Properties of Specific Alcohol Binding Sites

Summary

Principal Investigator: James Trudell
Affiliation: Stanford University
Country: USA
Abstract: Alcohol abuse and alcoholism are major health problems. It is likely that a solution to these problems will require an understanding of the effects of alcohol on neuronal ion channel proteins. Specific binding sites for alcohols have been described in the transmembrane (TM) domain of the superfamily of ligand-gated ion channels (LGIC's) that includes glycine (GlyRa1), GABA, nicotinic acetylcholine, and 5-HT3 receptors. Our global hypothesis is that alcohols bind within cavities that are bounded by TM segments of these receptors and preferentially stabilize specific channel substates. Our goal is to define the properties of those sites that mediate binding and efficacy of alcohol and alcohol antagonists in GlyRa1. These binding sites may provide a common motif for binding of alcohols within other classes of ion channels and other important proteins. We will build computational models of binding sites in GlyRa1 and design specific site-directed mutations to test these hypothesis. These mutations will be constructed and tested by our collaborator, Dr. R. A. Harris. Aim 1. We will test the hypothesis that amino acid residues from all four transmembrane helices of GlyRa1 contribute to a binding site for alcohols. We will develop computational models to delineate the dimensions of these sites. We will use these models to predict where covalent binding of alkyl methanethiosulfonate (MTS) reagents would mimic alcohol binding. The predictions will be tested in the Harris laboratory by expressing GlyRa1 containing site-directed cysteine substitutions in oocytes. They will apply MTS reagents to the oocytes and measure the effects on glycine-induced currents. Aim 2. We will test the hypothesis that double site directed cysteine mutations can clarify the refined tertiary structure of the GlyRa1 and distinguish our model from one based on the torpedo nAChR. While the overall structure of our GlyRa1 model and the nAChR model of Unwin are in global agreement, there are important differences in the orientation of transmembrane helices and residues bounding a possible alcohol- binding site. The Harris laboratory will test these predictions by crosslinking site-directed di-cysteines. In summary, knowledge of alcohol binding sites in GlyRa1 will increase our understanding of alcohol action in LGIC's. The results may reveal general motifs for action in other systems affected by alcohol and aid in the design of alcohol antagonists.
Funding Period: 2001-12-01 - 2010-06-30
more information: NIH RePORT

Top Publications

  1. ncbi Homology modeling of a human glycine alpha 1 receptor reveals a plausible anesthetic binding site
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 45:128-35. 2005
  2. ncbi Identifying the binding site(s) for antidepressants on the Torpedo nicotinic acetylcholine receptor: [3H]2-azidoimipramine photolabeling and molecular dynamics studies
    Mitesh Sanghvi
    Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
    Biochim Biophys Acta 1778:2690-9. 2008
  3. ncbi Roles for loop 2 residues of alpha1 glycine receptors in agonist activation
    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, USA
    J Biol Chem 283:27698-706. 2008
  4. ncbi Targets for ethanol action and antagonism in loop 2 of the extracellular domain of glycine receptors
    Daya I Perkins
    Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
    J Neurochem 106:1337-49. 2008
  5. ncbi Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 48:855-60. 2008
  6. ncbi 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
    James R Trudell
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 48:344-9. 2008
  7. ncbi Cross-linking of sites involved with alcohol action between transmembrane segments 1 and 3 of the glycine receptor following activation
    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
    J Neurochem 104:1649-62. 2008
  8. ncbi Normal-mode analysis of the glycine alpha1 receptor by three separate methods
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 47:1572-9. 2007
  9. ncbi Evidence that ethanol acts on a target in Loop 2 of the extracellular domain of alpha1 glycine receptors
    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, USA
    J Neurochem 102:2097-109. 2007
  10. ncbi The minimum alveolar anesthetic concentration of 2-, 3-, and 4-alcohols and ketones in rats: relevance to anesthetic mechanisms
    Albert Won
    Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143-0464, USA
    Anesth Analg 102:1419-26. 2006

Scientific Experts

  • James Trudell
  • Edward J Bertaccini
  • Daniel K Crawford
  • Daya I Perkins
  • Daryl L Davies
  • Ronald L Alkana
  • Ingrid A Lobo
  • R Adron Harris
  • Mitesh Sanghvi
  • Erik Lindahl
  • Albert Won
  • Liana Asatryan
  • Michael P Blanton
  • Hugo R Arias
  • Krzysztof Jozwiak
  • Ayman K Hamouda
  • Titia Sixma
  • Kaixun Li
  • Irene Oh
  • Edmond I Eger
  • Mark Liao
  • James M Sonner
  • Michael J Laster
  • Robert Brosnan
  • Douglas L Brutlag
  • Jessica Shapiro

Detail Information

Publications12

  1. ncbi Homology modeling of a human glycine alpha 1 receptor reveals a plausible anesthetic binding site
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 45:128-35. 2005
    ..This suggests that the binding sites for volatile anesthetics in the LGICs are the cavities formed within the core of transmembrane four-helix bundles...
  2. ncbi Identifying the binding site(s) for antidepressants on the Torpedo nicotinic acetylcholine receptor: [3H]2-azidoimipramine photolabeling and molecular dynamics studies
    Mitesh Sanghvi
    Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
    Biochim Biophys Acta 1778:2690-9. 2008
    ..Collectively, these results are consistent with a model where PCP and TCA bind to overlapping sites within the lumen of the Torpedo nAChR ion channel...
  3. ncbi Roles for loop 2 residues of alpha1 glycine receptors in agonist activation
    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, USA
    J Biol Chem 283:27698-706. 2008
    ....
  4. ncbi Targets for ethanol action and antagonism in loop 2 of the extracellular domain of glycine receptors
    Daya I Perkins
    Alcohol and Brain Research Laboratory, Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
    J Neurochem 106:1337-49. 2008
    ..These findings should help in the development of pharmacological agents that antagonize ethanol...
  5. ncbi Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 48:855-60. 2008
    ..The results suggest that alterations in receptor dynamics could be a general feature of ligand binding...
  6. ncbi 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
    James R Trudell
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 48:344-9. 2008
    ..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...
  7. ncbi Cross-linking of sites involved with alcohol action between transmembrane segments 1 and 3 of the glycine receptor following activation
    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
    J Neurochem 104:1649-62. 2008
    ....
  8. ncbi Normal-mode analysis of the glycine alpha1 receptor by three separate methods
    Edward J Bertaccini
    Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305 5117, USA
    J Chem Inf Model 47:1572-9. 2007
    ..Such analyses may someday allow the use of protein dynamics elucidated via normal-mode calculations as additional endpoints for future drug design...
  9. ncbi Evidence that ethanol acts on a target in Loop 2 of the extracellular domain of alpha1 glycine receptors
    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, USA
    J Neurochem 102:2097-109. 2007
    ....
  10. ncbi The minimum alveolar anesthetic concentration of 2-, 3-, and 4-alcohols and ketones in rats: relevance to anesthetic mechanisms
    Albert Won
    Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143-0464, USA
    Anesth Analg 102:1419-26. 2006
    ..The oil/gas partition coefficient predicted potency as well as, or better than, either chain length or oxygen placement. Hydrophilicity, as indicated by the saline/gas partition coefficient, also seemed to influence potency...
  11. ncbi Accessibility to residues in transmembrane segment four of the glycine receptor
    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
    Neuropharmacology 50:174-81. 2006
    ..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...
  12. ncbi Loop 2 structure in glycine and GABA(A) receptors plays a key role in determining ethanol sensitivity
    Daya I Perkins
    Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, USA
    J Biol Chem 284:27304-14. 2009
    ..In addition to being the first GlyR model threaded on GLIC, the juxtaposition of the two structures led to a possible mechanistic explanation for the effects of ethanol on GlyR-based on changes in Loop 2 structure...