Synthetic ion channels

File:Tabushi channel.svg

While semi-synthetic ion channels, often based on modified peptidic channels like gramicidin, had been prepared since the 1970s, the first attempt to prepare a synthetic ion channel was made in 1982 using a substituted β-cyclodextrin.{{cite journal | title=A,C,D,F-tetrasubstituted β-cyclodextrin as an artificial channel compound. |author1=Tabushi, Iwao |author2=Kuroda, Yasuhisa |author3=Yokota, Kanichi. | journal=Tetrahedron Letters | year=1982 | volume=23 | issue=44 | pages=4601–4604 | doi = 10.1016/S0040-4039(00)85664-6 }}

Inspired by gramicidin, this molecule was designed to be a barrel-shaped entity spanning a single leaflet of a bilayer membrane, 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).

Na⁺ transport by such channels was first reported by two groups of investigators in 1989–1990.V. E. Carmichael, P. J. Dutton, T. M. Fyles, T. D. James, J. A. Swan, M. Zojaji Biomimetic ion transport: a functional model of a unimolecular ion channel J. Am. Chem. Soc., 1989, 111, 767–769.A. Nakano, Q. Xie, J. V. Mallen, L. Echegoyen, G. W. Gokel Synthesis of a membrane-insertable, sodium cation conducting channel: kinetic analysis by dynamic sodium-23 NMR J. Am. Chem. Soc., 1990, 112, 1287–1289.G. W. Gokel, I. A. Carasel Biologically active, synthetic ion transporters Chem. Soc. Rev., 2007, 36, 378.

With the adoption of voltage clamp 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,{{cite web | url=http://www.jkwchui.com/science/synthetic-ion-channel-bibliography/ | title=Synthetic Ion Channel Bibliography | year=2011 | accessdate=April 21, 2011 | author=Chui, JKW | archive-url=https://web.archive.org/web/20110621040537/http://www.jkwchui.com/science/synthetic-ion-channel-bibliography/ | archive-date=June 21, 2011 | url-status=dead }} and a series of comprehensive reviews are available.

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File:Ion-transport mechanisms.svg

Passive transport 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, detergent, and ion channel 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.

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File:Vesicle technique.svg

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 methods.

In a typical case, a dye is entrapped within the population of vesicles. This dye is selected to be respond colorimetrically or fluorometrically 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.

File:Voltage-clamp-concept.svg

An alternative to the ensemble-based method described above is the voltage-clamp experiment.{{cite book | title=Ion Channels: A Practical Approach | publisher=Oxford University Press | author=Ashley, R. H. | year=1995 | location=Oxford | pages=302 | isbn=978-0-19-963474-3}} In a voltage-clamp experiment, two compartments of electrolyte 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.

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 - 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 staircase like appearance (Panel C in figure); these ideal events are often modelled as Markov processes.

By using the activity grid notation,{{cite book | title=A New Paradigm for the Voltage-Clamp Studies of Synthetic Ion Channels | publisher=University of Victoria | author=Chui, J. K. W. | year=2011 | location=Victoria BC, Canada | pages=927}} synthetic ion channels studied with the voltage-clamp method during the period 1982-2010 have been critically reviewed.{{cite journal | url=http://pubs.rsc.org/en/content/articlelanding/2011/CS/C1CS15099E | title=Ionic conductance of synthetic channels: analysis, lessons, and recommendations |author1=Chui, J. K. W. |author2=Fyles, T. M. | journal=Chemical Society Reviews |date=June 2011 | doi=10.1039/C1CS15099E | pmid=21691671 | volume=41 | issue=1 | pages=148–175| url-access=subscription }} 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.{{cite journal | title=Apparent fractal distribution of open durations in cyclodextrin-based ion channels |author1=Chui, J. K. W. |author2=Fyles, T. M. | journal=Chem. Comm. |date=May 2010 | volume=46 | issue=23 | pages=4169–4171 | doi=10.1039/C0CC00366B| pmid=20454723 }} Developing methods for analyzing these non-ideal traces and clarifying their relationship to transport mechanism is an area of contemporary research.

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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.

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.

File:FylesCrownBarrel.svg

File:Hydraphiles (synthetic ion channels).svg

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Ion channels containing calixarenes 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.

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File:CDchannels.svg

The first synthetic ion channel was constructed by partial substitution on the primary rim of β-cyclodextrin. Other substituted β-cyclodextrins have since been reported, including thiol-modified cyclodextrins,{{cite journal | title=Ionic Channel Behavior of Modified Cyclodextrins Inserted in Lipid Membranes |author1=Bacri, Laurent |author2=Benkhaled, Amal |author3=Guégan, Philippe |author4=Auvray, Loïc | journal=Langmuir |date=May 2005 | volume=21 | issue=13 | pages=5842–5846 | doi=10.1021/la047211s |pmid=15952831 }} an anion-selective oligobutylene channel,{{cite journal | title=A Highly Active Anion-Selective Aminocyclodextrin Ion Channel |author1=Madhavan, Nandita |author2=Robert, Erin C. |author3=Gin, Mary S. | journal=Angewandte Chemie International Edition |date=November 2005 | volume=44 | issue=46 | pages=7584–7587 | doi=10.1002/anie.200501625 | pmid=16247816}} and various poly-ethyleneoxide linked starburst oligomers.{{cite journal | title=Synthesis of Half-Channels by the Anionic Polymerization of Ethylene Oxide Initiated by Modified Cyclodextrin |author1=Badi, Nezha |author2=Auvray, Loïc |author3=Guégan, Philippe | journal=Advanced Materials |date=October 2009 | volume=21 | issue=40 | pages=4054–4057 | doi=10.1002/adma.200802982|bibcode=2009AdM....21.4054B |s2cid=96554181 }} Structure-activity relationships for a large suite of cyclodextrin "half-channels" prepared by "click"-chemistry has been recently reported.

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File:GhadiriStack.svg

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.

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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.

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Semi-synthetic bio-hybrid channels constructed by modifications of natural ion channels had been constructed. Leveraging modern synthetic organic chemistry, these allows pinpoint modifications of existing structures to either elucidate their transport mechanisms or to graft on new functionalities.

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Gramicidin and alamethicin had been popular starting points for selective modifications.{{cite journal | title=Alamethicin−Leucine Zipper Hybrid Peptide: A Prototype for the Design of Artificial Receptors and Ion Channels |author1=Shiroh Futaki |author2=Masayuki Fukuda |author3=Masayuki Omote |author4=Kayoko Yamauchi |author5=Takeshi Yagami |author6=Mineo Niwa |author7=Yukio Sugiura |name-list-style=amp | journal=Journal of the American Chemical Society | year=2001 | volume=123 | issue=49 | pages=12127–12134 | doi=10.1021/ja011166i|pmid=11734010 |bibcode=2001JAChS.12312127F }} The above diagram illustrates one example, where a crown-ether was fixed across the mouth of the ion-passing portal.{{cite journal | title=Crown Ether–Gramicidin Hybrid Ion Channels: Dehydration-Assisted Ion Selectivity |author1=Jochen R. Pfeifer |author2=Philipp Reiß |author3=Ulrich Koert | journal=Angewandte Chemie International Edition | year=2005 | volume=45 | issue=3 | pages=501–504 | doi=10.1002/anie.200502570 | pmid=16342124}} This channel shows discrete conductance but different ion selectivity than wild type gramicidin in voltage-clamp experiments.

While modification of large protein channels using mutagenesis 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.{{cite journal | title=Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores |author1=Arijit Banerjee |author2=Ellina Mikhailova |author3=Stephen Cheley |author4=Li-Qun Gu |author5=Michelle Montoya |author6=Yasuo Nagaoka |author7=Eric Gouaux |author8=Hagan Bayley |name-list-style=amp | journal=PNAS |date=May 2010 | volume=107 | issue=18 | pages=8165–8170 | doi=10.1073/pnas.0914229107|bibcode = 2010PNAS..107.8165B | pmid=20400691 | pmc=2889592|doi-access=free }}

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.

File:Varieties of Voltage Clamp Traces.png

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.

The majority of synthetic ion channels follow an Eisenman I sequence (Cs⁺ > Rb⁺ > K⁺ > Na⁺ >> Li⁺){{cite journal | title=Ionic selectivity revisited: The role of kinetic and equilibrium processes in ion permeation through channels |author1=Eisenman, George |author2=Horn, Richard | journal=Journal of Membrane Biology | year=1983 | volume=76 | issue=3 | pages=197–225 | doi=10.1007/BF01870364|pmid=6100862 |s2cid=26390118 }} in their selectivity for alkali metal 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.{{cite journal | title=Synthetic Ion Channel Based on Metal–Organic Polyhedra |author1=Jung, Minseon |author2=Kim, Hyunuk |author3=Baek, Kangkyun |author4=Kim, Kimoon |author-link4= Kim Kimoon | journal=Angewandte Chemie International Edition |date=June 2008 | volume=47 | issue=31 | pages=5755–5757 | doi=10.1002/anie.200802240 | pmid=18576447}}

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File:IVPossibilities.svg

Most synthetic channels are Ohmic 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. an 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.{{cite journal | title=Voltage-Dependent Formation of Anion Channels by Synthetic Rigid-Rod Push–Pull β-Barrels |author1=Naomi Sakai |author2=David Houdebert |author3=Stefan Matile | journal=Chemistry: A European Journal |date=December 2002 | volume=9 | issue=1 | pages=223–232 | doi=10.1002/chem.200390016|pmid=12506379 }}{{cite journal | title=Artificial Ion Channels Showing Rectified Current Behavior |author1=Chigusa Goto |author2=Mika Yamamura |author3=Akiharu Satake |author4=Yoshiaki Kobuke |name-list-style=amp | journal=Journal of the American Chemical Society | year=2001 | volume=123 | issue=49 | pages=12152–12159 | doi=10.1021/ja010761h|pmid=11734013 |bibcode=2001JAChS.12312152G }}{{cite journal | title=A Voltage-Gated Ion Channel Based on a Bis-Macrocyclic Bolaamphiphile |author1=T. M. Fyles |author2=D. Loock |author3=X. Zhou |name-list-style=amp | journal=Journal of the American Chemical Society | year=1998 | volume=120 | issue=13 | pages=2997–3003 | doi=10.1021/ja972648q|bibcode=1998JAChS.120.2997F }} The latter, demonstrated in natural channels such as alamethicin, is rarely encountered in synthetic ion channels. They may be related to lipid ion channels, but to date their mechanism remains elusive.

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,{{cite journal | title=Ligand-Gated Synthetic Ion Channels |author1=Talukdar, Pinaki |author2=Bollot, Guillaume |author3=Mareda, Jiri |author4=Sakai, Naomi |author5=Matile, Stefan | journal=Chemistry: A European Journal |date=August 2005 | volume=11 | issue=22 | pages=6525–6532 | doi=10.1002/chem.200500516|pmid=16118825 }}{{cite journal | title=Palladium(II)-gated ion channels |author1=Wilson, C. P. |author2=Webb, S. J. |s2cid=27837694 | journal=Chem. Comm. |date=July 2008 | pages=4007–4009 | doi=10.1039/B809087D | issue=34|pmid=18758608 }} as well as inter- and intramolecular{{cite journal | title=Voltage-dependent behavior of a "ball-and-chain" gramicidin channel |author1=G A Woolley |author2=V Zunic |author3=J Karanicolas |author4=A S Jaikaran |author5=A V Starostin |name-list-style=amp | journal=Biophysical Journal |date=November 1997 | volume=73 | issue=5 | pages=2465–2475 | doi = 10.1016/S0006-3495(97)78275-4 | pmc=1181148 | pmid=9370440|bibcode = 1997BpJ....73.2465W }} blockage.

Regulatory elements that responds to other signals are known; examples include photomodulated conductances{{cite journal | title=A Light-Gated Synthetic Ion Channel |author1=Parag V. Jog |author2=Mary S. Gin |name-list-style=amp | journal=Organic Letters | year=2008 | volume=10 | issue=17 | pages=3693–3696 | doi=10.1021/ol8013045|pmid = 18656946}}{{cite journal | title=Optical Switching of Ion−Dipole Interactions in a Gramicidin Channel Analogue |author1=Vitali Borisenko |author2=Darcy C. Burns |author3=Zhihua Zhang |author4=G. Andrew Woolley |name-list-style=amp | journal=Journal of the American Chemical Society |date=June 2000 | volume=122 | issue=27 | pages=6343–6370 | doi=10.1021/ja000736w|bibcode=2000JAChS.122.6364B }}{{cite journal | title=Engineering Light-Gated Ion Channels |author1=Matthew R. Banghart |author2=Matthew Volgraf |author3=Dirk Trauner | authorlink3 = Dirk Trauner | name-list-style=amp | journal=Biochemistry | year=2006 | volume=45 | issue=51 | pages=15129–15141 | doi=10.1021/bi0618058 | pmid=17176035|citeseerx = 10.1.1.70.6273}} as well as "thermal switches" constructed by isomerization of the carbamate group.{{cite journal | title=Design of Regulated Ion Channels Using Measurements of Cis-Trans Isomerization in Single Molecules |author1=G. Andrew Woolley |author2=Anna S. I. Jaikaran |author3=Zhihua Zhang |author4=Shuyun Peng | journal=Journal of the American Chemical Society | year=1995 | volume=117 | issue=16 | pages=4448–4454 | doi=10.1021/ja00121a002|bibcode=1995JAChS.117.4448W }} To date, no mechanosensitive synthetic ion channels have been reported.

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• Nanotechnology
• Supramolecular chemistry
• Macrocycles
• Amphiphile
• Ionophore
• Membrane biophysics
• Membrane protein
• Voltage-gated ion channel
• Pore-forming toxin
• Antimicrobial peptides
• Electrophysiology

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Category:Supramolecular chemistry

Category:Molecular biology

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Category:Ion channels

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