not flow through the funny channel as easily as does potassium, sodium does permeate well enough to allow for depolarization of cells following a strong hyperpolarization. This is critical for the function of funny channels in places like the heart and brain. Computational analyses using recent structures of the funny channels have provided a possible mechanism for their unusual permeation properties.

Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design

Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.

Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity

Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated.

IMPORTANCE Eukaryotic homologs of the progestin and AdipoQ receptor family (PAQR) have been shown to regulate membrane fluidity by affecting, through unknown mechanisms, unsaturated fatty acid (FA) metabolism. The bacterial homologs studied here mediate small and consistent changes in unsaturated FA metabolism that do not seem to impact membrane fluidity but, rather, alter membrane energetics homeostasis. Together, the findings here suggest that bacterial and eukaryotic PAQRs share functions in maintaining membrane homeostasis (fluidity in eukaryotes and energetics for bacteria with TrhA homologs).

Direct proof of soft knock-on mechanism of ion permeation in a voltage gated sodium channel

Sodium channels selectively conduct Na⁺ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na⁺ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na⁺ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug.

Nonselective cation permeation in an AMPA-type glutamate receptor

Fast excitatory synaptic transmission in the central nervous system relies on the AMPA-type glutamate receptor (AMPAR). This receptor incorporates a nonselective cation channel, which is opened by the binding of glutamate. Although the open pore structure has recently became available from cryo-electron microscopy (Cryo-EM), the molecular mechanisms governing cation permeability in AMPA receptors are not understood. Here, we combined microsecond molecular dynamic (MD) simulations on a putative open-state structure of GluA2 with electrophysiology on cloned channels to elucidate ion permeation mechanisms. Na⁺, K⁺, and Cs⁺ permeated at physiological rates, consistent with a structure that represents a true open state. A single major ion binding site for Na⁺ and K⁺ in the pore represents the simplest selectivity filter (SF) structure for any tetrameric cation channel of known structure. The minimal SF comprised only Q586 and Q587, and other residues on the cytoplasmic side formed a water-filled cavity with a cone shape that lacked major interactions with ions. We observed that Cl^- readily enters the upper pore, explaining anion permeation in the RNA-edited (Q586R) form of GluA2. A permissive architecture of the SF accommodated different alkali metals in distinct solvation states to allow rapid, nonselective cation permeation and copermeation by water. Simulations suggested Cs⁺ uses two equally populated ion binding sites in the filter, and we confirmed with electrophysiology of GluA2 that Cs⁺ is slightly more permeant than Na⁺, consistent with serial binding sites preferentially driving selectivity.

Ion Selectivity and Permeation Mechanism in a Cyclodextrin-Based Channel

Synthetic ion channels are a promising technology in the medical and materials sciences because of their ability to conduct ions. Channels based on cyclodextrin, a cyclic oligomer of glucose, are of particular interest because of their nontoxicity and biocompatibility. Using molecular dynamics-based free energy calculations, this study identifies cyclodextrin channel types that are best suited to serve as synthetic ion channels. Free energy profiles show that the connectivity in the channel determines whether the channel is cation-selective or anion-selective. Furthermore, the energy barrier for ion transport is governed by the number of glucose molecules making up the cyclodextrin units of the channel. A detailed mechanism is proposed for ion transport through these channels. Findings from this study will aid in designing cyclodextrin-based channels that could be either cation-selective or anion-selective, by modifying the linkages of the channel or the number of glucose molecules in the cyclodextrin rings.

Determinants of conductance of a bacterial voltage-gated sodium channel

Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel Na_vMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Na_v channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na⁺ in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.

Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions

Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.

Fuel Cell Using Squid Axon Electrolyte and Its Proton Conductivity

Fuel cells using biomaterials have the potential for environmentally friendly clean energy and have attracted a lot of interest. Moreover, biomaterials are expected to develop into in vivo electrical devices such as pacemakers with no side effects. Ion channels, which are membrane proteins, are known to have a fast ion transport capacity. Therefore, by using ion channels, the realization of fuel cell electrolytes with high-proton conductivity can be expected. In this study, we have fabricated a fuel cell using an ion channel electrolyte for the first time and investigated the electrical properties of the ion channel electrolyte. It was found that the fuel cell using the ion channel membrane shows a power density of 0.78 W/cm² in the humidified condition. On the other hand, the power density of the fuel cell blocking the ion channel with the channel blocker drastically decreased. These results indicate that the fuel cell using the ion channel electrolyte operates through the existence of the ion channel and that the ion channel membrane can be used as the electrolyte of the fuel cell in humidified conditions. Furthermore, the proton conductivity of the ion channel electrolyte drastically increases above 85% relative humidity (RH) and becomes 2 × 10^-2 S/m at 96% RH. This result indicates that the ion channel becomes active above 96%RH. In addition, it was deduced from the impedance analysis that the high proton conductivity of the ion channel electrolyte above 96% RH is caused by the activation of ion channels, which are closely related to the fractionalization of water molecule clusters. From these results, it was found that a fuel cell using the squid axon becomes a new fuel cell using the function of the ion channel above 96% RH.

Surfactant exopolysaccharide of Ochrobactrum pseudintermedium C1 has antibacterial potential: Its bio-medical applications in vitro

Since the advent of biologics in human welfare various bio-molecules have been explored. Different bacterial exopolysaccharides have proved their worth in many industrial and commercial applications. In this perspective, while exploring a surfactant exopolysaccharide of Ochrobactrum pseudintermedium C1, it is strikingly observed that it possesses a potent antibacterial property which encourages its bio-medical applications. Following isolation and purification of the said exopolysaccharide, its structural configuration and functional attributes are studied by several analytical procedures involving FTIR, ¹³C- NMR, CHN-analysis, estimation of zeta potential, XRD-study and digital tensiometry. When treated with pathological samples in vitro, it distinctly elicits its antibacterial property by exhibiting a characteristic zone of inhibition. Combined with a standard antibiotic (like ciprofloxacin), it enhances the action of antibiotic also. Mechanism of its antibacterial action is evaluated by crystal violet entrapment assay with UV-vis spectrophotometry, bacterial cell viability assay by trypan blue staining and SEM study. Results show that its basic surfactant property, anionic character, crystalline nature and scaffolding architecture are supposed to facilitate its antibacterial property which is manifested by its capability of disrupting bacterial cell envelope causing eventual cell death. In the current global scenario, an increasing threat of antibiotic resistance is prevailing due to their indiscriminate use. If used as an adjuvant with a judicious dose of antibiotic, this bio-molecule might play a significant role in bio-medicine to combat such threat.

Selectivity filter modalities and rapid inactivation of the hERG1 channel

The human ether-á-go-go-related gene (hERG1) channel conducts small outward K⁺ currents that are critical for cardiomyocyte membrane repolarization. The gain-of-function mutation N629D at the outer mouth of the selectivity filter (SF) disrupts inactivation and K⁺-selective transport in hERG1, leading to arrhythmogenic phenotypes associated with long-QT syndrome. Here, we combined computational electrophysiology with Markov state model analysis to investigate how SF-level gating modalities control selective cation transport in wild-type (WT) and mutant (N629D) hERG1 variants. Starting from the recently reported cryogenic electron microscopy (cryo-EM) open-state channel structure, multiple microseconds-long molecular-dynamics (MD) trajectories were generated using different cation configurations at the filter, voltages, electrolyte concentrations, and force-field parameters. Most of the K⁺ permeation events observed in hERG1-WT simulations occurred at microsecond timescales, influenced by the spontaneous dehydration/rehydration dynamics at the filter. The SF region displayed conductive, constricted, occluded, and dilated states, in qualitative agreement with the well-documented flickering conductance of hERG1. In line with mutagenesis studies, these gating modalities resulted from dynamic interaction networks involving residues from the SF, outer-mouth vestibule, P-helices, and S5-P segments. We found that N629D mutation significantly stabilizes the SF in a state that is permeable to both K⁺ and Na⁺, which is reminiscent of the SF in the nonselective bacterial NaK channel. Increasing the external K⁺ concentration induced "WT-like" SF dynamics in N629D, in qualitative agreement with the recovery of flickering currents in experiments. Overall, our findings provide an understanding of the molecular mechanisms controlling selective transport in K⁺ channels with a nonconventional SF sequence.

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 (P_X/P_Na). The relative permeabilities varied inversely with relative K_d 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.

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.