Na(+)/Ca(2+) selectivity in the bacterial voltage-gated sodium channel NavAb

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.

Ca2+ entry through NaV channels generates submillisecond axonal Ca2+ signaling

Calcium ions (Ca²⁺) are essential for many cellular signaling mechanisms and enter the cytosol mostly through voltage-gated calcium channels. Here, using high-speed Ca²⁺ imaging up to 20 kHz in the rat layer five pyramidal neuron axon we found that activity-dependent intracellular calcium concentration ([Ca²⁺]_i) in the axonal initial segment was only partially dependent on voltage-gated calcium channels. Instead, [Ca²⁺]_i changes were sensitive to the specific voltage-gated sodium (Na_V) channel blocker tetrodotoxin. Consistent with the conjecture that Ca²⁺ enters through the Na_V channel pore, the optically resolved I_Ca in the axon initial segment overlapped with the activation kinetics of Na_V channels and heterologous expression of Na_V1.2 in HEK-293 cells revealed a tetrodotoxin-sensitive [Ca²⁺]_i rise. Finally, computational simulations predicted that axonal [Ca²⁺]_i transients reflect a 0.4% Ca²⁺ conductivity of Na_V channels. The findings indicate that Ca²⁺ permeation through Na_V channels provides a submillisecond rapid entry route in Na_V-enriched domains of mammalian axons.

Nerve cells communicate using tiny electrical impulses called action potentials. Special proteins termed ion channels produce these electric signals by allowing specific charged particles, or ions, to pass in or out of cells across its membrane. When a nerve cell ‘fires’ an action potential, specific ion channels briefly open to let in a surge of positively charged ions which electrify the cell. Action potentials begin in the same place in each nerve cell, at an area called the axon initial segment. The large number of sodium channels at this site kick-start the influx of positively charged sodium ions ensuring that every action potential starts from the same place.

Previous research has shown that, when action potentials begin, the concentration of calcium ions at the axon initial segment also increases, but it was not clear which ion channels were responsible for this entry of calcium. Channels that are selective for calcium ions are the prime candidates for this process. However, research in squid nerve cells gave rise to an unexpected idea by suggesting that sodium channels may not exclusively let in sodium but also allow some calcium ions to pass through. Hanemaaijer, Popovic et al. therefore wanted to test the routes that calcium ions take and see whether the sodium channels in mammalian nerve cells are also permeable to calcium.

Experiments using fluorescent dyes to track the concentration of calcium in rat and human nerve cells showed that calcium ions accumulated at the axon initial segment when action potentials fired. Most of this increase in calcium could be stopped by treating the neurons with a toxin that prevents sodium channels from opening. Electrical manipulations of the cells revealed that, in this context, the calcium ions were effectively behaving like sodium ions. Human kidney cells were then engineered to produce the sodium channel protein. This confirmed that calcium and sodium ions were indeed both passing through the same channel.

These results shed new light on the relationship between calcium ions and sodium channels within the mammalian nervous system and that this interplay occurs at the axon initial segment of the cell. Genetic mutations that ‘nudge’ sodium channels towards favoring calcium entry are also found in patients with autism spectrum disorders, and so this new finding may contribute to our understanding of these conditions.

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.

Mechanistic insights into the Orai channel by molecular dynamics simulations

Highly Ca²⁺ selective channels trigger a large variety of cellular signaling processes in both excitable and non-excitable cells. Among these channels, the Orai channel is unique in its activation mechanism and its structure. It mediates Ca²⁺ influx into the cytosol with an extremely small unitary conductance over longer time-scales, ranging from minutes up to several hours. Its activation is regulated by the Ca²⁺ content of the endoplasmic reticulum (ER). Depletion of luminal [Ca²⁺]_ER is sensed by the STIM1 single transmembrane protein that directly binds and gates the Orai1 channel. Orai mediated Ca²⁺ influx increases cytosolic Ca²⁺ from 100 nM up to low micromolar range close to the pore and thereby forms Ca²⁺ microdomains. Hence, these features of the Orai channel can trigger long-term signaling processes without affecting the overall Ca²⁺ content of a single living cell. Here we focus on the architecture and dynamic conformational changes within the Orai channel. This review summarizes current achievements of molecular dynamics simulations in combination with live cell recordings to address gating and permeation of the Orai channel with molecular precision.

Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaVAb Sodium Channel

The determination of the atomic structures of voltage-gated bacterial sodium channels using X-ray crystallography has provided a first view of this family of membrane proteins. Molecular dynamics simulations offer one approach to clarify the underlying mechanism of permeation and selectivity in these channels. However, it appears that the intracellular gate of the pore domain is either closed or only open partially in the available X-ray structures. The lack of structure with a fully open intracellular gate poses a special challenge to computational studies aimed at simulating ion conduction. To circumvent this problem, we simulated a model of the Na_VAb channel in which the transmembrane S5 and S6 helices of the pore domain have been truncated to provide direct open access to the intracellular entryway to the pore. Molecular dynamics simulations were carried out over a range of membrane potential and ion concentration of sodium and potassium. The simulations show that the Na_VAb selectivity filter is essentially a cationic pore supporting the conduction of ions at a rate comparable to aqueous diffusion with no significant selectivity for sodium. Conductance and selectivity vary as a function of ion concentration for both cations. Permeation occurs primarily via a knock-on mechanism for both sodium and potassium, although the ion ordering in single file along the pore is not strictly maintained. The character of the outward current appears quite different from the inward current, with a buildup on ions in the selectivity filter prior to escape toward the extracellular side, indicating the presence of a rectification effect that is overcome by nonphysiological applied voltages.

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.

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.

Modeling ion permeation through a bacterial voltage-gated calcium channel CaVAb using molecular dynamics simulations

Ca²⁺ion binds tightly to the center of the selectivity filter of voltage-gated calcium channels.

Molecular dynamics simulations for designing biomimetic pores based on internally functionalized self-assembling α,γ-peptide nanotubes

A molecular dynamics study on internally functionalized peptide nanotubes composed of α- and γ-amino acids self-assembled in lipid bilayers is presented. One of the main advantages of peptide nanotubes composed of γ-amino acids is that the properties of their inner cavities can be tuned by introducing different functions on β-carbon of the γ-amino acid. In the work described here we studied the effect of the presence of different numbers of hydroxyl groups in different positions in the lumen of these channels when they are inserted into a lipid bilayer and assessed how they affect the structural and dynamic behavior of the modified peptide nanotubes as well as the transmembrane transport of different ions. The results provided atomic information about the effect of polar groups on the dynamic, structural and transport properties of this type of peptidic channel upon insertion into lipid bilayers, projecting a promising future for their use as biomimetic channels when properly inner-derivatized. Furthermore, the chemical versatility of the hydroxyl groups in the lumen of the peptide nanotubes would enable appealing applications for these channels, such as a controlled method for the activation/inactivation of the transmembrane transport along the nanopore.

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.

K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na(v) Channels

Crystal structures of several bacterial Na_v channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Na_v channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial Na_vAb channel. This approach provided new insight into the mechanism of selective ion permeation in bacterial Na_v channels. The non-equilibrium simulations indicate that two or three extracellular K⁺ ions can block the entrance to the selectivity filter of Na_vAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K⁺ ions that can be ‘locked’ in place by modest applied forces. In contrast to K⁺, three Na⁺ ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similar local minimum in the two-dimensional free-energy landscape of two Na⁺ ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K⁺ block is equivalent to large applied potentials experimentally measured for two bacterial Na_v channels to induce inward currents of K⁺ ions. These results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free-energy landscapes.

In this paper we show that bacterial voltage-gated sodium channels (Na_v) conduct ions differently in the inward direction and in the outward direction because extracellular K⁺ blocks these channels. The mechanism of block by K⁺ is revealed in the simulations only when effects of applied forces in the inward direction are considered appropriately. The block of bacterial Na_v channels by K⁺ explains the experimental findings that inward K⁺ current in bacterial Na_v channels is very small under conditions where most mammalian Na_v channels conduct significant K⁺ current. The block by K⁺ ions can occur in the bacterial Na_v channels but is very unlikely to occur in mammalian channels due to differences in the amino acid sequences of the selectivity filters of the different channels.

Investigating the size and dynamics of voltage-gated sodium channel fenestrations

Eukaryotic voltage-gated sodium channels (VGSCs) are essential for the initiation and propagation of action potentials in electrically excitable cells, and are important pharmaceutical targets for the treatment of neurological disorders such as epilepsy, cardiac arrhythmias, and chronic pain. Evidence suggests that small, hydrophobic, VGSC-blocking drugs can gain access to binding residues within the central cavity of these channels by passing through lateral, lipid-filled “fenestrations” which run between the exterior of the protein and its central pore. Here, we use molecular dynamics simulations to investigate how the size and shape of fenestrations change over time in several bacterial VGSC models and a homology model of Nav1.4. We show that over the course of the simulations, the size of the fenestrations is primarily influenced by rapid protein motions, such as amino acid side-chain rotation, and highlight that differences between fenestration bottleneck-contributing residues are the primary cause of variations in fenestration size between the 6 bacterial models. In the eukaryotic channel model, 2 fenestrations are wide, but 2 are narrow due to differences in the amino acid sequence in the 4 domains. Lipid molecules are found to influence the size of the fenestrations by protruding acylchains into the fenestrations and displacing amino acid side-chains. Together, the results suggest that fenestrations provide viable pathways for small, flexible, hydrophobic drugs.

Effects of the protonation state of the EEEE motif of a bacterial Na(+)-channel on conduction and pore structure

A distinctive feature of prokaryotic Na(+)-channels is the presence of four glutamate residues in their selectivity filter. In this study, how the structure of the selectivity filter, and the free-energy profile of permeating Na(+) ions are altered by the protonation state of Glu177 are analyzed. It was found that protonation of a single glutamate residue was enough to modify the conformation of the selectivity filter and its conduction properties. Molecular dynamics simulations revealed that Glu177 residues may adopt two conformations, with the side chain directed toward the extracellular entrance of the channel or the intracellular cavity. The likelihood of the inwardly directed arrangement increases when Glu177 residues are protonated. The presence of one glutamate residue with its chain directed toward the intracellular cavity increases the energy barrier for translocation of Na(+) ions. These higher-energy barriers preclude Na(+) ions to permeate the selectivity filter of prokaryotic Na(+)-channels when one or more Glu177 residues are protonated.

Permeation and dynamics of an open-activated TRPV1 channel

Transient receptor potential (TRP) ion channels constitute a large and diverse protein family, found in yeast and widespread in the animal kingdom. TRP channels work as sensors for a wide range of cellular and environmental signals. Understanding how these channels respond to physical and chemical stimuli has been hindered by the limited structural information available until now. The three-dimensional structure of the vanilloid receptor 1 (TRPV1) was recently determined by single particle electron cryo-microscopy, offering for the first time the opportunity to explore ionic conduction in TRP channels at atomic detail. In this study, we present molecular dynamics simulations of the open-activated pore domain of TRPV1 in the presence of three cationic species: Na(+), Ca(2+) and K(+). The dynamics of these ions while interacting with the channel pore allowed us to rationalize their permeation mechanism in terms of a pathway involving three binding sites at the intracellular cavity, as well as the extracellular and intracellular entrance of the selectivity filter. Furthermore, conformational analysis of the pore in the presence of these ions reveals specific ion-mediated structural changes in the selectivity filter, which influences the permeability properties of the TRPV1 channel.

Locating the route of entry and binding sites of benzocaine and phenytoin in a bacterial voltage gated sodium channel

Sodium channel blockers are used to control electrical excitability in cells as a treatment for epileptic seizures and cardiac arrhythmia, and to provide short term control of pain. Development of the next generation of drugs that can selectively target one of the nine types of voltage-gated sodium channel expressed in the body requires a much better understanding of how current channel blockers work. Here we make use of the recently determined crystal structure of the bacterial voltage gated sodium channel NavAb in molecular dynamics simulations to elucidate the position at which the sodium channel blocking drugs benzocaine and phenytoin bind to the protein as well as to understand how these drugs find their way into resting channels. We show that both drugs have two likely binding sites in the pore characterised by nonspecific, hydrophobic interactions: one just above the activation gate, and one at the entrance to the the lateral lipid filled fenestrations. Three independent methods find the same sites and all suggest that binding to the activation gate is slightly more favourable than at the fenestration. Both drugs are found to be able to pass through the fenestrations into the lipid with only small energy barriers, suggesting that this can represent the long posited hydrophobic entrance route for neutral drugs. Our simulations highlight the importance of a number of residues in directing drugs into and through the fenestration, and in forming the drug binding sites.

The treatment of cardiac arrhythmia, epilepsy and pain usually involves blocking the protein channels responsible for initiating electrical activity in nerves and muscles. Current drugs block all such channels, but improved medication requires compounds that can differentiate between the channels present in different parts of the body. Achieving this goal calls for a better understanding of the interactions of current drugs with the proteins. Here we use computer simulation to understand where a local anesthetic and an anti-epileptic bind to a bacterial sodium channel and how they find their way to this position, helping to uncover ways to selectively target different human channels.

Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations

Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms. Here, we use molecular dynamics (MD) simulations with an applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs. 5.9 µs simulations with 500 mM NaCl suggest different mechanisms for inward and outward flux. The predicted inward conductance rate of ∼27±3 pS, agrees with experiment. The estimated outward conductance rate is 15±3 pS, which is considerably lower. Comparing inward and outward flux, the mean ion dwell time in the selectivity filter (SF) is prolonged from 13.5±0.6 ns to 20.1±1.1 ns. Analysis of the Na+ distribution revealed distinct patterns for influx and efflux events. In 32.0±5.9% of the simulation time, the E53 side chains adopted a flipped conformation during outward conduction, whereas this conformational change was rarely observed (2.7±0.5%) during influx. Further, simulations with dihedral restraints revealed that influx is less affected by the E53 conformational flexibility. In contrast, during outward conduction, our simulations indicate that the flipped E53 conformation provides direct coordination for Na+. The free energy profile (potential of mean force calculations) indicates that this conformational change lowers the putative barriers between sites SCEN and SHFS during outward conduction. We hypothesize that during an action potential, the increased Na+ outward transition propensities at depolarizing potentials might increase the probability of E53 conformational changes in the SF. Subsequently, this might be a first step towards initiating slow inactivation.

K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations

Generations of scientists have been captivated by ion channels and how they control the workings of the cell by admitting ions from one side of the cell membrane to the other. Elucidating the molecular determinants of ion conduction and selectivity are two of the most fundamental issues in the field of biophysics. Combined with ongoing progress in structural studies, modeling and simulation have been an integral part of the development of the field. As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. In this report, we give an overview of the recent progress made by simulation studies on the understanding of ion permeation in selective and nonselective ion channels.

A mechanical nanogate based on a carbon nanotube for reversible control of ion conduction

Control of mass transport through nanochannels is of critical importance in many nanoscale devices and nanofiltration membranes. The gates in biological channels, which control the transport of substances across cell membranes, can provide inspiration for this purpose. Gates in many biological channels are formed by a constriction ringed with hydrophobic residues which can prevent ion conduction even when they are not completely physically occluded. In this work, we use molecular dynamics simulations to design a nanogate inspired by this hydrophobic gating mechanism. Deforming a carbon nanotube (12,12) with an external force can form a hydrophobic constriction in the centre of the tube that controls ion conduction. The simulation results show that increasing the magnitude of the applied force narrows the constriction and lowers the fluxes of K(+) and Cl(-) found under an electric field. With the exerted force larger than 5 nN, the constriction blocks the conduction of K(+) and Cl(-) due to partial dehydration while allowing for a noticeable water flux. Ion conduction can revert back to the unperturbed level upon force retraction, suggesting the reversibility of the nanogate. The force can be exerted by available experimental facilities, such as atomic force microscope (AFM) tips. It is found that partial dehydration in a continuous water-filled hydrophobic constriction is enough to close the channel, while full dewetting is not necessarily required. This mechanically deformed nanogate has many potential applications, such as a valve in nanofluidic systems to reversibly control ion conduction and a high-performance nanomachine for desalination and water treatment.

Bacterial sodium channels: models for eukaryotic sodium and calcium channels

Eukaryotic sodium and calcium channels are made up of four linked homologous but different transmembrane domains. Bacteria express sodium channels comprised of four identical subunits, each being analogous to a single homologous domain of their eukaryotic counterparts. Key elements of primary structure are conserved between bacterial and eukaryotic sodium and calcium channels. The simple protein structure of the bacterial channels has allowed extensive structure-function probes of key regions as well as allowing determination of several X-ray crystallographic structures of these channels. The structures have revealed novel features of sodium and calcium channel pores and elucidated the structural importance of many of the conserved features of primary sequence. The structural information has also formed the basis for computational studies probing the basis for sodium and calcium selectivity and gating.

Bioinspired graphene nanopores with voltage-tunable ion selectivity for Na(+) and K(+)

Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na(+) and K(+), two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K(+) channel preferentially conducts K(+) over Na(+). A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na(+) channel selectively binds Na(+) but transports K(+) over Na(+). Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na(+) selectivity, dictated by the knock-on ion conduction and selective blockage by Na(+). Under higher voltage bias, the nanopore is K(+)-selective, as the blockage by Na(+) is destabilized and the stronger affinity for carboxylate groups slows the passage of Na(+) compared with K(+). The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na(+)/K(+) separation, and voltage-tunable nanofluidic devices.

Energetics of discrete selectivity bands and mutation-induced transitions in the calcium-sodium ion channels family

We use Brownian dynamics (BD) simulations to study the ionic conduction and valence selectivity of a generic electrostatic model of a biological ion channel as functions of the fixed charge Q(f) at its selectivity filter. We are thus able to reconcile the discrete calcium conduction bands recently revealed in our BD simulations, M0 (Q(f)=1e), M1 (3e), M2 (5e), with a set of sodium conduction bands L0 (0.5e), L1 (1.5e), thereby obtaining a completed pattern of conduction and selectivity bands vs Q(f) for the sodium-calcium channels family. An increase of Q(f) leads to an increase of calcium selectivity: L0 (sodium-selective, nonblocking channel) → M0 (nonselective channel) → L1 (sodium-selective channel with divalent block) → M1 (calcium-selective channel exhibiting the anomalous mole fraction effect). We create a consistent identification scheme where the L0 band is putatively identified with the eukaryotic sodium channel The scheme created is able to account for the experimentally observed mutation-induced transformations between nonselective channels, sodium-selective channels, and calcium-selective channels, which we interpret as transitions between different rows of the identification table. By considering the potential energy changes during permeation, we show explicitly that the multi-ion conduction bands of calcium and sodium channels arise as the result of resonant barrierless conduction. The pattern of periodic conduction bands is explained on the basis of sequential neutralization taking account of self-energy, as Q(f)(z,i)=ze(1/2+i), where i is the order of the band and z is the valence of the ion. Our results confirm the crucial influence of electrostatic interactions on conduction and on the Ca(2+)/Na(+) valence selectivity of calcium and sodium ion channels. The model and results could be also applicable to biomimetic nanopores with charged walls.

Detailed Examination of a Single Conduction Event in a Potassium Channel

Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using stratified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.1 paddle chimera and thereby identifies the expected stable configurations of ions and waters in the selectivity filter of the channel. We describe in detail the motions of the ions and waters during a conduction event, focusing on how waters and ions enter the filter, the rotation of water molecules inside the filter, and how potassium ions are coordinated as they move from a water to a protein environment. Finally, we analyze the small conformational changes undergone by the protein, showing that the stable configurations are most similar to the experimental crystal structure.

Catalysis of Na+ permeation in the bacterial sodium channel Na(V)Ab

Determination of a high-resolution 3D structure of voltage-gated sodium channel Na(V)Ab opens the way to elucidating the mechanism of ion conductance and selectivity. To examine permeation of Na(+) through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of Na(V)Ab in an explicit, hydrated lipid bilayer at 0 mV in 150 mM NaCl, for a total simulation time of 21.6 μs. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na(+) through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of Na(+) between the extracellular medium and the central cavity of the channel. Analysis of Na(+) dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na(+) ions, with a computed rate of translocation of (6 ± 1) × 10(6) ions⋅s(-1) that is consistent with expectations from electrophysiological studies. The binding of Na(+) is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na(+) ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. Structural fluctuations of these ionic clusters result in a myriad of ion binding modes and foster a highly degenerate, liquid-like energy landscape propitious to Na(+) diffusion. By stabilizing multiple ionic occupancy states while helping Na(+) ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na(+) permeation.

The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation

Voltage-gated sodium (Nav) channels and their Na⁺/K⁺ selectivity are of great importance in the mammalian neuronal signaling. According to mutational analysis, the Na⁺/K⁺ selectivity in mammalian Nav channels is mainly determined by the Lys and Asp/Glu residues located at the constriction site within the selectivity filter. Despite successful molecular dynamics simulations conducted on the prokaryotic Nav channels, the lack of Lys at the constriction site of prokaryotic Nav channels limits how much can be learned about the Na⁺/K⁺ selectivity in mammalian Nav channels. In this work, we modeled the mammalian Nav channel by mutating the key residues at the constriction site in a prokaryotic Nav channel (NavRh) to its mammalian counterpart. By simulating the mutant structure, we found that the Na⁺ preference in mammalian Nav channels is collaboratively achieved by the deselection from Lys and the selection from Asp/Glu within the constriction site.