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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models. J Mol Biol 2021; 433:167128. [PMID: 34224751 DOI: 10.1016/j.jmb.2021.167128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.
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McCracken ML, Gorini G, McCracken LM, Mayfield RD, Harris RA, Trudell JR. Inter- and Intra-Subunit Butanol/Isoflurane Sites of Action in the Human Glycine Receptor. Front Mol Neurosci 2016; 9:45. [PMID: 27378846 PMCID: PMC4906044 DOI: 10.3389/fnmol.2016.00045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/26/2016] [Indexed: 11/24/2022] Open
Abstract
Glycine receptors (GlyRs) mediate inhibitory neurotransmission and are targets for alcohols and anesthetics in brain. GlyR transmembrane (TM) domains contain critical residues for alcohol/anesthetic action: amino acid A288 in TM3 forms crosslinks with TM1 (I229) in the adjacent subunit as well as TM2 (S267) and TM4 (Y406, W407, I409, Y410) in the same subunit. We hypothesized that these residues may participate in intra-subunit and inter-subunit sites of alcohol/anesthetic action. The following double and triple mutants of GLRA1 cDNA (encoding human glycine receptor alpha 1 subunit) were injected into Xenopus laevis oocytes: I229C/A288C, I229C/A288C/C290S, A288C/Y406C, A288C/W407C, A288C/I409C, and A288C/Y410C along with the corresponding single mutants and wild-type GLRA1. Butanol (22 mM) or isoflurane (0.6 mM) potentiation of GlyR-mediated currents before and after application of the cysteine crosslinking agent HgCl2 (10 μM) was measured using two-electrode voltage clamp electrophysiology. Crosslinking nearly abolished butanol and isoflurane potentiation in the I229C/A288C and I229C/A288C/C290S mutants but had no effect in single mutants or wild-type. Crosslinking also inhibited butanol and isoflurane potentiation in the TM3-4 mutants (A288C/Y406C, A288C/W407C, A288C/I409C, A288C/Y410C) with no effect in single mutants or wild-type. We extracted proteins from oocytes expressing I229C/288C, A288C/Y410C, or wild-type GlyRs, used mass spectrometry to verify their expression and possible inter-subunit dimerization, plus immunoblotting to investigate the biochemical features of proposed crosslinks. Wild-type GlyR subunits measured about 50 kDa; after crosslinking, the dimeric/monomeric 100:50 kDa band ratio was significantly increased in I229C/288C but not A288C/Y410C mutants or wild-type, providing support for TM1-3 inter-subunit and TM3-4 intra-subunit crosslinking. A GlyR homology model based on the GluCl template provides further evidence for a multi-site model for alcohol/anesthetic interaction with human GLRA1.
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Affiliation(s)
- Mandy L McCracken
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA; Integrative Neuroscience Research Branch, Neurobiology of Addiction Section, National Institute on Drug Abuse, National Institutes of HealthBaltimore, MD, USA
| | - Giorgio Gorini
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - Lindsay M McCracken
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - James R Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine Stanford, CA, USA
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Howard RJ, Trudell JR, Harris RA. Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics. Pharmacol Rev 2014; 66:396-412. [PMID: 24515646 PMCID: PMC3973611 DOI: 10.1124/pr.113.007468] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.
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Affiliation(s)
- Rebecca J Howard
- Department of Chemistry, Skidmore College, Saratoga Springs, NY 12866.
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Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor. Anesthesiology 2013; 119:1087-95. [PMID: 23770602 DOI: 10.1097/aln.0b013e31829e47e3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling. METHODS The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s. RESULTS Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. CONCLUSION Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.
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X-ray structural studies of the entire extracellular region of the serine/threonine kinase PrkC from Staphylococcus aureus. Biochem J 2011; 435:33-41. [DOI: 10.1042/bj20101643] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacterial serine/threonine kinases modulate a wide number of cellular processes. The serine/threonine kinase PrkC from the human pathogen Staphylococcus aureus was also shown to induce germination of Bacillus subtilis spores, in response to cell wall muropeptides. The presence of muropeptides in the bacterial extracellular milieu is a strong signal that the growing conditions are promising. In the present paper, we report the X-ray structure of the entire extracellular region of PrkC from S. aureus. This structure reveals that the extracellular region of PrkC, EC-PrkC, is a linear modular structure composed of three PASTA (penicillin binding-associated and serine/threonine kinase-associated) domains and an unpredicted C-terminal domain, which presents the typical features of adhesive proteins. Using several solution techniques, we also found that EC-PrkC shows no tendency to dimerize even in the presence of high concentrations of muropeptides. X-ray structural results obtained in the present study provide molecular clues into the mechanism of muropeptide-induced PrkC activation.
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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.
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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.
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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.
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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.
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McCracken LM, McCracken ML, Gong DH, Trudell JR, Harris RA. Linking of Glycine Receptor Transmembrane Segments Three and Four Allows Assignment of Intrasubunit-Facing Residues. ACS Chem Neurosci 2010; 1:482. [PMID: 21326622 DOI: 10.1021/cn100019g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Glycine receptors (GlyRs) are pentameric ligand-gated ion channels that mediate inhibitory neurotransmission in the brain and spinal cord and are targets of alcohols and anesthetics. The transmembrane (TM) domain of GlyR subunits is composed of four α-helical segments (TM1-4), but there are conflicting data about the orientation of TM3 and TM4 and, therefore, also the proximity of residues (e.g., A288) that are important for alcohol and anesthetic effects. In the present study, we investigated the proximity of A288 in TM3 to residues in TM4 from M404 to K411. We generated eight double mutant GlyRs (A288C/M404C, A288C/F405C, A288C/Y406C, A288C/W407C, A288C/I408C, A288C/I409C, A288C/Y410C, and A288C/K411C), as well as the corresponding single mutants, and expressed them in Xenopus laevis oocytes. To measure glycine responses, we used two-electrode voltage clamp electrophysiology. We built homology models of the GlyR using structures of the nicotinic acetylcholine receptor (nAChR) and a prokaryotic ion channel (Gloeobacter violaceus, GLIC) as templates, and asked which model best fit our experimental data. Application of the cross-linking reagent HgCl(2) in the closed state produced a leftward shift in the glycine concentration-response curves of the A288C/W407C and A288C/Y410C mutants, suggesting they are able to form cross-links. In addition, when HgCl(2) was coapplied with glycine, responses were changed in the A288C/Y406C, A288C/I409C, and A288C/Y410C double mutants, suggesting that agonist-induced rotation of TM4 allows A288C/Y406C and A288C/I409C to cross-link. These results are consistent with a model of GlyR, based on nAChR, in which A288, Y406, W407, I409, and Y410 face into a four-helical bundle.
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Affiliation(s)
- L. M. McCracken
- Waggoner Center for Alcohol & Addiction Research, University of Texas at Austin, Austin, Texas
| | - M. L. McCracken
- Waggoner Center for Alcohol & Addiction Research, University of Texas at Austin, Austin, Texas
| | - D. H. Gong
- Waggoner Center for Alcohol & Addiction Research, University of Texas at Austin, Austin, Texas
| | - J. R. Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California 94305-5117
| | - R. A. Harris
- Waggoner Center for Alcohol & Addiction Research, University of Texas at Austin, Austin, Texas
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Molecular targets and mechanisms for ethanol action in glycine receptors. Pharmacol Ther 2010; 127:53-65. [PMID: 20399807 DOI: 10.1016/j.pharmthera.2010.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 03/23/2010] [Indexed: 11/23/2022]
Abstract
Glycine receptors (GlyRs) are recognized as the primary mediators of neuronal inhibition in the spinal cord, brain stem and higher brain regions known to be sensitive to ethanol. Building evidence supports the notion that ethanol acting on GlyRs causes at least a subset of its behavioral effects and may be involved in modulating ethanol intake. For over two decades, GlyRs have been studied at the molecular level as targets for ethanol action. Despite the advances in understanding the effects of ethanol in vivo and in vitro, the precise molecular sites and mechanisms of action for ethanol in ligand-gated ion channels in general, and in GlyRs specifically, are just now starting to become understood. The present review focuses on advances in our knowledge produced by using molecular biology, pressure antagonism, electrophysiology and molecular modeling strategies over the last two decades to probe, identify and model the initial molecular sites and mechanisms of ethanol action in GlyRs. The molecular targets on the GlyR are covered on a global perspective, which includes the intracellular, transmembrane and extracellular domains. The latter has received increasing attention in recent years. Recent molecular models of the sites of ethanol action in GlyRs and their implications to our understanding of possible mechanism of ethanol action and novel targets for drug development in GlyRs are discussed.
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Disruption of an intersubunit electrostatic bond is a critical step in glycine receptor activation. Proc Natl Acad Sci U S A 2010; 107:7987-92. [PMID: 20385800 DOI: 10.1073/pnas.1001845107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proper regulation of neurotransmission requires that ligand-activated ion channels remain closed until agonist binds. How channels then open remains poorly understood. Glycine receptor (GlyR) gating is initiated by agonist binding at interfaces between adjacent subunits in the extracellular domain. Aspartate-97, located at the alpha1 GlyR interface, is a conserved residue in the cys-loop receptor superfamily. The mutation of D97 to arginine (D97R) causes spontaneous channel opening, with open and closed dwell times similar to those of maximally activated WT GlyR. Using a model of the N-terminal domain of the alpha1 GlyR, we hypothesized that an arginine-119 residue was forming intersubunit electrostatic bonds with D97. The D97R/R119E charge reversal restored this interaction, stabilizing channels in their closed states. Cysteine substitution shows that this link occurs between adjacent subunits. This intersubunit electrostatic interaction among GlyR subunits thus contributes to the stabilization of the closed channel state, and its disruption represents a critical step in GlyR activation.
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Crawford DK, Perkins DI, Trudell JR, Bertaccini EJ, Davies DL, Alkana RL. Roles for loop 2 residues of alpha1 glycine receptors in agonist activation. J Biol Chem 2008; 283:27698-27706. [PMID: 18658152 PMCID: PMC2562068 DOI: 10.1074/jbc.m802384200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 06/20/2008] [Indexed: 11/06/2022] Open
Abstract
The present study tested the hypothesis that several residues in Loop 2 of alpha1 glycine receptors (GlyRs) play important roles in mediating the transduction of agonist activation to channel gating. This was accomplished by investigating the effect of cysteine point mutations at positions 50-60 on glycine responses in alpha1GlyRs using two-electrode voltage clamp of Xenopus oocytes. Cysteine substitutions produced position-specific changes in glycine sensitivity that were consistent with a beta-turn structure of Loop 2, with odd-numbered residues in the beta-turn interacting with other agonist-activation elements at the interface between extracellular and transmembrane domains. We also tested the hypothesis that the charge at position 53 is important for agonist activation by measuring the glycine response of wild type (WT) and E53C GlyRs exposed to methanethiosulfonate reagents. As earlier, E53C GlyRs have a significantly higher EC(50) than WT GlyRs. Exposing E53C GlyRs to the negatively charged 2-sulfonatoethyl methanethiosulfonate, but not neutral 2-hydroxyethyl methanethiosulfonate, positively charged 2-aminoethyl methanethiosulfonate, or 2-trimethylammonioethyl methanethiosulfonate, decreased the glycine EC(50) to resemble WT GlyR responses. Exposure to these reagents did not significantly alter the glycine EC(50) for WT GlyRs. The latter findings suggest that the negative charge at position 53 is important for activation of GlyRs through its interaction with positive charge(s) in other neighboring agonist activation elements. Collectively, the findings provide the basis for a refined molecular model of alpha1GlyRs based on the recent x-ray structure of a prokaryotic pentameric ligand-gated ion channel and offer insight into the structure-function relationships in GlyRs and possibly other ligand-gated ion channels.
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Affiliation(s)
- Daniel K Crawford
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089; Neuroscience Graduate Program, University of Southern California, Los Angeles, California 90089
| | - Daya I Perkins
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089
| | - James R Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California 94305
| | - Edward J Bertaccini
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California 94305; Department of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California 94304
| | - Daryl L Davies
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089.
| | - Ronald L Alkana
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089; Neuroscience Graduate Program, University of Southern California, Los Angeles, California 90089
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Tomita Y, Kato R, Okochi M, Honda H. A motif detection and classification method for peptide sequences using genetic programming. J Biosci Bioeng 2008; 106:154-61. [DOI: 10.1263/jbb.106.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 05/07/2008] [Indexed: 11/17/2022]
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Trudell JR, Yue ME, Bertaccini EJ, Jenkins A, Harrison NL. Molecular modeling and mutagenesis reveals a tetradentate binding site for Zn2+ in GABA(A) alphabeta receptors and provides a structural basis for the modulating effect of the gamma subunit. J Chem Inf Model 2008; 48:344-9. [PMID: 18197653 DOI: 10.1021/ci700324a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gamma-aminobutyric acid type A receptors (GABA(A)-R) containing alpha1beta2gamma2 subunits are weakly inhibited by Zn2+, whereas receptors containing only the alpha1beta2 subunits are strongly inhibited. We built homology models of the ion pores of alpha1beta2 and alpha1beta2gamma2 GABA(A)-R using coordinates of the nicotinic acetylcholine receptor as a template. Threading the GABA(A)-R beta2 sequence onto this template placed the 17' histidine and the 20' glutamate residues at adjacent locations in the mouth of the pore, such that a nearly ideal tetradentate site for Zn2+ was formed from two histidine and two glutamate residues between adjacent beta subunits in the alpha1beta2 GABA(A)-R. Following optimization with CHARMM, the distance between the alpha-carbons of the adjacent histidine residues was approximately 9.2 A, close to the ideal distance for a Zn2+ binding site. Loss of inhibition by Zn2+ in alpha1beta2gamma2 GABA(A)-R can be explained by the geometry of these residues in the arrangement alpha1beta2gamma2alpha1beta2, in which the nearest C-alpha-C-alpha distance between the histidine residues is 15.5 A, too far apart for an energetically optimal Zn2+ binding site. We then mutated the gamma subunit at the 17' and/or 20' positions. Zn2+ inhibition was not restored in alpha1beta2gamma2 (I282H) receptors. A novel finding is that the modeling shows the native 20' lysine in gamma2 can compete with Zn2+ for binding to the inserted 17' histidine. Sensitivity to Zn2+ was restored in the double mutant receptor, alpha1beta2gamma2 (I282H; K285E), in which the competition with lysine was removed and a more favorable Zn2+ binding site was formed.
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Affiliation(s)
- James R Trudell
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305-5117, USA.
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Wotring VE, Weiss DS. Charge scan reveals an extended region at the intracellular end of the GABA receptor pore that can influence ion selectivity. J Gen Physiol 2008; 131:87-97. [PMID: 18079559 PMCID: PMC2174155 DOI: 10.1085/jgp.200609701] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 11/23/2007] [Indexed: 12/02/2022] Open
Abstract
Selective permeability is a fundamental property of ion channels. The Cys-loop receptor superfamily is composed of both excitatory (ACh, 5-HT) and inhibitory (GABA, glycine) neurotransmitter-operated ion channels. In the GABA receptor, it has been previously shown that the charge selectivity of the integral pore can be altered by a single mutation near the intracellular end of the second transmembrane-spanning domain (TM2). We have extended these findings and now show that charge selectivity of the anionic rho1 GABA receptor can be influenced by the introduction of glutamates, one at a time, over an 8-amino acid stretch (-2' to 5') in the proposed intracellular end of TM2 and the TM1-TM2 intracellular linker. Depending on the position, glutamate substitutions in this region produced sodium to chloride permeability ratios (P(Na)+(/Cl)-) varying from 0.64 to 3.4 (wild type P(Na)+(/Cl)- = 0). In addition to providing insight into the mechanism of ion selectivity, this functional evidence supports a model proposed for the homologous nicotinic acetylcholine receptor in which regions of the protein, in addition to TM2, form the ion pathway.
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Affiliation(s)
- Virginia E Wotring
- Department of Neurobiology, University of Alabama at Birmingham, AL 35294, USA
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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.
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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
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Bertaccini EJ, Trudell JR, Lindahl E. Normal-mode analysis of the glycine alpha1 receptor by three separate methods. J Chem Inf Model 2007; 47:1572-9. [PMID: 17602605 PMCID: PMC2530920 DOI: 10.1021/ci600566j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Predicting collective dynamics and structural changes in biological macromolecules is pivotal toward a better understanding of many biological processes. Limitations due to large system sizes and inaccessible time scales have prompted the development of alternative techniques for the calculation of such motions. In this work, we present the results of a normal-mode analysis technique based on molecular mechanics that enables the calculation of accurate force-field based vibrations of extremely large molecules and compare it with two elastic network approximate models. When applied to the glycine alpha1 receptor, all three normal-mode analysis algorithms demonstrate an "iris-like" gating motion. Such gating motions have implications for understanding the effects of anesthetic and other ligand binding sites and for the means of transducing agonist binding into ion channel opening. Unlike the more approximate methods, molecular mechanics based analyses can also reveal approximate vibrational frequencies. Such analyses may someday allow the use of protein dynamics elucidated via normal-mode calculations as additional endpoints for future drug design.
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Affiliation(s)
- Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305-5117, USA.
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17
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Crawford DK, Trudell JR, Bertaccini EJ, Li K, Davies DL, Alkana RL. Evidence that ethanol acts on a target in Loop 2 of the extracellular domain of alpha1 glycine receptors. J Neurochem 2007; 102:2097-2109. [PMID: 17561937 DOI: 10.1111/j.1471-4159.2007.04680.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable evidence indicates that ethanol acts on specific residues in the transmembrane domains of glycine receptors (GlyRs). In this study, we tested the hypothesis that the extracellular domain is also a target for ethanol action by investigating the effect of cysteine substitutions at positions 52 (extracellular domain) and 267 (transmembrane domain) on responses to n-alcohols and propyl methanethiosulfonate (PMTS) in alpha1GlyRs expressed in Xenopus oocytes. In support of the hypothesis: (i) The A52C mutation changed ethanol sensitivity compared to WT GlyRs; (ii) PMTS produced irreversible alcohol-like potentiation in A52C GlyRs; and (iii) PMTS binding reduced the n-chain alcohol cutoff in A52C GlyRs. Further studies used PMTS binding to cysteines at positions 52 or 267 to block ethanol action at one site in order to determine its effect at other site(s). In these situations, ethanol caused negative modulation when acting at position 52 and positive modulation when acting at position 267. Collectively, these findings parallel the evidence that established the TM domain as a target for ethanol, suggest that positions 52 and 267 are part of the same alcohol pocket and indicate that the net effect of ethanol on GlyR function reflects the summation of its positive and negative modulatory effects on different targets.
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Affiliation(s)
- Daniel K Crawford
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
| | - James R Trudell
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
| | - Edward J Bertaccini
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
| | - Kaixun Li
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
| | - Daryl L Davies
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
| | - Ronald L Alkana
- Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USANeuroscience Graduate Program, University of Southern California, Los Angeles, California, USADepartment of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, California, USADepartment of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, USA
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18
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Wiles AM, Naider F, Becker JM. Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family. Res Microbiol 2006; 157:395-406. [PMID: 16364604 DOI: 10.1016/j.resmic.2005.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 10/06/2005] [Accepted: 10/07/2005] [Indexed: 11/25/2022]
Abstract
Few polytopic membrane proteins have had their topology determined experimentally. Often, researchers turn to an algorithm to predict where the transmembrane domains might lie. Here we use a consensus method, using six different transmembrane domain prediction algorithms on six members of the oligopeptide transport family, all of which have been experimentally characterized. PSI-BLAST results indicate that the six chosen oligopeptide transport family members are distributed throughout most branches of the phylogram, suggesting that these members represent a broad view of the oligopeptide transport family. We combined the prediction algorithms with a multiple sequence alignment, and consensus transmembrane domains were assigned not only based on algorithmic output, but also based on conserved familial motifs found by analysis of the PSI-BLAST results. The consensus method combined with the "charge-difference rule" yields a model topology for the family containing 12 transmembrane domains with the N- and C-termini facing extracellular.
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Affiliation(s)
- Amy M Wiles
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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19
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Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, Kasukawa T, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD. Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. PLoS Genet 2006; 2:e46. [PMID: 16683029 PMCID: PMC1449889 DOI: 10.1371/journal.pgen.0020046] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Accepted: 02/10/2006] [Indexed: 11/18/2022] Open
Abstract
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two features: endoplasmic reticulum signal peptides and alpha-helical transmembrane domains. These features allow protein sequences to be classified into one of five membrane organization categories: soluble intracellular proteins, soluble secreted proteins, type I membrane proteins, type II membrane proteins, and multi-spanning membrane proteins. Generation of protein isoforms with variable membrane organizations can change a protein's subcellular localization or association with the membrane. Application of MemO, a membrane organization annotation pipeline, to the FANTOM3 Isoform Protein Sequence mouse protein set revealed that within the 8,032 transcriptional units (TUs) with multiple protein isoforms, 573 had variation in their use of signal peptides, 1,527 had variation in their use of transmembrane domains, and 615 generated protein isoforms from distinct membrane organization classes. The mechanisms underlying these transcript variations were analyzed. While TUs were identified encoding all pairwise combinations of membrane organization categories, the most common was conversion of membrane proteins to soluble proteins. Observed within our high-confidence set were 156 TUs predicted to generate both extracellular soluble and membrane proteins, and 217 TUs generating both intracellular soluble and membrane proteins. The differential use of endoplasmic reticulum signal peptides and transmembrane domains is a common occurrence within the variable protein output of TUs. The generation of protein isoforms that are targeted to multiple subcellular locations represents a major functional consequence of transcript variation within the mouse transcriptome.
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Affiliation(s)
- Melissa J Davis
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
| | - Kelly A Hanson
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
| | - Francis Clark
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
- Advanced Computational Modeling Centre, University of Queensland, St. Lucia, Queensland, Australia
| | - J. Lynn Fink
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
| | - Fasheng Zhang
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
| | - Takeya Kasukawa
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
| | - Chikatoshi Kai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
| | - Jun Kawai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
| | - Piero Carninci
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
| | - Yoshihide Hayashizaki
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
| | - Rohan D Teasdale
- Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia
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20
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Bertaccini E, Trudell J, Lindahl E. Normal mode analysis reveals the channel gating motion within a ligand gated ion channel model. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.ics.2005.07.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Lobo IA, Harris RA. Sites of alcohol and volatile anesthetic action on glycine receptors. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2005; 65:53-87. [PMID: 16140053 DOI: 10.1016/s0074-7742(04)65003-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Ingrid A Lobo
- Institute for Cellular and Molecular Biology, Waggoner Center for Alcohol and Addiction Research, Section of Neurobiology, University of Texas at Austin, Austin, Texas 78712, USA
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22
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Lobo IA, Trudell JR, Harris RA. Accessibility to residues in transmembrane segment four of the glycine receptor. Neuropharmacology 2005; 50:174-81. [PMID: 16225893 DOI: 10.1016/j.neuropharm.2005.08.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Revised: 08/23/2005] [Accepted: 08/24/2005] [Indexed: 11/26/2022]
Abstract
Glycine receptors (GlyRs) are members of the ligand-gated ion channel superfamily. Each subunit has four transmembrane segments (TM1-TM4). Several studies suggest that amino acids in all four TMs face into a water-filled, alcohol and anesthetic binding cavity in the extracellular portion of the transmembrane domain. TM4 should contribute a "wall" to this cavity, but the residues involved are unknown. Here, we determined the ability of an alcohol analog, propyl methanethiosulfonate (propyl MTS), to covalently react with twelve GlyR TM4 positions (I401-I412) after mutating the original amino acids to cysteines. Reactivity of a cysteine with propyl MTS implies that the cysteine is exposed to water. W407C, I409C, Y410C, and K411C showed altered receptor function following reaction with propyl MTS in the presence or absence of glycine. The cysteine mutations alone eliminated the effects of ethanol for I409C, Y410C, and K411C, and reduced the effects of octanol for I409C and isoflurane for K411C. The ability of propyl MTS to reduce isoflurane and chloroform potentiation was examined in the reactive mutants. Potentiation by isoflurane was significantly reduced for I409C after reaction. These data demonstrate water-accessibility of specific TM4 positions in the GlyR and suggest involvement of these residues with alcohol and anesthetic action.
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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, 2500 Speedway, MBB 1.124, A4800 Austin, TX 78712, USA.
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23
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Beuming T, Weinstein H. Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT. Protein Eng Des Sel 2005; 18:119-25. [PMID: 15820982 DOI: 10.1093/protein/gzi013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The availability of both EM and high-resolution crystallographic data for several membrane proteins (MPs) permits a detailed evaluation of the ability of molecular modeling techniques to complement EM data in the development of models of MPs. A protocol for this purpose is presented, consisting of (1) identifying transmembrane (TM) domains from sequence; (2) assigning buried and lipid-exposed faces of the TM domains; and (3) assembling the TM domains into a bundle, based on geometric restraints obtained from the EM data. The protocol is validated by predicting the structures of several 7- and 12-TM MPs to within 3-5 A r.m.s.d. from their crystal structures. The protocol is applied to generate a model of the oxalate transporter OxlT, for which a high-resolution structure is not yet available.
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Affiliation(s)
- Thijs Beuming
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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24
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Bertaccini EJ, Shapiro J, Brutlag DL, Trudell JR. Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site. J Chem Inf Model 2004; 45:128-35. [PMID: 15667138 DOI: 10.1021/ci0497399] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The superfamily of ligand-gated ion channels (LGICs) has been implicated in anesthetic and alcohol responses. Mutations within glycine and GABA receptors have demonstrated that possible sites of anesthetic action exist within the transmembrane subunits of these receptors. The exact molecular arrangement of this transmembrane region remains at intermediate resolution with current experimental techniques. Homology modeling methods were therefore combined with experimental data to produce a more exact model of this region. A consensus from multiple bioinformatics techniques predicted the topology within the transmembrane domain of a glycine alpha one receptor (GlyRa1) to be alpha helical. This fold information was combined with sequence information using the SeqFold algorithm to search for modeling templates. Independently, the FoldMiner algorithm was used to search for templates that had structural folds similar to published coordinates of the homologous nAChR (1OED). Both SeqFold and Foldminer identified the same modeling template. The GlyRa1 sequence was aligned with this template using multiple scoring criteria. Refinement of the alignment closed gaps to produce agreement with labeling studies carried out on the homologous receptors of the superfamily. Structural assignment and refinement was achieved using Modeler. The final structure demonstrated a cavity within the core of a four-helix bundle. Residues known to be involved in modulating anesthetic potency converge on and line this cavity. This suggests that the binding sites for volatile anesthetics in the LGICs are the cavities formed within the core of transmembrane four-helix bundles.
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Affiliation(s)
- Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305-5117, USA.
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25
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Trudell JR, Bertaccini E. Comparative modeling of a GABAA alpha1 receptor using three crystal structures as templates. J Mol Graph Model 2004; 23:39-49. [PMID: 15331052 DOI: 10.1016/j.jmgm.2004.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 02/20/2004] [Accepted: 03/03/2004] [Indexed: 11/27/2022]
Abstract
We built a model of a GABAA alpha1 receptor (GABAAR) that combines the ligand binding (LBD) and the transmembrane domains (TMD). We used six steps: (1) a four-alpha helical bundle in the crystal structure of bovine cytochrome c oxidase (2OCC) was identified as a template for the TMD of a single subunit. (2) The five pore-forming alpha helices of a bacterial mechanosensitive channel (1MSL) served as a template for the pentameric ion channel. (3) Five copies of the tetrameric template from 2OCC were superimposed on 1MSL to produce a homopentamer containing 20 alpha helices arranged around a funnel-shaped central pore. (4) Five copies of the GABAAR sequence were threaded onto the alpha-helical segments of this template and inter-helical loops were generated to produce the TMD model. (5) A model of the LBD was built by threading the aligned sequence of GABAAR onto the crystal structure of the acetylcholine binding protein (1I9B). (6) The models of the LBD and the TMD were aligned along a common five-fold axis, moved together along that axis until in vdW contact, merged, and then optimized with restrained molecular dynamics. Our model corresponds closely with recently published coordinates of the acetylcholine receptor (1OED) but also explains additional features. Our model reveals structures of loops that were not visible in the cryoelectron micrograph and satisfies most labeling and mutagenesis data. It also suggests mechanisms for ligand binding transduction, ion selectivity, and anesthetic binding.
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Affiliation(s)
- J R Trudell
- Department of Anesthesia, Stanford University, CA 94305-5117, USA.
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26
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Lobo IA, Mascia MP, Trudell JR, Harris RA. Channel Gating of the Glycine Receptor Changes Accessibility to Residues Implicated in Receptor Potentiation by Alcohols and Anesthetics. J Biol Chem 2004; 279:33919-27. [PMID: 15169788 DOI: 10.1074/jbc.m313941200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The glycine receptor is a target for both alcohols and anesthetics, and certain amino acids in the alpha1 subunit transmembrane segments (TM) are critical for drug effects. Introducing larger amino acids at these positions increases the potency of glycine, suggesting that introducing larger residues, or drug molecules, into the drug-binding cavity facilitates channel opening. A possible mechanism for these actions is that the volume of the cavity expands and contracts during channel opening and closing. To investigate this hypothesis, mutations for amino acids in TM1 (I229C) and TM2 (G256C, T259C, V260C, M263C, T264C, S267C, S270C) and TM3 (A288C) were individually expressed in Xenopus laevis oocytes. The ability of sulfhydryl-specific alkyl methanethiosulfonate (MTS) compounds of different lengths to covalently react with introduced cysteines in both the closed and open states of the receptor was determined. S267C was accessible to short chain (C3-C8) MTS in both open and closed states, but was only accessible to longer chain (C10-C16) MTS compounds in the open state. Reaction with S267C was faster in the open state. I229C and A288C showed state-dependent reaction with MTS only in the presence of agonist. M263C and S270C were also accessible to MTS labeling. Mutated residues more intracellular than M263C did not react, indicating a floor of the cavity. These data demonstrate that the conformational changes accompanying channel gating increase accessibility to amino acids critical for drug action in TM1, TM2, and TM3, which may provide a mechanism by which alcohols and anesthetics can act on glycine (and likely other) receptors.
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Affiliation(s)
- Ingrid A Lobo
- Institute for Cellular and Molecular Biology, Waggoner Center for Alcohol and Addiction Research and Section of Neurobiology, The University of Texas, Austin, Texas 78712, USA.
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27
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Filippova N, Wotring VE, Weiss DS. Evidence that the TM1-TM2 Loop Contributes to the ρ1 GABA Receptor Pore. J Biol Chem 2004; 279:20906-14. [PMID: 15007065 DOI: 10.1074/jbc.m401012200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Considerable evidence indicates the second transmembrane domain (TM2) of the gamma-aminobutyric acid (GABA) receptor lines the integral ion pore. To further delineate the structures that constitute the ion pore and selectivity filter of the rho1 GABA receptor, we used the substituted cysteine accessibility method with charged reagents to identify anion- and cation-accessible surfaces. Twenty-one consecutive residues were mutated to cysteine, one at a time, in the presumed intracellular end of the first transmembrane domain (TM1; Ala(271)-Met(276)), the entire linker connecting TM1 to TM2 (Leu(277)-Arg(287)), and the presumed intracellular end of TM2 (Ala(288)-Ala(291)). Positively (MTSEA(+)) and negatively (pCMBS(-)) charged sulfhydryl reagents, as well as Cd(2+), were added extracellularly to test accessibility of the engineered cysteines. Four of the mutants, all at the intracellular end of TM2 (R287C, V289C, P290C, A291C), were accessible to positively charged reagents, whereas seven mutants (A271C, T272C, L277C, W279C, V280C, P290C, A291C) were functionally modified by negatively charged pCMBS(-). These seven modified residues were at the intracellular end of TM2, in the TM1-TM2 linker, and at the intracellular end of TM1. In nearly all cases (excluding P290C), the rate and the degree of modification were state-dependent, with greater accessibility in the presence of agonist. Select cysteine mutants were combined with a point mutation (A291E) that converted the pore from chloride- to non-selective. In this case, positively charged reagents could modify residues in the TM1-TM2 linker (Leu(277) and Val(280)), supporting the notion that the modifying reagents were reaching their target through the pore. Taken together, our results suggest that, up to its intracellular end, the TM2 domain is not charge selective. In addition, we propose that the TM1-TM2 linker and the intracellular end of TM1 are along the pathway of the permeating ion. These findings may lend new insights into the structure of the GABA receptor pore.
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Affiliation(s)
- Natalia Filippova
- Department of Neurobiology, University of Alabama at Birmingham School of Medicine, 1719 Sixth Avenue South, CIRC410, Birmingham, AL 35294, USA
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28
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Borghese CM, Henderson LA, Bleck V, Trudell JR, Harris RA. Sites of Excitatory and Inhibitory Actions of Alcohols on Neuronal α2β4 Nicotinic Acetylcholine Receptors. J Pharmacol Exp Ther 2003. [DOI: 10.1124/jpet.103.053710] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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29
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Sonner JM, Antognini JF, Dutton RC, Flood P, Gray AT, Harris RA, Homanics GE, Kendig J, Orser B, Raines DE, Trudell J, Vissel B, Eger EI. Inhaled anesthetics and immobility: mechanisms, mysteries, and minimum alveolar anesthetic concentration. Anesth Analg 2003; 97:718-740. [PMID: 12933393 DOI: 10.1213/01.ane.0000081063.76651.33] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Studies using molecular modeling, genetic engineering, neurophysiology/pharmacology, and whole animals have advanced our understanding of where and how inhaled anesthetics act to produce immobility (minimum alveolar anesthetic concentration; MAC) by actions on the spinal cord. Numerous ligand- and voltage-gated channels might plausibly mediate MAC, and specific amino acid sites in certain receptors present likely candidates for mediation. However, in vivo studies to date suggest that several channels or receptors may not be mediators (e.g., gamma-aminobutyric acid A, acetylcholine, potassium, 5-hydroxytryptamine-3, opioids, and alpha(2)-adrenergic), whereas other receptors/channels (e.g., glycine, N-methyl-D-aspartate, and sodium) remain credible candidates.
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Affiliation(s)
- James M Sonner
- *Department of Anesthesia and Perioperative Care, University of California, San Francisco, California; †Department of Anesthesiology, University of California, Davis, California; ‡Columbia University, New York, New York; §University of Texas, Austin, Texas; ∥University of Pittsburgh, Pittsburgh, Pennsylvania; ¶Stanford University, Palo Alto, California; #University of Toronto, Toronto, Canada; **Department of Anaesthesia, Harvard Medical School, Cambridge, Massachusetts; and ††Garvan Institute of Medical Research, Darlinghurst, Australia
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30
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Arias HR, Kem WR, Trudell JR, Blanton MP. Unique general anesthetic binding sites within distinct conformational states of the nicotinic acetylcholine receptor. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2003; 54:1-50. [PMID: 12785284 DOI: 10.1016/s0074-7742(03)54002-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
General anesthesia is a complex behavioral state provoked by the pharmacological action of a broad range of structurally different hydrophobic molecules called general anesthetics (GAs) on receptor members of the genetically linked ligand-gated ion channel (LGIC) superfamily. This superfamily includes nicotinic acetylcholine (AChRs), type A and C gamma-aminobutyric acid (GABAAR and GABACR), glycine (GlyR), and type 3 5-hydroxytryptamine (5-HT3R) receptors. This review focuses on recent advances in the localization of GA binding sites on conformationally and compositionally distinct AChRs. The experimental evidence outlined in this review suggests that: 1. Several neuronal-type AChRs might be targets for the pharmacological action of distinct GAs. 2. The molecular components of a specific GA binding site on a certain receptor subtype are different from the structural determinants of the locus for the same GA on a different receptor subtype. 3. There are unique binding sites for distinct GAs in the same receptor protein. 4. A GA can activate, potentiate, or inhibit an ion channel, indicating the existence of more than one binding site for the same GA. 5. The affinity of a specific GA depends on the conformational state of the receptor. 6. GAs inhibition channels by at least two mechanisms, an open-channel-blocking and/or an allosteric mechanism. 7. Certain GAs may inhibit AChR function by competing for the agonist binding sites or by augmenting the desensitization rate.
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Affiliation(s)
- Hugo R Arias
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, USA
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31
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Kash TL, Jenkins A, Kelley JC, Trudell JR, Harrison NL. Coupling of agonist binding to channel gating in the GABA(A) receptor. Nature 2003; 421:272-5. [PMID: 12529644 DOI: 10.1038/nature01280] [Citation(s) in RCA: 268] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2002] [Accepted: 10/21/2002] [Indexed: 11/08/2022]
Abstract
Neurotransmitters such as acetylcholine and GABA (gamma-aminobutyric acid) mediate rapid synaptic transmission by activating receptors belonging to the gene superfamily of ligand-gated ion channels (LGICs). These channels are pentameric proteins that function as signal transducers, converting chemical messages into electrical signals. Neurotransmitters activate LGICs by interacting with a ligand-binding site, triggering a conformational change in the protein that results in the opening of an ion channel. This process, which is known as 'gating', occurs rapidly and reversibly, but the molecular rearrangements involved are not well understood. Here we show that optimal gating in the GABA(A) receptor, a member of the LGIC superfamily, is dependent on electrostatic interactions between the negatively charged Asp 57 and Asp 149 residues in extracellular loops 2 and 7, and the positively charged Lys 279 residue in the transmembrane 2-3 linker region of the alpha1-subunit. During gating, Asp 149 and Lys 279 seem to move closer to one another, providing a potential mechanism for the coupling of ligand binding to opening of the ion channel.
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Affiliation(s)
- Thomas L Kash
- Graduate Program in Neuroscience, Weill Graduate School of Biomedical Sciences, Cornell University, New York, New York 10021, USA
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Trudell J. Unique assignment of inter-subunit association in GABA(A) alpha 1 beta 3 gamma 2 receptors determined by molecular modeling. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1565:91-6. [PMID: 12225856 DOI: 10.1016/s0005-2736(02)00512-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Recent publications defined requirements for inter-subunit contacts in a benzodiazepine-sensitive GABA(A) receptor (GABA(A)R alpha 1 beta 3 gamma 2). There is strong evidence that the heteropentameric receptor contains two alpha 1, two beta 3, and one gamma 2 subunit. However, the available data do not distinguish two possibilities: When viewed clockwise from an extracellular viewpoint the subunits could be arranged in either gamma 2 beta 3 alpha 1 beta 3 alpha 1 or gamma 2 alpha 1 beta 3 alpha 1 beta 3 configurations. Here we use molecular modeling to thread the relevant GABA(A)R subunit sequences onto a template of homopentameric subunits in the crystal structure of the acetylcholine binding protein (AChBP). The GABA(A) sequences are known to have 15-18% identity with the acetylcholine binding protein and nearly all residues that are conserved within the nAChR family are present in AChBP. The correctly aligned GABA(A) sequences were threaded onto the AChBP template in the gamma 2 beta 3 alpha 1 beta 3 alpha 1 or gamma 2 alpha 1 beta 3 alpha 1 beta 3 arrangements. Only the gamma 2 alpha 1 beta 3 alpha 1 beta 3 arrangement satisfied three known criteria: (1) alpha 1 His(102) binds at the gamma 2 subunit interface in proximity to gamma 2 residues Thr(142), Phe(77), and Met(130); (2) alpha 1 residues 80-100 bind near gamma 2 residues 91-104; and (3) alpha 1 residues 58-67 bind near the beta 3 subunit interface. In addition to predicting the most likely inter-subunit arrangement, the model predicts which residues form the GABA and benzodiazepine binding sites.
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Affiliation(s)
- James Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Stanford, CA 94305-5117, USA.
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Jenkins A, Andreasen A, Trudell JR, Harrison NL. Tryptophan scanning mutagenesis in TM4 of the GABA(A) receptor alpha1 subunit: implications for modulation by inhaled anesthetics and ion channel structure. Neuropharmacology 2002; 43:669-78. [PMID: 12367612 DOI: 10.1016/s0028-3908(02)00175-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Previous studies have shown that amino acid residues in trans-membrane (TM) segments 1, 2 and 3 of the alpha subunit are critical for the enhancement of GABA(A) receptor function by inhaled anesthetics. In this study we used tryptophan (Trp) scanning mutagenesis between Ile 406 and Asn 417 in the alpha1 subunit to determine the effects of Trp substitution in the fourth transmembrane segment (TM4) on receptor gating and anesthetic modulation. Wild-type and mutant alpha1 subunits were transiently expressed in HEK 293 cells with wild-type beta2 and gamma2s subunits and GABA-activated currents were recorded using whole-cell voltage clamp. The potentiation by three inhaled anesthetics (isoflurane, halothane and chloroform) of responses elicited by a submaximal concentration of GABA were also examined.EC(50) values for GABA at the mutant receptors were in the range 4-60 microM (wild-type=20 microM), indicating that Trp substitution can alter the apparent affinity of the receptor for GABA positively or negatively, dependent on position. The variation of the calculated EC(50) value for GABA exhibited an interesting periodicity, with the cycle length for each repeat corresponding to approximately 3.6 amino acids. These data are consistent with an alpha-helical structure for the TM4 segment of the alpha subunit. Several of these Trp point mutations altered the ability of one or more of the three inhaled anesthetics to modulate receptor function; four of the 12 mutations abolished receptor modulation by one or more of the anesthetics tested. These data are consistent with a role for these residues at the extracellular end of TM4 in anesthetic modulation of GABA(A) receptors.
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Affiliation(s)
- Andrew Jenkins
- Department of Anesthesiology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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Trudell JR, Bertaccini E. Molecular modelling of specific and non-specific anaesthetic interactions. Br J Anaesth 2002; 89:32-40. [PMID: 12173239 DOI: 10.1093/bja/aef157] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There has been rapid progress in molecular modelling in recent years. The convergence of improved software for molecular mechanics and dynamics, techniques for chimeric substitution and site-directed mutations, and the first x-ray structures of transmembrane ion channels have made it possible to build and test models of anaesthetic binding sites. These models have served as guides for site-directed mutagenesis and as starting points for understanding the molecular dynamics of anaesthetic-site interactions. Ligand-gated ion channels are targets for inhaled anaesthetics and alcohols in the central nervous system. The inhibitory strychnine-sensitive glycine and gamma-aminobutyric acid type A receptors are positively modulated by anaesthetics and alcohols; site-directed mutagenesis techniques have identified amino acid residues important for the action of volatile anaesthetics and alcohols in these receptors. Key questions are whether these amino acid mutations form part of alcohol- or anaesthetic-binding sites or if they alter protein stability in a way that allows anaesthetic molecules to act remotely by non-specific mechanisms. It is likely that molecular modelling will play a major role in answering these questions.
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Affiliation(s)
- J R Trudell
- Department of Anaesthesia, Beckman Program for Molecular and Genetic Medicine, Stanford University, Stanford, CA 94305-5117, USA
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