Thermal stability of the K+ channel tetramer: cation interactions and the conserved threonine residue at the innermost site (S4) of the KcsA selectivity filter

Conformational plasticity of NaK2K and TREK2 potassium channel selectivity filters

The K+ channel selectivity filter (SF) is defined by TxGYG amino acid sequences that generate four identical K+ binding sites (S1-S4). Only two sites (S3, S4) are present in the non-selective bacterial NaK channel, but a four-site K+-selective SF is obtained by mutating the wild-type TVGDGN SF sequence to a canonical K+ channel TVGYGD sequence (NaK2K mutant). Using single molecule FRET (smFRET), we show that the SF of NaK2K, but not of non-selective NaK, is ion-dependent, with the constricted SF configuration stabilized in high K+ conditions. Patch-clamp electrophysiology and non-canonical fluorescent amino acid incorporation show that NaK2K selectivity is reduced by crosslinking to limit SF conformational movement. Finally, the eukaryotic K+ channel TREK2 SF exhibits essentially identical smFRET-reported ion-dependent conformations as in prokaryotic K+ channels. Our results establish the generality of K+-induced SF conformational stability across the K+ channel superfamily, and introduce an approach to study manipulation of channel selectivity.

Molecular Events behind the Selectivity and Inactivation Properties of Model NaK-Derived Ion Channels

Y55W mutants of non-selective NaK and partly K⁺-selective NaK2K channels have been used to explore the conformational dynamics at the pore region of these channels as they interact with either Na⁺ or K⁺. A major conclusion is that these channels exhibit a remarkable pore conformational flexibility. Homo-FRET measurements reveal a large change in W55–W55 intersubunit distances, enabling the selectivity filter (SF) to admit different species, thus, favoring poor or no selectivity. Depending on the cation, these channels exhibit wide-open conformations of the SF in Na⁺, or tight induced-fit conformations in K⁺, most favored in the four binding sites containing NaK2K channels. Such conformational flexibility seems to arise from an altered pattern of restricting interactions between the SF and the protein scaffold behind it. Additionally, binding experiments provide clues to explain such poor selectivity. Compared to the K⁺-selective KcsA channel, these channels lack a high affinity K⁺ binding component and do not collapse in Na⁺. Thus, they cannot properly select K⁺ over competing cations, nor reject Na⁺ by collapsing, as K⁺-selective channels do. Finally, these channels do not show C-type inactivation, likely because their submillimolar K⁺ binding affinities prevent an efficient K⁺ loss from their SF, thus favoring permanently open channel states.

Conductance stability and Na+ interaction with Shab K+ channels under low K+ conditions

K+ ions exert a structural effect that brings stability to K+ selective pores. Thus, upon bathing Shab channels in 0 K+ solutions the ion conductance, GK, irreversibly collapses. Related to this, studies with isolated KcsA channels have suggested that there is a transition [K+] around which the pore takes one of two conformations, either the low (non-conducting) or high K+ (conducting) crystal structures. We examined this premise by looking at the K+-dependency of GK stability of Shab channels within the cell membrane environment. We found that: K+ effect on GK stability is highly asymmetrical, and that as internal K+ is replaced by Na+ GK drops in a way that suggests a transition internal [K+]. Additionally, we found that external permeant ions inhibit GK drop with a potency that differs from the global selectivity-sequence of K+ pores; the non-permeant TEA inhibited GK drop in a K+-dependent manner. Upon lowering internal [K+] we observed an influx of Na+ at negative potentials. Na+ influx was halted by physiological external [K+], which also restored GK stability. Hyperpolarized potentials afforded GK stability but, as expected, do not restore GK selectivity. For completeness, Na+ interaction with Shab was also assessed at depolarized potentials by looking at Na block followed by permeation (pore unblock) at positive potentials, in solutions approaching the 0 K+ limit. The stabilizing effect of negative potentials along with the non-parallel variation of Na+ permeability and conductance-stability herein reported, show that pore stability and selectivity, although related, are not strictly coupled.

Structural basis for ion selectivity in TMEM175 K+ channels

The TMEM175 family constitutes recently discovered K+channels that are important for autophagosome turnover and lysosomal pH regulation and are associated with the early onset of Parkinson Disease. TMEM175 channels lack a P-loop selectivity filter, a hallmark of all known K+ channels, raising the question how selectivity is achieved. Here, we report the X-ray structure of a closed bacterial TMEM175 channel in complex with a nanobody fusion-protein disclosing bound K+ ions. Our analysis revealed that a highly conserved layer of threonine residues in the pore conveys a basal K+ selectivity. An additional layer comprising two serines in human TMEM175 increases selectivity further and renders this channel sensitive to 4-aminopyridine and Zn2+. Our findings suggest that large hydrophobic side chains occlude the pore, forming a physical gate, and that channel opening by iris-like motions simultaneously relocates the gate and exposes the otherwise concealed selectivity filter to the pore lumen.

Potassium channel selectivity filter dynamics revealed by single-molecule FRET

Potassium (K) channels exhibit exquisite selectivity for conduction of K⁺ ions over other cations, particularly Na⁺. High-resolution structures reveal an archetypal selectivity filter (SF) conformation in which dehydrated K⁺ ions, but not Na⁺ ions, are perfectly coordinated. Using single-molecule FRET (smFRET), we show that the SF-forming loop (SF-loop) in KirBac1.1 transitions between constrained and dilated conformations as a function of ion concentration. The constrained conformation, essential for selective K⁺ permeability, is stabilized by K⁺ but not Na⁺ ions. Mutations that render channels nonselective result in dilated and dynamically unstable conformations, independent of the permeant ion. Further, while wild-type KirBac1.1 channels are K⁺ selective in physiological conditions, Na⁺ permeates in the absence of K⁺. Moreover, whereas K⁺ gradients preferentially support ⁸⁶Rb⁺ fluxes, Na⁺ gradients preferentially support ²²Na⁺ fluxes. This suggests differential ion selectivity in constrained versus dilated states, potentially providing a structural basis for this anomalous mole fraction effect.

Directed Self-Assembly of C4-Symmetric, Oxidovanadate-Centered, Vanadyl(V) Quadruplexes for Ba2+- and Hg2+-Specific Recognition, Transport, and Recovery

Directed assembly of loosely, Na⁺-bound, oxidovanadate-centered quartets of C₄-symmetry from tailor-made chiral N-salicylidene-vanadyl(V) complexes, for the first time, allows for highly efficient Ba²⁺- or Hg²⁺-specific detection (by ⁵¹V NMR and VCD), transport (forming a unique helical capsule or a capped square planar complex, respectively), and green recovery from an aqueous phase containing 4 different alkaline earth ions or from at least 10 different metal ions of similar size and charge capacity into the CHCl₃ layer without interference from oxa- or oxophilic ions like Mg²⁺, Ca²⁺, Cu²⁺, Cd²⁺, and Pb²⁺.

H. R, Thamleena A. H, Joseph A, Ben A, V. U. K. Roles of different amino-acid residues towards binding and selective transport of K+ through KcsA K+-ion channel

Each amino acid in the selectivity filter plays a distinct role towards binding and transport of K⁺ ion through KcsA.

Octa-Coordination and the Aqueous Ba(2+) Ion

The hydration structure of Ba(2+) ion is important for understanding blocking mechanisms in potassium ion channels. Here, we combine statistical mechanical theory, ab initio molecular dynamics simulations, and electronic structure methods to calculate the hydration free energy and local hydration structure of Ba(2+)(aq). The predicted hydration free energy (-304 ± 1 kcal/mol) agrees with the experimental value (-303 kcal/mol) when a maximally occupied, unimodal inner solvation shell is treated. In the local environment defined by the first shell of hydrating waters, Ba(2+) is directly and stably coordinated by eight (8) waters. Octa-coordination resembles the crystal structure of Ba(2+) and K(+) bound in potassium ion channels, but differs from the local hydration structure of K(+)(aq) determined earlier.

Equilibrium selectivity alone does not create K+-selective ion conduction in K+ channels

Potassium (K(+)) channels are selective for K(+) over Na(+) ions during their transport across membranes. We and others have previously shown that tetrameric K(+) channels are primarily occupied by K(+) ions in their selectivity filters under physiological conditions, demonstrating the channel's intrinsic equilibrium preference for K(+) ions. Based on this observation, we hypothesize that the preference for K(+) ions over Na(+) ions in the filter determines its selectivity during ion conduction. Here, we ask whether non-selective cation channels, which share an overall structure and similar individual ion-binding sites with K(+) channels, have an ion preference at equilibrium. The variants of the non-selective Bacillus cereus NaK cation channel we examine are all selective for K(+) over Na(+) ions at equilibrium. Thus, the detailed architecture of the K(+) channel selectivity filter, and not only its equilibrium ion preference, is fundamental to the generation of selectivity during ion conduction.

Role of methyl-induced polarization in ion binding

The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate transmembrane salt concentration gradients by transporting K(+) ions selectively. One of the K(+) binding sites in the channel's selectivity filter, the S4 site, also binds Ba(2+) ions, which blocks K(+) transport. This inhibitory property of Ba(2+) ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba(2+) block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine, because serine carries one less branched methyl group than threonine. A T→S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba(2+), the loss in K(+) binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups, especially those that are proximal to charged moieties, including ions, titratable amino acids, sulfates, phosphates, and nucleotides.

Interaction of local anesthetics with the K (+) channel pore domain: KcsA as a model for drug-dependent tetramer stability

Local anesthetics and related drugs block ionic currents of Na (+) , K (+) and Ca ( 2+) conducted across the cell membrane by voltage-dependent ion channels. Many of these drugs bind in the permeation pathway, occlude the pore and stop ion movement. However channel-blocking drugs have also been associated with decreased membrane stability of certain tetrameric K (+) channels, similar to the destabilization of channel function observed at low extracellular K (+) concentration. Such drug-dependent stability may result from electrostatic repulsion of K (+) from the selectivity filter by a cationic drug molecule bound in the central cavity of the channel. In this study we used the pore domain of the KcsA K (+) channel protein to test this hypothesis experimentally with a biochemical assay of tetramer stability and theoretically by computational simulation of local anesthetic docking to the central cavity. We find that two common local anesthetics, lidocaine and tetracaine, promote thermal dissociation of the KcsA tetramer in a K (+) -dependent fashion. Docking simulations of these drugs with open, open-inactivated and closed crystal structures of KcsA yield many energetically favorable drug-channel complexes characterized by nonbonded attraction to pore-lining residues and electrostatic repulsion of K (+) . The results suggest that binding of cationic drugs to the inner cavity can reduce tetramer stability of K (+) channels.

Contribution of ion binding affinity to ion selectivity and permeation in KcsA, a model potassium channel

Ion permeation and selectivity, key features in ion channel function, are believed to arise from a complex ensemble of energetic and kinetic variables. Here we evaluate the contribution of pore cation binding to ion permeation and selectivity features of KcsA, a model potassium channel. For this, we used E71A and M96V KcsA mutants in which the equilibrium between conductive and nonconductive conformations of the channel is differently shifted. E71A KcsA is a noninactivating channel mutant. Binding of K(+) to this mutant reveals a single set of low-affinity K(+) binding sites, similar to that seen in the binding of K(+) to wild-type KcsA that produces a conductive, low-affinity complex. This seems consistent with the observed K(+) permeation in E71A. Nonetheless, the E71A mutant retains K(+) selectivity, which cannot be explained on the basis of just its low affinity for this ion. At variance, M96V KcsA is a rapidly inactivating mutant that has lost selectivity for K(+) and also conducts Na(+). Here, low-affinity binding and high-affinity binding of both cations are detected, seemingly in agreement with both being permeating species in this mutant channel. In conclusion, binding of the ion to the channel protein seemingly explains certain gating, ion selectivity, and permeation properties. Ion binding stabilizes greatly the channel and, depending upon ion type and concentration, leads to different conformations and ion binding affinities. High-affinity states guarantee binding of specific ions and mediate ion selectivity but are nonconductive. Conversely, low-affinity states would not discriminate well among different ions but allow permeation to occur.

Synchrotron radiation circular dichroism spectroscopy-defined structure of the C-terminal domain of NaChBac and its role in channel assembly

Extramembranous domains play important roles in the structure and function of membrane proteins, contributing to protein stability, forming association domains, and binding ancillary subunits and ligands. However, these domains are generally flexible, making them difficult or unsuitable targets for obtaining high-resolution X-ray and NMR structural information. In this study we show that the highly sensitive method of synchrotron radiation circular dichroism (SRCD) spectroscopy can be used as a powerful tool to investigate the structure of the extramembranous C-terminal domain (CTD) of the prokaryotic voltage-gated sodium channel (Na(V)) from Bacillus halodurans, NaChBac. Sequence analyses predict its CTD will consist of an unordered region followed by an alpha-helix, which has a propensity to form a multimeric coiled-coil motif, and which could form an association domain in the homotetrameric NaChBac channel. By creating a number of shortened constructs we have shown experimentally that the CTD does indeed contain a stretch of approximately 20 alpha-helical residues preceded by a nonhelical region adjacent to the final transmembrane segment and that the efficiency of assembly of channels in the membrane progressively decreases as the CTD residues are removed. Analyses of the CTDs of 32 putative prokaryotic Na(V) sequences suggest that a CTD helical bundle is a structural feature conserved throughout the bacterial sodium channel family.

Selection of inhibitor-resistant viral potassium channels identifies a selectivity filter site that affects barium and amantadine block

Background

Understanding the interactions between ion channels and blockers remains an important goal that has implications for delineating the basic mechanisms of ion channel function and for the discovery and development of ion channel directed drugs.

Methodology/Principal Findings

We used genetic selection methods to probe the interaction of two ion channel blockers, barium and amantadine, with the miniature viral potassium channel Kcv. Selection for Kcv mutants that were resistant to either blocker identified a mutant bearing multiple changes that was resistant to both. Implementation of a PCR shuffling and backcrossing procedure uncovered that the blocker resistance could be attributed to a single change, T63S, at a position that is likely to form the binding site for the inner ion in the selectivity filter (site 4). A combination of electrophysiological and biochemical assays revealed a distinct difference in the ability of the mutant channel to interact with the blockers. Studies of the analogous mutation in the mammalian inward rectifier Kir2.1 show that the T→S mutation affects barium block as well as the stability of the conductive state. Comparison of the effects of similar barium resistant mutations in Kcv and Kir2.1 shows that neighboring amino acids in the Kcv selectivity filter affect blocker binding.

Conclusions/Significance

The data support the idea that permeant ions have an integral role in stabilizing potassium channel structure, suggest that both barium and amantadine act at a similar site, and demonstrate how genetic selections can be used to map blocker binding sites and reveal mechanistic features.

Protein dynamics detected in a membrane-embedded potassium channel using two-dimensional solid-state NMR spectroscopy

We report longitudinal (15)N relaxation rates derived from two-dimensional ((15)N, (13)C) chemical shift correlation experiments obtained under magic angle spinning for the potassium channel KcsA-Kv1.3 reconstituted in multilamellar vesicles. Thus, we demonstrate that solid-state NMR can be used to probe residue-specific backbone dynamics in a membrane-embedded protein. Enhanced backbone mobility was detected for two glycine residues within the selectivity filter that are highly conserved in potassium channels and that are of core relevance to the filter structure and ion selectivity.

Differential roles of blocking ions in KirBac1.1 tetramer stability

Potassium channels are tetrameric proteins that mediate K(+)-selective transmembrane diffusion. For KcsA, tetramer stability depends on interactions between permeant ions and the channel pore. We have examined the role of pore blockers on the tetramer stability of KirBac1.1. In 150 mm KCl, purified KirBac1.1 protein migrates as a monomer (approximately 40 kDa) on SDS-PAGE. Addition of Ba(2+) (K(1/2) approximately 50 microm) prior to loading results in an additional tetramer band (approximately 160 kDa). Mutation A109C, at a residue located near the expected Ba(2+)-binding site, decreased tetramer stabilization by Ba(2+) (K(1/2) approximately 300 microm), whereas I131C, located nearby, stabilized tetramers in the absence of Ba(2+). Neither mutation affected Ba(2+) block of channel activity (using (86)Rb(+) flux assay). In contrast to Ba(2+), Mg(2+) had no effect on tetramer stability (even though Mg(2+) was a potent blocker). Many studies have shown Cd(2+) block of K(+) channels as a result of cysteine substitution of cavity-lining M2 (S6) residues, with the implicit interpretation that coordination of a single ion by cysteine side chains along the central axis effectively blocks the pore. We examined blocking and tetramer-stabilizing effects of Cd(2+) on KirBac1.1 with cysteine substitutions in M2. Cd(2+) block potency followed an alpha-helical pattern consistent with the crystal structure. Significantly, Cd(2+) strongly stabilized tetramers of I138C, located in the center of the inner cavity. This stabilization was additive with the effect of Ba(2+), consistent with both ions simultaneously occupying the channel: Ba(2+) at the selectivity filter entrance and Cd(2+) coordinated by I138C side chains in the inner cavity.