Ligand-gated Ion Channel Protein Research Articles

De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light on parasitiform poultry mites evolution and its chemoreceptor repertoires.

The northern fowl mite (NFM), Ornithonyssus sylviarum, and the poultry red mite (PRM), Dermanyssus gallinae, are the most serious pests of poultry, both of which have an expanding global prevalence. Research on NFM has been constrained by a lack of genomic and transcriptomic data. Here, we report and analyze the first global transcriptome data across all mite live stages and sexes. A total of 28,999 unigenes were assembled, of which 19,750 (68.10%) were annotated using seven functional databases. The biological function of these unigenes was classified using the GO, KOG, and KEGG databases. To gain insight into the chemosensory receptor-based system of parasitiform mites, we furthermore assessed the gene repertoire of gustatory receptors (GRs) and ionotropic receptors (IRs), both of which encode putative ligand-gated ion channel proteins. While these receptors are well characterized in insect model species, our understanding of chemosensory detection in mites and ticks is in its infancy. To address this paucity of data, we identified 9 IR/iGluRs and 2 GRs genes by analyzing transcriptome data in the NFM, while 9 GRs and 41 IR/iGluRs genes were annotated in the PRM genome. Taken together, the transcriptomic and genomic annotation of these two species provide a valuable reference for studies of parasitiform mites and also help to understand how chemosensory gene family expansion/contraction events may have been reshaped by an obligate parasitic lifestyle compared with their free-living closest relatives. Future studies should include additional species to validate this observation and functional characterization of the identified proteins as a step forward in identifying tools for controlling these poultry pests.

Protein engineering and design in ion channels and receptors.

Acetylcholine receptors (AChRs) expressed at the neuromuscular junction synapses are typical allosteric proteins that shuttle between at least two stable conformational states: Closed (C) and Open (O). Agonist binding to their target sites on the receptor in the extracellular domain triggers a global C→O conformational change that results in an open channel pore that allows ion conduction. How the receptor senses the chemical signal of an agonist and communicates it to the channel pore, located ~50Å away, are key to understanding the receptor function. AChRs are indispensable for muscle contraction and their neuronal homologues play critical roles in the nervous system function. In this chapter, using a combination of single channel patch-clamp, computational approaches, and genetic engineering, we elucidate the principles of design and engineering to quantify the fundamental thermodynamic parameters of AChRs that regulate ligand binding and channel opening. The receptor engineering principles outlined here for the neuromuscular AChRs are applicable to the broader class of ligand-gated ion channel proteins.

Simulating ion channel activation mechanisms using swarms of trajectories.

Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's "swarms of trajectories" approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function. © 2019 Wiley Periodicals, Inc.

Structural effects of divalent calcium cations on the α7 nicotinic acetylcholine receptor: A molecular dynamics simulation study.

The α7 subtype of neuronal nicotinic acetylcholine receptor (nAChR) is a ligand-gated ion channel protein that is vital to various neurological functions, including modulation of neurotransmitter release. A relatively high concentration of extracellular Ca2+ in the neuronal environment is likely to exert substantial structural and functional influence on nAChRs, which may affect their interactions with agonists and antagonists. In this work, we employed atomistic molecular dynamics (MD) simulations to examine the effects of elevated Ca2+ on the structure and dynamics of α7 nAChR embedded in a model phospholipid bilayer. Our results suggest that the presence of Ca2+ in the α7 nAChR environment results in closure of loop C-in the extracellular ligand-binding domain, a motion normally associated with agonist binding and receptor activation. Elevated Ca2+ also alters the conformation of key regions of the receptor, including the inter-helical loops, pore-lining helices and the "gate" residues, and causes partial channel opening in the absence of an agonist, leading to an attendant reduction in the free energy of Ca2+ permeation through the pore as elucidated by umbrella sampling simulations. Overall, the structural and permeability changes in α7 nAChR suggest that elevated Ca2+ induces a partially activated receptor state that is distinct from both the resting and the agonist-activated states. These results are consistent with the notion that divalent ions can serve as a potentiator of nAChRs, resulting in a higher rate of receptor activation (and subsequent desensitization) in the presence of agonists, with possible implications for diseases involving calcium dysregulation.

The neural γ2α1β2α1β2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges.

While ~30% of the human genome encodes membrane proteins, only a handful of structures of membrane proteins have been resolved to high resolution. Here, we studied the structure of a member of the Cys-loop ligand gated ion channel protein superfamily of receptors, human type A γ2α1β2α1β2 gamma amino butyric acid receptor complex in a lipid bilayer environment. Studying the correlation between the structure and function of the gamma amino butyric acid receptor may enhance our understanding of the molecular basis of ion channel dysfunctions linked with epilepsy, ataxia, migraine, schizophrenia and other neurodegenerative diseases. The structure of human γ2α1β2α1β2 has been modeled based on the X-ray structure of the Caenorhabditis elegans glutamate-gated chloride channel via homology modeling. The template provided the first inhibitory channel structure for the Cys-loop superfamily of ligand-gated ion channels. The only available template structure before this glutamate-gated chloride channel was a cation selective channel which had very low sequence identity with gamma aminobutyric acid receptor. Here, our aim was to study the effect of structural corrections originating from modeling on a more reliable template structure. The homology model was analyzed for structural properties via a 100ns molecular dynamics (MD) study. Due to the structural shifts and the removal of an open channel potentiator molecule, ivermectin, from the template structure, helical packing changes were observed in the transmembrane segment. Namely removal of ivermectin molecule caused a closure around the Leu 9 position along the ion channel. In terms of the structural shifts, there are three potential disulfide bridges between the M1 and M3 helices of the γ2 and 2 α1 subunits in the model. The effect of these disulfide bridges was investigated via monitoring the differences in root mean square fluctuations (RMSF) of individual amino acids and principal component analysis of the MD trajectory of the two homology models-one with the disulfide bridge and one with protonated Cys residues. In all subunit types, RMSF of the transmembrane domain helices are reduced in the presence of disulfide bridges. Additionally, loop A, loop F and loop C fluctuations were affected in the extracellular domain. In cross-correlation analysis of the trajectory, the two model structures displayed different coupling in between the M2-M3 linker region, protruding from the membrane, and the β1-β2/D loop and cys-loop regions in the extracellular domain. Correlations of the C loop, which collapses directly over the bound ligand molecule, were also affected by differences in the packing of transmembrane helices. Finally, more localized correlations were observed in the transmembrane helices when disulfide bridges were present in the model. The differences observed in this study suggest that dynamic coupling at the interface of extracellular and ion channel domains differs from the coupling introduced by disulfide bridges in the transmembrane region. We hope that this hypothesis will be tested experimentally in the near future.

Analyzing the Effects of Lipid Type on the α-Hemolysin Nanopore and 5HT3 Receptor Structure and Gating using Molecular Dynamics Simulations

Alpha-hemolysin (α-HL) is a transmembrane protein used to measure the size and charge of macromolecules. In this process, α-HL is inserted into a tethered lipid bilayer composed of 1,2-diphytanoyl-sn-glycero-3-phosphocholine (PHPC) lipids. However, all previous molecular dynamics (MD) simulations attempting to model this system have used a more common lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), to represent the PHPC-tethered bilayer. PHPC possesses highly methylated hydrophobic chains which creates a more rigid structure. The result is that simulations using POPC lipids yield channel currents at least 20% less than experimental values. MD simulations conducted with both PHPC and POPC lipids for both the full and a reduced form of the protein containing just the β-barrel indicate that PHPC lipids could more accurately describe the experimentally observed parameters. The 5-hydroxytryptamine receptor (5HT3) is the principle receptor responsible for modulating a wide range of neurological and digestive functions. Here we aim to better understand the response of the 5HT3 receptor to 5HT (serotonin) in an environment that mimics the native lipid composition. This work supports the experimental design of a field effect transistor (FET) device we are developing to measure the presence of ligands such as neurotransmitters, neuropeptides and drug molecules. To this end, MD simulations were conducted on a system composed of the Cys-loop ligand-gated ion channel protein receptor 5HT3, a 7:7:6 ratio POPC/1-stearoyl-2-docosahexaenoyl-sn-glyerco-3-phosphocholine (SDPC)/cholesterol membrane, and 5HT to determine if ligand binding causes experimentally observed protein reassembly and channel opening. This work is unique in that these simulations possess a more realistic membrane composition and that they compare the conformation of the glycosylated protein to the non-glycosylated form providing structural details of the effects of glycosylation on the binding pocket and channel pore radius.

Characterizing Nanopore-Polymer Interactions and Cys-loop Protein Receptor Gating

The first objective is to better understand how the size and charge of an analyte affect the flow of ions through a transmembrane nanopore to support the development of a bio-nanosensor that can measure the mass and identify of complex macromolecules such as DNA. To this end, molecular dynamics (MD) simulations were conducted on a transmembrane nanopore system composed of the β-barrel region of the transmembrane protein α-hemolysin (α-HL), a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer membrane, and an aqueous solution of potassium chloride (KCl), in which the β-barrel forms a channel through the membrane. After the system was allowed to equilibrate, a single molecule of polyethylene glycol (PEG) was added into the channel and a transmembrane potential was applied to one side of the membrane. The ionic current through the channel was measured, and compared to the measured current without a PEG molecule present. This work concluded that a system composed of only the β-barrel region of α-HL (not including the head region) can accurately depict the flow of ions through the nanopore in response to an applied transmembrane potential with greater computational ease than with the entire protein.The second objective is to better understand the response of the 5HT3 receptor to the ligand 5HT (serotonin) in an environment that mimics the surface of a proposed microelectromechanical system (MEMS) device designed to measure the presence of ligands such as neurotransmitters, neuropeptides and drug molecules. To this end, MD simulations were conducted on a system composed of the Cys-loop ligand-gated ion channel protein receptor 5HT3, a 7:7:6 ratio POPC/1-stearoyl-2-docosahexaenoyl-sn-glyerco-3-phosphocholine (SDPC)/cholesterol membrane, and 5HT to determine if binding of the ligand causes protein reassembly and channel opening.

Ligand-induced structural changes in a membrane-reconstituted ion channel observed with atomic force microscopy

We investigated structural changes in ligand-gated ion channel proteins reconstituted into supported lipid bilayers. The ion channels’ extracellular parts were highly dynamic and exhibited agonist-induced changes, which were inhibited by antagonists. Our data demonstrate that, by using small exogenously applied compounds (i.e., ligands), ion channel proteins reconstituted into supported lipid bilayers on a substrate can be controlled.

Computational study of the transmembrane domain of the acetylcholine receptor

The nicotinic acetylcholine receptor (nAChR) is a ligand-gated ion channel protein whose transmembrane domain (TM-domain) is believed to be responsible for channel gating via a hydrophobic effect. In this work, we perform molecular dynamics and Brownian dynamics simulations to investigate the effect of transmembrane potential on the conformation and water occupancy of TM-domain, and the resulting ion permeation events. The results show that the behavior of the hydrophobic gate is voltage-dependent. Large hyperpolarized membrane potential can change the conformation of TM-domain and water occupancy in this region, which may enable ion conduction. An electrostatic gating mechanism is also proposed from our simulations, which seems to play a role in addition to the well-known hydrophobic effect.

Crystal structure and association behaviour of the GluR2 amino-terminal domain

Fast excitatory neurotransmission is mediated largely by ionotropic glutamate receptors (iGluRs), tetrameric, ligand-gated ion channel proteins comprised of three subfamilies, AMPA, kainate and NMDA receptors, with each subfamily sharing a common, modular-domain architecture. For all receptor subfamilies, active channels are exclusively formed by assemblages of subunits within the same subfamily, a molecular process principally encoded by the amino-terminal domain (ATD). However, the molecular basis by which the ATD guides subfamily-specific receptor assembly is not known. Here we show that AMPA receptor GluR1- and GluR2-ATDs form tightly associated dimers and, by the analysis of crystal structures of the GluR2-ATD, propose mechanisms by which the ATD guides subfamily-specific receptor assembly.

Role of acetylcholine receptor domains in ion selectivity

The nicotinic acetylcholine receptor (nAChR) is a ligand gated ion channel protein, composed of three domains: a transmembrane domain (TM-domain), extracellular domain (EC-domain), and intracellular domain (IC-domain). Due to its biological importance, much experimental and theoretical research has been carried out to explore its mechanisms of gating and selectivity, but there are still many unresolved issues, especially on the ion selectivity. Moreover, most of the previous theoretical work has concentrated on the TM-domain or EC-domain of nAChR, which may be insufficient to understand the entire structure–function relation. In this work, we perform molecular dynamics, Brownian dynamics simulations and continuum electrostatic calculations to investigate the role of different nAChR domains in ion conduction and selectivity. The results show that although both the EC and IC domains contain strong negative charges that create large cation concentrations at either end of the pore, this alone is not sufficient to create the observed cation selectivity and may play a greater role in determining the channel conductance. The presence of cations in the wide regions of the pore can screen out the protein charge allowing anions to enter, meaning that local regions of the TM-domain are most likely responsible for discriminating between ions. These new results complement our understanding about the ion conduction and selectivity mechanism of nAChR.

Tryptophan scanning of the acetylcholine receptor's βM4 transmembrane domain: Decoding allosteric linkage at the lipid-protein interface with ion-channel gating

The nicotinic acetylcholine receptor (nAChR) is a ligand-gated ion channel protein that mediates fast excitatory synaptic transmission in the peripheral and central nervous systems. Changes in the structure and function of the AChR can lead to serious impairment of physiological processes. In this study, we combined site-directed mutagenesis, radioligand binding assays, electrophysiological recordings, and Fourier analyses to characterize the functional role and structural aspects of the βM4 transmembrane domain of the Torpedo AChR. We performed tryptophan replacements, from residues L438 through F455, along the βM4 transmembrane domain. Expression levels of mutants F439W-G450W and F452W-I454W produced peak currents similar to or lower than those in wild-type (WT). Tryptophan substitutions at positions L438 and T451 led to a deficiency in either subunit expression or receptor assembly. Mutations L440W, V442W, C447W, and S453W produced a gain-of-function response. Mutation F455W produced a loss of ion channel function. The periodicity profile of the normalized expression level (closed state) and EC50 (open state) revealed a minor conformational change of 0.4 residues/turn of the βM4 domain. These findings suggest that a minor movement of the βM4 domain occurs during channel activation.

Molecular modelling of the GABA A ion channel protein

The GABA A ion channel protein is central to the mechanism of action of general anaesthetics and thus to the phenomenon of human consciousness. A molecular model of the α 1β 2γ 2 γ-aminobutyric acid type-A (GABA A) ligand-gated ion channel protein has been constructed. The cryo-electron microscopy structure of the nicotinic acetylcholine receptor (nAChR) from Torpedo marmorata and the X-ray crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis were used as starting templates for comparative modelling. Features of the modelling approach used in the development of this GABA A model include: (1) multiple sequence alignment of members of the Cys-loop superfamily; (2) the design and implementation of a quasi- ab initio loop modelling algorithm; (3) expansion of the transmembrane domain (TMD) ion pore to model the open-state of the GABA A channel; (4) hydrophobicity analysis of the TMD to refine the structure in regions involved in general anaesthetic binding. The final model of the α 1β 2γ 2 GABA A protein agrees with available experimental data concerning general anaesthetics.

Highly Electrically Insulating Tethered Lipid Bilayers for Probing the Function of Ion Channel Proteins

A method is presented to form gold-electrode-tethered lipid bilayers with exceptionally high electrical resistances. Electrical impedance spectroscopy is used to monitor the bilayer incorporation of a ligand-gated ion channel protein and the modulation of its channel activity by the selective binding of an antibody. Due to the low defect density of the tethered membrane, the effect of a few channels can be resolved thus opening the way to single-channel experiments on this highly stable and versatile platform. In turn, a minute quantity of analyte, here antibodies, can be measured, which is of great interest for bioanalytics.

Cloning and functional characterization of two glycine receptor alpha-subunits from the perch retina.

Glycine receptors are ligand-gated ion channel proteins mediating synaptic inhibition in the spinal cord, retina and brain of vertebrates. We have cloned and functionally characterized two glycine receptor alpha-subunits from the perch (Roccus americana) retina. Based on sequence homology with the mammalian counterparts, we termed these subunits alpha 1 and alpha 3. RT-PCR revealed the presence of both subunits in retina and brain, whereas alpha1 was predominant in spinal cord. A short splice variant of alpha1 was detected in the brain but not in the retina. Functional expression of the perch subunits in HEK-293 cells yielded robust glycine-gated currents sensitive to strychnine. The perch receptors displayed a high efficacy for taurine and GABA and thus differ from the mammalian counterparts. Because the retina is a rich source for taurine, this finding could be of physiological importance. The structural features of the ligand binding domain strongly support the notion of increased glycine/GABA discrimination in higher vertebrates.

Different efficacy of specific agonists at 5-HT3 receptor splice variants: the role of the extra six amino acid segment.

1. Whole cell voltage clamp electrophysiology and radioligand binding were used to examine the agonist characteristics of the two splice variants of the 5-HT3 receptor which have been cloned from neuronal cell lines. Homo-oligomeric 5-HT3 receptors were examined in HEK 293 cells stably transfected with either long (5-HT3-L) or short (5-HT3-S) receptor subunit DNAs. 2. Functional homo-oligomeric receptors were formed from both subunits, and responses to 5-HT3 receptor agonists (5-hydroxytryptamine (5-HT), 2-methyl 5-HT and m-chlorophenylbiguanide) were qualitatively similar. 3. Maximum currents (Rmax) elicited by the 5-HT3 receptor agonists m-chlorophenylbiguanide (mCPBG) and 2-methyl-5-HT (2-Me-5-HT), as compared to 5-HT, differed in the two splice variants: Rmax mCPBG/Rmax 5-HT values were 0.68+/-0.04 and 0.91+/-0.01 in 5-HT3-L and 5-HT3-S receptors, respectively. Comparable values for 2-Me-5-HT were 0.30+/-0.02 and 0.23+/-0.02. 4. Radioligand binding data showed no difference in affinity of agonist or antagonist binding sites; thus the six amino acid deletion appears to cause differences in agonist efficacy. 5. The role of the 6 amino acid insertion was further investigated by use of site-directed mutagenesis to create two mutant receptors, one where serine 286 was replaced with alanine, and the second where all 6 amino acids were replaced with alanines. 6. Examination of the mutant receptors when stably expressed in HEK 293 cells revealed agonist properties resembling long and not short 5-HT3 receptors. Thus specific amino acids in this region are not responsible for the observed differences. 7. The data show intracellular structure can have significant effects on ligand-gated ion channel function, and suggest that minor changes in structure may be responsible for differences in function observed when ligand-gated ion channel proteins are modulated intracellularly.

Regulation of excitatory and inhibitory neurotransmitter-gated ion channels by protein phosphorylation

Phosphorylation of ligand-gated ion channels is recognised as a potentially important mechanism for short- and long-term modulation of ion-channel function. Following the discovery of numerous sites of phosphorylation on ligand-gated ion channel proteins, recent studies have demonstrated that neurotransmitter-induced activation of serine/threonine, tyrosine and other kinases can result in the modulation of glutamate, type A γ-aminobutyric acid (GABA A) and glycine receptors. These findings may have important consequences for our understanding of synaptic transmission and neuronal excitability.

Cyanotriphenylborate: subtype-specific blocker of glycine receptor chloride channels.

The inhibitory glycine receptor is a ligand-gated ion-channel protein existing in different homo- and heterooligomeric isoforms. Here we show that the chloride channel of the recombinant alpha 1-subunit homooligomeric glycine receptor is efficiently blocked by cyanotriphenylborate (CTB) with a concentration effecting 50% inhibition (IC50) of 1.3 microM in the presence of 50 microM glycine. The antagonistic effect of CTB is noncompetitive, use dependent, and more pronounced at positive membrane potentials, suggesting open-channel block. In contrast to alpha 1-subunit receptors, alpha 2-subunit homooligomers are resistant to CTB (IC50 >> 20 microM). By exchanging the channel-lining transmembrane segment M2 of the alpha 1 polypeptide by that of the alpha 2 polypeptide, we could transfer this resistance to alpha 1 channels, indicating that a single glycine residue at position 254 of the alpha 1 subunit is critical for CTB sensitivity. The blocker did not affect the cation-selective channel of the nicotinic acetylcholine receptor. Thus, CTB may prove useful as a tool to probe the subunit structure of native glycine receptors in mammalian neurons.

Structural analysis of mouse glycine receptor alpha subunit genes. Identification and chromosomal localization of a novel variant.

The inhibitory glycine receptor is a ligand-gated ion channel protein that occurs in different developmentally regulated isoforms in the mammalian central nervous system. Here, we have analyzed genomic clones covering the coding regions of the murine glycine receptor alpha 1 and alpha 2 subunit genes. Both genes contain eight intronic regions with precisely conserved boundaries. The same structure was also found for seven exons of a third homologous gene, alpha 4, identified during screening. The predicted alpha 4 polypeptide displays very high homology to the alpha 2 subunit. Like the alpha 2 gene, the alpha 4 gene maps to the mouse X chromosome. Our data indicate that the genomic organization of glycine receptor alpha subunit genes is conserved during evolution.

Structure and function of inhibitory glycine receptors.

Ion transport by peptide channels has been the major theme in the work of the late P. Läuger. His theoretical and experimental approaches provided the basis for a deeper understanding of pore-mediated ion permeation through biological membranes. This review on a ligand–gated ion channel protein from the mammalian brain is dedicated to the memory of this outstanding scientist.