Neurotransmitter-gated ion-channel transmembrane region
Ligand-gated ion channel
Identifiers
Symbol	Neur_chan_memb
Pfam	PF02932
InterPro	IPR006029
PROSITE	PDOC00209
SCOP	1cek
SUPERFAMILY	1cek
TCDB	1.A.9
OPM superfamily	14
OPM protein	2bg9
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

1. Ion-channel-linked receptor
2. Ions
3. Ligand (such as acetylcholine)

When ligands bind to the receptor, the ion channel portion of the receptor opens, allowing ions to pass across the cell membrane.

Ligand-gated ion channels (LICs, LGIC), also commonly referred as ionotropic receptors, are a group of transmembrane ion-channel proteins which open to allow ions such as Na⁺, K⁺, Ca²⁺, and/or Cl⁻ to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand), such as a neurotransmitter.^[1][2][3]

When a presynaptic neuron is excited, it releases a neurotransmitter from vesicles into the synaptic cleft. The neurotransmitter then binds to receptors located on the postsynaptic neuron. If these receptors are ligand-gated ion channels, a resulting conformational change opens the ion channels, which leads to a flow of ions across the cell membrane. This, in turn, results in either a depolarization, for an excitatory receptor response, or a hyperpolarization, for an inhibitory response.

These proteins are typically composed of at least two different domains: a transmembrane domain which includes the ion pore, and an extracellular domain which includes the ligand binding location (an allosteric binding site). This modularity has enabled a 'divide and conquer' approach to finding the structure of the proteins (crystallising each domain separately). The function of such receptors located at synapses is to convert the chemical signal of presynaptically released neurotransmitter directly and very quickly into a postsynaptic electrical signal. Many LICs are additionally modulated by allosteric ligands, by channel blockers, ions, or the membrane potential. LICs are classified into three superfamilies which lack evolutionary relationship: cys-loop receptors, ionotropic glutamate receptors and ATP-gated channels.

Cys-loop receptors

Nicotinic acetylcholine receptor in closed state with predicted membrane boundaries shown, PDB 2BG9

The cys-loop receptors are named after a characteristic loop formed by a disulfide bond between two cysteine residues in the N terminal extracellular domain. They are part of a larger family of pentameric ligand-gated ion channels that usually lack this disulfide bond, hence the tentative name "Pro-loop receptors".^[4][5] A binding site in the extracellular N-terminal ligand-binding domain gives them receptor specificity for (1) acetylcholine (AcCh), (2) serotonin, (3) glycine, (4) glutamate and (5) γ-aminobutyric acid (GABA) in vertebrates. The receptors are subdivided with respect to the type of ion that they conduct (anionic or cationic) and further into families defined by the endogenous ligand. They are usually pentameric with each subunit containing 4 transmembrane helices constituting the transmembrane domain, and a beta sheet sandwich type, extracellular, N terminal, ligand binding domain.^[6] Some also contain an intracellular domain like shown in the image.

The prototypic ligand-gated ion channel is the nicotinic acetylcholine receptor. It consists of a pentamer of protein subunits (typically ααβγδ), with two binding sites for acetylcholine (one at the interface of each alpha subunit). When the acetylcholine binds it alters the receptor's configuration (twists the T2 helices which moves the leucine residues, which block the pore, out of the channel pathway) and causes the constriction in the pore of approximately 3 angstroms to widen to approximately 8 angstroms so that ions can pass through. This pore allows Na⁺ ions to flow down their electrochemical gradient into the cell. With a sufficient number of channels opening at once, the inward flow of positive charges carried by Na⁺ ions depolarizes the postsynaptic membrane sufficiently to initiate an action potential.

While single-cell organisms like bacteria would have little apparent need for the transmission of an action potential, a bacterial homologue to an LIC has been identified, hypothesized to act nonetheless as a chemoreceptor.^[4] This prokaryotic nAChR variant is known as the GLIC receptor, after the species in which it was identified; Gloeobacter Ligand-gated Ion C channel.

Structure

Cys-loop receptors have structural elements that are well conserved, with a large extracellular domain (ECD) harboring an alpha-helix and 10 beta-strands. Following the ECD, four transmembrane segments (TMSs) are connected by intracellular and extracellular loop structures.^[7] Except the TMS 3-4 loop, their lengths are only 7-14 residues. The TMS 3-4 loop forms the largest part of the intracellular domain (ICD) and exhibits the most variable region between all of these homologous receptors. The ICD is defined by the TMS 3-4 loop together with the TMS 1-2 loop preceding the ion channel pore.^[7] Crystallization has revealed structures for some members of the family, but to allow crystallization, the intracellular loop was usually replaced by a short linker present in prokaryotic cys-loop receptors, so their structures as not known. Nevertheless, this intracellular loop appears to function in desensitization, modulation of channel physiology by pharmacological substances, and posttranslational modifications. Motifs important for trafficking are therein, and the ICD interacts with scaffold proteins enabling inhibitory synapse formation.^[7]

Cationic cys-loop receptors

Anionic cys-loop receptors

Ionotropic glutamate receptors

The AMPA receptor bound to a glutamate antagonist showing the amino terminal, ligand binding, and transmembrane domain, PDB 3KG2

The ionotropic glutamate receptors bind the neurotransmitter glutamate. They form tetramers with each subunit consisting of an extracellular amino terminal domain (ATD, which is involved tetramer assembly), an extracellular ligand binding domain (LBD, which binds glutamate), and a transmembrane domain (TMD, which forms the ion channel). The transmembrane domain of each subunit contains three transmembrane helices as well as a half membrane helix with a reentrant loop. The structure of the protein starts with the ATD at the N terminus followed by the first half of the LBD which is interrupted by helices 1,2 and 3 of the TMD before continuing with the final half of the LBD and then finishing with helix 4 of the TMD at the C terminus. This means there are three links between the TMD and the extracellular domains. Each subunit of the tetramer has a binding site for glutamate formed by the two LBD sections forming a clamshell like shape. Only two of these sites in the tetramer need to be occupied to open the ion channel. The pore is mainly formed by the half helix 2 in a way which resembles an inverted potassium channel.

AMPA receptor

The AMPA receptor bound to a glutamate antagonist showing the amino terminal, ligand binding, and transmembrane domain, PDB 3KG2

The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (also known as AMPA receptor, or quisqualate receptor) is a non-NMDA-type ionotropic transmembrane receptor for glutamate that mediates fast synaptic transmission in the central nervous system (CNS). Its name is derived from its ability to be activated by the artificial glutamate analog AMPA. The receptor was first named the "quisqualate receptor" by Watkins and colleagues after a naturally occurring agonist quisqualate and was only later given the label "AMPA receptor" after the selective agonist developed by Tage Honore and colleagues at the Royal Danish School of Pharmacy in Copenhagen.^[10] AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The AMPA receptor GluA2 (GluR2) tetramer was the first glutamate receptor ion channel to be crystallized.

AMPA receptor trafficking

Ligands:

• Agonists: Glutamate, AMPA, 5-Fluorowillardiine, Domoic acid, Quisqualic acid, etc.
• Antagonists: CNQX, Kynurenic acid, NBQX, Perampanel, Piracetam, etc.
• Positive allosteric modulators: Aniracetam, Cyclothiazide, CX-516, CX-614, etc.
• Negative allosteric modulators: Ethanol, Perampanel, Talampanel, GYKI-52,466, etc.

NMDA receptors

Stylized depiction of an activated NMDAR

The N-methyl-D-aspartate receptor (NMDA receptor) – a type of ionotropic glutamate receptor – is a voltage-dependent ligand-gated ion channel that is gated by the simultaneous binding of glutamate and a co-agonist (i.e., either D-serine or glycine).^[11] Studies show that the NMDA receptor is involved in regulating synaptic plasticity and memory.^[12][13]

The name "NMDA receptor" is derived from the ligand N-methyl-D-aspartate (NMDA), which acts as a selective agonist at these receptors. When the NMDA receptor is activated by the binding of two co-agonists, the cation channel opens, allowing Na⁺ and Ca²⁺ to flow into the cell, in turn raising the cell's electric potential. Thus, the NMDA receptor is an excitatory receptor. At resting potentials, the binding of Mg²⁺ or Zn²⁺ at their extracellular binding sites on the receptor blocks ion flux through the NMDA receptor channel. "However, when neurons are depolarized, for example, by intense activation of colocalized postsynaptic AMPA receptors, the voltage-dependent block by Mg²⁺ is partially relieved, allowing ion influx through activated NMDA receptors. The resulting Ca²⁺ influx can trigger a variety of intracellular signaling cascades, which can ultimately change neuronal function through activation of various kinases and phosphatases".^[14]

Ligands:

• Primary endogenous co-agonists: glutamate and either D-serine or glycine
• Other agonists : aminocyclopropanecarboxylic acid; D-cycloserine; L-aspartate; quinolinate, etc.
• Partial agonists : N-methyl-D-aspartic acid (NMDA); NRX-1074; 3,5-dibromo-L-phenylalanine,^[15] etc.
• Antagonists: ketamine, PCP, dextropropoxyphene, ketobemidone, tramadol, kynurenic acid (endogenous), etc.

GABA receptors

GABA receptors are major inhibitory neurotransmitter expressed in the major interneurons in animal cortex.

GABA_A receptor

GABA_A receptor schematic

GABA_A receptors are ligand-gated ion channels. GABA (gamma-aminobutyric acid), the endogenous ligand for these receptors, is the major inhibitory neurotransmitter in the central nervous system. When activated, it mediates Cl^– flow into the neuron, hyperpolarizing the neuron. GABA_A receptors occur in all organisms that have a nervous system. Due to their wide distribution within the nervous system of mammals, they play a role in virtually all brain functions.^[16]

Various ligands can bind specifically to GABA_A receptors, either activating or inhibiting the Cl^– channel.

Ligands:

• Agonists: GABA, muscimol, progabide, gaboxadol
• Antagonists: bicuculine, gabazine
• Partial agonist: piperidine-4-sulfonic acid

5-HT receptors

3D structure model of the 5-HT1B receptor in complex with ergotamine based on crystallographic data for PDB 4IAR

5-HT receptors, also known as the serotonin receptors, or 5-hydroxytryptamine receptors, are ligand-gated ion channels. They activate an intracellular second messenger cascade to produce an excitatory/inhibitory response. They are found in mammals, both central nervous system (CNS) and peripheral nervous system (PNS), as well as other animals.^[17] Its natural ligand is Serotonin, and it modulates the release of multiple neurotransmitters, such as dopamine, epinephrine/norepinephrine, glutamate, and GABA.
Research confirm that the 5-HT receptors are involved in many neurological processes, such as anxiety, depression, sleep, cognition, memory, and so on. Thus there are several drugs targeting the 5-HT system, including some antidepressants, antipsychotics, anxiolytics, antiemetics, and antimigraine drugs, as well as the psychedelic drugs and empathogens.^[18][19][20]

ATP-gated channels

Figure 1. Schematic representation showing the membrane topology of a typical P2X receptor subunit. First and second transmembrane domains are labeled TM1 and TM2.

ATP-gated channels open in response to binding the nucleotide ATP. They form trimers with two transmembrane helices per subunit and both the C and N termini on the intracellular side.

PIP₂-gated channels

Phosphatidylinositol 4,5-bisphosphate (PIP₂) binds to and directly activates inwardly rectifying potassium channels (K_ir).^[21] PIP₂ is a cell membrane lipid, and its role in gating ion channels represents a novel role for the molecule.^[22][23]

Indirect modulation

In contrast to ligand-gated ion channels, there are also receptor systems in which the receptor and the ion channel are separate proteins in the cell membrane, instead of a single molecule. In this case, ion channels are indirectly modulated by activation of the receptor, instead of being gated directly.

G-protein-linked receptors

G-protein-coupled receptor mechanism

Also called G protein-coupled receptor, seven-transmembrane domain receptor, 7 TM receptor, constitute a large protein family of receptors that sense molecules outside the cell and activate inside signal transduction pathways and, ultimately, cellular responses. They pass through the cell membrane 7 times. G-protein-Linked receptors are a huge family that have hundreds of members identified. Ion-channel-linked receptors (e.g. GABAB, NMDA, etc.) are only a part of them.

Table 1. Three major families of Trimeric G Proteins^[24]

GABA_B receptor

GABAB receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid. They are linked via G-proteins to K+ channels, when active, they create hyperpolarized effect and lower the potential inside the cell.^[25]

Ligands:

• Agonists: GABA, Baclofen, gamma-Hydroxybutyrate, Phenibut etc.
• Positive Allosteric Modulators: CGP-7930,^[26] Fendiline, BSPP, etc.
• Antagonists:2-OH-saclofen, Saclofen, SCH-50911

Gα signaling

The cyclic-adenosine monophosphate (cAMP)-generating enzyme adenylate cyclase is the effector of both the G_αs and G_αi/o pathways. Ten different AC gene products in mammals, each with subtle differences in tissue distribution and/or function, all catalyze the conversion of cytosolic adenosine triphosphate (ATP) to cAMP, and all are directly stimulated by G-proteins of the G_αs class. Interaction with Gα subunits of the G_αi/o type, on the contrary, inhibits AC from generating cAMP. Thus, a GPCR coupled to G_αs counteracts the actions of a GPCR coupled to G_αi/o, and vice versa. The level of cytosolic cAMP may then determine the activity of various ion channels as well as members of the ser/thr-specific protein kinase A (PKA) family. As a result, cAMP is considered a second messenger and PKA a secondary effector.

The effector of the G_αq/11 pathway is phospholipase C-β (PLCβ), which catalyzes the cleavage of membrane-bound phosphatidylinositol 4,5-biphosphate (PIP2) into the second messengers inositol (1,4,5) trisphosphate (IP3) and diacylglycerol (DAG). IP3 acts on IP3 receptors found in the membrane of the endoplasmic reticulum (ER) to elicit Ca²⁺ release from the ER, DAG diffuses along the plasma membrane where it may activate any membrane localized forms of a second ser/thr kinase called protein kinase C (PKC). Since many isoforms of PKC are also activated by increases in intracellular Ca²⁺, both these pathways can also converge on each other to signal through the same secondary effector. Elevated intracellular Ca²⁺ also binds and allosterically activates proteins called calmodulins, which in turn go on to bind and allosterically activate enzymes such as Ca²⁺/calmodulin-dependent kinases (CAMKs).

The effectors of the G_α12/13 pathway are three RhoGEFs (p115-RhoGEF, PDZ-RhoGEF, and LARG), which, when bound to G_α12/13 allosterically activate the cytosolic small GTPase, Rho. Once bound to GTP, Rho can then go on to activate various proteins responsible for cytoskeleton regulation such as Rho-kinase (ROCK). Most GPCRs that couple to G_α12/13 also couple to other sub-classes, often G_αq/11.

Gβγ signaling

The above descriptions ignore the effects of Gβγ–signalling, which can also be important, in particular in the case of activated G_αi/o-coupled GPCRs. The primary effectors of Gβγ are various ion channels, such as G-protein-regulated inwardly rectifying K⁺ channels (GIRKs), P/Q- and N-type voltage-gated Ca²⁺ channels, as well as some isoforms of AC and PLC, along with some phosphoinositide-3-kinase (PI3K) isoforms.

Clinical relevance

Ligand-gated ion channels are likely to be the major site at which anaesthetic agents and ethanol have their effects, although unequivocal evidence of this is yet to be established.^[27][28] In particular, the GABA and NMDA receptors are affected by anaesthetic agents at concentrations similar to those used in clinical anaesthesia.^[29]

By understanding the mechanism and exploring the chemical/biological/physical component that could function on those receptors, more and more clinical applications are proven by preliminary experiments or FDA.

• Addiction treatment:

A series recent study shows that GABA receptors are involved with addiction-related behaviors, such as cocaine,^[30] heroin, alcohol,^[31] etc. Understanding the mechanism of receptors helped scientist develop pharmaceutical tools to treat addictions by modifying the receptors' activity.^[32][33]

• Memantine

Memantine is approved by the U.S. F.D.A and the European Medicines Agency for the treatment of moderate-to-severe Alzheimer's disease,^[34] and has now received a limited recommendation by the UK's National Institute for Health and Care Excellence for patients who fail other treatment options.^[35]

• Antidepressant treatment

Agomelatine, is a type of drug that acts on a dual melatonergic-serotonergic pathway, which have shown its efficacy in the treatment of anxious depression during clinical trails,^[36][37] study also suggests the efficacy in the treatment of atypical and melancholic depression.^[38]

See also

• Receptor (biochemistry)
• Action potential
• Voltage-dependent calcium channel
• Calcium-activated potassium channel
• Cyclic nucleotide-gated ion channel
• Acid-sensing ion channel
• Ryanodine receptor
• Inositol trisphosphate receptor

References

External links

• Ligand-Gated Ion Channel database at European Bioinformatics Institute. Verified availability April 11, 2007.
• "Revised Recommendations for Nomenclature of Ligand-Gated Ion Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology. 
• http://www.esf.edu/efb/course/EFB325/lectures/29HormoneSignals.htm
• https://www.genenames.org/

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