Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels

Physics of Selective Conduction and Point Mutation in Biological Ion Channels

We introduce a statistical and linear response theory of selective conduction in biological ion channels with multiple binding sites and possible point mutation. We derive an effective grand-canonical ensemble and generalized Einstein relations for the selectivity filter, assuming strongly coordinated ionic motion, and allowing for ionic Coulomb blockade. The theory agrees well with data from the KcsA K^{+} channel and a mutant. We show that the Eisenman relations for thermodynamic selectivity follow from the condition for fast conduction and find that maximum conduction requires the binding sites to be nearly identical.

Molecular simulation of the Kv7.4[ΔS269] mutant channel reveals that ion conduction in the cavity is perturbed due to hydrophobic gating

Mutations in the voltage-gated potassium channel Kv7.4 (encoded as KCNQ4) lead to the early onset of non-syndromic hearing loss, which is significant during language acquisition. The deletion of the S269 pore residue (genetic Δ mutation) in Kv7.4 has been reported to be associated with hearing loss. So far, there is no mechanistic understanding of how this mutation modulates channel function. To understand the role of S269 in ion conduction, we performed molecular dynamics simulations for both wild type and ΔS269 mutant channels. Simulations indicate that the ΔS269 mutation suppresses the fluctuations in the neighboring Y269 residue and thereby consolidates the ring formed by I307 and F310 residues in the adjacent S6 helixes in the cavity region. We show that the long side chains of I307 near the entrance to the cavity form a hydrophobic gate. Comparison of the free energy profiles of a cavity ion in Kv7.4 and Kv7.4[ΔS269] channels reveals a sizable energy barrier in the latter case, which suppresses ion conduction. Thus the simulation studies reveal that the hydrophobic gate resulting from the ΔS269 mutation appears to be responsible for sensorineural hearing loss.

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DeltaS269 mutation in the Kv7.4 channel is associated with hearing loss (SNHL).

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The mutation effects on channel function are studied via MD simulations.

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DeltaS269 mutation imposes a constriction at the cavity to suppress K⁺ conductance.

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Understanding the mutation effects on channel function will help to treat SNHL.

Queueing arrival and release mechanism for K+ permeation through a potassium channel

The mechanism underlying ion permeation through potassium channels still remains controversial. K+ ions permeate across a narrow selectivity filter (SF) in a single file. Conventional scenarios assume that K+ ions are tightly bound in the SF, and, thus, they are displaced from their energy well by ion-ion repulsion with an incoming ion. This tight coupling between entering and exiting ions has been called the "knock-on" mechanism. However, this paradigm is contradicted by experimental data measuring the water-ion flux coupling ratio, demonstrating fewer ion occupancies. Here, the results of molecular dynamics simulations of permeation through the KcsA potassium channel revealed an alternative mechanism. In the aligned ions in the SF (an ion queue), the outermost K+ was readily and spontaneously released toward the extracellular space, and the affinity of the relevant ion was ~ 50 mM. Based on this low-affinity regime, a simple queueing mechanism described by loose coupling of entering and exiting ions is proposed.

Computational Study of the Loss-of-Function Mutations in the Kv1.5 Channel Associated with Atrial Fibrillation

Atrial fibrillation (AF) is a heart disease caused by defective ion channels in the atria, which affect the action potential (AP) duration and disturb normal heart rhythm. Rapid firing of APs in neighboring atrial cells is a common mechanism of AF, and therefore, therapeutic approaches have focused on extending the AP duration by inhibiting the K⁺ channels involved in repolarization. Of these, Kv1.5 that carries the I _Kur current is a promising target because it is expressed mainly in atria and not in ventricles. In genetic studies of AF patients, both loss-of-function and gain-of-function mutations in Kv1.5 have been identified, indicating that either decreased or increased I _Kur currents could trigger AF. Blocking of already downregulated Kv1.5 channels could cause AF to become chronic. Thus, a molecular-level understanding of how the loss-of-function mutations in Kv1.5 affect I _Kur would be useful for developing new therapeutics. Here, we perform molecular dynamics simulations to study the effect of three loss-of-function mutations in the pore domain of Kv1.5 on ion permeation. Comparison of the pore structures and ion free energies in the wild-type and mutant Kv1.5 channels indicates that conformational changes in the selectivity filter could hinder ion permeation in the mutant channels.

Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter

Computational evaluation of the energetics of substrate binding, transport, and release events of neurotransmitter transporters at the molecular level is a challenge, as the structural transitions of these membrane proteins involve coupled global and local changes that span time scales of several orders of magnitude, from nanoseconds to seconds. Here, we provide a quantitative assessment of the energetics of dopamine (DA) translocation through the human DA transporter (hDAT), using a combination of molecular modeling, simulation, and analysis tools. DA-binding and -unbinding events, which generally involve local configurational changes, are evaluated using free-energy perturbation or adaptive biasing force methods. The global transitions between the outward-facing state and the inward-facing state, on the other hand, require a dual-boost accelerated molecular dynamics simulation. We present results on DA-binding/unbinding energetics under different conditions, as well as the conformational energy landscape of hDAT in both DA-bound and -unbound states. The study provides a tractable method of approach for quantitative evaluation of substrate-binding energetics and efficient estimation of conformational energy landscape, in general.

Venom-derived peptide inhibitors of voltage-gated potassium channels

Voltage-gated potassium channels play a key role in human physiology and pathology. Reflecting their importance, numerous channelopathies have been characterised that arise from mutations in these channels or from autoimmune attack on the channels. Voltage-gated potassium channels are also the target of a broad range of peptide toxins from venomous organisms, including sea anemones, scorpions, spiders, snakes and cone snails; many of these peptides bind to the channels with high potency and selectivity. In this review we describe the various classes of peptide toxins that block these channels and illustrate the broad range of three-dimensional structures that support channel blockade. The therapeutic opportunities afforded by these peptides are also highlighted. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'

Computational Study of Binding of μ-Conotoxin GIIIA to Bacterial Sodium Channels NaVAb and NaVRh

Structures of several voltage-gated sodium (NaV) channels from bacteria have been determined recently, but the same feat might not be achieved for the mammalian counterparts in the near future. Thus, at present, computational studies of the mammalian NaV channels have to be performed using homology models based on the bacterial crystal structures. A successful homology model for the mammalian NaV1.4 channel was recently constructed using the extensive mutation data for binding of μ-conotoxin GIIIA to NaV1.4, which was further validated through studies of binding of other μ-conotoxins and ion permeation. Understanding the similarities and differences between the bacterial and mammalian NaV channels is an important issue, and the NaV1.4-GIIIA system provides a good opportunity for such a comparison. To this end, we study the binding of GIIIA to the bacterial channels NaVAb and NaVRh. The complex structures are obtained using docking and molecular dynamics simulations, and the dissociation of GIIIA is studied through umbrella sampling simulations. The results are compared to those obtained from the NaV1.4-GIIIA system, and the differences in the binding modes arising from the changes in the selectivity filters are highlighted.

Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels

Recent determination of the crystal structures of bacterial voltage-gated sodium (NaV) channels have raised hopes that modeling of the mammalian counterparts could soon be achieved. However, there are substantial differences between the pore domains of the bacterial and mammalian NaV channels, which necessitates careful validation of mammalian homology models constructed from the bacterial NaV structures. Such a validated homology model for the NaV1.4 channel was constructed recently using the extensive mutagenesis data available for binding of μ-conotoxins. Here we use this NaV1.4 model to study the ion permeation mechanism in mammalian NaV channels. Linking of the DEKA residues in the selectivity filter with residues in the neighboring domains is found to be important for keeping the permeation pathway open. Molecular dynamics simulations and potential of mean force calculations reveal that there is a binding site for a Na+ ion just inside the DEKA locus, and 1-2 Na+ ions can occupy the vestibule near the EEDD ring. These sites are separated by a low free energy barrier, suggesting that inward conduction occurs when a Na+ ion in the vestibule goes over the free energy barrier and pushes the Na+ ion in the filter to the intracellular cavity, consistent with the classical knock-on mechanism. The NaV1.4 model also provides a good description of the observed Na+/K+ selectivity.

Water molecules response to an external GHz electric field in KcsA potassium channel: A molecular modeling approach

KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K + and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel.

Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels

Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion-water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.

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.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Computational studies of marine toxins targeting ion channels

Toxins from marine animals offer novel drug leads for treatment of diseases involving ion channels. Computational methods could be very helpful in this endeavour in several ways, e.g., (i) constructing accurate models of the channel-toxin complexes using docking and molecular dynamics (MD) simulations; (ii) determining the binding free energies of toxins from umbrella sampling MD simulations; (iii) predicting the effect of mutations from free energy MD simulations. Using these methods, one can design new analogs of toxins with improved affinity and selectivity properties. Here we present a review of the computational methods and discuss their applications to marine toxins targeting potassium and sodium channels. Detailed examples from the potassium channel toxins—ShK from sea anemone and κ-conotoxin PVIIA—are provided to demonstrate capabilities of the computational methods to give accurate descriptions of the channel-toxin complexes and the energetics of their binding. An example is also given from sodium channel toxins (µ-conotoxin GIIIA) to illustrate the differences between the toxin binding modes in potassium and sodium channels.

Why the Drosophila Shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels

The Drosophila Shaker K(+) channel is the first cloned voltage-gated potassium channel and has, therefore, played an important role in structural and functional studies of those channels. While such a role is well justified for ion permeation, it is not clear whether this also extends to ligand binding. Despite the high degree of homology among Shaker and Kv1 channels, κ-conotoxin PVIIA (κ-PVIIA) binds to Shaker with high affinity but not to Kv1 channels. Here we address this issue by studying binding of κ-PVIIA to Shaker and Kv1 channels using molecular dynamics (MD) simulations. The structures of the channel-toxin complexes are constructed via docking and refinement with MD. The binding mode of each complex is characterized and compared to available mutagenesis data to validate the complex models. The potential of mean force for dissociation of the Shaker-κ-PVIIA complex is calculated from umbrella sampling MD simulations, and the corresponding binding free energy is determined, which provides further validation of the complex structure. Comparison of the Shaker and Kv1 complex models shows that a few mutations in the turret and extended regions are sufficient to abolish the observed sensitivity of Shaker to κ-PVIIA. This study demonstrates that Shaker is not always a good model for Kv1 channels for ligand binding. It also provides insights into the binding of the toxin to potassium channels that will be useful for improving affinity and selectivity properties of Kv1 channels.

High-risk long QT syndrome mutations in the Kv7.1 (KCNQ1) pore disrupt the molecular basis for rapid K(+) permeation

Type 1 long QT syndrome (LQT1) is caused by loss-of-function mutations in the KCNQ1 gene, which encodes the K(+) channel (Kv7.1) that underlies the slowly activating delayed rectifier K(+) current in the heart. Intragenic risk stratification suggests LQT1 mutations that disrupt conserved amino acid residues in the pore are an independent risk factor for LQT1-related cardiac events. The purpose of this study is to determine possible molecular mechanisms that underlie the loss of function for these high-risk mutations. Extensive genotype-phenotype analyses of LQT1 patients showed that T322M-, T322A-, or G325R-Kv7.1 confers a high risk for LQT1-related cardiac events. Heterologous expression of these mutations with KCNE1 revealed they generated nonfunctional channels and caused dominant negative suppression of WT-Kv7.1 current. Molecular dynamics simulations of analogous mutations in KcsA (T85M-, T85A-, and G88R-KcsA) demonstrated that they disrupted the symmetrical distribution of the carbonyl oxygen atoms in the selectivity filter, which upset the balance between the strong attractive and K(+)-K(+) repulsive forces required for rapid K(+) permeation. We conclude high-risk LQT1 mutations in the pore likely disrupt the architectural and physical properties of the K(+) channel selectivity filter.

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins-ion channels and transporters-which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.

Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations

The stability and ion binding properties of the homo-tetrameric pore domain of a prokaryotic, voltage-gated sodium channel are studied by extensive all-atom molecular dynamics simulations, with the channel protein being embedded in a fully hydrated lipid bilayer. It is found that Na(+) ion presents in a mostly hydrated state inside the wide pore of the selectivity filter of the sodium channel, in sharp contrast to the nearly fully dehydrated state for K(+) ions in potassium channels. Our results also indicate that Na(+) ions make contact with only one or two out of the four polypeptide chains forming the selectivity filter, and surprisingly, the selectivity filter exhibits robust stability for various initial ion configurations even in the absence of ions. These findings are quite different from those in potassium channels. Furthermore, an electric field above 0.5V/nm is suggested to be able to induce Na(+) permeation through the selectivity filter.

Modeling the binding of three toxins to the voltage-gated potassium channel (Kv1.3)

The conduction properties of the voltage-gated potassium channel Kv1.3 and its modes of interaction with several polypeptide venoms are examined using Brownian dynamics simulations and molecular dynamics calculations. Employing an open-state homology model of Kv1.3, we first determine current-voltage and current-concentration curves and ascertain that simulated results accord with experimental measurements. We then investigate, using a molecular docking method and molecular dynamics simulations, the complexes formed between the Kv1.3 channel and several Kv-specific polypeptide toxins that are known to interfere with the conducting mechanisms of several classes of voltage-gated K(+) channels. The depths of potential of mean force encountered by charybdotoxin, α-KTx3.7 (also known as OSK1) and ShK are, respectively, -19, -27, and -25 kT. The dissociation constants calculated from the profiles of potential of mean force correspond closely to the experimentally determined values. We pinpoint the residues in the toxins and the channel that are critical for the formation of the stable venom-channel complexes.

Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations

The voltage-gated potassium channel Kv1.3 is an attractive target for treatment of autoimmune diseases. ShK toxin from sea anemone is one of the most potent blockers of Kv1.3, and therefore ShK and its analogues have been proposed as therapeutic leads for such diseases. Increasing the selectivity of the proposed leads for Kv1.3 over other Kv1 channels is a major issue in this endeavor. Here we study binding of ShK toxin to Kv1 channels using free energy simulation methods. Homology models for Kv1.1 and Kv1.3 channels are constructed using the crystal structure of Kv1.2. The initial poses for the Kv1.x-ShK complexes are obtained using HADDOCK, which are then refined via molecular dynamics simulations. The binding mode in each complex is characterized by identifying the strongly interacting residues, which compare well with available mutagenesis studies. For each complex, the potential of mean force is calculated from umbrella sampling simulations, and the corresponding absolute binding free energy is determined. The computed binding free energies are in good agreement with the experimental data, which increases the confidence on the model complexes. The insights gained on Kv1.x-ShK binding modes will be valuable in the development of new ShK analogues with better selectivity properties.

Blockade of permeation by potassium but normal gating of the G628S nonconducting hERG channel mutant

G628S is a mutation in the signature sequence that forms the selectivity filter of the human ether-a-go-go-related gene (hERG) channel (GFG) and is associated with long-QT2 syndrome. G628S channels are known to have a dominant-negative effect on hERG currents, and the mutant is therefore thought to be nonfunctional. This study aims to assess the physiological mechanism that prevents the surface-expressing G628S channels from conducting ions. We used voltage-clamp fluorimetry along with two-microelectrode voltage clamping in Xenopus oocytes to confirm that the channels express well at the surface, and to show that they are actually functional, with activation kinetics comparable to that of wild-type, and that the mutation leads to a reduced selectivity to potassium. Although ionic currents are not detected in physiological solutions, removing extracellular K(+) results in the appearance of an inward Na(+)-dependent current. Using whole-cell patch clamp in mammalian transfected cells, we demonstrate that the G628S channels conduct Na(+), but that this can be blocked by both intracellular and higher-than-physiological extracellular K(+). Using solutions devoid of K(+) allows the appearance of nA-sized Na(+) currents with activation and inactivation gating analogous to wild-type channels. The G628S channels are functionally conducting but are normally blocked by intracellular K(+).