1
|
Yuan X, Zhang D, Mao S, Wang Q. Filling the Gap in Understanding the Mechanism of GABA AR and Propofol Using Computational Approaches. J Chem Inf Model 2021; 61:1889-1901. [PMID: 33823589 DOI: 10.1021/acs.jcim.0c01290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
γ-Aminobutyric acid type-A receptors (GABAARs) play a critical role in neural transmission by mediating the inhibitory neural firing and are the target of many psychiatric drugs. Among them, propofol is one of the most widely used and important general anesthetics in clinics. Recent advances in structural biology revealed the structure of a human GABAAR in both open and closed states. Yet, the detailed mechanism of the receptor and propofol remains to be fully understood. Therefore, in this study, based on the previous successes in structural biology, a variety of computational techniques were applied to fill the gap between previous experimental studies. This study investigated the ion-conducting mechanism of GABAAR, predicted the possible binding mechanism of propofol, and revealed a new motion mechanism of transmembrane domain (TMD) helices. We hope that this study may contribute to future studies on ion-channel receptors, general anesthetics, and drug development.
Collapse
Affiliation(s)
- Xinghang Yuan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Di Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shengjun Mao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| |
Collapse
|
2
|
Abstract
Ethanol is a chemoattractant for Bacillus subtilis even though it is not metabolized and inhibits growth. B. subtilis likely uses ethanol to find ethanol-fermenting microorganisms to utilize as prey. Two chemoreceptors sense ethanol: HemAT and McpB. HemAT’s myoglobin-like sensing domain directly binds ethanol, but the heme group is not involved. McpB is a transmembrane receptor consisting of an extracellular sensing domain and a cytoplasmic signaling domain. While most attractants bind the extracellular sensing domain, we found that ethanol directly binds between intermonomer helices of the cytoplasmic signaling domain of McpB, using a mechanism akin to those identified in many mammalian ethanol-binding proteins. Our results indicate that the sensory repertoire of chemoreceptors extends beyond the sensing domain and can directly involve the signaling domain. Motile bacteria sense chemical gradients using chemoreceptors, which consist of distinct sensing and signaling domains. The general model is that the sensing domain binds the chemical and the signaling domain induces the tactic response. Here, we investigated the unconventional sensing mechanism for ethanol taxis in Bacillus subtilis. Ethanol and other short-chain alcohols are attractants for B. subtilis. Two chemoreceptors, McpB and HemAT, sense these alcohols. In the case of McpB, the signaling domain directly binds ethanol. We were further able to identify a single amino acid residue, Ala431, on the cytoplasmic signaling domain of McpB that, when mutated to serine, reduces taxis to alcohols. Molecular dynamics simulations suggest that the conversion of Ala431 to serine increases coiled-coil packing within the signaling domain, thereby reducing the ability of ethanol to bind between the helices of the signaling domain. In the case of HemAT, the myoglobin-like sensing domain binds ethanol, likely between the helices encapsulating the heme group. Aside from being sensed by an unconventional mechanism, ethanol also differs from many other chemoattractants because it is not metabolized by B. subtilis and is toxic. We propose that B. subtilis uses ethanol and other short-chain alcohols to locate prey, namely, alcohol-producing microorganisms.
Collapse
|
3
|
Cottone G, Chiodo L, Maragliano L. Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. J Chem Inf Model 2020; 60:5045-5056. [PMID: 32803965 PMCID: PMC8011927 DOI: 10.1021/acs.jcim.0c00549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Molecular
studies of human pentameric ligand-gated ion channels
(LGICs) expressed in neurons and at neuromuscular junctions are of
utmost importance in the development of therapeutic strategies for
neurological disorders. We focus here on the nicotinic acetylcholine
receptor nAChR-α7, a homopentameric channel widely expressed
in the human brain, with a proven role in a wide spectrum of disorders
including schizophrenia and Alzheimer’s disease. By exploiting
an all-atom structural model of the full (transmembrane and extracellular)
protein in the open, agonist-bound conformation we recently developed,
we evaluate the free energy and the mean first passage time of single-ion
permeation using molecular dynamics simulations and the milestoning
method with Voronoi tessellation. The results for the wild-type channel
provide the first available mapping of the potential of mean force
in the full-length α7 nAChR, reveal its expected cationic nature,
and are in good agreement with simulation data for other channels
of the LGIC family and with experimental data on nAChRs. We then investigate
the role of a specific mutation directly related to ion selectivity
in LGICs, the E-1′ → A-1′ substitution at the
cytoplasmatic selectivity filter. We find that the mutation strongly
affects sodium and chloride permeation in opposite directions, leading
to a complete inversion of selectivity, at variance with the limited
experimental results available that classify this mutant as cationic.
We thus provide structural determinants for the observed cationic-to-anionic
inversion, revealing a key role of the protonation state of residue
rings far from the mutation, in the proximity of the hydrophobic channel
gate.
Collapse
Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
| |
Collapse
|
4
|
Selvaraj C, Selvaraj G, Kaliamurthi S, Cho WC, Wei DQ, Singh SK. Ion Channels as Therapeutic Targets for Type 1 Diabetes Mellitus. Curr Drug Targets 2020; 21:132-147. [PMID: 31538892 DOI: 10.2174/1389450119666190920152249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
Abstract
Ion channels are integral proteins expressed in almost all living cells and are involved in muscle contraction and nutrient transport. They play a critical role in the normal functioning of the excitable tissues of the nervous system and regulate the action potential and contraction events. Dysfunction of genes encodes ion channel proteins, which disrupt the channel function and lead to a number of diseases, among which is type 1 diabetes mellitus (T1DM). Therefore, understanding the complex mechanism of ion channel receptors is necessary to facilitate the diagnosis and management of treatment. In this review, we summarize the mechanism of important ion channels and their potential role in the regulation of insulin secretion along with the limitations of ion channels as therapeutic targets. Furthermore, we discuss the recent investigations of the mechanism regulating the ion channels in pancreatic beta cells, which suggest that ion channels are active participants in the regulation of insulin secretion.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Department of Bioinformatics, Computer-Aided Drug Design, and Molecular Modeling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, 630004, India
| | - Gurudeeban Selvaraj
- Center of Interdisciplinary Sciences-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Satyavani Kaliamurthi
- Center of Interdisciplinary Sciences-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Dong-Qing Wei
- Center of Interdisciplinary Sciences-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China
- Department of Bioinformatics, The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer-Aided Drug Design, and Molecular Modeling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, 630004, India
| |
Collapse
|
5
|
Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| |
Collapse
|
6
|
Ayan M, Essiz S. The neural γ 2α 1β 2α 1β 2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges. J Mol Model 2018; 24:206. [PMID: 30008086 DOI: 10.1007/s00894-018-3739-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Abstract
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 100 ns 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.
Collapse
Affiliation(s)
- Meral Ayan
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey
| | - Sebnem Essiz
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Fatih, Istanbul, Turkey.
| |
Collapse
|
7
|
Bhattarai JP, Park SJ, Chun SW, Cho DH, Han SK. Activation of synaptic and extrasynaptic glycine receptors by taurine in preoptic hypothalamic neurons. Neurosci Lett 2015; 608:51-6. [PMID: 26453764 DOI: 10.1016/j.neulet.2015.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/28/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
Abstract
Taurine is an essential amino-sulfonic acid having a fundamental function in the brain, participating in both cell volume regulation and neurotransmission. Using a whole cell voltage patch clamp technique, the taurine-activated neurotransmitter receptors in the preoptic hypothalamic area (PHA) neurons were investigated. In the first set of experiments, different concentrations of taurine were applied on PHA neurons. Taurine-induced responses were concentration-dependent. Taurine-induced currents were action potential-independent and sensitive to strychnine, suggesting the involvement of glycine receptors. In addition, taurine activated not only α-homomeric, but also αβ-heteromeric glycine receptors in PHA neurons. Interestingly, a low concentration of taurine (0.5mM) activated glycine receptors, whereas a higher concentration (3mM) activated both glycine and gamma-aminobutyric acid A (GABAA) receptors in PHA neurons. These results suggest that PHA neurons are influenced by taurine and respond via glycine and GABAA receptors.
Collapse
Affiliation(s)
- Janardhan Prasad Bhattarai
- Department of Oral Physiology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Soo Joung Park
- Department of Oral Physiology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Sang Woo Chun
- Department of Oral Physiology, College of Dentistry, Institute of Wonkwang Biomaterial and Implant, Wonkwang University, 344-2 Shinyong Dong, Iksan 570-749, Republic of Korea
| | - Dong Hyu Cho
- Department of Obstetrics and Gynecology, Chonbuk National University Hospital and School of Medicine, Jeonj 561-756, Republic of Korea.
| | - Seong Kyu Han
- Department of Oral Physiology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju 561-756, Republic of Korea.
| |
Collapse
|
8
|
Meiselbach H, Vogel N, Langlhofer G, Stangl S, Schleyer B, Bahnassawy L, Sticht H, Breitinger HG, Becker CM, Villmann C. Single expressed glycine receptor domains reconstitute functional ion channels without subunit-specific desensitization behavior. J Biol Chem 2014; 289:29135-47. [PMID: 25143388 DOI: 10.1074/jbc.m114.559138] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cys loop receptors are pentameric arrangements of independent subunits that assemble into functional ion channels. Each subunit shows a domain architecture. Functional ion channels can be reconstituted even from independent, nonfunctional subunit domains, as shown previously for GlyRα1 receptors. Here, we demonstrate that this reconstitution is not restricted to α1 but can be transferred to other members of the Cys loop receptor family. A nonfunctional GlyR subunit, truncated at the intracellular TM3-4 loop by a premature stop codon, can be complemented by co-expression of the missing tail portion of the receptor. Compared with α1 subunits, rescue by domain complementation was less efficient when GlyRα3 or the GABAA/C subunit ρ1 was used. If truncation disrupted an alternative splicing cassette within the intracellular TM3-4 loop of α3 subunits, which also regulates receptor desensitization, functional rescue was not possible. When α3 receptors were restored by complementation using domains with and without the spliced insert, no difference in desensitization was found. In contrast, desensitization properties could even be transferred between α1/α3 receptor chimeras harboring or lacking the α3 splice cassette proving that functional rescue depends on the integrity of the alternative splicing cassette in α3. Thus, an intact α3 splicing cassette in the TM3-4 loop environment is indispensable for functional rescue, and the quality of receptor restoration can be assessed from desensitization properties.
Collapse
Affiliation(s)
| | - Nico Vogel
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander University Erlangen-Nürnberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Georg Langlhofer
- the Institute for Clinical Neurobiology, University of Würzburg, Versbacherstrasse 5, 97078 Würzburg, Germany, and
| | - Sabine Stangl
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander University Erlangen-Nürnberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Barbara Schleyer
- the Institute for Clinical Neurobiology, University of Würzburg, Versbacherstrasse 5, 97078 Würzburg, Germany, and
| | - Lamia'a Bahnassawy
- the Biochemistry Department, German University Cairo, New Cairo City, Cairo 11835, Egypt
| | | | - Hans-Georg Breitinger
- the Biochemistry Department, German University Cairo, New Cairo City, Cairo 11835, Egypt
| | - Cord-Michael Becker
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander University Erlangen-Nürnberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Carmen Villmann
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander University Erlangen-Nürnberg, Fahrstrasse 17, 91054 Erlangen, Germany, the Institute for Clinical Neurobiology, University of Würzburg, Versbacherstrasse 5, 97078 Würzburg, Germany, and
| |
Collapse
|
9
|
Amyloid β peptide (25–35) in picomolar concentrations modulates the function of glycine receptors in rat hippocampal pyramidal neurons through interaction with extracellular site(s). Brain Res 2014; 1558:1-10. [DOI: 10.1016/j.brainres.2014.02.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 01/08/2023]
|
10
|
Mowrey DD, Kinde MN, Xu Y, Tang P. Atomistic insights into human Cys-loop receptors by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:307-14. [PMID: 24680782 DOI: 10.1016/j.bbamem.2014.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/12/2014] [Accepted: 03/20/2014] [Indexed: 12/13/2022]
Abstract
Cys-loop receptors are pentameric ligand-gated ion channels (pLGICs) mediating fast neurotransmission in the central and peripheral nervous systems. They are important targets for many currently used clinical drugs, such as general anesthetics, and for allosteric modulators with potential therapeutic applications. Here, we provide an overview of advances in the use of solution NMR in structural and dynamic characterization of ion channels, particularly human Cys-loop receptors. We present challenges to overcome and realistic solutions for achieving high-resolution structural information for this family of receptors. We discuss how subtle structural differences among homologous channels define unique channel pharmacological properties and advocate the necessity to determine high-resolution structures for individual receptor subtypes. Finally, we describe drug binding to the TMDs of Cys-loop receptors identified by solution NMR and the associated dynamics changes relevant to channel functions.
Collapse
Affiliation(s)
- David D Mowrey
- Department of Anesthesiology, University of Pittsburgh School of Medicine, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, USA
| | - Monica N Kinde
- Department of Anesthesiology, University of Pittsburgh School of Medicine, USA
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, USA; Department of Structural Biology, University of Pittsburgh School of Medicine, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, USA.
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, USA.
| |
Collapse
|
11
|
Activation of glycine and extrasynaptic GABA(A) receptors by taurine on the substantia gelatinosa neurons of the trigeminal subnucleus caudalis. Neural Plast 2013; 2013:740581. [PMID: 24379976 PMCID: PMC3863572 DOI: 10.1155/2013/740581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/05/2013] [Accepted: 11/12/2013] [Indexed: 11/23/2022] Open
Abstract
The substantia gelatinosa (SG) of the trigeminal subnucleus caudalis (Vc) has been known for the processing and transmission of orofacial nociceptive information. Taurine, one of the most plentiful free amino-acids in humans, has proved to be involved in pain modulation. In this study, using whole-cell patch clamp technique, we investigated the direct membrane effects of taurine and the action mechanism behind taurine-mediated responses on the SG neurons of the Vc. Taurine showed non-desensitizing and repeatable membrane depolarizations and inward currents which remained in the presence of amino-acid receptors blocking cocktail (AARBC) with tetrodotoxin, indicating that taurine acts directly on the postsynaptic SG neurons. Further, application of taurine at different doses (10 μM to 3 mM) showed a concentration dependent depolarizations and inward currents with the EC50 of 84.3 μM and 723 μM, respectively. Taurine-mediated responses were partially blocked by picrotoxin (50 μM) and almost completely blocked by strychnine (2 μM), suggesting that taurine-mediated responses are via glycine receptor (GlyR) activation. In addition, taurine (1 mM) activated extrasynaptic GABAA receptor (GABAAR)-mediated currents. Taken together, our results indicate that taurine can be a target molecule for orofacial pain modulation through the activation of GlyRs and/or extrasynaptic GABAARs on the SG neurons.
Collapse
|
12
|
Cheng MH, Coalson RD. Energetics and ion permeation characteristics in a glutamate-gated chloride (GluCl) receptor channel. J Phys Chem B 2012; 116:13637-43. [PMID: 23088363 DOI: 10.1021/jp3074915] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An invertebrate glutamate-gated chloride channel (GluCl) has recently been crystallized in an open-pore state. This channel is homologous to the human Cys-loop receptor family of pentameric ligand-gated ion channels, including anion-selective GlyR and GABAR and cation-selective nAChR and 5HT(3). We implemented molecular dynamics (MD) in conjunction with an elastic network model to perturb the X-ray structure of GluCl and investigated the open channel stability and its ion permeation characteristics. Our study suggests that TM2 helical tilting may close GluCl near the hydrophobic constriction L254 (L9'), similar to its cation-selective homologues. Ion permeation characteristics were determined by Brownian dynamics simulations using a hybrid MD/continuum electrostatics approach to evaluate the free energy profiles for ion transport. Near the selectivity filter region (P243 or P-2'), the free energy barrier for Na(+) transport is over 4 k(B)T higher than that for Cl(-), indicating anion selectivity of the channel. Furthermore, three layers of positivity charged rings in the extracellular domain also contribute to charge selectivity and facilitate Cl(-) permeability over Na(+). Collectively, the charge selectivity of GluCl may be determined by overall electrostatic and ion dehydration effects, perhaps not deriving from a single region of the channel (the selectivity filter region near the intracellular entrance).
Collapse
Affiliation(s)
- Mary Hongying Cheng
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | |
Collapse
|
13
|
Perkins DI, Trudell JR, Asatryan L, Davies DL, Alkana RL. Charge and geometry of residues in the loop 2 β hairpin differentially affect agonist and ethanol sensitivity in glycine receptors. J Pharmacol Exp Ther 2012; 341:543-51. [PMID: 22357974 DOI: 10.1124/jpet.111.190942] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Recent studies highlighted the importance of loop 2 of α1 glycine receptors (GlyRs) in the propagation of ligand-binding energy to the channel gate. Mutations that changed polarity at position 52 in the β hairpin of loop 2 significantly affected sensitivity to ethanol. The present study extends the investigation to charged residues. We found that substituting alanine with the negative glutamate at position 52 (A52E) significantly left-shifted the glycine concentration response curve and increased sensitivity to ethanol, whereas the negative aspartate substitution (A52D) significantly right-shifted the glycine EC₅₀ but did not affect ethanol sensitivity. It is noteworthy that the uncharged glutamine at position 52 (A52Q) caused only a small right shift of the glycine EC₅₀ while increasing ethanol sensitivity as much as A52E. In contrast, the shorter uncharged asparagine (A52N) caused the greatest right shift of glycine EC₅₀ and reduced ethanol sensitivity to half of wild type. Collectively, these findings suggest that charge interactions determined by the specific geometry of the amino acid at position 52 (e.g., the 1-Å chain length difference between aspartate and glutamate) play differential roles in receptor sensitivity to agonist and ethanol. We interpret these results in terms of a new homology model of GlyR based on a prokaryotic ion channel and propose that these mutations form salt bridges to residues across the β hairpin (A52E-R59 and A52N-D57). We hypothesize that these electrostatic interactions distort loop 2, thereby changing agonist activation and ethanol modulation. This knowledge will help to define the key physical-chemical parameters that cause the actions of ethanol in GlyRs.
Collapse
Affiliation(s)
- Daya I Perkins
- Alcohol and Brain Research Laboratories, Departments of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | |
Collapse
|
14
|
Chen WW, Sing Tay DK, Leong SSJ, Kwak SK. Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.604854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
15
|
Fernández-Ballester G, Fernández-Carvajal A, González-Ros JM, Ferrer-Montiel A. Ionic channels as targets for drug design: a review on computational methods. Pharmaceutics 2011; 3:932-53. [PMID: 24309315 PMCID: PMC3857065 DOI: 10.3390/pharmaceutics3040932] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/26/2011] [Accepted: 11/30/2011] [Indexed: 01/21/2023] Open
Abstract
Ion channels are involved in a broad range of physiological and pathological processes. The implications of ion channels in a variety of diseases, including diabetes, epilepsy, hypertension, cancer and even chronic pain, have signaled them as pivotal drug targets. Thus far, drugs targeting ion channels were developed without detailed knowledge of the molecular interactions between the lead compounds and the target channels. In recent years, however, the emergence of high-resolution structures for a plethora of ion channels paves the way for computer-assisted drug design. Currently, available functional and structural data provide an attractive platform to generate models that combine substrate-based and protein-based approaches. In silico approaches include homology modeling, quantitative structure-activity relationships, virtual ligand screening, similarity and pharmacophore searching, data mining, and data analysis tools. These strategies have been frequently used in the discovery and optimization of novel molecules with enhanced affinity and specificity for the selected therapeutic targets. In this review we summarize recent applications of in silico methods that are being used for the development of ion channel drugs.
Collapse
|
16
|
Ruthstein S, Stone KM, Cunningham TF, Ji M, Cascio M, Saxena S. Pulsed electron spin resonance resolves the coordination site of Cu²(+) ions in α1-glycine receptor. Biophys J 2011; 99:2497-506. [PMID: 20959090 DOI: 10.1016/j.bpj.2010.08.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/09/2010] [Accepted: 08/26/2010] [Indexed: 11/19/2022] Open
Abstract
Herein, we identify the coordination environment of Cu²(+) in the human α1-glycine receptor (GlyR). GlyRs are members of the pentameric ligand-gated ion channel superfamily (pLGIC) that mediate fast signaling at synapses. Metal ions like Zn²(+) and Cu²(+) significantly modulate the activity of pLGICs, and metal ion coordination is essential for proper physiological postsynaptic inhibition by GlyR in vivo. Zn²(+) can either potentiate or inhibit GlyR activity depending on its concentration, while Cu²(+) is inhibitory. To better understand the molecular basis of the inhibitory effect we have used electron spin resonance to directly examine Cu²(+) coordination and stoichiometry. We show that Cu²(+) has one binding site per α1 subunit, and that five Cu²(+) can be coordinated per GlyR. Cu²(+) binds to E192 and H215 in each subunit of GlyR with a 40 μM apparent dissociation constant, consistent with earlier functional measurements. However, the coordination site does not include several residues of the agonist/antagonist binding site that were previously suggested to have roles in Cu²(+) coordination by functional measurements. Intriguingly, the E192/H215 site has been proposed as the potentiating Zn²(+) site. The opposing modulatory actions of these cations at a shared binding site highlight the sensitive allosteric nature of GlyR.
Collapse
Affiliation(s)
- Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pennsylvania, USA
| | | | | | | | | | | |
Collapse
|
17
|
Bertaccini EJ, Wallner B, Trudell JR, Lindahl E. Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4. J Chem Inf Model 2010; 50:2248-55. [PMID: 21117677 DOI: 10.1021/ci100266c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ligand-gated ion channels (LGICs) significantly modulate anesthetic effects. Their exact molecular structure remains unknown. This has led to ambiguity regarding the proper amino acid alignment within their 3D structure and, in turn, the location of any anesthetic binding sites. Current controversies suggest that such a site could be located in either an intra- or intersubunit locale within the transmembrane domain of the protein. Here, we built a model of the glycine alpha one receptor (GlyRa1) based on the open-state structures of two new high-resolution ion channel templates from the prokaryote, Gloebacter violaceus (GLIC). Sequence scoring suggests reasonable homology between GlyRa1 and GLIC. Three of the residues notable for modulating anesthetic action are on transmembrane segments 1-3 (TM1-3): (ILE229, SER 267, and ALA 288). They line an intersubunit interface, in contrast to previous models. However, residues from the fourth transmembrane domain (TM4) that are known to modulate a variety of anesthetic effects are quite distant from this putative anesthetic binding site. While this model can account for a large proportion of the physicochemical data regarding such proteins, it cannot readily account for the alterations on anesthetic effects that are due to mutations within TM4.
Collapse
Affiliation(s)
- Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California, United States.
| | | | | | | |
Collapse
|
18
|
Cheng MH, Coalson RD, Tang P. Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel. J Am Chem Soc 2010; 132:16442-9. [PMID: 20979415 PMCID: PMC3071019 DOI: 10.1021/ja105001a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.
Collapse
Affiliation(s)
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA 15260
| |
Collapse
|
19
|
Pittel I, Witt-Kehati D, Degani-Katzav N, Paas Y. Probing pore constriction in a ligand-gated ion channel by trapping a metal ion in the pore upon agonist dissociation. J Biol Chem 2010; 285:26519-31. [PMID: 20466725 PMCID: PMC2924088 DOI: 10.1074/jbc.m110.102327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 04/24/2010] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic pentameric ligand-gated ion channels (pLGICs) are receptors activated by neurotransmitters to rapidly transport ions across cell membranes, down their electrochemical gradients. Recent crystal structures of two prokaryotic pLGICs were interpreted to imply that the extracellular side of the transmembrane pore constricts to close the channel (Hilf, R. J., and Dutzler, R. (2009) Nature 457, 115-118; Bocquet, N., Nury, H., Baaden, M., Le Poupon, C., Changeux, J. P., Delarue, M., and Corringer, P. J. (2009) Nature 457, 111-114). Here, we utilized a eukaryotic acetylcholine (ACh)-serotonin chimeric pLGIC that was engineered with histidines to coordinate a metal ion within the channel pore, at its cytoplasmic side. In a previous study, the access of Zn(2+) ions to the engineered histidines had been explored when the channel was either at rest (closed) or active (open) (Paas, Y., Gibor, G., Grailhe, R., Savatier-Duclert, N., Dufresne, V., Sunesen, M., de Carvalho, L. P., Changeux, J. P., and Attali, B. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 15877-15882). In this study, the interactions of Zn(2+) with the pore were probed upon agonist (ACh) dissociation that triggers the transition of the receptor from the active conformation to the resting conformation (i.e. during deactivation). Application of Zn(2+) onto ACh-bound open receptors obstructed their pore and prevented ionic flow. Removing ACh from its extracellular binding sites to trigger deactivation while Zn(2+) is still bound led to tight trapping of Zn(2+) within the pore. Together with single-channel recordings, made to explore single pore-blocking events, we show that dissociation of ACh causes the gate to shut on a Zn(2+) ion that effectively acts as a "foot in the door." We infer that, upon deactivation, the cytoplasmic side of the pore of the ACh-serotonin receptor chimera constricts to close the channel.
Collapse
Affiliation(s)
- Ilya Pittel
- From the Laboratory of Ion Channels, The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Dvora Witt-Kehati
- From the Laboratory of Ion Channels, The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Nurit Degani-Katzav
- From the Laboratory of Ion Channels, The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yoav Paas
- From the Laboratory of Ion Channels, The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| |
Collapse
|
20
|
Herrera AI, Al-Rawi A, Cook GA, Gao J, Iwamoto T, Prakash O, Tomich JM, Chen J. Structural characterization of two pore-forming peptides: consequences of introducing a C-terminal tryptophan. Proteins 2010; 78:2238-50. [PMID: 20544961 PMCID: PMC2909830 DOI: 10.1002/prot.22736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic channel-forming peptides that can restore chloride conductance across epithelial membranes could provide a novel treatment of channelopathies such as cystic fibrosis. Among a series of 22-residue peptides derived from the second transmembrane segment of the glycine receptor alpha(1)-subunit (M2GlyR), p22-S22W (KKKKP ARVGL GITTV LTMTT QW) is particularly promising with robust membrane insertion and assembly. The concentration to reach one-half maximal short circuit current is reduced to 45 +/- 6 microM from that of 210 +/- 70 microM of peptide p22 (KKKKP ARVGL GITTV LTMTT QS). However, this is accompanied with nearly 50% reduction in conductance. Toward obtaining a molecular level understanding of the channel activities, we combine information from solution NMR, existing biophysical data, and molecular modeling to construct atomistic models of the putative pentameric channels of p22 and p22-S22W. Simulations in membrane bilayers demonstrate that these structural models, even though highly flexible, are stable and remain adequately open for ion conductance. The membrane-anchoring tryptophan residues not only rigidify the whole channel, suggesting increased stability, but also lead to global changes in the pore profile. Specifically, the p22-S22W pore has a smaller opening on average, consistent with lower measured conductance. Direct observation of several incidences of chloride transport suggests several qualitative features of how these channels might selectively conduct anions. The current study thus helps to rationalize the functional consequences of introducing a single C-terminal tryptophan. Availability of these structural models also paves the way for future work to rationally modify and improve M2GlyR-derived peptides toward potential peptide-based channel replacement therapy.
Collapse
Affiliation(s)
| | | | | | - Jian Gao
- Department of Biochemistry, Kansas State University, Manhattan KS 66506, USA
| | - Takeo Iwamoto
- Department of Biochemistry, Kansas State University, Manhattan KS 66506, USA
| | - Om Prakash
- Department of Biochemistry, Kansas State University, Manhattan KS 66506, USA
| | - John M. Tomich
- Department of Biochemistry, Kansas State University, Manhattan KS 66506, USA
| | - Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan KS 66506, USA
| |
Collapse
|
21
|
Bertaccini EJ. The Molecular Mechanisms of Anesthetic Action: Updates and Cutting Edge Developments from the Field of Molecular Modeling. Pharmaceuticals (Basel) 2010; 3:2178-2196. [PMID: 27713348 PMCID: PMC4036663 DOI: 10.3390/ph3072178] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 06/10/2010] [Accepted: 07/06/2010] [Indexed: 12/01/2022] Open
Abstract
For over 160 years, general anesthetics have been given for the relief of pain and suffering. While many theories of anesthetic action have been purported, it has become increasingly apparent that a significant molecular focus of anesthetic action lies within the family of ligand-gated ion channels (LGIC’s). These protein channels have a transmembrane region that is composed of a pentamer of four helix bundles, symmetrically arranged around a central pore for ion passage. While initial and some current models suggest a possible cavity for binding within this four helix bundle, newer calculations postulate that the actual cavity for anesthetic binding may exist between four helix bundles. In either scenario, these cavities have a transmembrane mode of access and may be partially bordered by lipid moieties. Their physicochemical nature is amphiphilic. Anesthetic binding may alter the overall motion of a ligand-gated ion channel by a “foot-in-door” motif, resulting in the higher likelihood of and greater time spent in a specific channel state. The overall gating motion of these channels is consistent with that shown in normal mode analyses carried out both in vacuo as well as in explicitly hydrated lipid bilayer models. Molecular docking and large scale molecular dynamics calculations may now begin to show a more exact mode by which anesthetic molecules actually localize themselves and bind to specific protein sites within LGIC’s, making the design of future improvements to anesthetic ligands a more realizable possibility.
Collapse
Affiliation(s)
- Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine, Co-Director of Operating Room and Intensive Care Services, Palo Alto VA Health Care System, 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.
| |
Collapse
|
22
|
Affiliation(s)
- Alex Dickson
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637;
| | - Aaron R. Dinner
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637;
| |
Collapse
|
23
|
Hernandes MS, Troncone LRP. Glycine as a neurotransmitter in the forebrain: a short review. J Neural Transm (Vienna) 2009; 116:1551-60. [DOI: 10.1007/s00702-009-0326-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 09/20/2009] [Indexed: 11/30/2022]
|
24
|
Identifying the binding site(s) for antidepressants on the Torpedo nicotinic acetylcholine receptor: [3H]2-azidoimipramine photolabeling and molecular dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2690-9. [DOI: 10.1016/j.bbamem.2008.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 08/18/2008] [Accepted: 08/21/2008] [Indexed: 11/22/2022]
|
25
|
Cheng MH, Coalson RD, Cascio M, Kurnikova M. Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. J Comput Aided Mol Des 2008; 22:563-70. [PMID: 18368498 PMCID: PMC2822900 DOI: 10.1007/s10822-008-9200-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 02/18/2008] [Indexed: 11/27/2022]
Abstract
We conduct computational analyses of ion permeation characteristics in a model glycine receptor (GlyR) modified by photo-sensitive compounds. In particular, we consider hypothetical attachment to the channel of charge-neutral chemical groups which can be photo-activated by shining light of an appropriate wavelength on the system. After illumination, the attached molecules become charged via a photodissociation process or excited into a charge-separated state (thus generating a significant electric dipole). We carry out Brownian Dynamics simulations of ion flow through the channel in the presence of the additional charges generated in this fashion. Based on these calculations, we predict that photo-activation of appropriately positioned photo-sensitive compounds near the channel mouth can significantly modify the rate of ion permeation and the current rectification ratio. Possible implications for GlyR-based device designs are briefly discussed.
Collapse
Affiliation(s)
- Mary Hongying Cheng
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael Cascio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Maria Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15260, USA
| |
Collapse
|
26
|
Abstract
Ethanol produces a wide variety of behavioral and physiological effects in the body, but exactly how it acts to produce these effects is still poorly understood. Although ethanol was long believed to act nonspecifically through the disordering of lipids in cell membranes, proteins are at the core of most current theories of its mechanisms of action. Although ethanol affects various biochemical processes such as neurotransmitter release, enzyme function, and ion channel kinetics, we are only beginning to understand the specific molecular sites to which ethanol molecules bind to produce these myriad effects. For most effects of ethanol characterized thus far, it is unknown whether the protein whose function is being studied actually binds ethanol, or if alcohol is instead binding to another protein that then indirectly affects the functioning of the protein being studied. In this Review, we describe criteria that should be considered when identifying alcohol binding sites and highlight a number of proteins for which there exists considerable molecular-level evidence for distinct ethanol binding sites.
Collapse
Affiliation(s)
- R Adron Harris
- Section of Neurobiology and Waggoner Center for Alcohol and Addiction Research, Institutes for Neuroscience and Cell & Molecular Biology, University of Texas, Austin, TX 78712, USA.
| | | | | |
Collapse
|
27
|
Lobo IA, Harris RA, Trudell JR. Cross-linking of sites involved with alcohol action between transmembrane segments 1 and 3 of the glycine receptor following activation. J Neurochem 2007; 104:1649-62. [PMID: 18036150 DOI: 10.1111/j.1471-4159.2007.05090.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The glycine receptor is a member of the Cys-loop, ligand-gated ion channel family and is responsible for inhibition in the CNS. We examined the orientation of amino acids I229 in transmembrane 1 (TM1) and A288 in TM3, which are both critical for alcohol and volatile anesthetic action. We mutated these two amino acids to cysteines either singly or in double mutants and expressed the receptors in Xenopus laevis oocytes. We tested whether disulfide bonds could form between A288C in TM3 paired with M227C, Y228C, I229C, or S231C in TM1. Application of cross-linking (mercuric chloride) or oxidizing (iodine) agents had no significant effect on the glycine response of wild-type receptors or the single mutants. In contrast, the glycine response of the I229C/A288C double mutant was diminished after application of either mercuric chloride or iodine only in the presence of glycine, indicating that channel gating causes I229C and A288C to fluctuate to be within 6 A apart and form a disulfide bond. Molecular modeling was used to thread the glycine receptor sequence onto a nicotinic acetylcholine receptor template, further demonstrating that I229 and A288 are near-neighbors that can cross-link and providing evidence that these residues contribute to a single binding cavity.
Collapse
Affiliation(s)
- Ingrid A Lobo
- Waggoner Center for Alcohol and Addiction Research, Section of Neurobiology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712-1065, USA
| | | | | |
Collapse
|
28
|
Cheng MH, Coalson RD, Cascio M. Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism. Proteins 2007; 71:972-81. [DOI: 10.1002/prot.21784] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|