Structure-based prediction of the conductance properties of ion channels

The HOLE procedure allows the prediction of the absolute conductance of an ion channel model from its structure. The original prediction method uses an empirically corrected Ohmic method. It is most successful, with predictions being reliable to within a factor of two. A new modification of the procedure is presented in which the self-diffusion coefficients of water molecules from molecular dynamics simulation are used to replace the empirical correction factor. A "prediction" of the conductance for the porin OmpF by the new method is made and shown to be very close to the experimental value. HOLE also allows the prediction of the effect that the addition of non-electrolyte polymers will have on channel conductance. The method has great potential to yield structural information from data provided by single channel recordings but needs further validation by making measurements on channels of known structure. Preliminary results are given of single channel records establishing the effects of non-electrolytes on the conductance of gramicidin D channels. As an example of the potential uses of the procedure application is made to examine the oligomerization of alpha-toxin (alpha-hemolysin) channels. A model for the alpha-toxin hexamer, based on the crystal structure for the heptamer, is generated using molecular mechanics methods. The compatibility of the structures with single channel conductance data is assessed using HOLE.     

Synthetic ion channel activity documented by electrophysiological methods in living cells

Hydraphiles are synthetic ion channels that use crown ethers as entry portals and that span phospholipid bilayer membranes. Proton and sodium cation transport by these compounds has been demonstrated in liposomes and planar bilayers. In the present work, whole cell patch clamp experiments show that hydraphiles integrate into the membranes of human embryonic kidney (HEK 293) cells and significantly increase membrane conductance. The altered membrane permeability is reversible, and the cells under study remain vital during the experiment. Control compounds that are too short (C(8)-benzyl channel) to span the bilayer or are inactive owing to a deficiency in the central relay do not induce similar conductance increases. Control experiments confirm that the inactive channel analogues do not show nonspecific effects such as activation of native channels. These studies show that the combination of structural features that have been designed into the hydraphiles afford true, albeit simple, channel function in live cells.     

Molecular design and synthesis of artificial ion channels based on cyclic peptides containing unnatural amino acids

A series of novel cyclic peptides composed of 3 to 5 dipeptide units with alternating natural-unnatural amino acid units, have been designed and synthesized, employing 5-(N-alkanoylamino)-3-aminobenzoic acid with a long alkanoyl chain as the unnatural amino acid. All cyclic peptides with systematically varying pore size, shape, and lipophilicity are found to form ion channels with a conductance of ca. 9 pS in aqueous KCl (500 mM) upon examination by the voltage clamp method. These peptide channels are cation selective with the permeability ratio P(Cl(-))/P(K(+)) of around 0.17. The ion channels formed by the neutral, cationic, and anionic cyclic peptides containing L-alanine, L-lysine, and L-aspartate, respectively, show the monovalent cation selectivity with the permeability ratio P(Na(+))/P(K(+)) of ca. 0.39. On the basis of structural information provided by voltage-dependent blockade of the single channel current of all the tested peptides by Ca(2+), we inferred that each channel is formed from a dimer of the peptide with its peptide ring constructing the channel entrance and its alkanoyl chains lining across the membrane to build up the channel pore. The experimental results are consistent with an idea that the rate of ion conduction is determined by the nature of the hydrophobic alkanoyl chain region, which is common to all the channels.     

Effect of channel block on the collective spiking activity of coupled stochastic Hodgkin-Huxley neurons

Toxins, such as tetraethylammonium (TEA) and tetrodotoxin (TTX), can make potassium or sodium ion channels poisoned, respectively, and hence reduce the number of working ion channels and lead to the diminishment of conductance. In this paper, we have studied by numerical simulations the effects of sodium and potassium ion channel poisoning on the collective spiking activity of an array of coupled stochastic Hodgkin-Huxley (HH) neurons. It is found for a given number of neurons sodium or potas- sium ion channel block can either enhance or reduce the collective spiking regularity, depending on the membrane patch size. For a given smaller or larger patch size, potassium and sodium ion channel block can reduce or enhance the collective spiking regularity, but they have different patch size ranges for the transformation. This result shows that sodium or potassium ion channel block might have dif- ferent effects on the collective spiking activity in coupled HH neurons from the effects for a single neuron, which represents the interplay among the diminishment of maximal conductance and the in- crease of channel noise strength due to the channel blocks, as well as the bi-directional coupling be- tween the neurons.     

Ion channels from linear and branched bola-amphiphiles

The synthesis and characterization of the ion channel activity of three new bola-amphiphiles is described. These compounds are conceptually derived from a previously reported bis-cyclophane bola-amphiphile through opening of the cyclophanes to acyclic structures and were found to readily form ion channels in planar bilayer membranes as assessed by bilayer clamp single-channel analysis. All three compounds behaved very similarly: the dominant channels formed by all three are Ohmic with specific conductance of 10 +/- 1 pS (NaCl electrolyte) and 39 +/- 1 pS (CsCl electrolyte). Single-ion permeability ratios, determined from dissymmetric electrolyte experiments, showed the selectivity P(Cs(+)) > P(Na(+)) > P(Cl(-)). Less frequently, lower conductance channels were also observed to act independently of the dominant channels. The lifetimes of the dominant channels range from 70 to 280 ms for the three compounds with some very long-lived openings (20-40 s) observed for two of the three. The lower conductance states have shorter lifetimes. This study demonstrates that bis-macrocyclic compounds are not essential for channel formation by bola-amphiphiles, and opens a new class of channel-forming compounds for structure-activity optimization.     

Reconstitution of the Torpedo californica nicotinic acetylcholine receptor into planar lipid bilayers

Detergent-solubilized acetylcholine receptor (nAcChR) proteins can be purified by affinity chromatography and reconstituted into lipid vesicles and afterwards into planar lipid bilayer membranes via, in principle, two methods: fusion or assembly from two vesicle-spread monolayers. In the presence of agonists (carbamoylcholine, suberoyldicholine) different kinds of channel openings are recorded: fast single channels, bursts and long openings with short closures in between. Similar results have been obtained with reconstituted membrane fragments rich in nAcChR. In addition, Torpedo californica nAcChR proteins give rise to fuzzy channels and less defined events of conductivity, which “reemerge” again all the time. Frequently the channel events have conductance levels of about 200 to 300 pS, obviously simultaneous openings of several aggregated receptors. Under these conditions 40 pS conductance events occur also. It appears that the conductance of the channels measured is a multiple of 6.3 pS. Often, with the same sample, no channel openings are seen. Contrary to patch-clamp investigations on whole cells, AcChR-channel openings in reconstituted systems occur only several minutes after agonist application and not immediately. It is not clear whether the “reconstituted channels” reflect rapid activation or whether they result from desensitized receptor states only. Although a clear-cut correlation of channel event and channel protein unit is only possible by reconstitution of the biochemically characterized protein, e.g. monomer, dimer or higher oligomers, the reconstitution technique is still in its infancy.     

Ion channels in the human red blood cell membrane: their further investigation and physiological relevance.

Using the patch-clamp technique, two different ion channels have been characterized further in the human red blood cell (RBC) membrane. We demonstrate that the non-selective cation channel (NSC) is permeable to Ca(2+) and can be activated by prostaglandin E(2) (PGE(2)). Therefore, the physiological role of this channel could be, together with the Ca(2+)-activated K(+) channel, the participation in the process of blood clot formation. We give also evidence that another channel in the RBC membrane, so far assumed to be a small conductance anion channel, is more likely to be a proton or a hydroxyl ion channel.     

Membrane‐Length Amphiphiles Exhibiting Structural Simplicity and Ion Channel Activity

A number of synthetic ion channels have been reported in recent years that incorporate unusual or sophisticated design elements. The present work demonstrates that extremely simple compounds can function as ion channels (insert in bilayers, exhibit open–close behavior) if they meet minimum criteria. A simple membrane spanning structure may function as a channel if 1) it possesses polar headgroups (is bolaamphiphilic), 2) possesses a “central relay,” and 3) channel function (open–close behavior) must be detected after insertion of the amphiphile directly into the aqueous liposomal or cellular suspension. We show here compounds that are simple spans to which we have given the name “aplosspan” (from the Greek απλoσ + span) that meet these criteria. They are similar to, but simpler than, structures reported in the literatures that incorporate more complex design features.     

Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family

Understanding the mechanisms of gating and ion permeation in biological channels and receptors has been a long-standing challenge in biophysics. Recent advances in structural biology have revealed the architecture of a number of transmembrane channels and allowed detailed, molecular-level insight into these systems. Herein, we have examined the barriers to ion conductance and origins of ion selectivity in models of the cationic human alpha7 nicotinic acetylcholine receptor (nAChR) and the anionic alpha1 glycine receptor (GlyR), based on the structure of Torpedo nAChR. Molecular dynamics simulations were used to determine water density profiles along the channel length, and they established that both receptor pores were fully hydrated. The very low water density in the middle of the nAChR pore indicated the existence of a hydrophobic constriction. By contrast, the pore of GlyR was lined with hydrophilic residues and remained well-hydrated throughout. Adaptive biasing force simulations allowed us to reconstruct potentials of mean force (PMFs) for chloride and sodium ions in the two receptors. For the nicotinic receptor we observed barriers to ion translocation associated with rings of hydrophobic residues-Val13' and Leu9'-in the middle of the transmembrane domain. This finding further substantiates the hydrophobic gating hypothesis for nAChR. The PMF revealed no significant hydrophobic barrier for chloride translocation in GlyR. For both receptors nonpermeant ions displayed considerable barriers. Thus, the overall electrostatics and the presence of rings of charged residues at the entrance and exit of the channels were sufficient to explain the experimentally observed anion and cation selectivity.     

Cation selective ion channels formed by macrodiolide antibiotic elaiophylin in lipid bilayer membranes

The macrodiolide antibiotic elaiophylin (1) forms stable, long-lasting cation selective ion channels in planar lipid bilayer membranes prepared from soybean phosphatidylcholine. Current of the single ion channel displayed two sublevels corresponding to the two substates of the channel conductance: a slow substate, with about 5 s of mean dwell time in the open state at 40% level of the total amplitude conductance, and a fast substate of higher conductance with dwell times in the open and closed state of about 0.1 s. Amplitude conductances of the single ion channels in 200 mM of LiCl, NaCl, KCl, RbCl and CsCl were 75, 140, 220, 240 and 226 pS, and the conductance was linear function of the electrolyte concentration. Ratios of cation to anion permeabilities of the channel for NaCl and KCl were 8+/-2 and >24, respectively. A molecular model of the channel structure is suggested.     

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.     

Molecular dynamics simulation links conformation of a pore-flanking region to hyperekplexia-related dysfunction of the inhibitory glycine receptor

Inhibitory glycine receptors mediate rapid synaptic inhibition in mammalian spinal cord and brainstem. The previously identified hyperekplexia mutation GLRA1(P250T), located within the intracellular TM1-2 loop of the GlyR alpha1 subunit, results in altered receptor activation and desensitization. Here, elementary steps of ion channel function of alpha1(250) mutants were resolved and shown to correlate with hydropathy and molar volume of residue alpha1(250). Single-channel recordings and rapid activation kinetic studies using laser pulse photolysis showed reduced conductance but similar open probability of alpha1(P250T) mutant channels. Molecular dynamics simulation of a helix-turn-helix motif representing the intracellular TM1-2 domain revealed alterations in backbone conformation, indicating an increased flexibility in these mutants that paralleled changes in elementary steps of channel function. Thus, the architecture of the TM1-2 loop is a critical determinant of ion channel conductance and receptor desensitization.     

Ion channel drug potency assay with an artificial bilayer chip

The potency of pharmaceutical compounds acting on ion channels can be determined through measurements of ion channel conductance as a function of compound concentration. We have developed an artificial lipid bilayer chip for simple, fast, and high-yield measurement of ion channel conductance with simultaneous solution perfusion. Here we show the application of this chip to the measurement of the mammalian cold and menthol receptor TRPM8. Ensemble measurements of TRPM8 as a function of concentration of menthol and 2-aminoethoxydiphenyl borate (2-APB) enabled efficient determination of menthol's EC(50) (111.8 μM ± 2.4 μM) and 2-APB's IC(50) (4.9 μM ± 0.2 μM) in agreement with published values. This validation, coupled with the compatibility of this platform with automation and parallelization, indicates significant potential for large-scale pharmaceutical ion channel screening.     

beta-Barrel membrane bacterial proteins: structure, function, assembly and interaction with lipids

Membrane proteins, although constituting about one-third of all proteins encoded by the genomes of living organisms, are still strongly underrepresented in the database of 3D protein structures, which reflects the big challenge presented by this class of proteins. Structural biologists, by employing electron and x-ray approaches, are continuously revealing new and fundamental insights into the structure, function, assembly and interaction with lipids of membrane proteins. To date, two structural motifs, alpha-helices and beta-sheets, have been found in membrane proteins and interestingly these two structural motives correlate with the location: while alpha-helical bundles are most often found in the receptors and ion channels of plasma and endoplasmic reticulum membranes, beta-barrels are restricted to the outer membrane of Gram-negative bacteria and in the mitochondrial membrane, and represent the structural motif used by several microbial toxins to form cytotoxic transmembrane channels. The beta-barrel, while being a rigid and stable motif is a versatile scaffold, having a wide variation in the size of the barrel, in the mechanism to open or close the gate and to impose selectivity on substrates. Even if the number of x-ray structures of integral membrane proteins has greatly increased in recent years, only a few of them provide information at a molecular level on how proteins interact with lipids that surround them in the membrane. The detailed mechanism of protein lipid interactions is of fundamental importance for understanding membrane protein folding, membrane adsorption, insertion and function in lipid bilayers. Both specific and unspecific interactions with lipids may participate in protein folding and assembly.     

Physical organic chemistry on the brain

The challenges to obtaining chemical-scale information on the molecules of neuroscience are considerable. Most targets are complex integral membrane proteins that are not amenable to direct structural characterization. However, by combining the tools of organic synthesis, molecular biology, and electrophysiology, rational and systematic structure-function studies can be performed in what we have termed physical organic chemistry on the brain. Using these tools, we have probed hydrophobic effects, hydrogen bonding, cation-pi interactions, and conformational changes associated with channel gating. The insights gained provide important guidance for drug discovery efforts targeting ion channels and neuroreceptors and mechanistic insights for the complex proteins of neuroscience.     

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.     

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.     

Divalent cations reduce the pH sensitivity of OmpF channel inducing the pK(a) shift of key acidic residues

In contrast to the highly-selective channels of neurophysiology employing mostly the exclusion mechanism, different factors account for the selectivity of large channels. Elucidation of these factors is essential for understanding the permeation mechanisms in ion channels and their regulation in vivo. The interaction between divalent cations and a protein channel, the bacterial porin OmpF, has been investigated paying attention to the channel selectivity and its dependence on the solution pH. Unlike the experiments performed in salts of monovalent cations, the channel is now practically insensitive to pH, being anion selective all over the pH range considered. Electrostatic calculations based on the available structural data suggest that the binding of divalent cations has two main effects: (i) the pK(a) values of key ionizable groups differ significantly from those of the isolated groups in solution and (ii) the cation binding has a decisive impact on the effective electric charge regulating the channel selectivity. A simple molecular model based on statistical thermodynamics provides additional qualitative explanations to the experimental findings that could also be useful for other related systems like synthetic nanopores, ion exchange membranes, and polyelectrolyte multilayers.     

Reconstitution of channel proteins from Torpedo electroplax into virtually solvent-free lipid bilayers

The Torpedo electric organ has been the subject of intensive biochemical and biophysical investigations. It is a standard source of vesicle preparations containing large amounts of acetylcholine receptor protein as well as other proteins. Of these, the acetylcholine receptor channel and the chloride channel have been reconstituted into lipid bilayer membranes to date.In reconstitution experiments with virtually solvent-free lipid bilayers, we have detected a number of other ion channels, not described before, in bilayers containing solvents. This suggests that these channels are affected by the amount of solvent in the membrane, and that the Torpedo electroplax vesicles are a useful source for many physiologically relevant ion channel proteins.