Structure Of Ion Channels Research Articles

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.

Critical sizes for PET cylindrical and hourglass shaped pores for selective ion channels

The development of artificial transmembrane channels that are capable of transporting ions, water and small molecules across cell membrane is crucial for applications in drug delivery and gene therapy. In this paper, we determine the interaction between ions and artificial channels in order to understand the mechanisms underlying the selection and transport of ions through the channels. Particularly, the concept of suction energy is employed to determine the interaction of ions (Na + , Cl − , Ca 2＋ , K + ) and cylindrical and hourglass shaped channels made from polyethylene terephthalate (PET). Based on this concept, we find critical pore sizes for cylindrical and hourglass shaped channels that can be used for selective separation of positive charged ions. Further, we find that coating PET channel with different materials can reduce these values of the critical pore sizes. These results are also confirmed by molecular dynamics studies. The main contribution of this work is mathematical expressions for the interaction energy as a function of ion type, channel structure and size of the channel, and this method can be applied to study other pores with different shapes and sizes.

Light-Controlled Ionic/Molecular Transport through Solid-State Nanopores and Nanochannels.

Biological nanochannels perfectly operate in organisms and exquisitely control mass transmembrane transport for complex life process. Inspired by biological nanochannels, plenty of intelligent artificial solid-state nanopores and nanochannels are constructed based on various materials and methods with the development of nanotechnology. Specially, the light-controlled nanopores/nanochannels have attracted much attention due to the unique advantages in terms of that ion and molecular transport can be regulated remotely, spatially and temporally. According to the structure and function of biological ion channels, light-controlled solid-state nanopores/nanochannels can be divided into light-regulated ion channels with ion gating and ion rectification functions, and light-driven ion pumps with active ion transport property. In this review, we present a systematic overview of light-controlled ion channels and ion pumps according to the photo-responsive components in the system. Then, the related applications of solid-state nanopores/nanochannels for molecular sensing, water purification and energy conversion are discussed. Finally, a brief conclusion and short outlook are offered for future development of the nanopore/nanochannel field.

Paramecium, a Model to Study Ciliary Beating and Ciliogenesis: Insights From Cutting-Edge Approaches.

Cilia are ubiquitous and highly conserved extensions that endow the cell with motility and sensory functions. They were present in the first eukaryotes and conserved throughout evolution (Carvalho-Santos et al., 2011). Paramecium has around 4,000 motile cilia on its surface arranged in longitudinal rows, beating in waves to ensure movement and feeding. As with cilia in other model organisms, direction and speed of Paramecium ciliary beating is under bioelectric control of ciliary ion channels. In multiciliated cells of metazoans as well as paramecia, the cilia become physically entrained to beat in metachronal waves. This ciliated organism, Paramecium, is an attractive model for multidisciplinary approaches to dissect the location, structure and function of ciliary ion channels and other proteins involved in ciliary beating. Swimming behavior also can be a read-out of the role of cilia in sensory signal transduction. A cilium emanates from a BB, structurally equivalent to the centriole anchored at the cell surface, and elongates an axoneme composed of microtubule doublets enclosed in a ciliary membrane contiguous with the plasma membrane. The connection between the BB and the axoneme constitutes the transition zone, which serves as a diffusion barrier between the intracellular space and the cilium, defining the ciliary compartment. Human pathologies affecting cilia structure or function, are called ciliopathies, which are caused by gene mutations. For that reason, the molecular mechanisms and structural aspects of cilia assembly and function are actively studied using a variety of model systems, ranging from unicellular organisms to metazoa. In this review, we will highlight the use of Paramecium as a model to decipher ciliary beating mechanisms as well as high resolution insights into BB structure and anchoring. We will show that study of cilia in Paramecium promotes our understanding of cilia formation and function. In addition, we demonstrate that Paramecium could be a useful tool to validate candidate genes for ciliopathies.

Calmodulin interactions with model lipid membranes: the interplay of Ca2+and lipid composition

Interactions of ionic proteins and lipids are believed to be crucial for the structure and function of membrane receptors and ion-channels. Calmodulin (CaM) is a highly conserved, multifunctional calcium-modulated protein, expressed in all eukaryotic cells. It binds to a wide variety of target proteins, influencing their function. Moreover, CaM binds up to four calcium ions through four EF-hand motifs, consisting of helix-loop-helix domains. This is known to lead to a conformational change that allows the binding with other target proteins, essential in many biological processes and driven by hydrophobic interactions.

Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels

Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.

Structural and Functional Insights into the Role of Guard Cell Ion Channels in Abiotic Stress-Induced Stomatal Closure

A stomatal pore is formed by a pair of specialized guard cells and serves as a major gateway for water transpiration and atmospheric CO2 influx for photosynthesis in plants. These pores must be tightly controlled, as inadequate CO2 intake and excessive water loss are devastating for plants. When the plants are exposed to extreme weather conditions such as high CO2 levels, O3, low air humidity, and drought, the turgor pressure of the guard cells exhibits an appropriate response against these stresses, which leads to stomatal closure. This phenomenon involves a complex network of ion channels and their regulation. It is well-established that the turgor pressure of guard cells is regulated by ions transportation across the membrane, such as anions and potassium ions. In this review, the guard cell ion channels are discussed, highlighting the structure and functions of key ion channels; the SLAC1 anion channel and KAT1 potassium channel, and their regulatory components, emphasizing their significance in guard cell response to various stimuli.

Neuron Class and Target Variability in the Three-Dimensional Localization of SK2 Channels in Hippocampal Neurons as Detected by Immunogold FIB-SEM.

Small-conductance calcium-activated potassium (SK) channels are crucial for learning and memory. However, many aspects of their spatial organization in neurons are still unknown. In this study, we have taken a novel approach to answering these questions combining a pre-embedding immunogold labeling with an automated dual-beam electron microscope that integrates focused ion beam milling and scanning electron microscopy (FIB/SEM) to gather 3D map ultrastructural and biomolecular information simultaneously. Using this new approach, we evaluated the number and variability in the density of extrasynaptic SK2 channels in 3D reconstructions from six dendritic segments of excitatory neurons and six inhibitory neurons present in the stratum radiatum of the CA1 region of the mouse. SK2 immunoparticles were observed throughout the surface of hippocampal neurons, either scattered or clustered, as well as at intracellular sites. Quantitative volumetric evaluations revealed that the extrasynaptic SK2 channel density in spines was seven times higher than in dendritic shafts and thirty-five times higher than in interneurons. Spines showed a heterogeneous population of SK2 expression, some spines having a high SK2 content, others having a low content and others lacking SK2 channels. SK2 immunonegative spines were significantly smaller than those immunopositive. These results show that SK2 channel density differs between excitatory and inhibitory neurons and demonstrates a large variability in the density of SK2 channels in spines. Furthermore, we demonstrated that SK2 expression was associated with excitatory synapses, but not with inhibitory synapses in CA1 pyramidal cells. Consequently, regulation of excitability and synaptic plasticity by SK2 channels is expected to be neuron class- and target-specific. These data show that immunogold FIB/SEM represent a new powerful EM tool to correlate structure and function of ion channels with nanoscale resolution.

Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels.

Many physiologic effects of l-glutamate, the major excitatory neurotransmitter in the mammalian central nervous system, are mediated via signaling by ionotropic glutamate receptors (iGluRs). These ligand-gated ion channels are critical to brain function and are centrally implicated in numerous psychiatric and neurologic disorders. There are different classes of iGluRs with a variety of receptor subtypes in each class that play distinct roles in neuronal functions. The diversity in iGluR subtypes, with their unique functional properties and physiologic roles, has motivated a large number of studies. Our understanding of receptor subtypes has advanced considerably since the first iGluR subunit gene was cloned in 1989, and the research focus has expanded to encompass facets of biology that have been recently discovered and to exploit experimental paradigms made possible by technological advances. Here, we review insights from more than 3 decades of iGluR studies with an emphasis on the progress that has occurred in the past decade. We cover structure, function, pharmacology, roles in neurophysiology, and therapeutic implications for all classes of receptors assembled from the subunits encoded by the 18 ionotropic glutamate receptor genes.Significance StatementGlutamate receptors play important roles in virtually all aspects of brain function and are either involved in mediating some clinical features of neurological disease or represent a therapeutic target for treatment. Therefore, understanding the structure, function, and pharmacology of this class of receptors will advance our understanding of many aspects of brain function at molecular, cellular, and system levels and provide new opportunities to treat patients.

Electromechanical response performance of a reinforced biomass gel artificial muscle based on natural polysaccharide of sodium alginate doped with an ionic liquid for micro-nano regulation

In this paper, a reinforced Biomass Gel Artificial Muscle (BGAM) was fabricated by natural polysaccharide of Sodium Alginate (SA) doped with an Ionic Liquid (IL) of 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIm][BF4]). Micro-nano regulation effect and reinforcement mechanism of IL doping content on electromechanical response performance of BGAM were researched during a single cycle and repeated cycles. Then, a green fabrication process and a set of valid test methods for BGAM were proposed in detail. The experimental results showed that when IL doping content was 4 mL, the BGAM achieved optimal modification, with a porosity of 70.47%, where it internally adopted the porous polymer structure of ion channels. Additionally, specific capacitance of BGAM attained a maximum value of 126.98 mF/g, and the inner resistance and elastic modulus reached minimum values of 2.018 Ω and 1.871 MPa, separately. Thus, the optimal working life and output-force density values, namely, 1720 s and 13.072 mN/g, respectively, were also determined for the BGAM.

ICDI-W2vCom: Identifying the Ion Channel-Drug Interaction in Cellular Networking Based on word2vec and node2vec.

Ion channels are the second largest drug target family. Ion channel dysfunction may lead to a number of diseases such as Alzheimer’s disease, epilepsy, cephalagra, and type II diabetes. In the research work for predicting ion channel–drug, computational approaches are effective and efficient compared with the costly, labor-intensive, and time-consuming experimental methods. Most of the existing methods can only be used to deal with the ion channels of knowing 3D structures; however, the 3D structures of most ion channels are still unknown. Many predictors based on protein sequence were developed to address the challenge, while most of their results need to be improved, or predicting web servers are missing. In this paper, a sequence-based classifier, called “iCDI-W2vCom,” was developed to identify the interactions between ion channels and drugs. In the predictor, the drug compound was formulated by SMILES-word2vec, FP2-word2vec, SMILES-node2vec, and ECFPs via a 1184D vector, ion channel was represented by the word2vec via a 64D vector, and the prediction engine was operated by the LightGBM classifier. The accuracy and AUC achieved by iCDI-W2vCom via the fivefold cross validation were 91.95% and 0.9703, which outperformed other existing predictors in this area. A user-friendly web server for iCDI-W2vCom was established at http://www.jci-bioinfo.cn/icdiw2v. The proposed method may also be a potential method for predicting target–drug interaction.

The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels

Membrane proteins, including ion channels, became the focus of structural proteomics midway through the 20th century. Methods for studying ion channels are diverse and include structural (X-ray crystallography, cryoelectron microscopy, currently X-ray free electron lasers) and functional (e.g., patch clamp) approaches. This review highlights the evolution of approaches to study of the structure of cardiac ion channels, provides an overview of new techniques of structural biology concerning ion channels, including the use of lipo- and nanodiscs, and discusses the contribution of electrophysiological studies and molecular dynamics to obtain a complete picture of the structure and functioning of cardiac ion channels. Electrophysiological studies have become a powerful tool for deciphering the mechanisms of ion conductivity and selectivity, gating and regulation, as well as testing molecules of pharmacological interest. Obtaining the atomic structure of ion channels became possible by the active development of X-ray crystallography and cryoelectron micro-scopy, and, recently, with the use of XFEL.

Impact of F80M and F83M mutations on the functionality of fluoride ion channel elucidated in microsecond level molecular dynamic simulation

Fluoride ion channels of the Fluc family plays a critically important role in combating environmental fluoride toxicity. As per the crystal structure of these fluoride ion channels, the pore region is densely packed with a series of hydrogen bond donating residues arranged in a ladder fashion creating an ion conducting pathway. In earlier studies, it was revealed that although the ion conducting pathway polarity is highly conserved, however the functionality of the channel protein depends on several residues at particular positions. While, a threonine at end of the pore is critically important in forming initial interactions, two phenylalanines at the central region coordinate F- transportation through the channel. It was also revealed that these two phenylalanines cannot be substituted by any other aromatic, polar or non-polar residues without hindering the functionality with exception of methionine. In another study, it was revealed that these two phenylalanines F80 and F83 when mutated with methionine; F80M lead to active state, while the F83M has lead to inactivity of F- anion conductivity. However, the exact atomic level detailing on how exactly these mutations have impacted the conductivity remained elusive. In this scenario, in this present study, we have modeled these two mutations and performed a microsecond level simulation on each mutation compared with wild type towards understanding the atomic level detailing revealing several insights on what exactly happening at these residues responsible for the selective conductivity of F- ions. Communicated by Ramaswamy H. Sarma

Brugada syndrome: current concepts and genetic background

Brugada syndrome (BrS) is a hereditary clinical-electrocardiographic arrhythmic entity with low worldwide prevalence. The syndrome is caused by changes in the structure and function of certain cardiac ion channels and reduced expression of Connexin 43 (Cx43) in the Right Ventricle (RV), predominantly in the Right Ventricular Outflow Tract (VSVD), causing electromechanical abnormalities. The diagnosis is based on the presence of spontaneous or medicated ST elevation, characterized by boost of the J point and the ST segment ≥2 mm, of superior convexity "hollow type" (subtype 1A) or descending rectilinear model (subtype 1B). BrS is associated with an increased risk of syncope, palpitations, chest pain, convulsions, difficulty in breathing (nocturnal agonal breathing) and/or Sudden Cardiac Death (SCD) secondary to PVT/VF, unexplained cardiac arrest or documented PVT/VF or Paroxysmal atrial fibrillation (AF) in the absence of apparent macroscopic or structural heart disease, electrolyte disturbance, use of certain medications or coronary heart disease and fever. In less than three decades since the discovery of Brugada syndrome, the concept of Mendelian heredity has come undone. The enormous variants and mutations found mean that we are still far from being able to concretely clarify a genotype-phenotype relationship. There is no doubt that the entity is oligogenetic, associated with environmental factors, and that there are variants of uncertain significance, especially the rare variants of the SCN5A mutation, with European or Japanese ancestors, as well as a spontaneous type 1 or induced pattern, thanks to gnomAD (coalition) researchers who seek to aggregate and harmonize exome and genome sequencing data from a variety of large scale sequencing projects and make summary data available to the scientific community at large). Thus, we believe that this in depth analytical study of the countless mutations attributed to BrS may constitute a real cornerstone that will help to better understand this intriguing syndrome.

Efficient Chiral Nanosenor Based on Tip-Modified Nanochannels.

Enantiomers of various drug molecules have a specific effect on living organisms. Accordingly, developing a sample method for the efficient and rapid recognition of chiral drug enantiomers is of great industrial value and physiological significance. Here, inspired by the structure of ion channels in living organisms, we developed a chiral nanosensor based on an artificial tip-modified nanochannel system that allows efficient selective recognition of chiral drugs. In this system, l-alanine-pillar[5]arenes as selective receptors were introduced on the tip side of conical nanochannels to form an enantioselective "gate". The selective coefficient of our system toward R-propranolol is 4.96, which is higher than the traditional fully modified nanochannels in this work.

Structure and Function of Ion Channels Regulating Sperm Motility-An Overview.

Sperm motility is linked to the activation of signaling pathways that trigger movement. These pathways are mainly dependent on Ca2+, which acts as a secondary messenger. The maintenance of adequate Ca2+ concentrations is possible thanks to proper concentrations of other ions, such as K+ and Na+, among others, that modulate plasma membrane potential and the intracellular pH. Like in every cell, ion homeostasis in spermatozoa is ensured by a vast spectrum of ion channels supported by the work of ion pumps and transporters. To achieve success in fertilization, sperm ion channels have to be sensitive to various external and internal factors. This sensitivity is provided by specific channel structures. In addition, novel sperm-specific channels or isoforms have been found with compositions that increase the chance of fertilization. Notably, the most significant sperm ion channel is the cation channel of sperm (CatSper), which is a sperm-specific Ca2+ channel required for the hyperactivation of sperm motility. The role of other ion channels in the spermatozoa, such as voltage-gated Ca2+ channels (VGCCs), Ca2+-activated Cl-channels (CaCCs), SLO K+ channels or voltage-gated H+ channels (VGHCs), is to ensure the activation and modulation of CatSper. As the activation of sperm motility differs among metazoa, different ion channels may participate; however, knowledge regarding these channels is still scarce. In the present review, the roles and structures of the most important known ion channels are described in regard to regulation of sperm motility in animals.

Computational Electrophysiology from a Single Molecular Dynamics Simulation and the Electrodiffusion Model.

The availability of high-resolution structures of ion channels opens the doors to reliable computations of electrophysiological properties, such as the dependence of ionic currents and selectivities on applied voltage. We develop two theoretical approaches for calculating these properties from molecular dynamics simulations at a single voltage, or even in the absence of voltage, combined with the electrodiffusion model in which ion motion in the channel is represented as one-dimensional diffusion in the potential of mean force exerted by other components of the system and the applied electric field. No knowledge of diffusivity or ion densities at other voltages is needed. Instead, in one approach, one-sided ion fluxes and density profiles are used to determine the free energy profile. In the other approach, committor probabilities for ions transported at the selected voltage are used for this purpose. Both approaches have been validated in an example of a simple ion channel formed by trichotoxin. The potentials of mean force calculated by way of the proposed approaches and obtained from traditional methods are in excellent agreement. Furthermore, the current-voltage dependence agrees very well with results obtained by way of computationally more demanding methods. We also have readily calculated the reversal potential, a computationally challenging electrophysiological property. The key assumptions of the electrodiffusion model, such as the independence of crossing events or the insensitivity of the potential of mean force to applied voltage, have been found to be satisfied. We also show that the voltage changes linearly in the hydrophobic core of the membrane and is constant elsewhere.

Solution Structure of the Gloeobacter Violaceus Ligand-Gated Ion Channel Probed by Small-Angle Neutron Scattering

Pentameric ligand-gated ion channels transform chemical signals into electrical ones, a process during which they undergo subtle conformational cycling resulting in rapid, reversible gating of an intrinsic transmembrane pore. The pH-gated bacterial channel GLIC has proved a valuable model system for this receptor family, in part due to its accessibility to X-ray crystallography - which has provided structures of closed, open, and intermediate conformations. However, such models raise critical questions as to whether the X-ray structures represent actual functional states, and if the cycle includes additional conformations such as highly contracted or expanded states. Small-angle neutron scattering (SANS) offers an approach to characterizing solution-phase structure, increasingly applicable to biomolecular problems on this scale. Here we characterized GLIC by SANS, in combination with inline size-exclusion chromatography (SEC), match-out deuterated detergents, and computational modeling of multiple putative structural models. SEC-SANS under resting conditions (pH 7) enabled the characterization of non-aggegated species which fit predictions from resting-state models, particularly following unrestrained molecular dynamics simulation of X-ray structures. Curves collected under activating conditions (pH 3) best fit a mixture of resting- and open-state models, whereas they diverged from expanded-pore models. in addition to supporting less-expanded models of the open state, this work demonstrates that SEC-SANS, in combination with molecular modeling and simulations, can distinguish solution-phase functional states of an ion channel. As neutron source brilliance increases and inline SEC-SANS set-ups become increasingly accessible, such methods will offer valuable tools for the elucidation of receptor conformational cycling and pharmaceutical development.

Influence of Hydrophobicity on Anion Selectivity

Hydrophobic interfaces play a central role in biological anion transport. Crystal structures of ion channels and transporter proteins have recently suggested that chloride ions may form favourable interactions with hydrophobic pore-lining sidechains. Molecular dynamics (MD) have revealed the surface affinity of polarizable anions to hydrophobic/water interfaces through the inclusion of polarisation. Classical force fields neglect electronic polarisability which in turn dismisses the effects of electronic shielding and overestimates the strength of interactions between interacting charges. The electronic continuum correction (ECC) is a mean-field approach for approximating polarisation effects and is achieved by simply rescaling ionic charges in non-polarisable force fields. Here, we used MD simulations to investigate the behavior of water, sodium and chloride ions in a model hydrophobic nanopore by constructing a modified carbon nanotube (CNT). The distributions of ions and water relative to the nanopore walls were analysed and compared for simulations with and without the use of ECC. Radial density profiles revealed an internal layer-by-layer structure of ions and water, with chloride ions showing a preference for the hydrophobic pore walls. A similar yet stronger effect is seen with ECC. Our findings provide insight into the localisation of chloride ions to hydrophobic surfaces in nanopore geometries which contributes to our understanding of anion permeation and selectivity in biological ion channels.

Investigation of Cation Permeation Through AMPA Receptors by Molecular Dynamics Simulations

AMPA Receptors (AMPAR) belong to the family of ionotropic glutamate receptors and are responsible for fast excitatory signal transduction at vertebrate synapses. They are crucial for all higher brain functions and defects in AMPARs can lead to severe neurodevelopmental disorders. We performed extensive molecular dynamics simulations (over 20 microseconds) of the transmembrane domain of a putative open AMPAR structure. These simulations revealed that the structure is indeed open and molecular dynamics (MD) are able to simulate ionic current through the ion channel structure derived from cryogenic electron microscopy. Permeation proceeded at physiological rates during the simulations, but depended on the force field used. We cross validated permeation rates of the monovalent cations potassium, sodium and caesium with single channel recordings. MD simulations of permeation of those ion types showed that the narrowest part with two glutamines in each subunit play the most important role in cation permeation. Rather than a single permissive structure, the selectivity filter of the ion channel is flexible, and allows different ions to permeate using distinct mechanisms but at similar rates.