PIP2-dependent coupling of voltage sensor and pore domains in Kv7.2 channel

Biophysical and structural mechanisms of epilepsy-associated mutations in the S4-S5 Linker of KCNQ2 channels

Mutations in KCNQ2 are linked to various neurological disorders, including neonatal-onset epilepsy. The severity of these conditions often correlates with the mutation's location and the biochemical properties of the altered amino acid side chains. Two mutations affecting aspartate at position 212 (D212) in the S4-S5 linker of KCNQ2 have been identified. Interestingly, while the charge-conserved D212E mutation leads to severe neonatal-onset developmental and epileptic encephalopathy (DEE), the more dramatic substitution to glycine (D212G) results in self-limited familial neonatal epilepsy (SLFNE), a much milder pathology. To elucidate the underlying mechanisms, we performed electrophysiological studies and in silico simulations to investigate these mutations' biophysical and structural effects. Our findings reveal that the D212E mutation stabilizes the channel in the voltage sensor down-state and destabilizes the up-state, leading to a rightward shift in the voltage-dependent activation curve, slower activation kinetics, and accelerated deactivation kinetics. This disruption in KCNQ2 voltage sensitivity persists even in the more physiologically relevant KCNQ2/3 heterotetrameric channels. In contrast, the D212G mutation primarily destabilizes the up-state, but its impact on voltage sensitivity is significantly reduced in KCNQ2/3 heterotetrameric channels. These findings provide key insights into the biophysical and structural basis of KCNQ2 D212 mutations and their contribution to epilepsy-related symptoms, offering a clearer understanding of how these mutations drive the varied clinical outcomes observed in patients.

Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies

Membrane transporters are integral membrane proteins that act as gatekeepers of the cell, controlling fundamental processes such as recruitment of nutrients and expulsion of waste material. At a basic level, transporters operate using the "alternating access model," in which transported substances are accessible from only one side of the membrane at a time. This model usually involves large-scale structural changes in the transporter, which often cannot be captured using unbiased, conventional molecular simulation techniques. In this article, we provide an overview of some of the major simulation techniques that have been applied to characterize the structural dynamics and energetics involved in the transition of membrane transporters between their functional states. After briefly introducing each technique, we discuss some of their advantages and limitations and provide some recent examples of their application to membrane transporters.

Phosphatidylinositol 4,5-bisphosphate activation mechanism of human KCNQ5

The human voltage-gated potassium channels KCNQ2, KCNQ3, and KCNQ5 can form homo- and heterotetrameric channels that are responsible for generating the neuronal M current and maintaining the membrane potential stable. Activation of KCNQ channels requires both the depolarization of membrane potential and phosphatidylinositol 4,5-bisphosphate (PIP2). Here, we report cryoelectron microscopy structures of the human KCNQ5-calmodulin (CaM) complex in the apo, PIP2-bound, and both PIP2- and the activator HN37-bound states in either a closed or an open conformation. In the closed conformation, a PIP2 molecule binds in the middle of the groove between two adjacent voltage-sensing domains (VSDs), whereas in the open conformation, one additional PIP2 binds to the interface of VSD and the pore domain, accompanying structural rearrangement of the cytosolic domain of KCNQ and CaM. The structures, along with electrophysiology analyses, reveal the two different binding modes of PIP2 and elucidate the PIP2 activation mechanism of KCNQ5.

Genetic features and pharmacological rescue of novel Kv7.2 variants in patients with epilepsy

BACKGROUND

Increasing evidence indicates a robust correlation between epilepsy and variants of the Kv7.2 (KCNQ2) channel, which is critically involved in directing M-currents and regulating neuronal excitability within the nervous system. With the advancement of next-generation sequencing, the identification of KCNQ2 variants has surged. Nonetheless, their functional impacts are still being determined, introducing uncertainty into the diagnostic process for affected families and potentially hindering their ability to participate in targeted precision medicine trials. This study aims to elucidate the pathogenicity of these novel variants and explore potential therapeutic interventions.

METHODS

Whole-cell patch-clamp recordings, western blotting, and immunofluorescent staining were performed to elucidate the functional consequences of the identified variants. Moreover, coimmunoprecipitation techniques were conducted to explore protein interactions, thus facilitating a deeper understanding of the underlying pathogenetic mechanisms contributing to the disease. Ultimately, the effects of pharmacological interventions were evaluated in vitro using the patch-clamp technique.

RESULTS

Herein, we identified 12 novel KCNQ2 variants, further expanding the mutational spectrum of KCNQ2. Our investigation revealed that one gain-of-function variant (p.L102V (c.304C>G)) and three loss-of-function variants (p.H328Q (c.984C>G), p.A336V (c.1007C>T) and p.D563Efs*22 (c.1688_1689insACTT)) had different impacts on the binding of calmodulin and phosphati-dylinositol-4,5-bisphosphate, potentially altering their localisation and protein stability. Furthermore, the application of ML213, unlike Retigabine and ICA-069673, led to a significant increase in the current of p.H328Q.

CONCLUSION

This study expanded the mutational spectrum of KCNQ2 and analysed the genetic and functional consequences, as well as the pharmacological rescue, of four de novo KCNQ2 variants. These findings offer valuable insights into the precise medicine of KCNQ2-related epilepsy.

Investigating the Dynamics of the KCNN4 Channel: From the Determination of the Complete K+ Permeation Pathway Across the Channel to Its Opening by PIP2

KCNN4 is a calcium (Ca)-activated potassium channel for which Ca2+ sensitivity is conferred by calmodulin (CaM) that constitutively binds to the channel. Until the main part of the structure bound to CaM has been resolved, in silico studies had used homology models derived from the well characterized transmembrane domain of other K+ channels, limiting the functional investigation to this particular region. Thus, how the regulatory domains of KCNN4 communicate with each other and where the possible gates are located across the complete structure are still not well understood. Here we present for the first time results obtained from the investigation of full-length models of the channel in different conformational states and molecular contexts using classical all-atom molecular dynamic simulations. The simulations covered two activated states (open and closed) and a preactivated state of the channel embedded in a simple membrane model and a model of red blood cell membrane, where the channel is functionally expressed in vivo. Surprisingly, the intracellular domain was refractory to the entrance of K+, whatever the state of the channel was, allowing the K+ ions to enter and exit the channel only through two newly identified restrained diffusion spots. Inside the channel, the K+ flux was controlled by the V282 residue closing the pore region when the CaM N-lobes were not bound. This flux was compatible with the passage of fully or partially hydrated K+, depending on the opening level. Finally, the presence of phosphatidylinositol-4,5-bisphosphate (PIP2), a well-known K+-channel modulator, in a putative binding site of KCNN4 clearly facilitated the opening of the V282 restriction. Thus, in addition to the elucidation of the possible complete K+ permeation pathway throughout KCNN4, our results confirmed the direct activatory role of PIP2, associated with the channel opening, and provide a first insight into the architecture and the behavior of the complete intracellular region of KCNN4.

The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations

The phosphoinositide family of membrane lipids play diverse and critical roles in eukaryotic molecular biology. Much of this biological activity derives from interactions of phosphoinositide lipids with integral and peripheral membrane proteins, leading to modulation of protein structure, function, and cellular distribution. Since the discovery of phosphoinositides in the 1940s, combined molecular biology, biophysical, and structural approaches have made enormous progress in untangling this vast and diverse cellular network of interactions. More recently, in silico approaches such as molecular dynamics simulations have proven to be an asset in prospectively identifying, characterising, explaining the structural basis of these interactions, and in the best cases providing atomic level testable hypotheses on how such interactions control the function of a given membrane protein. This review details a number of recent seminal discoveries in phosphoinositide biology, enabled by advanced biomolecular simulation, and its integration with molecular biology, biophysical, and structural biology approaches. The results of the simulation studies agree well with experimental work, and in a number of notable cases have arrived at the key conclusion several years in advance of the experimental structures. SUMMARY: Hedger and Yen review developments in simulations of phosphoinositides and membrane proteins.

Lipids shape brain function through ion channel and receptor modulations: physiological mechanisms and clinical perspectives

Lipids represent the most abundant molecular type in the brain, with a fat content of ∼60% of the dry brain weight in humans. Despite this fact, little attention has been paid to circumscribe the dynamic role of lipids in brain function and disease. Membrane lipids such as cholesterol, phosphoinositide, sphingolipids, arachidonic acid, and endocannabinoids finely regulate both synaptic receptors and ion channels that ensure critical neural functions. After a brief introduction on brain lipids and their respective properties, we review here their role in regulating synaptic function and ion channel activity, action potential propagation, neuronal development, and functional plasticity and their contribution in the development of neurological and neuropsychiatric diseases. We also provide possible directions for future research on lipid function in brain plasticity and diseases.

Constitutive opening of the Kv7.2 pore activation gate causes KCNQ2-developmental encephalopathy

Pathogenic variants in KCNQ2 encoding Kv7.2 voltage-gated potassium channel subunits cause developmental encephalopathies (KCNQ2-encephalopathies), both with and without epilepsy. We herein describe the clinical, in vitro, and in silico features of two encephalopathy-causing variants (A317T, L318V) in Kv7.2 affecting two consecutive residues in the S6 activation gate that undergoes large structural rearrangements during pore opening; the disease-causing A356T variant in KCNQ3, paralogous to the A317T variant in KCNQ2, was also investigated. Currents through KCNQ2 mutant channels displayed increased density, hyperpolarizing shifts in activation gating, faster activation and slower deactivation kinetics, and resistance to changes in the cellular concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2), a critical regulator of Kv7 channel function; all these features are consistent with a strong gain-of-function effect. An increase in the probability of single-channel opening, with no change in membrane abundance or single-channel conductance, was responsible for the observed gain-of-function effects. All-atom molecular dynamics simulations revealed that the mutations widened the inner pore gate and stabilized a constitutively open channel configuration in the closed state, with minimal effects on the open conformation. Thus, mutation-induced stabilization of the inner pore gate open configuration is a molecular pathogenetic mechanism for KCNQ2-related encephalopathies.

PIP2 inhibits pore opening of the cyclic nucleotide-gated channel SthK

The signaling lipid phosphatidylinositol-4,5-bisphosphate (PIP2) regulates many ion channels. It inhibits eukaryotic cyclic nucleotide-gated (CNG) channels while activating their relatives, the hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels. The prokaryotic SthK channel from Spirochaeta thermophila shares features with CNG and HCN channels and is an established model for this channel family. Here, we show SthK activity is inhibited by PIP2. A cryo-EM structure of SthK in nanodiscs reveals a PIP2-fitting density coordinated by arginine and lysine residues from the S4 helix and the C-linker, located between voltage-sensing and pore domains of adjacent subunits. Mutation of two arginine residues weakens PIP2 inhibition with the double mutant displaying insensitivity to PIP2. We propose that PIP2 inhibits SthK by gluing S4 and S6 together, stabilizing a resting channel conformation. The PIP2 binding site is partially conserved in CNG channels suggesting the possibility of a similar inhibition mechanism in the eukaryotic homologs.

The plasma membrane inner leaflet PI(4,5)P2 is essential for the activation of proton-activated chloride channels

Proton-activated chloride (PAC) channels, ubiquitously expressed in tissues, regulate intracellular Cl- levels and cell death following acidosis. However, molecular mechanisms and signaling pathways involved in PAC channel modulation are largely unknown. Herein, we determine that phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] of the plasma membrane inner leaflet is essential for the proton activation of PAC channels. PI(4,5)P2 depletion by activating phosphatidylinositol 5-phosphatases or Gq protein-coupled muscarinic receptors substantially inhibits human PAC currents. In excised inside-out patches, PI(4,5)P2 application to the cytoplasmic side increases the currents. Structural simulation reveals that the putative PI(4,5)P2-binding site is localized within the cytosol in resting state but shifts to the cell membrane's inner surface in an activated state and interacts with inner leaflet PI(4,5)P2. Alanine neutralization of basic residues near the membrane-cytosol interface of the transmembrane helice 2 significantly attenuates PAC currents. Overall, our study uncovers a modulatory mechanism of PAC channel through inner membrane PI(4,5)P2.

Dehydroepiandrosterone Sulfate (DHEAS) Is an Endogenous Kv7 Channel Modulator That Reduces Kv7/M-Current Suppression and Inflammatory Pain

Neuronal Kv7 voltage-gated potassium channels generate the M-current and regulate neuronal excitability. Here, we report that dehydroepiandrosterone sulfate (DHEAS) is an endogenous Kv7 channel modulator that attenuates Gq-coupled receptor-induced M-current suppression. DHEAS reduced muscarinic agonist-induced Kv7-current suppression of Kv7.1, Kv7.2, Kv7.4, or Kv7.5 homomeric currents and endogenous M-currents in rat sympathetic ganglion neurons. However, DHEAS per se did not alter the voltage dependence of these Kv7 homomeric channels or the m1 receptor-induced activation of phospholipase C or protein kinase C. DHEAS-treated Kv7.2 homomeric currents became resistant to depletion of phosphatidylinositol 4,5-bisphosphate (PIP2) induced by voltage-activated phosphatase, Ci-VSP or eVSP. Our computational models predicted a novel binding site for DHEAS in the cytoplasmic domain of Kv7 subunits. A single-point mutation of the predicted key histidine into cysteine in the rat Kv7.2 subunit, rKv7.2(H558C), resulted in a loss of effects of DHEAS on muscarinic Kv7 current suppression. Furthermore, in vivo administration of DHEAS in mice of both sexes reduced late phase pain responses in the formalin paw test. However, it did not have effects on early phase responses in the formalin paw test or responses in the hot plate test. Coadministration of a selective Kv7 inhibitor, XE991, and DHEAS eliminated analgesic effects of DHEAS in late phase responses in the formalin paw test. Collectively, these results suggest that DHEAS attenuates M-current suppression by stabilizing PIP2-Kv7 subunit interaction and can mitigate inflammatory pain.SIGNIFICANCE STATEMENT M-current suppression induced by stimulation of Gq-coupled receptors is a form of Kv7 current modulation that can reversibly increase neuronal excitability. This study demonstrates that DHEAS, an endogenous steroid hormone, is a novel Kv7 channel modulator that can attenuate M-current suppression without affecting basal Kv7 channel kinetics. Administration of DHEAS in vivo alleviated inflammatory pain in rodents. These results suggest that the degree of M-current suppression can be dynamically regulated by small molecules. Therefore, this novel form of Kv7 channel regulation holds promising potential as a therapeutic target for sensitized nervous activities, such as inflammatory pain.

What voltage-sensing phosphatases can reveal about the mechanisms of ion channel regulation by phosphoinositides

Many membrane proteins including ion channels and ion transporters are regulated by membrane phospholipids such as phosphoinositides in cell membranes and organelles. Voltage-sensing phosphatase, VSP, is a voltage-sensitive phosphoinositide phosphatase which dephosphorylates PI(4,5)P2 into PI(4)P. VSP rapidly reduces the level of PI(4,5)P2 upon membrane depolarization, thus serving as a useful tool to quantitatively study phosphoinositide-regulation of ion channels and ion transporters using a cellular electrophysiology system. In this review, we focus on the application of VSPs to Kv7 family potassium channels, which have been important research targets in biophysics, pharmacology and medicine.

Potassium channelopathies associated with epilepsy-related syndromes and directions for therapeutic intervention

A number of mutations to members of several CNS potassium (K) channel families have been identified which result in rare forms of neonatal onset epilepsy, or syndromes of which one prominent characteristic is a form of epilepsy. Benign Familial Neonatal Convulsions or Seizures (BFNC or BFNS), also referred to as Self-Limited Familial Neonatal Epilepsy (SeLNE), results from mutations in 2 members of the K_V7 family (KCNQ) of K channels; while generally self-resolving by about 15 weeks of age, these mutations significantly increase the probability of generalized seizure disorders in the adult, in some cases they result in more severe developmental syndromes. Epilepsy of Infancy with Migrating Focal Seizures (EIMSF), or Migrating Partial Seizures of Infancy (MMPSI), is a rare severe form of epilepsy linked primarily to gain of function mutations in a member of the sodium-dependent K channel family, KCNT1 or SLACK. Finally, KCNMA1 channelopathies, including Liang-Wang syndrome (LIWAS), are rare combinations of neurological symptoms including seizure, movement abnormalities, delayed development and intellectual disabilities, with Liang-Wang syndrome an extremely serious polymalformative syndrome with a number of neurological sequelae including epilepsy. These are caused by mutations in the pore-forming subunit of the large-conductance calcium-activated K channel (BK channel) KCNMA1. The identification of these rare but significant channelopathies has resulted in a resurgence of interest in their treatment by direct pharmacological or genetic modulation. We will briefly review the genetics, biophysics and pharmacology of these K channels, their linkage with the 3 syndromes described above, and efforts to more effectively target these syndromes.

Crystal Structure and Noncovalent Interactions of Heterocyclic Energetic Molecules

Nitrogen-rich heterocyclic compounds are important heterocyclic substances with extensive future applications for energetic materials due to their outstanding density and excellent physicochemical properties. However, the weak intermolecular interactions of these compounds are not clear, which severely limits their widespread application. Three nitrogen-rich heterocyclic compounds were chosen to detect their molecular geometry, stacking mode and intermolecular interactions by crystal structure, Hirshfeld surface, RDG and ESP. The results show that all atoms in each molecule are coplanar and that the stacking mode of the three crystals is a planar layer style. A large amount of inter- and intramolecular interaction exists in the three crystals. All principal types of intermolecular contacts in the three crystals are N···H interactions and they account for 40.9%, 38.9% and 32.9%, respectively. Hydrogen bonding, vdW interactions and steric effects in Crystal c are stronger than in Crystals a and b. The negative ESPs all concentrate on the nitrogen atoms in the three molecules. This work is expected to benefit the crystal engineering of heterocyclic energetic materials.

Human KCNQ5 de novo mutations underlie epilepsy and intellectual disability

We identified six novel de novo human KCNQ5 variants in children with motor/language delay, intellectual disability (ID), and/or epilepsy by whole exome sequencing. These variants, comprising two nonsense and four missense alterations, were functionally characterized by electrophysiology in HEK293/CHO cells, together with four previously reported KCNQ5 missense variants (Lehman A, Thouta S, Mancini GM, Naidu S, van Slegtenhorst M, McWalter K, Person R, Mwenifumbo J, Salvarinova R; CAUSES Study; EPGEN Study; Guella I, McKenzie MB, Datta A, Connolly MB, Kalkhoran SM, Poburko D, Friedman JM, Farrer MJ, Demos M, Desai S, Claydon T. Am J Hum Genet 101: 65-74, 2017). Surprisingly, all eight missense variants resulted in gain of function (GOF) due to hyperpolarized voltage dependence of activation or slowed deactivation kinetics, whereas the two nonsense variants were confirmed to be loss of function (LOF). One severe GOF allele (P369T) was tested and found to extend a dominant GOF effect to heteromeric KCNQ5/3 channels. Clinical presentations were associated with altered KCNQ5 channel gating: milder presentations with LOF or smaller GOF shifts in voltage dependence [change in voltage at half-maximal conduction (ΔV₅₀) = ∼-15 mV] and severe presentations with larger GOF shifts in voltage dependence (ΔV₅₀ = ∼-30 mV). To examine LOF pathogenicity, two Kcnq5 LOF mouse lines were created with CRISPR/Cas9. Both lines exhibited handling- and thermal-induced seizures and abnormal cortical EEGs consistent with epileptiform activity. Our study thus provides evidence for in vivo KCNQ5 LOF pathogenicity and strengthens the contribution of both LOF and GOF mutations to global pediatric neurological impairment, including ID/epilepsy.NEW & NOTEWORTHY Six novel de novo human KCNQ5 variants were identified from children with neurodevelopmental delay, intellectual disability, and/or epilepsy. Expression of these variants along with four previously reported KCNQ5 variants from a similar cohort revealed GOF potassium channels, negatively shifted in V₅₀ of activation and/or delayed deactivation kinetics. GOF is extended to KCNQ5/3 heteromeric channels, making these the predominant channels affected in heterozygous de novo patients. Kcnq5 LOF mice exhibited seizures, consistent with in vivo pathogenicity.

Noncovalent Interactions and Crystal Structure Prediction of Energetic Materials

The crystal and molecular structures, intermolecular interactions, and energy of CL-20, HATO, and FOX-7 were comparatively predicted based on molecular dynamic (MD) simulations. By comparison, the 2D fingerprint plot, Hirshfeld surface, reduced density gradient isosurface, and electrostatic potential surface were studied to detect the intermolecular interactions. Meanwhile, the effects of vacuum and different solvents on the crystal habit of CL-20, HATO, and FOX-7 were studied by AE and MAE model, respectively. The energy calculation was also analysed based on the equilibrium structures of these crystal models by MD simulations. Our results would provide fundamental insights for the crystal engineering of energetic materials.