Synthetic ion channels
Encyclopedia
Synthetic ion channels are de novo chemical compounds that insert into lipid bilayer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...

s, form pores, and allow ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

s to flow from one side to the other. They are man-made analogues of natural ion channel
Ion channel
Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane of cells by allowing the flow of ions down their electrochemical gradient. They are present in the membranes that surround all biological cells...

s, and are thus also known as artificial ion channels. Compared to biological channels, they usually allow fluxes of similar magnitude but are
  1. minuscule in size (less than 5k Dalton vs. > 100k Dalton),
  2. diverse in molecular architecture, and
  3. may rely on diverse supramolecular interactions
    Supramolecular chemistry
    Supramolecular chemistry refers to the area of chemistry beyond the molecules and focuses on the chemical systems made up of a discrete number of assembled molecular subunits or components...

     to pre-form the active, conducting structures.


Synthetic channels, like natural channels, are usually characterized by a combination of single-molecule (e.g., voltage-clamp
Voltage clamp
The voltage clamp is used by electrophysiologists to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. Cell membranes of excitable cells contain many different kinds of ion channels, some of which are voltage gated...

 of planar bilayers
Model lipid bilayer
A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering various sub-cellular structures like the nucleus. A model bilayer can be made with either synthetic or natural lipids. The simplest model systems contain only a single pure...

) and ensemble techniques (flux in vesicles). The study of synthetic ion channels can potentially lead to new single-molecule sensing technologies as well as new therapeutics.

History

While semi-synthetic ion channels, often based on modified peptidic
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...

 channels like gramicidin
Gramicidin
Gramicidin is a heterogeneous mixture of six antibiotic compounds, gramicidins A, B and C, making up 80%, 6%,and 14% respectively, all of which are obtained from the soil bacterial species Bacillus brevis and called collectively gramicidin D. Gramicidin D are linear pentadecapeptides; that is...

, had been prepared since the 1970s, the first attempt to prepare a synthetic ion channel was made in 1982 using a substituted β-cyclodextrin
Cyclodextrin
Cyclodextrins are a family of compounds made up of sugar molecules bound together in a ring ....

. Inspired by gramicidin, this molecule was designed to be a barrel-shaped entity spanning a single leaflet of a bilayer membrane
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...

, becoming "active" only when two molecules in opposite leaflets come together in an end-to-end fashion. While the compound does induce ion-fluxes in vesicles, the data does not unambiguously show channel formation (as opposed to other transport mechanisms; see Mechanism).

With the adoption of voltage clamp
Voltage clamp
The voltage clamp is used by electrophysiologists to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. Cell membranes of excitable cells contain many different kinds of ion channels, some of which are voltage gated...

 technique to synthetic channel research in the early 1990s, researchers were able to observe quantized electrical activities from synthetic molecules, often considered the signature evidence for ion channels. This led to a sustained increase in research activity over the next two decades. In 2009, over 25 peer-reviewed papers were published on the topic, and a series of comprehensive reviews are available.

Characterization and mechanisms

Passive transport
Passive transport
Passive transport means moving biochemicals and other atomic or molecular substances across membranes. Unlike active transport, this process does not involve chemical energy, because, unlike in an active transport, the transport across membrane is always coupled with the growth of entropy of the...

 of ions across a membrane can take place by three main mechanisms: by ferrying, through defects in a disrupted membrane, or through a defined trajectory; these corresponds to ionophore
Ionophore
An ionophore is a lipid-soluble molecule usually synthesized by microorganisms to transport ions across the lipid bilayer of the cell membrane...

, detergent
Detergent
A detergent is a surfactant or a mixture of surfactants with "cleaning properties in dilute solutions." In common usage, "detergent" refers to alkylbenzenesulfonates, a family of compounds that are similar to soap but are less affected by hard water...

, and ion channel
Ion channel
Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane of cells by allowing the flow of ions down their electrochemical gradient. They are present in the membranes that surround all biological cells...

transporters. While synthetic ion channel research attempts to prepare compounds that show conductance via a defined path, the elucidation of mechanism is difficult and seldom unambiguous. The two main methods of characterization both have their drawbacks, and as a consequence, often function is defined but mechanism presumed.

Ensemble, vesicle-based time course

One line of evidence for ion transport comes from macroscopic examination of statistical ensembles. All these techniques use intact vesicles with an entrapped volume, with ion channel activities reported by different spectroscopic
Spectroscopy
Spectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...

 methods.

In a typical case, a dye
Dye
A dye is a colored substance that has an affinity to the substrate to which it is being applied. The dye is generally applied in an aqueous solution, and requires a mordant to improve the fastness of the dye on the fiber....

 is entrapped within the population of vesicles. This dye is selected to be respond colorimetrically
Colorimetry (chemical method)
In physical and analytical chemistry, colorimetry or colourimetry is a technique "used to determine the concentration of colored compounds in solution."...

 or fluorometrically
Fluorescence spectroscopy
Fluorescence spectroscopy aka fluorometry or spectrofluorometry, is a type of electromagnetic spectroscopy which analyzes fluorescence from a sample. It involves using a beam of light, usually ultraviolet light, that excites the electrons in molecules of certain compounds and causes them to emit...

 to the presence of an ion; this ion is typically absent from the inside of the vesicle but present in the outside. Without an ion transporter, the lipid bilayer as a kinetic barrier to block ion flux, and the dye remains "dark" indefinitely.

As an ion transporter allows ions on the outside to diffuse in, its addition will affect the color/fluorescence property of the dye. By macroscopically monitoring the dye's properties over time, and controlling outside factors, the ability of a compound to act as an ion transporter can be measured.

Observing ion transport, however, does not pin down ion channel as the mechanism. Any class of transporter can lead to the same observation, and additional corroborating evidence is usually required. Sophisticated experiments intended to probe selectivity, gating, and other channel parameters have been developed over the past two decades and recently summarized.

Vesicle assay variations

Method Reporter Example
NMR sodium-23 line width Hydraphiles
Fluoroscent HPTS ex/em ratios Oligoesters
pH-stat H+ Crown ether-barrels
Ion-selective electrodes Cl "SCMTR"

Stochastic, planar bilayer-based current traces

An alternative to the ensemble-based method described above is the voltage-clamp experiment. In a voltage-clamp
Voltage clamp
The voltage clamp is used by electrophysiologists to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. Cell membranes of excitable cells contain many different kinds of ion channels, some of which are voltage gated...

 experiment, two compartments of electrolyte
Electrolyte
In chemistry, an electrolyte is any substance containing free ions that make the substance electrically conductive. The most typical electrolyte is an ionic solution, but molten electrolytes and solid electrolytes are also possible....

 are divided by an aperture, usually between 5-250 micrometres in diameter. A lipid bilayer is painted across this aperture, thus electrically separating the compartments; the molecular nature can be ascertained by measuring its capacitance
Capacitance
In electromagnetism and electronics, capacitance is the ability of a capacitor to store energy in an electric field. Capacitance is also a measure of the amount of electric potential energy stored for a given electric potential. A common form of energy storage device is a parallel-plate capacitor...

.

Upon the addition of an (ideal) ion channel, a defined path between the two compartments is formed. Through this pore, ions flow down the potential and electrochemical gradient rapidly (>106/second), the maximum flux limited by the geometry and dimensions of the pore. At some later instant the pore may close or collapse, whereupon the current returns to zero. This open-state current, originating and amplified from a single-molecule event, is typically on the order of pA to nA, with time-resolution of approx. millisecond. Ideal or close-to-ideal events is termed "square-tops" in the literature, and have been considered as signature for a channel-based mechanism.

It is notable that the events observed at this scale are truly stochastic
Stochastic
Stochastic refers to systems whose behaviour is intrinsically non-deterministic. A stochastic process is one whose behavior is non-deterministic, in that a system's subsequent state is determined both by the process's predictable actions and by a random element. However, according to M. Kac and E...

 - that is, they are the result of random molecular collision and conformation changes. As the membrane area is much larger than that of a pore, multiple copies may open and close independently of one another, giving rise to the stair-case like appearance (Panel C in figure); these ideal events are often modelled as Markov process
Markov process
In probability theory and statistics, a Markov process, named after the Russian mathematician Andrey Markov, is a time-varying random phenomenon for which a specific property holds...

es.

By using the activity grid notation, synthetic ion channels studied with the voltage-clamp method during the period 1982-2010 have been critically reviewed. While the ideal traces are most frequently analyzed and reported in the literature, many records are decidedly non-ideal, with a subset was shown to be fractal. Developing methods for analyzing these non-ideal traces and clarifying their relationship to transport mechanism is an area of contemporary research.

Examples

A diverse and large pool of synthetic molecules have been reported to act as ion transporters in lipid membranes. A selection is described here to demonstrate the breadth of feasible structures and attainable functions. Comprehensive reviews for the literature up to 2010 are available in a tripartite series.

By chemical structure

Most (but not all; see minimalist channels) synthetic channels have chemical structures substantially larger than typical small molecules (molecular weights ~1-5kDa). This originates from the need to be amphiphilic, that is, have both sufficient hydrophobic portions to allow partitioning into lipid bilayer, as well as polar or charged "headgroups" to assert a defined orientation and geometry with respect to the membrane.
Crown ethers-based

Calixarene-based

Ion channels containing calixarene
Calixarene
A calixarene is a macrocycle or cyclic oligomer based on a hydroxyalkylation product of a phenol and an aldehyde. The word calixarene is derived from calix or chalice because this type of molecule resembles a vase and from the word arene that refers to the aromatic building block...

s of ring size 3 and 4 have both been reported. For calix[4]arene, two conformations are accessible, and examples of both 1,3-alt and cone conformation have been developed.
Cyclodextrin-based

The first synthetic ion channel was constructed by partial substitution on the primary rim of β-cyclodextrin
Cyclodextrin
Cyclodextrins are a family of compounds made up of sugar molecules bound together in a ring ....

. Other substituted β-cyclodextrins have since been reported, including an anion-selective oligobutylene channel and various poly-ethyleneoxide linked starburst oligomers. Structure-activity relationships for a large suite of cyclodextrin "half-channels" prepared by "click"-chemistry
Click chemistry
Click chemistry is a chemical philosophy introduced by K. Barry Sharpless of The Scripps Research Institute, in 2001 and describes chemistry tailored to generate substances quickly and reliably by joining small units together...

 has been recently reported.

Peptide-based

Alternating D/L peptide macrocycles are known to self-aggregate into nanotubes, and the resulting nanotubes have been shown to act as ion channels in lipid membranes.
Other architectures use peptide helices as a scaffold to attach other functionalities, such as crown ethers of different sizes. The property of these peptide-crown channels depend strongly on the identity of the capping end-groups.

Hybrid bio-channels

Semi-synthetic bio-hybrid channels constructed by modifications of natural ion channels had been constructed. Leveraging modern synthetic organic chemistry
Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation of carbon-based compounds, hydrocarbons, and their derivatives...

, these allows pinpoint modifications of existing structures to either elucidate their transport mechanisms or to graft on new functionalities.
Gramicidin
Gramicidin
Gramicidin is a heterogeneous mixture of six antibiotic compounds, gramicidins A, B and C, making up 80%, 6%,and 14% respectively, all of which are obtained from the soil bacterial species Bacillus brevis and called collectively gramicidin D. Gramicidin D are linear pentadecapeptides; that is...

 and alamethicin
Alamethicin
Alamethicin is a peptide antibiotic, produced by the fungus Trichoderma viride. It contains the non-proteinogenic amino acid 2-aminoisobutyric acid , which strongly induces helical peptide structures...

 had been popular starting points for selective modifications. The above diagram illustrates one example, where a crown-ether was fixed across the mouth of the ion-passing portal. This channel shows discrete conductance but different ion selectivity than wild type
Wild type
Wild type refers to the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard, "normal" allele at a locus, in contrast to that produced by a non-standard, "mutant" allele...

 gramicidin in voltage-clamp experiments.

While modification of large protein channels using mutagenesis
Mutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...

 are generally considered out of the scope of synthetic channels, the demarcation is not sharp, as supramolecular or covalent bonding of cyclodextrins to alpha-hemolysin demonstrates.

By transport characteristics

An ion channel can be characterized by its opening characteristics, ion selectivity, and control of flux (gating). Many synthetic ion channels show unique properties in one or more of these aspects.

Opening characteristics

An "ion-channel forming" molecule can often show multiple types of conductance activities in planar bilayer membranes. Each of these modes of action can be characterized by their
  • open duration (sub-ms---hours) , related to whether the active structure is kinetically labile,
  • unit conductance (pS---nS), related to the geometry of the active structure, and
  • open probability, a fraction related to the thermodynamic stability of that active structure relative to inactive forms.


These events are not necessarily uniform throughout their durations, and as a result a variety of shapes of conducting traces are possible.

Ion selectivity

The majority of synthetic ion channels follow an Eisenman I sequence (Cs+ > Rb+ > K+ > Na+ >> Li+) in their selectivity for alkali metal
Alkali metal
The alkali metals are a series of chemical elements in the periodic table. In the modern IUPAC nomenclature, the alkali metals comprise the group 1 elements, along with hydrogen. The alkali metals are lithium , sodium , potassium , rubidium , caesium , and francium...

 cations, suggesting that the origin of the selectivity is governed by the difference in energy required to remove water from a fully hydrated cation. A few synthetic channels show other patterns of ion selectivity, and only a single instance in which a synthetic channel following the opposite selectivity sequence (Eisenman XI; Cs+ < Rb+ < K+ < Na+ << Li+) had been reported.

Voltage response

Most synthetic channels are Ohm
Ohm
The ohm is the SI unit of electrical resistance, named after German physicist Georg Simon Ohm.- Definition :The ohm is defined as a resistance between two points of a conductor when a constant potential difference of 1 volt, applied to these points, produces in the conductor a current of 1 ampere,...

ic in conductance, that is, the current passed (both individually and as an ensemble) is proportional to the potential across the membrane. Some rare channels, however, show current-voltage characteristics that is non-linear. Specifically, two different types of non-Ohmic conductance are known:
  1. a rectifying behaviour, where current passes depends on the sign of the applied potential, and
  2. a exponential potential dependence, where the current passed scales exponentially with the applied potential.


The former requires asymmetry with respect to the mid-plane of the lipid bilayer, and is realized often by introducing an overall molecular dipole. The latter, demonstrated in natural channels such as alamethicin
Alamethicin
Alamethicin is a peptide antibiotic, produced by the fungus Trichoderma viride. It contains the non-proteinogenic amino acid 2-aminoisobutyric acid , which strongly induces helical peptide structures...

, is rarely encountered in synthetic ion channels. They may be related to lipid ion channels, but to date their mechanism remains elusive.
Ligand response

Certain synthetic ion channels have conductances that can be modulated by additional of external chemicals. Both up-modulation (channels are turned on by ligand) and down-modulation (channels are turned off by ligands) are known: different mechanisms, including formation of supramolecular aggregates, as well as inter- and intramolecular blockage.
Others

Regulatory elements that responds to other signals are known; examples include photomodulated conductances as well as "thermal switches" constructed by isomerization of the carbamate group. To date, no mechanosensitive synthetic ion channels have been reported.

See also

  • Nanotechnology
    Nanotechnology
    Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...

  • Supramolecular chemistry
    Supramolecular chemistry
    Supramolecular chemistry refers to the area of chemistry beyond the molecules and focuses on the chemical systems made up of a discrete number of assembled molecular subunits or components...

  • Macrocycle
    Macrocycle
    A macrocycle is, as defined by IUPAC, "a cyclic macromolecule or a macromolecular cyclic portion of a molecule." In the chemical literature, organic chemists may consider any molecule containing a ring of nine or more atoms to be a macrocycle...

    s
  • Amphiphile
  • Ionophore
    Ionophore
    An ionophore is a lipid-soluble molecule usually synthesized by microorganisms to transport ions across the lipid bilayer of the cell membrane...

  • Membrane biophysics
    Membrane biophysics
    Membrane biophysics is the study of biological membranes using physical, computational, mathematical, and biophysical methods....

  • Membrane protein
    Membrane protein
    A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.-Function:...

  • Voltage-gated ion channel
    Voltage-gated ion channel
    Voltage-gated ion channels are a class of transmembrane ion channels that are activated by changes in electrical potential difference near the channel; these types of ion channels are especially critical in neurons, but are common in many types of cells....

  • Pore-forming toxin
  • Antimicrobial peptides
    Antimicrobial peptides
    Antimicrobial peptides are an evolutionarily conserved component of the innate immune response and are found among all classes of life. Fundamental differences exist between prokaryotic and eukaryotic cells that may represent targets for antimicrobial peptides...

  • Electrophysiology
    Electrophysiology
    Electrophysiology is the study of the electrical properties of biological cells and tissues. It involves measurements of voltage change or electric current on a wide variety of scales from single ion channel proteins to whole organs like the heart...

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