Gramicidin-based channel systems for the detection of protein-ligand interaction

Formation of lipid bilayer membrane in a poly(dimethylsiloxane) microchip integrated with a stacked polycarbonate membrane support and an on-site nanoinjector

This paper describes a new and facile approach for the formation of pore-spanning bilayer lipid membranes (BLMs) within a poly(dimethylsiloxane) (PDMS) microfluidic device. Commercially, readily available polycarbonate (PC) membranes are employed for the support of BLMs. PC sheets with 5 μm, 2 μm, and 0.4 μm pore diameters, respectively, are thermally bonded into a multilayer-stack, reducing the pore density of 0.4 μm-pore PC by a factor of 200. The BLMs on this support are considerably stable (a mean lifetime: 17 h). This multilayer-stack PC (MSPC) membrane is integrated into the PDMS chip by an epoxy bonding method developed to secure durable bonding under the use of organic solvents. The microchip has a special channel for guiding a micropipette in the proximity of the MSPC support. With this on-site injection technique, tens to hundreds of nanoliters of solutions can be directly dispensed to the support. Incorporating gramicidin ion channels into BLMs on the MSPC support has confirmed the formation of single BLMs, which is based on the observation from current signals of 20 pS conductance that is typical to single channel opening. Based on the bilayer capacitance (1.4 pF), about 15% of through pores across the MSPC membrane are estimated to be covered with BLMs.

Pore-forming compounds as signal transduction elements for highly sensitive biosensing

Pore-forming compounds are attracting much attention due to the signal transduction ability for the development of highly sensitive biosensing. In this review, we describe an overview of the recent advances made by our group in the design of molecular sensing interfaces of spherical and planar lipid bilayers and natural bilayers. The potential uses of pore-forming compounds, such as gramicidin and MCM-41, in lipid bilayers and natural glutamate receptor channels in biomembrane are presented.

Engineered ion channels as emerging tools for chemical biology

Over the last 25 years, researchers have developed exogenously expressed, genetically engineered, semi-synthetic, and entirely synthetic ion channels. These structures have sufficient fidelity to serve as unique tools that can reveal information about living organisms. One of the most exciting success stories is optogenetics: the use of light-gated channels to trigger action potentials in specific neurons combined with studies of the response from networks of cells or entire live animals. Despite this breakthrough, the use of molecularly engineered ion channels for studies of biological systems is still in its infancy. Historically, researchers studied ion channels in the context of their own function in single cells or in multicellular signaling and regulation. Only recently have researchers considered ion channels and pore-forming peptides as responsive tools to report on the chemical and physical changes produced by other biochemical processes and reactions. This emerging class of molecular probes has a number of useful characteristics. For instance, these structures can greatly amplify the signal of chemical changes: the binding of one molecule to a ligand-gated ion channel can result in flux of millions of ions across a cell membrane. In addition, gating occurs on sub-microsecond time scales, resulting in fast response times. Moreover, the signal is complementary to existing techniques because the output is ionic current rather than fluorescence or radioactivity. And finally, ion channels are also localized at the membrane of cells where essential processes such as signaling and regulation take place. This Account highlights examples, mostly from our own work, of uses of ion channels and pore-forming peptides such as gramicidin in chemical biology. We discuss various strategies for preparing synthetically tailored ion channels that range from de novo designed synthetic molecules to genetically engineered or simply exogenously expressed or reconstituted wild-type channels. Next we consider aspects of experimental design by comparing various membrane environments or systems that make it possible to quantify the response of ion channels to biochemical processes of interest. We present applications of ion channels to answer questions in chemical biology, and propose potential future developments and applications of these single molecule probes. Finally we discuss the hurdles that impede the routine use of ion channel probes in biochemistry and cell biology laboratories and developments and strategies that could overcome these problems. Optogenetics has facilitated breakthroughs in neuroscience, and these results give a dramatic idea of what may lie ahead for designed ion channels as a functional class of molecular probes. If researchers can improve molecular engineering to increase ion channel versatility and can overcome the barriers to collaborating across disciplines, we conclude that these structures could have tremendous potential as novel tools for chemical biology studies.

Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels

Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability.

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.

Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation

Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Metal-assisted channel stabilization: disposition of a single histidine on the N-terminus of alamethicin yields channels with extraordinarily long lifetimes

Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn(2+), suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination.

A semi-synthetic ion channel platform for detection of phosphatase and protease activity

Sensitive methods to probe the activity of enzymes are important for clinical assays and for elucidating the role of these proteins in complex biochemical networks. This paper describes a semi-synthetic ion channel platform for detecting the activity of two different classes of enzymes with high sensitivity. In the first case, this method uses single ion channel conductance measurements to follow the enzyme-catalyzed hydrolysis of a phosphate group attached to the C-terminus of gramicidin A (gA, an ion channel-forming peptide) in the presence of alkaline phosphatase (AP). Enzymatic hydrolysis of this phosphate group removes negative charges from the entrance of the gA pore, resulting in a product with measurably reduced single ion channel conductance compared to the original gA-phosphate substrate. This technique employs a standard, commercial bilayer setup and takes advantage of the catalytic turnover of enzymes and the amplification characteristics of ion flux through individual gA pores to detect picomolar concentrations of active AP in solution. Furthermore, this technique makes it possible to study the kinetics of an enzyme and provides an estimate for the observed rate constant (k(cat)) and the Michaelis constant (K(M)) by following the conversion of the gA-phosphate substrate to product over time in the presence of different concentrations of AP. In the second case, modification of gA with a substrate for proteolytic cleavage by anthrax lethal factor (LF) afforded a sensitive method for detection of LF activity, illustrating the utility of ion channel-based sensing for detection of a potential biowarfare agent. This ion channel-based platform represents a powerful, novel approach to monitor the activity of femtomoles to picomoles of two different classes of enzymes in solution. Furthermore, this platform has the potential for realizing miniaturized, cost-effective bioanalytical assays that complement currently established assays.

Determinants of water permeability through nanoscopic hydrophilic channels

Naturally occurring pores show a variety of polarities and sizes that are presumably directly linked to their biological function. Many biological channels are selective toward permeants similar or smaller in size than water molecules, and therefore their pores operate in the regime of single-file water pores. Intrinsic factors affecting water permeability through such pores include the channel-membrane match, the structural stability of the channel, the channel geometry and channel-water affinity. We present an extensive molecular dynamics study on the role of the channel geometry and polarity on the water osmotic and diffusive permeability coefficients. We show that the polarity of the naturally occurring peptidic channels is close to optimal for water permeation, and that the water mobility for a wide range of channel polarities is essentially length independent. By systematically varying the geometry and polarity of model hydrophilic pores, based on the fold of gramicidin A, the water density, occupancy, and permeability are studied. Our focus is on the characterization of the transition between different permeation regimes in terms of the structure of water in the pores, the average pore occupancy and the dynamics of the permeating water molecules. We show that a general relationship between osmotic and diffusive water permeability coefficients in the single-file regime accounts for the time averaged pore occupancy, and that the dynamics of the permeating water molecules through narrow non single file channels effectively behaves like independent single-file columns.

Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels

The effect of channel length on the barrier for potassium ion permeation through single-file channels has been studied by means of all-atom molecular dynamics simulations. Using series of peptidic gramicidin-like and simplified ring-structured channels, both embedded in model membranes, we obtained two distinct types of behavior: saturation of the central free energy barriers for peptidic channels and a linear increase in simplified ring-structured channels with increasing channel length. The saturation of the central free energy barrier for the peptidic channels occurs at relatively short lengths, and it is correlated with the desolvation from the bulk water. Remarkably, decomposition of free energy barriers into enthalpic and entropic terms reveals an entropic cost for ion permeation. Furthermore, this entropic cost dominates the ion permeation free energy barrier, since the corresponding free energy contribution is higher than the enthalpic barrier. We conclude that the length dependence of the free energy is enthalpy-dominated, but the entropy is the major contribution to the permeation barrier. The decrease in rotational water motion and the reduction of channel mobility are putative origins for the overall entropic penalty.

Using ion channel-forming peptides to quantify protein-ligand interactions

This paper proposes a method for sensing affinity interactions by triggering disruption of self-assembly of ion channel-forming peptides in planar lipid bilayers. It shows that the binding of a derivative of alamethicin carrying a covalently attached sulfonamide ligand to carbonic anhydrase II (CA II) resulted in the inhibition of ion channel conductance through the bilayer. We propose that the binding of the bulky CA II protein (MW approximately 30 kD) to the ion channel-forming peptides (MW approximately 2.5 kD) either reduced the tendency of these peptides to self-assemble into a pore or extracted them from the bilayer altogether. In both outcomes, the interactions between the protein and the ligand lead to a disruption of self-assembled pores. Addition of a competitive inhibitor, 4-carboxybenzenesulfonamide, to the solution released CA II from the alamethicin-sulfonamide conjugate and restored the current flow across the bilayer by allowing reassembly of the ion channels in the bilayer. Time-averaged recordings of the current over discrete time intervals made it possible to quantify this monovalent ligand binding interaction. This method gave a dissociation constant of approximately 2 microM for the binding of CA II to alamethicin-sulfonamide in the bilayer recording chamber: this value is consistent with a value obtained independently with CA II and a related sulfonamide derivative by isothermal titration calorimetry.

Increasing pH Causes Faster Anion- and Cation-Transport Rates through a Synthetic Ion Channel

Ion-channel mimics are able to transmit electrical signals across phospholipid membranes, and can be envisioned as nanoswitches for molecular electronics. Here, we reported the use of pH to alter ion-transport rates through a synthetic aminocyclodextrin ion channel. Both cation- and anion-transport rates were found to increase with an increase in pH due to the unique electrostatics of the multiple ammonium groups that line the channel pore. Such pH regulation of ion transport rates is unique and can be exploited for sensing applications.

Transmission of extramembrane conformational change into current: construction of metal-gated ion channel

Interaction with Fe(III) induces the reversible conformational switch of the extramembrane segment in the artificial receptor channel, which is transmitted into membranes as an increase in channel current (ion flux).

Ligand-induced extramembrane conformation switch controlling alamethicin assembly and the channel current

In this review, we describe our approach to creating artificial receptor-channel proteins or sensor systems, using an extramembrane segment conformationally switchable by external stimuli. Alamethicin is known to self-assemble in membranes to form ion channels with various open states. Employment of an alpha-helical leucine-zipper segment resulted in the effective modulation of the association states of alamethicin to produce a single predominant channel-open state. A decrease in the helical content of the extramembrane segments was found to induce a channel-current increase. Therefore, conformational changes in the extramembrane segments induced by the interaction with ligands can be reflected in the current levels.

Designing nanosensors based on charged derivatives of gramicidin A

Detection of chemical processes on a single molecule scale is the ultimate goal of sensitive analytical assays. We recently reported the possibility to detect chemical modifications on individual molecules by monitoring a change in the single ion channel conductance of derivatives of gramicidin A (gA) upon reaction with analytes in solution. These peptide-based nanosensors detect reaction-induced changes in the charge of gA derivatives that were engineered to carry specific functional groups near their C-terminus.1 Here, we discuss five key design parameters to optimize the performance of such chemomodulated ion channel sensors. In order to realize an effective sensor that measures changes in charge of groups attached to the C-terminus of a gA pore, the following conditions should be fulfilled: (1) the change in charge should occur as close to the entrance of the pore as possible; (2) the charge before and after reaction should be well-defined within the operational pH range; (3) the ionic strength of the recording buffer should be as low as possible while maintaining a detectable flow of ions through the pore; (4) the applied transmembrane voltage should be as high as possible while maintaining a stable membrane; (5) the lipids in the supporting membrane should either be zwitterionic or charged differently than the derivative of gA. We show that under the condition of high applied transmembrane potential (>100 mV) and low ionic strength of the recording buffer (< or =0.10 M), a change in charge at the entrance of the pore is the dominant requirement to distinguish between two differently charged derivatives of gA; the conductance of the heterodimeric gA pore reported here does not depend on a difference in charge at the exit of the pore. We provide a simple explanation for this asymmetric characteristic based on charge-induced local changes in the concentration of cations near the lipid bilayer membrane. Charge-based ion channel sensors offer tremendous potential for ultrasensitive functional detection since a single chemical modification of each individual sensing element can lead to readily detectable changes in channel conductance.

Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length

We investigated the structural and energetic determinants underlying water permeation through peptidic nanopores, motivated by recent experimental findings that indicate that water mobility in single-file water channels displays nonlinear length dependence. To address the molecular mechanism determining the observed length dependence, we studied water permeability in a series of designed gramicidin-like channels of different length using atomistic molecular dynamics simulations. We found that within the studied range of length the osmotic water permeability is independent of pore length. This result is at variance with textbook models, where the relationship is assumed to be linear. Energetic analysis shows that loss of solvation rather than specific water binding sites in the pore form the main energetic barrier for water permeation, consistent with our dynamics results. For this situation, we propose a modified expression for osmotic permeability that fully takes into account water motion collectivity and does not depend on the pore length. Different schematic barrier profiles are discussed that explain both experimental and computational interpretations, and we propose a set of experiments aimed at validation of the presented results. Implications of the results for the design of peptidic channels with desired permeation characteristics are discussed.

Lipid Bilayer Formation by Contacting Monolayers in a Microfluidic Device for Membrane Protein Analysis

Artificial planar lipid bilayers are a powerful tool for the functional study of membrane proteins, yet they have not been widely used due to their low stability and reproducibility. This paper describes an accessible method to form a planar lipid bilayer, simply by contacting two monolayers assembled at the interface between water and organic solvent in a microfluidic chip. The membrane of an organic solvent containing phospholipids at the interface was confirmed to be a bilayer by the capacitance measurement and by measuring the ion channel signal from reconstituted antibiotic peptides. We present two different designs for bilayer formation. One equips two circular wells connected, in which the water/solvent/water interface was formed by simply injecting a water droplet into each well. Another equips the cross-shaped microfluidic channel. In the latter design, formation of the interface at the sectional area was controlled by external syringe pumps. Both methods are extremely simple and reproducible, especially in microdevices, and will lead to automation and multiple bilayer formation for the high-throughput screening of membrane transport in physiological and pharmaceutical studies.

Redox-regulated ion channel activity of a cysteine-containing gramicidin A analogue

According to recent data, gramicidin A analogues having positively charged amino acid sequences at the C-termini exhibit two types of channel activity in lipid membranes: classical cation-selective channels and large unselective pores. The induction of unselective pores was shown here to strongly depend on the redox state of the membrane-bathing solution, if the gramicidin analogue contained a cysteine residue in the sequence GSGPKKKRKVC attached to the C-terminus. In particular, the addition of H2O2 led to an increase in the transmembrane current and the loss of cationic selectivity on planar bilayer lipid membranes and an increase in the carboxyfluorescein leakage of liposomes. The effect was observed at high concentration of the peptide while was absent at the single-channel level. It was concluded that oxidation led to possible formation of dimers of the peptide, which promoted the formation of large unselective pores.