DeepIon: Deep learning approach for classifying ion transporters and ion channels from membrane proteins

The movement of ions across the cell membrane is an essential for many biological processes. This study is focused on ion channels and ion transporters (pumps) as types of border guards control the incessant traffic of ions across cell membranes. Ion channels and ion transporters function to regulate membrane potential and electrical signaling and play important roles in cell proliferation, migration, apoptosis, and differentiation. In their behaviors, it is found that ion channels differ significantly from ion transporters. Therefore, a method for automatically classifying ion transporters and ion channels from membrane proteins is proposed by training deep neural networks and using the position-specific scoring matrix profile as an input. The key of novelty is the three-stage approach, in which five techniques for data normalization are used; next three imbalanced data techniques are applied to the minority classes and then, six classifiers are compared with the proposed method. © 2019 Wiley Periodicals, Inc.     

An efficient approach for the prediction of ion channels and their subfamilies

Ion channels are integral membrane proteins that are responsible for controlling the flow of ions across the cell. There are various biological functions that are performed by different types of ion channels. Therefore for new drug discovery it is necessary to develop a novel computational intelligence techniques based approach for the reliable prediction of ion channels families and their subfamilies. In this paper random forest based approach is proposed to predict ion channels families and their subfamilies by using sequence derived features. Here, seven feature vectors are used to represent the protein sample, including amino acid composition, dipeptide composition, correlation features, composition, transition and distribution and pseudo amino acid composition. The minimum redundancy and maximum relevance feature selection is used to find the optimal number of features for improving the prediction performance. The proposed method achieved an overall accuracy of 100%, 98.01%, 91.5%, 93.0%, 92.2%, 78.6%, 95.5%, 84.9%, MCC values of 1.00, 0.92, 0.88, 0.88, 0.90, 0.79, 0.91, 0.81 and ROC area values of 1.00, 0.99, 0.99, 0.99, 0.99, 0.95, 0.99 and 0.96 using 10-fold cross validation to predict the ion channels and non-ion channels, voltage gated ion channels and ligand gated ion channels, four subfamilies (calcium, potassium, sodium and chloride) of voltage gated ion channels, and four subfamilies of ligand gated ion channels and predict subfamilies of voltage gated calcium, potassium, sodium and chloride ion channels respectively.     

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

Microscopic calculations of free energy profiles for ion transport through biological ion channels present a very serious challenge to modern simulation approaches. The main problem is due to the major convergence problems associated with the heterogeneous landscape of the electrostatic environment in ion channels and with the need to evaluate the profile associated with the transfer of the ion from bulk water to the channel environment. This problem is compounded by the lack of reliable and relevant benchmarks that can discriminate between alternative approaches. The present study is aimed at reducing the above problems by defining benchmarks that are directly relevant to ion channels and can also give converging results. This is done by constructing a series of models of a truncated gramicidin channel with different numbers of water molecules and by comparing the profiles for going around the channel and through the channel. These discriminating models are then used to validate and compare the adiabatic charging free energy perturbation (FEP) approach combined with an umbrella sampling approach (Warshel, A. J. Phys. Chem. 1982, 86, 2218) and the potential of mean force (PMF) approach used frequently in studies of ion channels. It is found that both approaches work quite well until one moves to the case of the fully solvated channel. In this limit, the PMF approach may give different results for the overall work of going through the channel and around the channel, while the FEP approach gives physically consistent results. The present benchmark also indicates that the weighted histogram analysis method (WHAM) approach does not offer a significant advantage over earlier approaches at least as much as studies of ion channels are concerned. Finally, it is concluded that the FEP approach may be more useful in evaluating the overall barrier for moving ions from water to ion channels and that in some cases it might be beneficial to use the FEP approach for selective points along the channel and then to connect these points by PMF calculations.     

Crystal Channel Engineering for Rapid Ion Transport: From Nature to Batteries

Ion transport behaviours through cell membranes are commonly identified in biological systems, which are crucial for sustaining life for organisms. Similarly, ion transport is significant for electrochemical ion storage in rechargeable batteries, which has attracted much attention in recent years. Rapid ion transport can be well achieved by crystal channels engineering, such as creating pores or tailoring interlayer spacing down to the nanometre or even sub-nanometre scale. Furthermore, some functional channels, such as ion selective channels and stimulus-responsive channels, are developed for smart ion storage applications. In this review, the typical ion transport phenomena in the biological systems, including ion channels and pumps, are first introduced, and then ion transport mechanisms in solid and liquid crystals are comprehensively reviewed, particularly for the widely studied porous inorganic/organic hybrid crystals and ultrathin inorganic materials. Subsequently, recent progress on the ion transport properties in electrodes and electrolytes is reviewed for rechargeable batteries. Finally, current challenges in the ion transport behaviours in rechargeable batteries are analysed and some potential research approaches, such as bioinspired ultrafast ion transport structures and membranes, are proposed for future studies. It is expected that this review can give a comprehensive understanding on the ion transport mechanisms within crystals and provide some novel design concepts on promoting electrochemical ion storage capability in rechargeable batteries.     

A dual sensor of fluorescent and colorimetric for the rapid detection of lead

This study demonstrated a simple and reliable method to rapidly detect Pb(2+) in aqueous solution, exploiting gold nanoparticles as a lead ion probe; the results indicated that the dual channels sensor showed high selectivity and sensitivity for Pb(2+) as low as ppm levels in aqueous environment.     

Structure-based discovery of potassium channel blockers from natural products: virtual screening and electrophysiological assay testing

Potassium ion (K(+)) channels are attractive targets for rational drug design. Based upon a three-dimensional model of the eukaryotic K(+) channels, the docking virtual screening approach was employed to search the China Natural Products Database. Compounds were ranked according to the relative binding energy, favorable shape complementarity, and potential of forming hydrogen bonds with the K(+) channel. Four candidate compounds found by virtual screening were investigated by using the whole-cell voltage-clamp recording in rat dissociated hippocampal neurons. When applied extracellularly, compound 1 markedly depressed the delayed rectifier K(+) current (I(K)) and fast transient K(+) current (I(A)), whereas compounds 2, 3, and 4 exerted a more potent and selective inhibitory effect on I(K). Intracellular application of the four compounds had no effect on both the K(+) currents.     

Detection of single ion channel activity on a chip using tethered bilayer membranes

Membrane-bound ion channels are promising biological receptors since they allow for the stochastic detection of analytes at high sensitivity. For stochastic sensing, it is necessary to measure the ion currents associated with single ion channel opening and closing events. However, this calls for stability, high reproducibility, and long lifetimes. A critical issue to overcome is the low stability of the ion channel environment, that is, the bilayer membrane. A promising technique to surmount this is to connect the lower part of the membrane to a surface forming a tethered bilayer membrane. By reconstituting the synthetic ion channel, gramicidin A, into a tethered bilayer as part of a microchip design, we have been able to record the activity of single ion channels. The observed activity was compared with that obtained by a conventional electrophysiology method, tip dipping, to confirm its authenticity. These findings allow for the construction of stable biosensors based on ion channels and provide a novel technique for the characterization of ion channel activity.     

Synthetische Ionenkanäle

Membrane-bound ion channels play an important role in biological systems. They are involved in key processes such as neural signal transduction, muscle contraction, and vision. The understanding of the structure of natural ion channels is growing, but it is still far from satisfactory. Synthetic ion channels can have the advantage of a well-defined conformation of the active state. This information facilitates the study of the structure-function relationships of their biological counterparts.     

双分子层膜人工离子通道的合成

离子通道(ion channels)是由细胞膜上的一类特殊亲水性蛋白质构成的微孔道,它的主要功能就是传输离子跨膜,相当于细胞的通气孔。其结构与功能的异常往往引起上千种疾病,统称为离子通道病,这种疾病目前不能靠常规的仪器来检查,在确诊上有一定的难度。因此通过化学手段合成人工离子通道来模拟生物体内细胞膜上的离子通道的结构与功能,对于深入研究这些疾病并发现特异性治疗药物均具有十分重要的理论和实际意义。本论文就近三十年来人们设计合成的不同种类人工离子通道进行了综述,介绍了其研究进展并总结了各种人工离子通道的分子结构设计以及在膜上传输离子行为,展望了其在模拟天然离子通道功能的同时在生物医药以及生命科学等领域的应用前景。     

Modeling membranes under a transmembrane potential

Accurate modeling of ion transport through synthetic and biological transmembrane channels has been so far a challenging problem. We introduce here a new method that allows one to study such transport under realistic biological conditions. We present results from molecular dynamics simulations of an ion channel formed by a peptide nanotube, embedded in a lipid bilayer, and subject to transmembrane potentials generated by asymmetric distributions of ions on both sides of the membrane. We show that the method is efficient for generating ionic currents and allows us to estimate the intrinsic conductance of the channel.     

Optimized precursor ion selection for labile ions in a linear ion trap mass spectrometer and its impact on quantification using selected reaction monitoring

The fragmentation of fragile ions during the application of an isolation waveform for precursor ion selection and the resulting loss of isolated ion intensity is well‐known in ion trap mass spectrometry (ITMS). To obtain adequate ion intensity in the selected reaction monitoring (SRM) of fragile precursor ions, a wider ion isolation width is required. However, the increased isolation width significantly diminishes the selectivity of the channels chosen for SRM, which is a serious problem for samples with complex matrices. The sensitive and selective quantification of many lipid molecules, including ceramides from real biological samples, using a linear ion trap mass spectrometer is also hindered by the same problem because of the ease of water loss from protonated ceramide ions. In this study, a method for the reliable quantification of ceramides using SRM with near unity precursor ion isolation has been developed for ITMS by utilizing alternative precursor ions generated by in‐source dissociation. The selected precursor ions allow the isolation of ions with unit mass width and the selective analysis of ceramides using SRM with negligible loss of sensitivity. The quantification of C18:0‐, C24:0‐ and C24:1‐ceramides using the present method shows excellent linearity over the concentration ranges from 6 to 100, 25 to 1000 and 25 to 1000 nM, respectively. The limits of detection of C18:0‐, C24:0‐ and C24:1‐ceramides were 0.25, 0.25 and 5 fmol, respectively. The developed method was successfully applied to quantify ceramides in fetal bovine serum. Copyright © 2014 John Wiley & Sons, Ltd.     

Natural and artificial ion channels for biosensing platforms

The single-molecule selectivity and specificity of the binding process together with the expected intrinsic gain factor obtained when utilizing flow through a channel have attracted the attention of analytical chemists for two decades. Sensitive and selective ion channel biosensors for high-throughput screening are having an increasing impact on modern medical care, drug screening, environmental monitoring, food safety, and biowarefare control. Even virus antigens can be detected by ion channel biosensors. The study of ion channels and other transmembrane proteins is expected to lead to the development of new medications and therapies for a wide range of illnesses. From the first attempts to use membrane proteins as the receptive part of a sensor, ion channels have been engineered as chemical sensors. Several other types of peptidic or nonpeptidic channels have been investigated. Various gating mechanisms have been implemented in their pores. Three technical problems had to be solved to achieve practical biosensors based on ion channels: the fabrication of stable lipid bilayer membranes, the incorporation of a receptor into such a structure, and the marriage of the modified membrane to a transducer. The current status of these three areas of research, together with typical applications of ion-channel biosensors, are discussed in this review.     

Atomic force microscopy imaging and electrical recording of lipid bilayers supported over microfabricated silicon chip nanopores: lab-on-a-chip system for lipid membranes and ion channels

We describe a silicon chip-based supported bilayer system to detect the presence of ion channels and their electrical conductance in lipid bilayers. Nanopores were produced in microfabricated silicon membranes by electron beam lithography as well as by using a finely focused ion beam. Thermal oxide was used to shrink pore sizes, if necessary, and to create an insulating surface. The chips with well-defined pores were easily mounted on a double-chamber plastic cell recording system, allowing for controlling the buffer conditions both above and below the window. The double-chamber system allowed using an atomic force microscopy (AFM) tip as one electrode and inserting a platinum wire as the second electrode under the membrane window, to measure electrical current across lipid bilayers that are suspended over the pores. Atomic force imaging, stiffness measurement, and electrical capacitance measurement show the feasibility of supporting lipid bilayers over defined nanopores: a key requirement to use any such technique for structure-function study of ion channels. Online addition of gramicidin, an ion-channel-forming peptide, resulted in electrical current flow across the bilayer, and the I-V curve that was measured using the conducting AFM tip indicates the presence of many conducting gramicidin ion channels.     

Potential analytical applications of gated artificial ion channels

Biosensors based on natural ion channels combine a biological recognition mechanism with a physical transduction technique in a very selective and sensitive manner. This kind of molecular sensor will contribute to drug screening and environmental screening. Key information about channel gating, ion transport, and molecular mechanism is provided by the patch-clamp technique, commonly used for electrophysiological analysis. Here we report the synthesis of light-gated artificial ion channels, necessary constituents for construction of biosensors based on natural ion channels. The artificial gated ion channels described here are based on calix[4]resorcinarene. Opening and closing of the artificial ion channel is achieved by azo groups, which work like a lid. Azo groups alter their conformation on irradiation with light, and are chemically quite stable. Addition of a gate function will enhance the potential of synthetic channels to be used in sensors as molecular switches.Dedicated to the memory of Wilhelm Fresenius     

Self-assembled Supramolecular Artificial Transmembrane Ion Channels: Recent Progress and Application

Natural protein channels have evolved with fantastic spatial structures, which play pivotal physiological functions in all living systems. Learning from nature, chemical scientists have developed a myriad of artificial transmembrane ion channels by using various chemical strategies, among which the non-covalent supramolecular ion channels exhibit remarkable advantages over other forms(e.g., single-molecule ion channel), which exhibited facile preparation methods, easier structural modification and functionalization. In this review, we have systematically summarized the recent progress of supramolecular self-assembled artificial transmembrane ion channels, which were classified by different self-assembly mechanisms, such as hydrogen bonds, π-π interactions, etc. Detailed preparation process and self-assembly strategies of the supramolecular ion channels have been described. Moreover, potential biomedical applications of the supramolecular ion channels have also been carefully discussed in this review. Finally, future opportunities and challenges facing this field were also elaborately discussed. It is anticipated that this review could provide a panoramic sketch and future directions towards the construction of novel artificial ion channels with novel functions and biomedical applications.     

Characteristics of Single Ionic Channels Induced by Sulfonic Acid Derivatives of Dibenzo-18-Crown-6 in Bilayers

Sulfonic acid derivatives of dibenzo-18-crown-6 (DB18C6) have been shown to induce formation of ion channels permeable to monovalent cations in bilayer lipid membranes (BLM). Some electric characteristics of channels have been studied by means of the voltage clamp method. Channels displayed little interionic discrimination. The voltage dependence as well as the multiple state behaviors of the channels functioning was observed. The channels formation has been shown to be dependent on pH of bath solutions and on the presence of bivalent cations in them. The channels supposed to be formed from aggregates of complexes associates assembled in aqueous salt solutions.     

Photo- and Redox-Regulated Transmembrane Ion Transporters

Synthetic supramolecular ion transporters find applications as potential therapeutics and as tools for engineering functional membranes. Stimuli-responsive systems enable external control over transport, which is necessary for targeted activation. The Minireview provides an overview of current approaches to developing stimuli-responsive ion transport systems, including channels and mobile carriers, that can be controlled using photo or redox inputs.     

Ion Channels as Sensing Elements-Investigations by Patch-Clamp Technique

Ion channels are transmembrane proteins. Their high recognition capability together with an intrinsic amplification effects makes them outstanding candidates as constituents of biosensors. The patch-clamp technique is an extremely powerful and versatile method for studying the functioning of ion channels reconstituted into biological or synthetic membranes. Two well characterized types of natural ion channels were studied, (i) the simple transmembrane protein gramicidin A and (ii) the rather complex ligand-gated nicotinic acetylcholine receptor.     

Single molecule measurements within individual membrane-bound ion channels using a polymer-based bilayer lipid membrane chip

The measurement of single poly(ethylene glycol) (PEG) molecules interacting with individual bilayer lipid membrane-bound ion channels is presented. Measurements were performed within a polymer microfluidic system including an open-well bilayer lipid membrane formation site, integrated Ag/AgCl reference electrodes for on-chip electrical measurements, and multiple microchannels for independent ion channel and analyte delivery. Details of chip fabrication, bilayer membrane formation, and alpha-hemolysin ion channel incorporation are discussed, and measurements of interactions between the membrane-bound ion channels and single PEG molecules are presented.     

Application of nonresonance excitation to ion trap tandem mass spectrometry and selected ejection chemical ionization

Nonresonance excitation is a universal ion excitation and ejection method in which increased ion kinetic energy is achieved by the combination of an axial dc dipole and the rf trapping fields. The method does not require the applied excitation frequency to match with the secular frequency of the precursor ions to effect collision-induced dissociation (CID) for tandem mass spectrometry applications. Therefore, it is free of the effects of secular frequency changes caused by space-charge and simplifies the optimization of tandem mass spectrometry parameters when combined with gas chromatography-tandem mass spectrometry (GC-MS/MS). Computer simulations show that in contrast to the resonance excitation process, the nonresonance excitation process is able to accelerate thermal ions to kinetic energies in excess of 40 eV in a few microseconds. Based on simulations, we expect that the rapid deposition of energy by this method may allow the study, in ion traps, of high energy decomposition channels of precursor ions with multiple decomposition channels. Furthermore, the method is able to simultaneously excite multiple precursor ions, for example, excite both analyte and its coeluting isotopically labeled internal standard for GC-MS/MS analysis. A GC-MS/MS analysis of 100 pg of n-butylbenzene is demonstrated with a signal-to-noise ratio of 3624, which is over an order of magnitude higher than the signal-to-noise ratio of 345 obtained by full scan gas chromatography-mass spectrometry. In addition, the nonresonance excitation method can be used as a low pass mass filter in the chemical ionization (CI) mode to eject undesired fragment ions that result from direct electron ionization. This new CI method, selected ejection chemical ionization, can produce a CI spectrum without contamination of sample fragment ions from electron ionization.