Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling

Sub-femtomolar drug monitoring via co-calibration mechanism with nanoconfined DNA probes

Synthetic drugs fundamentally reshape the illicit drug market due to their low cost, ease of production, and rapid manufacturing processes. However, current drug detection methods, which rely on complex instruments, have limited applicability and often neglect the influence of pH fluctuations, leading to potential bias and unreliable results. Herein, we propose co-calibration DNA probes on a nanoconfined biosensor (NCBS), covering the range of sweat pH 3-8 to achieve significantly enhanced target signal recognition. The NCBS exhibits a linear response range of 103-108 fM with a low limit of detection (LOD) of 3.58 fM in artificial sweat. Compared to the single-aptamer NCBS, the dual-aptamer NCBS offers a broader linear response range, primarily due to the synergistic effects of changes in surface wettability and the capture of hydrion, which together reduce signal interference in proton transport. The linear response range doubles, and its detection sensitivity improves by 4-5 orders of magnitude compared to existing drug detection methods. This sensing strategy expands the application scope of aptamer-based composite probes, offering an approach for ultra-sensitive drug detection and demonstrating significant potential in sweat sensing and drug monitoring fields.

Direct visualization of electric-field-stimulated ion conduction in a potassium channel

Understanding protein function would be facilitated by direct, real-time observation of chemical kinetics in the atomic structure. The selectivity filter (SF) of the K+ channel provides an ideal model, catalyzing the dehydration and transport of K+ ions across the cell membrane through a narrow pore. We used a "pump-probe" method called electric-field-stimulated time-resolved X-ray crystallography (EFX) to initiate and observe K+ conduction in the NaK2K channel in both directions on the timescale of the transport process. We observe both known and potentially new features in the high-energy conformations visited along the conduction pathway, including the associated dynamics of protein residues that control selectivity and conduction rate. A single time series of one channel in action shows the orderly appearance of features observed in diverse homologs with diverse methods, arguing for deep conservation of the dynamics underlying the reaction coordinate in this protein family.

Transmembrane Ion Channels: From Natural to Artificial Systems

Natural channel proteins allow the selective permeation of ions, water or other nutritious entities across bilayer membranes, facilitating various essential physiological functions in living systems. Inspired by nature, chemists endeavor to simulate the structural features and transport behaviors of channel proteins through biomimetic strategies. In this review, we start from introducing the inherent traits of channel proteins such as their crystal structures, functions and mechanisms. Subsequently, different kind of synthetic ion channels including their design principles, dynamic regulations and therapeutic applications were carefully reviewed. Finally, the potential challenges and opportunities in this research field were also carefully discussed. It is anticipated that this review could provide some inspiring ideas and future directions towards the construction of novel bionic ion channels with higher-level structures, properties, functions and practical applications.

Structures of TASK-1 and TASK-3 K2P channels provide insight into their gating and dysfunction in disease

TASK-1 and TASK-3 are pH-sensitive two-pore domain (K2P/KCNK) K+ channels. Their functional roles make them promising targets for treatment of multiple disorders including sleep apnea, pain, and atrial fibrillation. Mutations in these channels are also associated with neurodevelopmental and hypertensive disorders. A previous crystal structure of TASK-1 revealed a lower "X-gate" as a hotspot for missense gain-of-function (GoF) mutations associated with DDSA (developmental delay with sleep apnea). However, the mechanisms of gating in TASK channels are still not fully understood. Here, we resolve structures for both human TASK-1 and TASK-3 by cryoelectron microscopy (cryo-EM), as well as a recurrent TASK-3 variant (G236R) associated with KCNK9 imprinting syndrome (KIS) (formerly known as Birk-Barel syndrome). Combined with functional studies of the X-gating mechanism, we provide evidence for how a highly conserved gating mechanism becomes defective in disease, and also provide further insight into the pathway of conformational changes that underlie the pH-dependent inhibition of TASK channel activity.

Binding kinetics of quaternary ammonium ions in Kcv potassium channels

Kcv channels from plant viruses represent the autonomous pore module of potassium channels, devoid of any regulatory domains. These small proteins show very reproducible single-channel behavior in planar lipid bilayers. Thus, they are an optimum system for the study of the biophysics of ion transport and gating. Structural models based on homology modeling have been used successfully, but experimental structural data are currently not available. Here we determine the size of the cytosolic pore entrance by studying the blocker kinetics. Blocker binding and dissociation rate constants ranging from 0.01 to 1000 ms-1 were determined for different quaternary ammonium ions. We found that the cytosolic pore entrance of KcvNTS must be at least 11 Å wide. The results further indicate that the residues controlling a cytosolic gate in one of the Kcv isoforms influence blocker binding/dissociation as well as a second gate even when the cytosolic gate is in the open state. The voltage dependence of the rate constant of blocker release is used to test, which blockers bind to the same binding site.

Do selectivity filter carbonyls in K+ channels flip away from the pore? Two-dimensional infrared spectroscopy study

Molecular dynamics simulations revealed that the carbonyls of the Val residue in the conserved selectivity filter sequence TVGTG of potassium ion channels can flip away from the pore to form hydrogen bonds with the network of water molecules residing behind the selectivity filter. Such a configuration has been proposed to be relevant for C-type inactivation. Experimentally, X-ray crystallography of the KcsA channel admits the possibility that the Val carbonyls can flip, but it cannot decisively confirm the existence of such a configuration. In this study, we combined molecular dynamics simulations and line shape theory to design two-dimensional infrared spectroscopy experiments that can corroborate the existence of the selectivity filter configuration with flipped Val carbonyls. This ability to distinguish between flipped and unflipped carbonyls is based on the varying strength of the electric field inside and outside the pore, which is directly linked to carbonyl stretching frequencies that can be resolved using infrared spectroscopy.

Ion and water permeation through claudin-10b and claudin-15 paracellular channels

The structural scaffold of epithelial and endothelial tight junctions (TJs) comprises multimeric strands of claudin (Cldn) proteins that anchor adjacent cells and control the paracellular flux of water and solutes. Based on the permeability properties they confer to the TJs, Cldns are classified as channel- or barrier-forming. For instance, Cldn10b, expressed in kidneys, lungs, and other tissues, displays high permeability for cations and low permeability for water. Along with its high sequence similarity to the cation- and water-permeable TJ protein Cldn15, this makes Cldn10b a valuable test case for investigating the molecular determinants of paracellular transport. In lack of high-resolution experimental information on TJ architectures, here we use molecular dynamics simulations to determine whether atomistic models recapitulate the differences in ion and water transport between of Cldn10b and Cldn15. Our data, based on extensive standard simulations and free energy calculations, reveal that Cldn10b models form cation-permeable pores narrower than Cldn15, which, together with the stable coordination of Na+ ions to acidic pore-lining residues (E153, D36, D56), limit the passage of water molecules. By providing a mechanism driving a peculiar case of paracellular transport, these results provide a structural basis for the specific permeability properties of Cldn subtypes that define their physiological role.

Computational engineering of water-soluble human potassium ion channels through QTY transformation

Transmembrane potassium ion channels are crucial for ion transport, metabolism, and signaling, and serve as promising targets for anti-cancer therapies. However, their hydrophobic transmembrane nature requires detergents, posing a major bottleneck for experimental handling. In this paper, we present a structural bioinformatics study of six experimentally determined and twelve modeled potassium channel structures, in which hydrophobic amino acids (L, I/V, and F) were systematically replaced with neutral hydrophilic ones (Q, T, and Y), making the proteins more water-soluble. QTY (computationally predicted) and native (experimental and repredicted) variants show remarkable structural similarity (RMSD: ~0.50 Å - ~2.14 Å) despite significant sequence differences. QTY variants, both rigid and refined with MD simulations, maintain comparable to native variants stability, solvent-accessible surface area (SASA), and ionic, aromatic, and van der Waals interactions but differ in the grand average of hydropathy (GRAVY), solubility, and hydrophobic contacts. Overall, our study presents a computational approach for designing hydrophilic potassium ion channels while maintaining the native global structure that could potentially simplify their practical use by eliminating the need for detergents.

Isoleucine gate blocks K+ conduction in C-type inactivation

Many voltage-gated potassium (Kv) channels display a time-dependent phenomenon called C-type inactivation, whereby prolonged activation by voltage leads to the inhibition of ionic conduction, a process that involves a conformational change at the selectivity filter toward a non-conductive state. Recently, a high-resolution structure of a strongly inactivated triple-mutant channel kv1.2-kv2.1-3m revealed a novel conformation of the selectivity filter that is dilated at its outer end, distinct from the well-characterized conductive state. While the experimental structure was interpreted as the elusive non-conductive state, our molecular dynamics simulations and electrophysiological measurements show that the dilated filter of kv1.2-kv2.1-3m is conductive and, as such, cannot completely account for the inactivation of the channel observed in the structural experiments. The simulation shows that an additional conformational change, implicating isoleucine residues at position 398 along the pore lining segment S6, is required to effectively block ion conduction. The I398 residues from the four subunits act as a state-dependent hydrophobic gate located immediately beneath the selectivity filter. These observations are corroborated by electrophysiological experiments showing that ion permeation can be resumed in the kv1.2-kv2.1-3m channel when I398 is mutated to an asparagine-a mutation that does not abolish C-type inactivation since digitoxin (AgTxII) fails to block the ionic permeation of kv1.2-kv2.1-3m_I398N. As a critical piece of the C-type inactivation machinery, this structural feature is the potential target of a broad class of quaternary ammonium (QA) blockers and negatively charged activators thus opening new research directions toward the development of drugs that specifically modulate gating states of Kv channels.

Effect of two activators on the gating of a K2P channel

TWIK-related potassium channel 1 (TREK1), a two-pore-domain mammalian potassium (K+) channel, regulates the resting potential across cell membranes, presenting a promising therapeutic target for neuropathy treatment. The gating of this channel converges in the conformation of the narrowest part of the pore: the selectivity filter (SF). Various hypotheses explain TREK1 gating modulation, including the dynamics of loops connecting the SF with transmembrane helices and the stability of hydrogen bond (HB) networks adjacent to the SF. Recently, two small molecules (Q6F and Q5F) were reported as activators that affect TREK1 by increasing its open probability in single-channel current measurements. Here, using molecular dynamics simulations, we investigate the effect of these ligands on the previously proposed modulation mechanisms of TREK1 gating compared to the apo channel. Our findings reveal that loop dynamics at the upper region of the SF exhibit only a weak correlation with permeation events/nonpermeation periods, whereas the HB network behind the SF appears more correlated. These nonpermeation periods arise from both distinct mechanisms: a C-type inactivation (resulting from dilation at the top of the SF), which has been described previously, and a carbonyl flipping in an SF binding site. We find that, besides the prevention of C-type inactivation in the channel, the ligands increase the probability of permeation by modulating the dynamics of the carbonyl flipping, influenced by a threonine residue at the bottom of the SF. These results offer insights for rational ligand design to optimize the gating modulation of TREK1 and related K+ channels.

Ion occupancy of the selectivity filter controls opening of a cytoplasmic gate in the K2P channel TALK-2

Two-pore domain K+ (K2P) channel activity was previously thought to be controlled primarily via a selectivity filter (SF) gate. However, recent crystal structures of TASK-1 and TASK-2 revealed a lower gate at the cytoplasmic pore entrance. Here, we report functional evidence of such a lower gate in the K2P channel K2P17.1 (TALK-2, TASK-4). We identified compounds (drugs and lipids) and mutations that opened the lower gate allowing the fast modification of pore cysteine residues. Surprisingly, stimuli that directly target the SF gate (i.e., pHe., Rb+ permeation, membrane depolarization) also opened the cytoplasmic gate. Reciprocally, opening of the lower gate reduced the electric work to open the SF via voltage driven ion binding. Therefore, it appears that the SF is so rigidly locked into the TALK-2 protein structure that changes in ion occupancy can pry open a distant lower gate and, vice versa, opening of the lower gate concurrently promote SF gate opening. This concept might extent to other K+ channels that contain two gates (e.g., voltage-gated K+ channels) for which such a positive gate coupling has been suggested, but so far not directly demonstrated.

Selectivity filter mutations shift ion permeation mechanism in potassium channels

Potassium (K+) channels combine high conductance with high ion selectivity. To explain this efficiency, two molecular mechanisms have been proposed. The "direct knock-on" mechanism is defined by water-free K+ permeation and formation of direct ion-ion contacts in the highly conserved selectivity filter (SF). The "soft knock-on" mechanism involves co-permeation of water and separation of K+ by water molecules. With the aim to distinguish between these mechanisms, crystal structures of the KcsA channel with mutations in two SF residues-G77 and T75-were published, where the arrangements of K+ ions and water display canonical soft knock-on configurations. These data were interpreted as evidence of the soft knock-on mechanism in wild-type channels. Here, we test this interpretation using molecular dynamics simulations of KcsA and its mutants. We show that while a strictly water-free direct knock-on permeation is observed in the wild type, conformational changes induced by these mutations lead to distinct ion permeation mechanisms, characterized by co-permeation of K+ and water. These mechanisms are characterized by reduced conductance and impaired potassium selectivity, supporting the importance of full dehydration of potassium ions for the hallmark high conductance and selectivity of K+ channels. In general, we present a case where mutations introduced at the critical points of the permeation pathway in an ion channel drastically change its permeation mechanism in a nonintuitive manner.

Fine-tuning pH sensor H98 by remote essential residues in the hydrogen-bond network of mTASK-3

TASK-3 generates a background K+ conductance which when inhibited by acidification depolarizes membrane potential and increases cell excitability. These channels sense pH by protonation of histidine residue H98, but recent evidence revealed that several other amino acid residues also contribute to TASK-3 pH sensitivity, suggesting that the pH sensitivity is determined by an intermolecular network. Here we use electrophysiology and molecular modeling to characterize the nature and requisite role(s) of multiple amino acids in pH sensing by TASK-3. Our results suggest that the pH sensor H98 and consequently pH sensitivity is influenced by remote amino acids that function as a hydrogen-bonding network to modulate ionic conductivity. Among the residues in the network, E30 and K79 are the most important for passing external signals near residue S31 to H98. The hydrogen-bond network plays a key role in selectivity or pH sensing in mTASK-3, and E30 and S31 in the network can modulate the conductive properties (E30) or reverse the pH sensitivity and selectivity of the channel (S31). Molecular dynamics simulations and pK1/2 calculation revealed that double mutants involving H98 + S31 primarily regulate the structure stability of the pore selectivity filter and pore loop regions, further strengthen the stability of the cradle suspension system, and alter the ionization state of E30 and K79, thereby preventing pore conformational change that normally occurs in response to varying extracellular pH. These results demonstrate that crucial residues in the hydrogen-bond network can remotely tune the pH sensing of mTASK-3 and may be a potential allosteric regulatory site for therapeutic molecule development.

Structure of the Ion Channel Kir7.1 and Implications for its Function in Normal and Pathophysiologic States

Hereditary defects in the function of the Kir7.1 in the retinal pigment epithelium are associated with the ocular diseases retinitis pigmentosa, Leber congenital amaurosis, and snowflake vitreal degeneration. Studies also suggest that Kir7.1 may be regulated by a GPCR, the melanocortin-4 receptor, in certain hypothalamic neurons. We present the first structures of human Kir7.1 and describe the conformational bias displayed by two pathogenic mutations, R162Q and E276A, to provide an explanation for the basis of disease and illuminate the gating pathway. We also demonstrate the structural basis for the blockade of the channel by a small molecule ML418 and demonstrate that channel blockade in vivo activates MC4R neurons in the paraventricular nucleus of the hypothalamus (PVH), inhibiting food intake and inducing weight loss. Preliminary purification, and structural and pharmacological characterization of an in tandem construct of MC4R and Kir7.1 suggests that the fusion protein forms a homotetrameric channel that retains regulation by liganded MC4R molecules.

Short-term plasticity as 'energetic memory' of ion channel components of action potential

Information transfer in the nervous system is traditionally understood by the transmission of action potentials along neuronal dendrites, with ion channels in the membrane as the basic unit operator for their creation and propagation. We present here a new model for the multiphysics behaviour of ion channels and the action potential dynamics in nervous and other signal-transmitting systems. This model is based on the long-term suppression of an action potential as a response to mechanical input. While other models focus on electrical aspects of the action potential, an increasing body of experiments highlights its electro-mechanical nature and points in particular towards an alteration of the action potential when subjected to a mechanical input. Here, we propose a new phenomenological framework able to capture the mechanical aspect of ion channel dynamics and the resulting effect on the overall electrophysiology of the membrane. The model is introduced here through a set of coupled differential equations that describe the system while agreeing with the general findings of the experiments that support an electro-mechanical model. It also confirms that transient quasi-static mechanical loads reversibly affect the amplitude and rate of change of neuronal action potentials, which are smaller and slower under indentation loading conditions. Changes after the loading release are also reversible, albeit on a different time scale.

Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics (MD) simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes, while the up-state structure maintains a stable and conductive SF. This suggests an atomistic mechanism for the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, experimentally by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. Based on MD simulations, we propose two gating pathways by which movement of the pCt controls the stability (i.e., conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.

Mutation in pore-helix modulates interplay between filter gate and Ba2+ block in a Kcv channel pore

The selectivity filter of K+ channels catalyzes a rapid and highly selective transport of K+ while serving as a gate. To understand the control of this filter gate, we use the pore-only K+ channel KcvNTS in which gating is exclusively determined by the activity of the filter gate. It has been previously shown that a mutation at the C-terminus of the pore-helix (S42T) increases K+ permeability and introduces distinct voltage-dependent and K+-sensitive channel closures at depolarizing voltages. Here, we report that the latter are not generated by intrinsic conformational changes of the filter gate but by a voltage-dependent block caused by nanomolar trace contaminations of Ba2+ in the KCl solution. Channel closures can be alleviated by extreme positive voltages and they can be completely abolished by the high-affinity Ba2+ chelator 18C6TA. By contrast, the same channel closures can be augmented by adding Ba2+ at submicromolar concentrations to the cytosolic buffer. These data suggest that a conservative exchange of Ser for Thr in a crucial position of the filter gate increases the affinity of the filter for Ba2+ by >200-fold at positive voltages. While Ba2+ ions apparently remain only for a short time in the filter-binding sites of the WT channel before passing the pore, they remain much longer in the mutant channel. Our findings suggest that the dwell times of permeating and blocking ions in the filter-binding sites are tightly controlled by interactions between the pore-helix and the selectivity filter.

Connexin Gap Junction Channels and Hemichannels: Insights from High-Resolution Structures

Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca2+ overload. Surprisingly, the binding of 12 Ca2+ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a "ball-and-chain" fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein-protein and protein-lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation.

C-type inactivation and proton modulation mechanisms of the TASK3 channel

The TWIK-related acid-sensitive K+ channel 3 (TASK3) belongs to the two-pore domain (K2P) potassium channel family, which regulates cell excitability by mediating a constitutive "leak" potassium efflux in the nervous system. Extracellular acidification inhibits TASK3 channel, but the molecular mechanism by which channel inactivation is coupled to pH decrease remains unclear. Here, we report the cryo-electron microscopy structures of human TASK3 at neutral and acidic pH. Structural comparison revealed selectivity filter (SF) rearrangements upon acidification, characteristic of C-type inactivation, but with a unique structural basis. The extracellular mouth of the SF was prominently dilated and simultaneously blocked by a hydrophobic gate. His98 protonation shifted the conformational equilibrium between the conductive and C-type inactivated SF toward the latter by engaging a cation-π interaction with Trp78, consistent with molecular dynamics simulations and electrophysiological experiments. Our work illustrated how TASK3 is gated in response to extracellular pH change and implies how physiological stimuli might directly modulate the C-type gating of K2P channels.

Asymmetric contribution of a selectivity filter gate in triggering inactivation of CaV1.3 channels

Voltage-dependent and Ca2+-dependent inactivation (VDI and CDI, respectively) of CaV channels are two biologically consequential feedback mechanisms that fine-tune Ca2+ entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultrahighly conserved tryptophan residues in the interdomain interfaces near the selectivity filter of CaV1.3, we demonstrate a critical role for asymmetric conformational changes in mediating VDI and CDI. Specifically, mutagenesis of the domain III-IV interface, but not others, enhanced VDI. Molecular dynamics simulations demonstrate that mutations in distinct selectivity filter interfaces differentially impact conformational flexibility. Furthermore, mutations in distinct domains preferentially disrupt CDI mediated by the N- versus C-lobes of CaM, thus uncovering a scheme of structural bifurcation of CaM signaling. These findings highlight the fundamental importance of the asymmetric arrangement of the pseudotetrameric CaV pore domain for feedback inhibition.

Computational Studies Show How the H463R Mutation Turns hKv1.5 into an Inactivation State

The KCNA5 gene provides the code for the α-subunit of the potassium channel Kv1.5. The genetic variant H463R in the Kv1.5 channel has been reported to cause a functional loss in atrial fibrillation (AF) patients. Understanding the mutations at a molecular level is key to developing improved therapeutics concerning cardiac hKv1.5 and hKv1.4 channels. Molecular dynamics and umbrella sampling free energy simulations are an effective tool to understand the mutation's effect on ion conduction, which we have employed and found that the hKv1.5[H463R] mutation imposes an energy barrier on the ion conduction pathway compared to the wild-type channel's ion free energy and pore structure. These results imply that the arginine mutation associated with the AF disease in particular modulates the inactivation process of hKv1.5. Kv1.4, encoded by the KCNA4 gene, is also present in the heart. Therefore, we considered simulation studies of the equivalent H507R mutation in the hKv1.4 channel and found that the mutation slightly reduces the ion conduction barrier in the ion conduction pathway, making it insignificant.

The molecular mechanism of the effects of the anti-neuropathic ligands on the modulation of the Sigma-2 receptor: An in-silico study

Neuropathic pain (NP) is a prevalent medical condition that lacks an effective treatment. Recently, the Sigma-2 receptor (S2R) has been proposed as a potential therapeutic target for NP. Some highly-selective S2R ligands (UKH1114, CM398, and YTD) have shown promising results in vivo, but the molecular interaction between the S2R and these ligands has been scarcely investigated. This work explores changes in the S2R upon interaction with the three mentioned ligands using in silico approaches. The results indicated that the ICL1, H1, ICL2, and ECL are the most dynamic regions of S2R in all systems. Binding interaction analysis identified amino acids with significant contribution to the binding free energy. Notably, the UKH1114-S2R simulation trajectory revealed that small alterations in the ICL1, H1, ICL2, and ECL form a new stable opening in the S2R, linking the occluded S2R binding pocket to the endoplasmic reticulum lumen, providing more evidence for the assumptions about the EBP and S2R mechanism of function. Further, the agreement between the membrane parameters in our study and experimental values confirms the validity of the MD simulations. Overall, this study provides new insights into the interaction between anti-NP ligands and the S2R.

Brownian Aging as One of the Mechanistic Components That Shape the Single-Channel Ionic Currents through Biological and Synthetic Membranes

Semipermeable membranes enable the separation of a given system from its environment. In biological terms, they are responsible for cells' identity. In turn, the functioning of ion channels is crucial for the control of ionic fluxes across the membranes and, consequently, for the exchange of chemical and electrical signals. This paper presents a model and simulations of currents through ionic nanochannels in an attempt to better understand the physical mechanism(s) of open/closed (O/C) sequences, i.e., random interruptions of ionic flows through channels observed in all known biochannels and in some synthetic nanopores. We investigate whether aging, i.e., the changes in Brownian motion characteristics with the lapse of time, may be at least one of the sources of the O/C sequences (in addition to the gating machinery in biochannels). The simulations based on the approximated nanostructure of ion channels confirm this postulation. The results also show the possibility of changing the O/C characteristics through an appropriate alteration of the channel surroundings. This observation may be valuable in technical uses of nanochannels in synthetic membranes and allow for a better understanding of the reason for the differences between the biochannels' activity in diverse biological membranes. Proposals of experimental verification of this aging O/C hypothesis are also presented.

Structural Fluctuation, Relaxation, and Folding of Protein: An Approach Based on the Combined Generalized Langevin and RISM/3D-RISM Theories

In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water's degrees of freedom onto the protein's degrees of freedom. Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix. The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.

Alkali metal cations modulate the geometry of different binding sites in HCN4 selectivity filter for permeation or block

Hyperpolarization-activated cyclic-nucleotide gated (HCN) channels are important for timing biological processes like heartbeat and neuronal firing. Their weak cation selectivity is determined by a filter domain with only two binding sites for K+ and one for Na+. The latter acts as a weak blocker, which is released in combination with a dynamic widening of the filter by K+ ions, giving rise to a mixed K+/Na+ current. Here, we apply molecular dynamics simulations to systematically investigate the interactions of five alkali metal cations with the filter of the open HCN4 pore. Simulations recapitulate experimental data like a low Li+ permeability, considerable Rb+ conductance, a block by Cs+ as well as a punch through of Cs+ ions at high negative voltages. Differential binding of the cation species in specific filter sites is associated with structural adaptations of filter residues. This gives rise to ion coordination by a cation-characteristic number of oxygen atoms from the filter backbone and solvent. This ion/protein interplay prevents Li+, but not Na+, from entry into and further passage through the filter. The site equivalent to S3 in K+ channels emerges as a preferential binding and presumably blocking site for Cs+. Collectively, the data suggest that the weak cation selectivity of HCN channels and their block by Cs+ are determined by restrained cation-generated rearrangements of flexible filter residues.

Extreme Ion-Transport Inorganic 2D Membranes for Nanofluidic Applications

Inorganic 2D materials offer a new approach to controlling mass diffusion at the nanoscale. Controlling ion transport in nanofluidics is key to energy conversion, energy storage, water purification, and numerous other applications wherein persistent challenges for efficient separation must be addressed. The recent development of 2D membranes in the emerging field of energy harvesting, water desalination, and proton/Li-ion production in the context of green energy and environmental technology is herein discussed. The fundamental mechanisms, 2D membrane fabrication, and challenges toward practical applications are highlighted. Finally, the fundamental issues of thermodynamics and kinetics are outlined along with potential membrane designs that must be resolved to bridge the gap between lab-scale experiments and production levels.

Asymmetric Contribution of a Selectivity Filter Gate in Triggering Inactivation of CaV1.3 Channels

Voltage-dependent and Ca2+-dependent inactivation (VDI and CDI, respectively) of CaV channels are two biologically consequential feedback mechanisms that fine-tune Ca2+ entry into neurons and cardiomyocytes. Although known to be initiated by distinct molecular events, how these processes obstruct conduction through the channel pore remains poorly defined. Here, focusing on ultra-highly conserved tryptophan residues in the inter-domain interfaces near the selectivity filter of CaV1.3, we demonstrate a critical role for asymmetric conformational changes in mediating VDI and CDI. Specifically, mutagenesis of the domain III-IV interface, but not others, enhanced VDI. Molecular dynamics simulations demonstrate that mutations in distinct selectivity filter interfaces differentially impact conformational flexibility. Furthermore, mutations in distinct domains preferentially disrupt CDI mediated by the N- versus C-lobes of CaM, thus uncovering a scheme of structural bifurcation of CaM signaling. These findings highlight the fundamental importance of the asymmetric arrangement of the pseudo-tetrameric CaV pore domain for feedback inhibition.

Solid-state nanochannels for bio-marker analysis

Bio-markers, such as ions, small molecules, nucleic acids, peptides, proteins and cells, participate in the construction of living organisms and play important roles in biological processes. It is of great significance to accurately detect these bio-markers for studying their basic functions, the development of molecular diagnosis and to better understand life processes. Solid-state nanochannel-based sensing systems have been demonstrated for the detection of bio-markers, due to their rapid, label-free and high-throughput screening, with high sensitivity and specificity. Generally, studies on solid-state nanochannels have focused on probes on the inner-wall (PIW), ignoring probes on the outer-surface (POS). As a result, the direct detection of cells is difficult to realize by these inner-wall focused nanochannels. Moreover, the sensitivity for detecting ions, small molecules, nucleic acids, peptides and proteins requires further improvement. Recent research has focused on artificial solid-state nanochannels with POS, which have demonstrated the ability to independently regulate ion transport. This design not only contributes to the in situ detection of large analytes, such as cells, but also provides promising opportunities for ultra-high sensitivity detection with a clear mechanism. In this tutorial review, we present an overview of the detection principle used for solid-state nanochannels, inner-wall focused nanochannels and outer-surface focused nanochannels. Furthermore, we discuss the remaining challenges faced by current nanochannel technologies and provide insights into their prospects.

Voltage-Mediated Water Dynamics Enables On-Demand Transport of Sugar Molecules in Two-Dimensional Channels

The constructing of artificial channels with gating functions is an important undertaking for gaining insight into biological process and achieving efficient bionic functions. Typically, controllable transport within such channels relies on either electrostatic or specific interactions between the transporting species and the channel. However, for molecules with weak interactions with the channel, achieving precise gating of the transport remains a significant challenge. In this regard, this study proposes a voltage gating membrane of two-dimensional channels that selectively transport of neutral molecules glucose with a dimension of 0.60 nm. The permeation of glucose is switched on/off by electrochemically manipulating the water dynamics in the nanochannel. Voltage driven-intercalation of ion into the two-dimensional channel causes water to stratify and move closer to the channel walls, thereby resulting in the channel center being emptier for glucose diffusion. Due to the sub-nanometer size dimension of the channel, selective permeation of glucose over sucrose is also achieved in this approach.

Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy

The potassium ion (K+) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single 13C-18O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K+ transport mechanisms: soft-knock and hard-knock. According to the former, water molecules alternate between K+ ions in the selectivity filter while the latter assumes that K+ ions occupy the adjacent sites. Molecular dynamics simulations and computational spectroscopy are employed to interpret experimental 2D IR spectra. We find that in the closed conductive state of the KcsA channel, K+ ions do not occupy adjacent binding sites. The experimental data is consistent with simulated 2D IR spectra of soft-knock ion configurations. In contrast, the simulated spectra for the hard-knock ion configurations do not reproduce the experimental results. 2D IR spectra of the hard-knock mechanism have lower frequencies, homogeneous 2D lineshapes, and multiple peaks. In contrast, ion configurations of the soft-knock model produce 2D IR spectra with a single peak at a higher frequency and inhomogeneous lineshape. We conclude that under equilibrium conditions, in the absence of transmembrane voltage, both water and K+ ions occupy the selectivity filter of the KcsA channel in the closed conductive state. The ion configuration is central to the mechanism of ion transport through potassium channels.

A peek behind the scenes of selectivity filter gating

JGP study (Kopec et al. 2023. J. Gen. Physiol.https://doi.org/10.1085/jgp.202213166) reveals how interactions with pore-helix residues control filter inactivation in the prokaryotic potassium channel MthK.

Interactions between selectivity filter and pore helix control filter gating in the MthK channel

K+ channel activity can be limited by C-type inactivation, which is likely initiated in part by dissociation of K+ ions from the selectivity filter and modulated by the side chains that surround it. While crystallographic and computational studies have linked inactivation to a "collapsed" selectivity filter conformation in the KcsA channel, the structural basis for selectivity filter gating in other K+ channels is less clear. Here, we combined electrophysiological recordings with molecular dynamics simulations, to study selectivity filter gating in the model potassium channel MthK and its V55E mutant (analogous to KcsA E71) in the pore-helix. We found that MthK V55E has a lower open probability than the WT channel, due to decreased stability of the open state, as well as a lower unitary conductance. Simulations account for both of these variables on the atomistic scale, showing that ion permeation in V55E is altered by two distinct orientations of the E55 side chain. In the "vertical" orientation, in which E55 forms a hydrogen bond with D64 (as in KcsA WT channels), the filter displays reduced conductance compared to MthK WT. In contrast, in the "horizontal" orientation, K+ conductance is closer to that of MthK WT; although selectivity filter stability is lowered, resulting in more frequent inactivation. Surprisingly, inactivation in MthK WT and V55E is associated with a widening of the selectivity filter, unlike what is observed for KcsA and reminisces recent structures of inactivated channels, suggesting a conserved inactivation pathway across the potassium channel family.

Cloxyquin activates hTRESK by allosteric modulation of the selectivity filter

The TWIK-related spinal cord K⁺ channel (TRESK, K_2P18.1) is a K_2P channel contributing to the maintenance of membrane potentials in various cells. Recently, physiological TRESK function was identified as a key player in T-cell differentiation rendering the channel a new pharmacological target for treatment of autoimmune diseases. The channel activator cloxyquin represents a promising lead compound for the development of a new class of immunomodulators. Identification of cloxyquin binding site and characterization of the molecular activation mechanism can foster the future drug development. Here, we identify the cloxyquin binding site at the M2/M4 interface by mutational scan and analyze the molecular mechanism of action by protein modeling as well as in silico and in vitro electrophysiology using different permeating ion species (K⁺ / Rb⁺). In combination with kinetic analyses of channel inactivation, our results suggest that cloxyquin allosterically stabilizes the inner selectivity filter facilitating the conduction process subsequently activating hTRESK.

A multi-stimuli-responsive nanochannel inspired by biological disulfide bond

Disulfide bonds exist widely in channel protein and play an essential role in matter exchange and signal transduction (e.g., rhodopsin, canonical transient receptor potential 5 (TRPC5)). The research on disulfide bond in nanochannel is significant for the cognition of their biological functions. However, the fragility of biological channel limits the in-situ study and practical application. Herein, an innovative biologically-inspired artificial nanochannel based on disulfide bond (NCDS) with excellent durability, adjustable surface property is proposed. The constructed NCDS has a multi-response to UV-light, thiol (e.g., cysteine (Cys)) or pH stimulation, and can obtain reversibility after regulation by hydrogen peroxide (H₂O₂) or H⁺. The biomimetic NCDS shows great potential in biosensor and intelligent response design. This study also shines new light to channel protein based on disulfide bond that despite the nanochannel has specificity, it will be modulated by the change of nature environment, such as UV-light and chemical microenvironment (e.g., redox state and pH), which might be the reason of some disease.

How Azide Ion/Hydrazoic Acid Passes Through Biological Membranes: An Experimental and Computational Study

Hydrazoic acid (HN₃) and its deprotonated form azide ion (N₃^-) (AHA) are toxic because they inhibit the cytochrome c oxidase complex IV (CoX IV) embedded in the inner mitochondrial membrane that forms part of the enzyme complexes involved in cellular respiration. Critical to its toxicity is the inhibition of CoX IV in the central nervous system and cardiovascular system. Hydrazoic acid is an ionizable species and its affinity for membranes, and the associated permeabilities, depend on the pH values of aqueous media on both sides of the membranes. In this article, we address the permeability of AHA through the biological membrane. In order to understand the affinity of the membrane for the neutral and ionized form of azide, we measured the octanol/water partition coefficients at pH values of 2.0 and 8.0, which are 2.01 and 0.00034, respectively. Using a Parallel Artificial Membrane Permeability Assay (PAMPA) experiment, we measured the effective permeability through the membrane, which is logP_e - 4.97 and - 5.26 for pH values of 7.4 and pH 8.0, respectively. Experimental permeability was used to validate theoretical permeability, which was estimated by numerically solving a Smoluchowski equation for AHA diffusion through the membrane. We demonstrated that the rate of permeation through the cell membrane of 8.46·10⁴ s^-1 is much higher than the rate of the chemical step of CoX IV inhibition by azide of 200 s^-1. The results of this study show that transport through the membrane does not represent the rate-limiting step and therefore does not control the rate of CoX IV inhibition in the mitochondria. However, the observed dynamics of azide poisoning is controlled by circulatory transport that takes place on a time scale of minutes.

TREK channels in Mechanotransduction: a Focus on the Cardiovascular System

Mechano-electric feedback is one of the most important subsystems operating in the cardiovascular system, but the underlying molecular mechanism remains rather unknown. Several proteins have been proposed to explain the molecular mechanism of mechano-transduction. Transient receptor potential (TRP) and Piezo channels appear to be the most important candidates to constitute the molecular mechanism behind of the inward current in response to a mechanical stimulus. However, the inhibitory/regulatory processes involving potassium channels that operate on the cardiac system are less well known. TWIK-Related potassium (TREK) channels have emerged as strong candidates due to their capacity for the regulation of the flow of potassium in response to mechanical stimuli. Current data strongly suggest that TREK channels play a role as mechano-transducers in different components of the cardiovascular system, not only at central (heart) but also at peripheral (vascular) level. In this context, this review summarizes and highlights the main existing evidence connecting this important subfamily of potassium channels with the cardiac mechano-transduction process, discussing molecular and biophysical aspects of such a connection.

Mechanism of external K+ sensitivity of KCNQ1 channels

KCNQ1 voltage-gated K+ channels are involved in a wide variety of fundamental physiological processes and exhibit the unique feature of being markedly inhibited by external K+. Despite the potential role of this regulatory mechanism in distinct physiological and pathological processes, its exact underpinnings are not well understood. In this study, using extensive mutagenesis, molecular dynamics simulations, and single-channel recordings, we delineate the molecular mechanism of KCNQ1 modulation by external K+. First, we demonstrate the involvement of the selectivity filter in the external K+ sensitivity of the channel. Then, we show that external K+ binds to the vacant outermost ion coordination site of the selectivity filter inducing a diminution in the unitary conductance of the channel. The larger reduction in the unitary conductance compared to whole-cell currents suggests an additional modulatory effect of external K+ on the channel. Further, we show that the external K+ sensitivity of the heteromeric KCNQ1/KCNE complexes depends on the type of associated KCNE subunits.

Hydrogen sulfide inhibits lipopolysaccharide-based neuroinflammation-induced astrocyte polarization after cerebral ischemia/reperfusion injury

The effect of lipopolysaccharide (LPS)-based neuroinflammation following cerebral ischemia/reperfusion (I/R) on the genotypic transformation of reactive astrocytes and its relationship with endogenous hydrogen sulfide (H₂S) were investigated in present study. We found that LPS promoted the cerebral I/R-induced A1 astrocytes proliferation in mouse hippocampal tissues and deteriorated the reduction of hydrogen sulfide (H₂S) content in mouse sera, H₂S donor NaHS could inhibitA1 astrocytes proliferation. Similarly, knockout of cystathionine γ-lyase (CSE), one of endogenous H₂S synthases, likewise up-regulated the cerebral I/R-induced A1 astrocytes proliferation, which could also be blocked by NaHS. Besides, supplement with H₂S promoted the A2 astrocytes proliferation in hippocampal tissues of CSE knockout (CSE KO) mice or LPS-treated mice following cerebral I/R. In the oxygen glucose deprivation/reoxygenation (OGD/R) model of astrocytes, H₂S also promoted the transformation of astrocytes into A2 subtype. Moreover, we found that H₂S could up-regulate the expression of α-subunit of large-conductance Ca²⁺-activated K⁺ (BK_Ca) channels in astrocytes, and the channel opener BMS-191011 likewise promoted the transformation of astrocyte into A2 subtype. In conclusion, H₂S inhibits the proliferation of A1 astrocytes induced by LPS-based neuroinflammation following cerebral I/R and promotes the transformation of astrocytes into A2 subtype, which may be related to up-regulation of BK_Ca channels.

A theory of chemical reactions in biomolecules in solution: Generalized Langevin mode analysis (GLMA)

The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier-crossing process, similar to the Marcus theory. The barrier is defined as the crossing point of two free-energy surfaces that are attributed to the reactant and product of the reaction. It is assumed that both free-energy surfaces are quadratic or harmonic. The assumption is based on the Kim-Hirata theory of structural fluctuation of protein, which proves that the fluctuation around an equilibrium structure is quadratic with respect to the structure or atomic coordinates. The quadratic surface is a composite of many harmonic functions with different modes or frequencies. The height of the activation barrier will be dependent on the mode or frequency-the less the frequency, the lower the barrier. Hence, it is essential to decouple the fluctuational modes into a hierarchical order. GLMA is impeccable for this purpose. It is essential for a theoretical study of chemical reactions to choose a reaction coordinate along which the reaction proceeds. We suppose that the mode whose center of coordinate and/or the frequency changes most before and after the reaction is the one relevant to the chemical reaction and choose the coordinate as the reaction coordinate. The rate of reaction along the reaction coordinate is k_rate=ν⁡exp-ΔF^(†)/k_BT, which is similar to the Marcus expression for the electron transfer reaction. In the equation, ΔF^(†) is the activation barrier defined by ΔF^(†)≡F^(r)Q^†-F^(r)(Q_eq ^(r)), where F^(r)(Q_eq ^(r)) and F^(r)Q^† denote the free energies at equilibrium Q_eq ^(r) and the crossing point Q^†, respectively, both on the free energy surface of the reactant.

Inner pore hydration free energy controls the activation of big potassium channels

Hydrophobic gating is an emerging mechanism in regulation of protein ion channels where the pore remains physically open but becomes dewetted to block ion permeation. Atomistic molecular dynamics simulations have played a crucial role in understanding hydrophobic gating by providing the molecular details to complement mutagenesis and structural studies. However, existing studies rely on direct simulations and do not quantitatively describe how the sequence and structural changes may control the delicate liquid-vapor equilibrium of confined water in the pore of the channel protein. To address this limitation, we explore two enhanced sampling methods, namely metadynamics and umbrella sampling, to derive free-energy profiles of pore hydration in both the closed and open states of big potassium (BK) channels, which are important in cardiovascular and neural systems. It was found that metadynamics required substantially longer sampling times and struggled to generate stably converged free-energy profiles due to the slow dynamics of cooperative pore water diffusion even in the barrierless limit. Using umbrella sampling, well-converged free-energy profiles can be readily generated for the wild-type BK channels as well as three mutants with pore-lining mutations experimentally known to dramatically perturb the channel gating voltage. The results show that the free energy of pore hydration faithfully reports the gating voltage of the channel, providing further support for hydrophobic gating in BK channels. Free-energy analysis of pore hydration should provide a powerful approach for quantitative studies of how protein sequence, structure, solution conditions, and/or drug binding may modulate hydrophobic gating in ion channels.

Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors

Ionotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became available recently by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as positioning of the side-chains in the SF is still missing. Here, in an attempt to obtain high-resolution information about glutamate receptor SFs, we incorporated partial SF sequences of the AMPA and kainate receptors into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, previously unobserved structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.

Voltage-Dependent FTIR and 2D Infrared Spectroscopies within the Electric Double Layer Using a Plasmonic and Conductive Electrode

Strong electric fields exist between the electric double layer and charged surfaces. These fields impact molecular structures and chemistry at interfaces. We have developed a transparent electrode with infrared plasmonic enhancement sufficient to measure FTIR and two-dimensional infrared spectra at submonolayer coverages on the surface to which a voltage can be applied. Our device consists of an infrared transparent substrate, a 10-20 nm layer of conductive indium tin oxide (ITO), an electrically resistive layer of 3-5 nm Al₂O₃, and a 3 nm layer of nonconductive plasmonic gold. The materials and thicknesses are set to maximize the surface number density of the monolayer molecules, electrical conductivity, and plasmonic enhancement while minimizing background signals and avoiding Fano line shape distortions. The design was optimized by iteratively characterizing the material roughness and thickness with atomic force microscopy and electron microscopy and by monitoring the plasmon resonance enhancement with spectroscopy. The design is robust to repeated fabrication. This new electrode is tested on nitrile functional groups using a monolayer of 4-mercaptobenzonitrile as well as on CO and CC stretching modes using 4-mercaptobenzoic acid methyl ester. A voltage-dependent Stark shift is observed on both monolayers. We also observe that the transition dipole strength of the CN mode scales linearly with the applied voltage, providing a second way of measuring the surface electric field strength. We anticipate that this cell will enable many new voltage-dependent infrared experiments under applied voltages.

Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1

Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators.

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.

Molecular dynamics study of Cl- permeation through cystic fibrosis transmembrane conductance regulator (CFTR)

The recent elucidation of atomistic structures of Cl^- channel CFTR provides opportunities for understanding the molecular basis of cystic fibrosis. Despite having been activated through phosphorylation and provided with ATP ligands, several near-atomistic cryo-EM structures of CFTR are in a closed state, as inferred from the lack of a continuous passage through a hydrophobic bottleneck region located in the extracellular portion of the pore. Here, we present repeated, microsecond-long molecular dynamics simulations of human CFTR solvated in a lipid bilayer and aqueous NaCl. At equilibrium, Cl^- ions enter the channel through a lateral intracellular portal and bind to two distinct cationic sites inside the channel pore but do not traverse the narrow, de-wetted bottleneck. Simulations conducted in the presence of a strong hyperpolarizing electric field led to spontaneous Cl^- translocation events through the bottleneck region of the channel, suggesting that the protein relaxed to a functionally open state. Conformational changes of small magnitude involving transmembrane helices 1 and 6 preceded ion permeation through diverging exit routes at the extracellular end of the pore. The pore bottleneck undergoes wetting prior to Cl^- translocation, suggesting that it acts as a hydrophobic gate. Although permeating Cl^- ions remain mostly hydrated, partial dehydration occurs at the binding sites and in the bottleneck. The observed Cl^- pathway is largely consistent with the loci of mutations that alter channel conductance, anion binding, and ion selectivity, supporting the model of the open state of CFTR obtained in the present study.

Full opening of helix bundle crossing does not lead to NaK channel activation

A critical part of ion channel function is the ability to open and close in response to stimuli and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels suggested a general steric gating mechanism located at the helix bundle crossing (HBC), recent functional studies on several channels indicate that the helix bundle crossing is wide-open even in functionally nonconductive channels. Two NaK channel variants were crystallized in very different open and closed conformations, which served as important models of the HBC gating hypothesis. However, neither of these NaK variants is conductive in liposomes unless phenylalanine 92 is mutated to alanine (F92A). Here, we use NMR to probe distances at near-atomic resolution of the two NaK variants in lipid bicelles. We demonstrate that in contrast to the crystal structures, both NaK variants are in a fully open conformation, akin to Ca2+-bound MthK channel structure where the HBC is widely open. While we were not able to determine what a conductive NaK structure is like, our further inquiry into the gating mechanism suggests that the selectivity filter and pore helix are coupled to the M2 helix below and undergo changes in the structure when F92 is mutated. Overall, our data show that NaK exhibits coupling between the selectivity filter and HBC, similar to K+ channels, and has a more complex gating mechanism than previously thought, where the full opening of HBC does not lead to channel activation.

Synergistic Effect of Bio-Inspired Nanochannels: Hydrophilic DNA Probes at Inner Wall and Hydrophobic Coating at Outer Surface for Highly Sensitive Detection

During the past few decades, bio-inspired nanochannels have been well developed and applied in biosensing, energy transfer, separation, and so on. Here, inspired by the synergistic effect of biological nanopores, biomimetic solid-state nanochannels with hydrophilic DNA probes at the inner wall (DNA@IW_Hydrophilic ) and hydrophobic coating at the outer surface (None@OS_Hydrophobic ) are designed. To demonstrate their prompted sensing properties, Hg²⁺ and its specific probe are selected as target and hydrophilic DNA probes, respectively. Compared with the traditional solid-state nanochannels with hydrophilic probes distributed on both the inner wall and outer surface, the nanochannels with DNA@IW_Hydrophilic +None@OS_Hydrophobic significantly decrease the limit of detection (LOD) by 10⁵ -fold. The obvious improvement of sensitivity (with LOD of 1 nM) is attributed to the synergistic effect: None@OS_Hydrophobic results in the nanochannel's effective diameter decrease and DNA@IW_Hydrophilic induces a specific sensing target. Meanwhile, nanomolar detection of Hg²⁺ in human serum and in vivo fish muscle are achieved. Through molecular dynamics simulation, the synergistic effect can be confirmed by ion fluxes increasement; the relative carbon nanotube increases from 135.64% to 135.84%. This work improves the understanding of nanochannels' synergistic effect and provides a significant insight for nanochannels with improved sensitivity.

Microglia-derived PDGFB promotes neuronal potassium currents to suppress basal sympathetic tonicity and limit hypertension

Although many studies have addressed the regulatory circuits affecting neuronal activities, local non-synaptic mechanisms that determine neuronal excitability remain unclear. Here, we found that microglia prevented overactivation of pre-sympathetic neurons in the hypothalamic paraventricular nucleus (PVN) at steady state. Microglia constitutively released platelet-derived growth factor (PDGF) B, which signaled via PDGFRα on neuronal cells and promoted their expression of Kv4.3, a key subunit that conducts potassium currents. Ablation of microglia, conditional deletion of microglial PDGFB, or suppression of neuronal PDGFRα expression in the PVN elevated the excitability of pre-sympathetic neurons and sympathetic outflow, resulting in a profound autonomic dysfunction. Disruption of the PDGFB^MG-Kv4.3^Neuron pathway predisposed mice to develop hypertension, whereas central supplementation of exogenous PDGFB suppressed pressor response when mice were under hypertensive insult. Our results point to a non-immune action of resident microglia in maintaining the balance of sympathetic outflow, which is important in preventing cardiovascular diseases.

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.

TUPÃ: Electric field analyses for molecular simulations

We introduce TUPÃ, a Python-based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/.