1
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Infield DT, Schene ME, Galpin JD, Ahern CA. Genetic Code Expansion for Mechanistic Studies in Ion Channels: An (Un)natural Union of Chemistry and Biology. Chem Rev 2024. [PMID: 39207057 DOI: 10.1021/acs.chemrev.4c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Ion channels play central roles in biology and human health by catalyzing the transmembrane flow of electrical charge. These proteins are ideal targets for genetic code expansion (GCE) methods because it is feasible to measure ion channel activity from miniscule amounts of protein and to analyze the resulting data via rigorous, established biophysical methods. In an ideal scenario, the encoding of synthetic, noncanonical amino acids via GCE allows the experimenter to ask questions inaccessible to traditional methods. For this reason, GCE has been successfully applied to a variety of ligand- and voltage-gated channels wherein extensive structural, functional, and pharmacological data exist. Here, we provide a comprehensive summary of GCE as applied to ion channels. We begin with an overview of the methods used to encode noncanonical amino acids in channels and then describe mechanistic studies wherein GCE was used for photochemistry (cross-linking; caged amino acids) and atomic mutagenesis (isosteric manipulation of charge and aromaticity; backbone mutation). Lastly, we cover recent advances in the encoding of fluorescent amino acids for the real-time study of protein conformational dynamics.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Miranda E Schene
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
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2
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Schene ME, Infield DT, Ahern CA. Expression and purification of fluorinated proteins from mammalian suspension culture. Methods Enzymol 2024; 696:341-354. [PMID: 38658087 DOI: 10.1016/bs.mie.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The site-specific encoding of noncanonical amino acids allows for the introduction of rationalized chemistry into a target protein. Of the methods that enable this technology, evolved tRNA and synthetase pairs offer the potential for expanded protein production and purification. Such an approach combines the versatility of solid-phase peptide synthesis with the scalable features of recombinant protein production. We describe the large scale production and purification of eukaryotic proteins bearing fluorinated phenylalanine in mammalian suspension cell preparations. Downstream applications of this approach include scalable recombinant protein preparation for ligand binding assays with small molecules and ligands, protein structure determination, and protein stability assays.
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Affiliation(s)
- Miranda E Schene
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA.
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3
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Lummis SCR, Dougherty DA. Expression of Mutant Glycine Receptors in Xenopus Oocytes Using Canonical and Non-Canonical Amino Acids Reveals Distinct Roles of Conserved Proline Residues. MEMBRANES 2022; 12:1012. [PMID: 36295771 PMCID: PMC9607081 DOI: 10.3390/membranes12101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Pentameric ligand-gated ion channels (pLGIC) play important roles in fast neuronal signal transmission. Functional receptors are pentamers, with each subunit having an extracellular domain (ECD), a transmembrane domain (TMD) and an intracellular domain. The binding of the agonist to the ECD induces a structural change that is transduced to the TMD to open the channel. Molecular details of this process are emerging, but a comprehensive understanding is still lacking. Proline (Pro) is one amino acid that has attracted much interest; its unusual features generate bends in loops and kinks and bulges in helices, which can be essential for function in some pLGICs. Here, we explore the roles of four conserved Pros in the glycine receptor (GlyR), creating substitutions with canonical and noncanonical amino acids, characterizing them using two electrode voltage clamp electrophysiology in Xenopus oocytes, and interpreting changes in receptor parameters using structural data from the open and closed states of the receptor. The data reveal that for efficient function, the Pro in the α1β1 loop is needed to create a turn and to be the correct size and shape to interact with nearby residues; the peptide bond of the Pro in the Cys-loop requires the cis conformation; and the Pros in loop A and M1 allow efficient function because of their reduced hydrogen bonding capacity. These data are broadly consistent with data from other pLGICs, and therefore likely represent the important features of these Pros in all members of the family.
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Affiliation(s)
- Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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4
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Bhatt M, Di Iacovo A, Romanazzi T, Roseti C, Cinquetti R, Bossi E. The "www" of Xenopus laevis Oocytes: The Why, When, What of Xenopus laevis Oocytes in Membrane Transporters Research. MEMBRANES 2022; 12:membranes12100927. [PMID: 36295686 PMCID: PMC9610376 DOI: 10.3390/membranes12100927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 05/16/2023]
Abstract
After 50 years, the heterologous expression of proteins in Xenopus laevis oocytes is still essential in many research fields. New approaches and revised protocols, but also classical methods, such as the two-electrode voltage clamp, are applied in studying membrane transporters. New and old methods for investigating the activity and the expression of Solute Carriers (SLC) are reviewed, and the kinds of experiment that are still useful to perform with this kind of cell are reported. Xenopus laevis oocytes at the full-grown stage have a highly efficient biosynthetic apparatus that correctly targets functional proteins at the defined compartment. This small protein factory can produce, fold, and localize almost any kind of wild-type or recombinant protein; some tricks are required to obtain high expression and to verify the functionality. The methodologies examined here are mainly related to research in the field of membrane transporters. This work is certainly not exhaustive; it has been carried out to be helpful to researchers who want to quickly find suggestions and detailed indications when investigating the functionality and expression of the different members of the solute carrier families.
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Affiliation(s)
- Manan Bhatt
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Angela Di Iacovo
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Tiziana Romanazzi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Cristina Roseti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Centre for Neuroscience—Via Manara 7, University of Insubria, 21052 Busto Arsizio, Italy
| | - Raffaella Cinquetti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
| | - Elena Bossi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Centre for Neuroscience—Via Manara 7, University of Insubria, 21052 Busto Arsizio, Italy
- Correspondence:
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5
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Knox HJ, Rego Campello H, Lester HA, Gallagher T, Dougherty DA. Characterization of Binding Site Interactions and Selectivity Principles in the α3β4 Nicotinic Acetylcholine Receptor. J Am Chem Soc 2022; 144:16101-16117. [PMID: 36006801 DOI: 10.1021/jacs.2c06495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) play an important role in neurotransmission and are also involved in addiction and several disease states. There is significant interest in therapeutic targeting of nAChRs; however, achieving selectivity for one subtype over others has been a longstanding challenge, given the close structural similarities across the family. Here, we characterize binding interactions in the α3β4 nAChR subtype via structure-function studies involving noncanonical amino acid mutagenesis and two-electrode voltage clamp electrophysiology. We establish comprehensive binding models for both the endogenous neurotransmitter ACh and the smoking cessation drug cytisine. We also use a panel of C(10)-substituted cytisine derivatives to probe the effects of subtle changes in the ligand structure on binding. By comparing our results to those obtained for the well-studied α4β2 subtype, we identify several features of both the receptor and agonist structure that can be utilized to enhance selectivity for either α3β4 or α4β2. Finally, we characterize binding interactions of the α3β4-selective partial agonist AT-1001 to determine factors that contribute to its selectivity. These results shed new light on the design of selective nAChR-targeted ligands and can be used to inform the design of improved therapies with minimized off-target effects.
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Affiliation(s)
- Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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6
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Shao J, Kuiper BP, Thunnissen AMWH, Cool RH, Zhou L, Huang C, Dijkstra BW, Broos J. The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach. J Am Chem Soc 2022; 144:13815-13822. [PMID: 35868012 PMCID: PMC9354243 DOI: 10.1021/jacs.2c04986] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
In proteins, the amino acids Phe, Tyr, and especially
Trp are frequently
involved in π interactions such as π–π, cation−π,
and CH−π bonds. These interactions are often crucial
for protein structure and protein–ligand binding. A powerful
means to study these interactions is progressive fluorination of these
aromatic residues to modulate the electrostatic component of the interaction.
However, to date no protein expression platform is available to produce
milligram amounts of proteins labeled with such fluorinated amino
acids. Here, we present a Lactococcus lactis Trp
auxotroph-based expression system for efficient incorporation (≥95%)
of mono-, di-, tri-, and tetrafluorinated, as well as a methylated
Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug
transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between
Trp96 and Trp96′ in the dimer interface. Progressive fluorination
of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly
establishing the importance of electrostatic π–π
interactions for drug binding. Presteady state kinetic data of the
LmrR–drug interaction support the enthalpic nature of the interaction,
while high resolution crystal structures of the labeled protein–drug
complexes provide for the first time a structural view of the progressive
fluorination approach. The L. lactis expression system
was also used to study the role of Trp68 in the binding of riboflavin
by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a
strong electrostatic component that contributed 15–20% to the
total riboflavin-RibU binding energy.
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Affiliation(s)
- Jinfeng Shao
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bastiaan P Kuiper
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Liang Zhou
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Chenxi Huang
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bauke W Dijkstra
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jaap Broos
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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7
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Sridhar A, Lummis SCR, Pasini D, Mehregan A, Brams M, Kambara K, Bertrand D, Lindahl E, Howard RJ, Ulens C. Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding site. J Biol Chem 2021; 297:100899. [PMID: 34157288 PMCID: PMC8327344 DOI: 10.1016/j.jbc.2021.100899] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are crucial mediators of electrochemical signal transduction in various organisms from bacteria to humans. Lipids play an important role in regulating pLGIC function, yet the structural bases for specific pLGIC-lipid interactions remain poorly understood. The bacterial channel ELIC recapitulates several properties of eukaryotic pLGICs, including activation by the neurotransmitter GABA and binding and modulation by lipids, offering a simplified model system for structure-function relationship studies. In this study, functional effects of noncanonical amino acid substitution of a potential lipid-interacting residue (W206) at the top of the M1-helix, combined with detergent interactions observed in recent X-ray structures, are consistent with this region being the location of a lipid-binding site on the outward face of the ELIC transmembrane domain. Coarse-grained and atomistic molecular dynamics simulations revealed preferential binding of lipids containing a positive charge, particularly involving interactions with residue W206, consistent with cation-π binding. Polar contacts from other regions of the protein, particularly M3 residue Q264, further support lipid binding via headgroup ester linkages. Aromatic residues were identified at analogous sites in a handful of eukaryotic family members, including the human GABAA receptor ε subunit, suggesting conservation of relevant interactions in other evolutionary branches. Further mutagenesis experiments indicated that mutations at this site in ε-containing GABAA receptors can change the apparent affinity of the agonist response to GABA, suggesting a potential role of this site in channel gating. In conclusion, this work details type-specific lipid interactions, which adds to our growing understanding of how lipids modulate pLGICs.
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Affiliation(s)
- Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah C R Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Diletta Pasini
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Aujan Mehregan
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Marijke Brams
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | | | | | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.
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8
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Baker BW, Dougherty DA, Lummis SCR. Proline Residues Contribute to Efficient GABA p Receptor Function. ACS Chem Neurosci 2020; 11:4215-4222. [PMID: 33201686 DOI: 10.1021/acschemneuro.0c00483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
GABAp receptors are homomeric pentameric ligand-gated ion channels (pLGICs) and are useful for probing the molecular details of the mechanism of action in this important protein family. Here, we explore the role of proline (Pro) residues by creating mutant receptors, expressing them in HEK293 cells, and using fluorescent membrane potential sensitive dye to monitor receptor activity. The data revealed that 3 of the Pro-to-alanine substitutions resulted in nonfunctional receptors (one in the Cys-loop, one in loop A and one in the β2-β3 loop), 7 resulted in increased EC50 values, and the remaining 13 resulted in receptors with properties similar to WT receptors. Further exploration of the nonfunctional mutants using expression in Xenopus laevis oocytes and whole-cell voltage-clamp electrophysiology, incorporating both canonical and noncanonical amino acids, revealed that the Pro in the Cys-loop had a preference for analogues with a high intrinsic cis bias, the Pro in loop A required a ring, and the β2-β3 loop Pro contributes to expression. The data from the Cys-loop Pro are consistent with those from other pLGICs, while those of the loop A Pro and some of the other Pros surprisingly differ. Thus, overall, the data clarify the roles of many of the Pros in the GABAp receptor and also suggest that caution must be applied in using data from one receptor to understand molecular details of all pLGICs.
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Affiliation(s)
- Benjamin W. Baker
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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9
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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10
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Blom AE, Campello HR, Lester HA, Gallagher T, Dougherty DA. Probing Binding Interactions of Cytisine Derivatives to the α4β2 Nicotinic Acetylcholine Receptor. J Am Chem Soc 2019; 141:15840-15849. [DOI: 10.1021/jacs.9b06580] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hugo Rego Campello
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Timothy Gallagher
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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11
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Blunt CEW, Dougherty DA. Binding Interactions of NS6740, a Silent Agonist of the α7 Nicotinic Acetylcholine Receptor. Mol Pharmacol 2019; 96:212-218. [PMID: 31175182 DOI: 10.1124/mol.119.116244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/28/2019] [Indexed: 11/22/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) is a potential drug target for the treatment of a number of neurologic and inflammatory disorders. Silent agonists are an emerging class of drugs that bind to the receptor but do not open the channel. Instead they shift the receptor to a desensitized state. Silent agonists may be able to target a subset of α7 nAChR-mediated signaling processes. Here we use noncanonical amino acid mutagenesis to characterize the binding to α7 by the silent agonist 1,4-diazabicyclo[3.2.2]nonan-4-yl(5-(3-(trifluoromethyl)phenyl)furan-2-yl)methanone (NS6740). We find that, like α7 agonists, NS6740 forms a cation-π interaction with Y115 (TyrA). We also showed that NS6740 makes a novel hydrogen bond to TyrA. This interaction is necessary for the silent agonist activity of NS6740; when the hydrogen bond is blocked, silent agonist NS6740 converts to a conventional partial agonist and appreciably opens the channel in the absence of a positive allosteric modulator (EC50 150 nM). SIGNIFICANCE STATEMENT: Noncanonical amino acids were used to show that a hydrogen bond to tyrosine (Y115) is required for silent agonist activity of NS6740 at the α7 nicotinic acetylcholine receptor.
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Affiliation(s)
- Catriona E W Blunt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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12
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Gasparri F, Wengel J, Grutter T, Pless SA. Molecular determinants for agonist recognition and discrimination in P2X2 receptors. J Gen Physiol 2019; 151:898-911. [PMID: 31126967 PMCID: PMC6605687 DOI: 10.1085/jgp.201912347] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/06/2019] [Indexed: 12/26/2022] Open
Abstract
P2X receptors (P2XRs) are ligand-gated cation channels involved in pain and inflammation. Gasparri et al. show that the backbone carbonyl atoms of amino acid residue Thr184 are involved in ligand discrimination, while those of Lys69 contribute mostly to ligand recognition by rat P2X2Rs. P2X receptors (P2XRs) are trimeric ligand-gated ion channels that open a cation-selective pore in response to ATP binding. P2XRs contribute to synaptic transmission and are involved in pain and inflammation, thus representing valuable drug targets. Recent crystal structures have confirmed the findings of previous studies with regards to the amino acid chains involved in ligand recognition, but they have also suggested that backbone carbonyl atoms contribute to ATP recognition and discrimination. Here we use a combination of site-directed mutagenesis, amide-to-ester substitutions, and a range of ATP analogues with subtle alterations to either base or sugar component to investigate the contributions of backbone carbonyl atoms toward ligand recognition and discrimination in rat P2X2Rs. Our findings demonstrate that while the Lys69 backbone carbonyl makes an important contribution to ligand recognition, the discrimination between different ligands is mediated by both the side chain and the backbone carbonyl oxygen of Thr184. Together, our data demonstrate how conserved elements in P2X2Rs recognize and discriminate agonists.
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Affiliation(s)
- Federica Gasparri
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Thomas Grutter
- University of Strasbourg, Centre National de la Recherche Scientifique, Conception et Application de Molécules Bioactives Unité Mixte de Recherche 7199, Strasbourg, France
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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13
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Sakata S, Okamura Y. Dynamic structural rearrangements and functional regulation of voltage-sensing phosphatase. J Physiol 2018; 597:29-40. [PMID: 30311949 DOI: 10.1113/jp274113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/02/2018] [Indexed: 11/08/2022] Open
Abstract
The voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a cytoplasmic catalytic region. The latter contains a phosphatase domain and a C2 domain, showing remarkable similarity to the tumour suppressor enzyme PTEN. In VSP, membrane depolarization induces a conformational change in the VSD, which activates the phosphoinositide phosphatase. The final outcome in VSP is enzymatic activity in the cytoplasmic region, unlike in voltage-gated ion channels where conformational change of the transmembrane pore is induced by the VSD. Therefore, it is crucial to detect structural change in the cytoplasmic catalytic region to gain insights into the operating mechanisms of VSP. This review summarizes a recent study in which a method of genetic incorporation of a non-canonical amino acid, Anap, was used to detect dynamic membrane voltage-controlled rearrangements of the structure of the catalytic region of sea squirt VSP (Ci-VSP). Upon membrane depolarization, both the phosphatase domain and the C2 domain move in a similar time frame, suggesting that the two regions are coupled to each other. Measurement of Förster resonance energy transfer (FRET) between Anap introduced into the C2 domain of Ci-VSP and dipicrylamine in the cell membrane suggested no large movement of the enzyme towards the membrane. Fluorescence changes in Anap induced by different membrane potentials indicate the presence of multiple conformations of the active enzyme.
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Affiliation(s)
- Souhei Sakata
- Department of Physiology, Division of Life Sciences, Faculty of Medicine, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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14
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Mosesso R, Dougherty DA, Lummis SCR. Probing Proline Residues in the Prokaryotic Ligand-Gated Ion Channel, ELIC. Biochemistry 2018; 57:4036-4043. [DOI: 10.1021/acs.biochem.8b00379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Richard Mosesso
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
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15
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Infield DT, Lee EEL, Galpin JD, Galles GD, Bezanilla F, Ahern CA. Replacing voltage sensor arginines with citrulline provides mechanistic insight into charge versus shape. J Gen Physiol 2018; 150:1017-1024. [PMID: 29866793 PMCID: PMC6028492 DOI: 10.1085/jgp.201812075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 01/06/2023] Open
Abstract
Activation of voltage-gated channels results from the outward movement of arginine residues on the S4 segments. Infield et al. use in vivo nonsense suppression to replace Shaker's S4 arginine residues with citrulline and reveal that a positive charge is required on R4 for voltage-dependent deactivation. Voltage-dependent activation of voltage-gated cation channels results from the outward movement of arginine-bearing helices within proteinaceous voltage sensors. The voltage-sensing residues in potassium channels have been extensively characterized, but current functional approaches do not allow a distinction between the electrostatic and steric contributions of the arginine side chain. Here we use chemical misacylation and in vivo nonsense suppression to encode citrulline, a neutral and nearly isosteric analogue of arginine, into the voltage sensor of the Shaker potassium channel. We functionally characterize the engineered channels and compare them with those bearing conventional mutations at the same positions. We observe effects on both voltage sensitivity and gating kinetics, enabling dissection of the roles of residue structure versus positive charge in channel function. In some positions, substitution with citrulline causes mild effects on channel activation compared with natural mutations. In contrast, substitution of the fourth S4 arginine with citrulline causes substantial changes in the conductance–voltage relationship and the kinetics of the channel, which suggests that a positive charge is required at this position for efficient voltage sensor deactivation and channel closure. The encoding of citrulline is expected to enable enhanced precision for the study of arginine residues located in crowded transmembrane environments in other membrane proteins. In addition, the method may facilitate the study of citrullination in vivo.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Elizabeth E L Lee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Grace D Galles
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA .,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
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16
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Abstract
Chemical aminoacylation of orthogonal tRNA allows for the genetic encoding of a wide range of synthetic amino acids without the need to evolve specific aminoacyl-tRNA synthetases. This method, when paired with protein expression in the Xenopus laevis oocyte expression system, can extract atomic scale functional data from a protein structure to advance the study of membrane proteins. The utility of the method depends on the orthogonality of the tRNA species used to deliver the amino acid. Here, we report that the pyrrolysyl tRNA (pylT) from Methanosarcina barkeri fusaro is orthogonal and highly competent for genetic code expansion experiments in the Xenopus oocyte. The data show that pylT is amendable to chemical acylation in vitro; it is then used to rescue a cytoplasmic site within a voltage-gated sodium channel. Further, the high fidelity of the pylT is demonstrated via encoding of lysine within the selectivity filter of the sodium channel, where sodium ion recognition by the distal amine of this side-chain is essential. Thus, pylT is an appropriate tRNA species for delivery of amino acids via nonsense suppression in the Xenopus oocyte. It may prove useful in experimental contexts wherein reacylation of suppressor tRNAs have been observed.
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17
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Callau-Vázquez D, Pless SA, Lynagh T. Investigation of Agonist Recognition and Channel Properties in a Flatworm Glutamate-Gated Chloride Channel. Biochemistry 2018; 57:1360-1368. [PMID: 29411605 DOI: 10.1021/acs.biochem.7b01245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glutamate-gated chloride channels (GluCls) are neurotransmitter receptors that mediate crucial inhibitory signaling in invertebrate neuromuscular systems. Their role in invertebrate physiology and their absence from vertebrates make GluCls a prime target for antiparasitic drugs. GluCls from flatworm parasites are substantially different from and are much less understood than those from roundworm and insect parasites, hindering the development of potential therapeutics targeting GluCls in flatworm-related diseases such as schistosomiasis. Here, we sought to dissect the molecular and chemical basis for ligand recognition in the extracellular glutamate binding site of SmGluCl-2 from Schistosoma mansoni, using site-directed mutagenesis, noncanonical amino acid incorporation, and electrophysiological recordings. Our results indicate that aromatic residues in ligand binding loops A, B, and C are important for SmGluCl-2 function. Loop C, which differs in length compared to other pentameric ligand-gated ion channels (pLGICs), contributes to ligand recognition through both an aromatic residue and two vicinal threonine residues. We also show that, in contrast to other pLGICs, the hydrophobic channel gate in SmGluCl-2 extends from the 9' position to the 6' position in the channel-forming M2 helix. The 6' and 9' positions also seem to control sensitivity to the pore blocker picrotoxin.
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Affiliation(s)
- Daniel Callau-Vázquez
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen , Jagtvej 160, 2100 Copenhagen, Denmark
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen , Jagtvej 160, 2100 Copenhagen, Denmark
| | - Timothy Lynagh
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen , Jagtvej 160, 2100 Copenhagen, Denmark
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18
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Lynagh T, Flood E, Boiteux C, Wulf M, Komnatnyy VV, Colding JM, Allen TW, Pless SA. A selectivity filter at the intracellular end of the acid-sensing ion channel pore. eLife 2017; 6. [PMID: 28498103 PMCID: PMC5449180 DOI: 10.7554/elife.24630] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/11/2017] [Indexed: 01/25/2023] Open
Abstract
Increased extracellular proton concentrations during neurotransmission are converted to excitatory sodium influx by acid-sensing ion channels (ASICs). 10-fold sodium/potassium selectivity in ASICs has long been attributed to a central constriction in the channel pore, but experimental verification is lacking due to the sensitivity of this structure to conventional manipulations. Here, we explored the basis for ion selectivity by incorporating unnatural amino acids into the channel, engineering channel stoichiometry and performing free energy simulations. We observed no preference for sodium at the “GAS belt” in the central constriction. Instead, we identified a band of glutamate and aspartate side chains at the lower end of the pore that enables preferential sodium conduction. DOI:http://dx.doi.org/10.7554/eLife.24630.001
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Affiliation(s)
- Timothy Lynagh
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Australia
| | - Matthias Wulf
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Vitaly V Komnatnyy
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Janne M Colding
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Australia
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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19
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Lynagh T, Komnatnyy VV, Pless SA. Unique Contributions of an Arginine Side Chain to Ligand Recognition in a Glutamate-gated Chloride Channel. J Biol Chem 2017; 292:3940-3946. [PMID: 28096462 PMCID: PMC5339774 DOI: 10.1074/jbc.m116.772939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/11/2017] [Indexed: 11/06/2022] Open
Abstract
Glutamate recognition by neurotransmitter receptors often relies on Arg residues in the binding site, leading to the assumption that charge-charge interactions underlie ligand recognition. However, assessing the precise chemical contribution of Arg side chains to protein function and pharmacology has proven to be exceedingly difficult in such large and complex proteins. Using the in vivo nonsense suppression approach, we report the first successful incorporation of the isosteric, titratable Arg analog, canavanine, into a neurotransmitter receptor in a living cell, utilizing a glutamate-gated chloride channel from the nematode Haemonchus contortus Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via a hydrogen bond network, where Arg interacts both with agonist and with a conserved Thr side chain within the receptor. Together, the data provide a new explanation for the reliance of neurotransmitter receptors on Arg side chains and highlight the exceptional capacity of unnatural amino acid incorporation for increasing our understanding of ligand recognition.
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Affiliation(s)
- Timothy Lynagh
- From the Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 H Copenhagen, Denmark
| | - Vitaly V Komnatnyy
- From the Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 H Copenhagen, Denmark
| | - Stephan A Pless
- From the Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 H Copenhagen, Denmark
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20
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Leisle L, Chadda R, Lueck JD, Infield DT, Galpin JD, Krishnamani V, Robertson JL, Ahern CA. Cellular encoding of Cy dyes for single-molecule imaging. eLife 2016; 5:e19088. [PMID: 27938668 PMCID: PMC5207767 DOI: 10.7554/elife.19088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022] Open
Abstract
A general method is described for the site-specific genetic encoding of cyanine dyes as non-canonical amino acids (Cy-ncAAs) into proteins. The approach relies on an improved technique for nonsense suppression with in vitro misacylated orthogonal tRNA. The data show that Cy-ncAAs (based on Cy3 and Cy5) are tolerated by the eukaryotic ribosome in cell-free and whole-cell environments and can be incorporated into soluble and membrane proteins. In the context of the Xenopus laevis oocyte expression system, this technique yields ion channels with encoded Cy-ncAAs that are trafficked to the plasma membrane where they display robust function and distinct fluorescent signals as detected by TIRF microscopy. This is the first demonstration of an encoded cyanine dye as a ncAA in a eukaryotic expression system and opens the door for the analysis of proteins with single-molecule resolution in a cellular environment.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - John D Lueck
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Venkatramanan Krishnamani
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
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21
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Rienzo M, Rocchi AR, Threatt SD, Dougherty DA, Lummis SCR. Perturbation of Critical Prolines in Gloeobacter violaceus Ligand-gated Ion Channel (GLIC) Supports Conserved Gating Motions among Cys-loop Receptors. J Biol Chem 2015; 291:6272-80. [PMID: 26668320 PMCID: PMC4813548 DOI: 10.1074/jbc.m115.694372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 11/30/2022] Open
Abstract
Gloeobacter violaceus ligand-gated ion channel (GLIC) has served as a valuable structural and functional model for the eukaryotic Cys-loop receptor superfamily. In Cys-loop and other receptors, we have previously demonstrated the crucial roles played by several conserved prolines. Here we explore the role of prolines in the gating transitions of GLIC. As conventional substitutions at some positions resulted in nonfunctional proteins, we used in vivo non-canonical amino acid mutagenesis to determine the specific structural requirements at these sites. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell electrophysiology was used to monitor channel activity. Pro-119 in the Cys-loop, Pro-198 and Pro-203 in the M1 helix, and Pro-299 in the M4 helix were sensitive to substitution, and distinct roles in receptor activity were revealed for each. In the context of the available structural data for GLIC, the behaviors of Pro-119, Pro-203, and Pro-299 mutants are consistent with earlier proline mutagenesis work. However, the Pro-198 site displays a unique phenotype that gives evidence of the importance of the region surrounding this residue for the correct functioning of GLIC.
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Affiliation(s)
- Matthew Rienzo
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Angela R Rocchi
- the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Stephanie D Threatt
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Dennis A Dougherty
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Sarah C R Lummis
- the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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22
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Kim RY, Yau MC, Galpin JD, Seebohm G, Ahern CA, Pless SA, Kurata HT. Atomic basis for therapeutic activation of neuronal potassium channels. Nat Commun 2015; 6:8116. [PMID: 26333338 PMCID: PMC4561856 DOI: 10.1038/ncomms9116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/21/2015] [Indexed: 12/25/2022] Open
Abstract
Retigabine is a recently approved anticonvulsant that acts by potentiating neuronal M-current generated by KCNQ2–5 channels, interacting with a conserved Trp residue in the channel pore domain. Using unnatural amino-acid mutagenesis, we subtly altered the properties of this Trp to reveal specific chemical interactions required for retigabine action. Introduction of a non-natural isosteric H-bond-deficient Trp analogue abolishes channel potentiation, indicating that retigabine effects rely strongly on formation of a H-bond with the conserved pore Trp. Supporting this model, substitution with fluorinated Trp analogues, with increased H-bonding propensity, strengthens retigabine potency. In addition, potency of numerous retigabine analogues correlates with the negative electrostatic surface potential of a carbonyl/carbamate oxygen atom present in most KCNQ activators. These findings functionally pinpoint an atomic-scale interaction essential for effects of retigabine and provide stringent constraints that may guide rational improvement of the emerging drug class of KCNQ channel activators. The antiepileptic drug retigabine potentiates neuronal KCNQ potassium channels. Here, the authors use a combination of unnatural amino acid mutagenesis and electrophysiology to show that retigabine acts by hydrogen bonding with a tryptophan indole nitrogen in the channel pore.
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Affiliation(s)
- Robin Y Kim
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, 2176 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Michael C Yau
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, 2176 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, 285 Newton Road, Iowa City, Iowa 52242, USA
| | - Guiscard Seebohm
- Department of Cardiovascular Medicine, University Hospital Münster, Albert-Schweitzer-Campus 1 (Gebäude D3), D-48149 Münster, Germany
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 285 Newton Road, Iowa City, Iowa 52242, USA
| | - Stephan A Pless
- Department of Drug Design and Pharmacology (Center for Biopharmaceuticals), University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Harley T Kurata
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, 2176 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
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23
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Marotta CB, Lester HA, Dougherty DA. An Unaltered Orthosteric Site and a Network of Long-Range Allosteric Interactions for PNU-120596 in α7 Nicotinic Acetylcholine Receptors. ACTA ACUST UNITED AC 2015. [PMID: 26211363 DOI: 10.1016/j.chembiol.2015.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are vital to neuronal signaling, are implicated in important processes such as learning and memory, and are therapeutic targets for neural diseases. The α7 nAChR has been implicated in Alzheimer's disease and schizophrenia, and allosteric modulators have become one focus of drug development efforts. We investigate the mode of action of the α7-selective positive allosteric modulator, PNU-120596, and show that the higher potency of acetylcholine in the presence of PNU-120596 is not due to an altered agonist binding site. In addition, we propose several residues in the gating interface and transmembrane region that are functionally important to transduction of allosteric properties, and link PNU-120596, the acetylcholine binding region, and the receptor gate. These results suggest global protein stabilization from a communication network through several key residues that alter the gating equilibrium of the receptor while leaving the agonist binding properties unperturbed.
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Affiliation(s)
- Christopher B Marotta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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24
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Pless SA, Kim RY, Ahern CA, Kurata HT. Atom-by-atom engineering of voltage-gated ion channels: magnified insights into function and pharmacology. J Physiol 2015; 593:2627-34. [PMID: 25640301 DOI: 10.1113/jphysiol.2014.287714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
Unnatural amino acid incorporation into ion channels has proven to be a valuable approach to interrogate detailed hypotheses arising from atomic resolution structures. In this short review, we provide a brief overview of some of the basic principles and methods for incorporation of unnatural amino acids into proteins. We also review insights into the function and pharmacology of voltage-gated ion channels that have emerged from unnatural amino acid mutagenesis approaches.
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Affiliation(s)
- Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Robin Y Kim
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | | | - Harley T Kurata
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, Vancouver, BC, Canada
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25
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Mruk K, Kobertz WR. Bioreactive Tethers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:77-100. [DOI: 10.1007/978-1-4939-2845-3_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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26
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Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
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27
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Photo-induced inhibition of Alzheimer's β-amyloid aggregation in vitro by rose bengal. Biomaterials 2015; 38:43-9. [DOI: 10.1016/j.biomaterials.2014.10.058] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/19/2014] [Indexed: 12/24/2022]
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28
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Miles TF, Lester HA, Dougherty DA. Allosteric activation of the 5-HT3AB receptor by mCPBG. Neuropharmacology 2014; 91:103-8. [PMID: 25541413 DOI: 10.1016/j.neuropharm.2014.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/16/2014] [Accepted: 12/10/2014] [Indexed: 10/25/2022]
Abstract
The 5-HT3AB receptor contains three A and two B subunits in an A-A-B-A-B order. However, serotonin function at the 5-HT3AB receptor has been shown to depend solely on the A-A interface present in the homomeric receptor. Using mutations at sites on both the primary (E122) and complementary (Y146) faces of the B subunit, we demonstrate that meta-chlorophenyl biguanide (mCPBG), a 5-HT3 selective agonist, is capable of binding to and activating the 5-HT3AB receptor at all five subunit interfaces of the heteromer. Further, mCPBG is capable of allosterically modulating the activity of serotonin from these sites. While these five binding sites are similar enough that they conform to a monophasic dose - response relationship, we uncover subtle differences in the heteromeric binding sites. We also find that the A-A interface appears to contribute disproportionately to the efficacy of 5-HT3AB receptor activation.
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Affiliation(s)
- Timothy F Miles
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA.
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29
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Rienzo M, Lummis SCR, Dougherty DA. Structural requirements in the transmembrane domain of GLIC revealed by incorporation of noncanonical histidine analogs. CHEMISTRY & BIOLOGY 2014; 21:1700-6. [PMID: 25525989 PMCID: PMC4291181 DOI: 10.1016/j.chembiol.2014.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/23/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022]
Abstract
The cyanobacterial pentameric ligand-gated ion channel GLIC, a homolog of the Cys-loop receptor superfamily, has provided useful structural and functional information about its eukaryotic counterparts. X-ray diffraction data and site-directed mutagenesis have previously implicated a transmembrane histidine residue (His234) as essential for channel function. Here, we investigated the role of His234 via synthesis and incorporation of histidine analogs and α-hydroxy acids using in vivo nonsense suppression. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell voltage-clamp electrophysiology was used to monitor channel activity. We show that an interhelix hydrogen bond involving His234 is important for stabilization of the open state, and that the shape and basicity of its side chain are highly sensitive to perturbations. In contrast, our data show that two other His residues are not involved in the acid-sensing mechanism.
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Affiliation(s)
- Matthew Rienzo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah C R Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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30
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Pless SA, Elstone FD, Niciforovic AP, Galpin JD, Yang R, Kurata HT, Ahern CA. Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains. ACTA ACUST UNITED AC 2014; 143:645-56. [PMID: 24778431 PMCID: PMC4003186 DOI: 10.1085/jgp.201311036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conserved acidic and aromatic residues in the four sodium channel voltage-sensor domains make domain-specific functional contributions. Voltage-gated sodium (NaV) channels mediate electrical excitability in animals. Despite strong sequence conservation among the voltage-sensor domains (VSDs) of closely related voltage-gated potassium (KV) and NaV channels, the functional contributions of individual side chains in Nav VSDs remain largely enigmatic. To this end, natural and unnatural side chain substitutions were made in the S2 hydrophobic core (HC), the extracellular negative charge cluster (ENC), and the intracellular negative charge cluster (INC) of the four VSDs of the skeletal muscle sodium channel isoform (NaV1.4). The results show that the highly conserved aromatic side chain constituting the S2 HC makes distinct functional contributions in each of the four NaV domains. No obvious cation–pi interaction exists with nearby S4 charges in any domain, and natural and unnatural mutations at these aromatic sites produce functional phenotypes that are different from those observed previously in Kv VSDs. In contrast, and similar to results obtained with Kv channels, individually neutralizing acidic side chains with synthetic derivatives and with natural amino acid substitutions in the INC had little or no effect on the voltage dependence of activation in any of the four domains. Interestingly, countercharge was found to play an important functional role in the ENC of DI and DII, but not DIII and DIV. These results suggest that electrostatic interactions with S4 gating charges are unlikely in the INC and only relevant in the ENC of DI and DII. Collectively, our data highlight domain-specific functional contributions of highly conserved side chains in NaV VSDs.
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Affiliation(s)
- Stephan A Pless
- Department of Anesthesiology, Pharmacology and Therapeutics, and 2 Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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31
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Daeffler KNM, Lester HA, Dougherty DA. Functional evaluation of key interactions evident in the structure of the eukaryotic Cys-loop receptor GluCl. ACS Chem Biol 2014; 9:2283-90. [PMID: 25051140 PMCID: PMC4201344 DOI: 10.1021/cb500323d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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The
publication of the first high-resolution crystal structure
of a eukaryotic Cys-loop receptor, GluClα, has provided valuable
structural information on this important class of ligand-gated ion
channels (LGIC). However, limited functional data exist for the GluCl
receptors. Before applying the structural insights from GluCl to mammalian
Cys-loop receptors such as nicotinic acetylcholine and GABA receptors,
it is important to ensure that established functional features of mammalian Cys-loop receptors are present in the more
distantly related GluCl receptors. Here, we seek to identify ligand-binding
interactions that are generally associated with Cys-loop receptors,
including the frequently observed cation−π interaction.
Our studies were performed on the highly homologous GluClβ receptor,
because GluClα is not activated by glutamate in Xenopus
laevis oocytes. Mutagenesis of the signal peptide and pore
lining helix was performed to enhance functional expression and sensitivity
to applied ligand, respectively. Conventional and unnatural amino
acid mutagenesis indicate a strong cation−π interaction
between Y206 and the protonated amine of glutamate, as well as other
important ionic and hydrogen bond interactions between the ligand
and the binding site, consistent with the crystal structure.
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Affiliation(s)
- Kristina N.-M. Daeffler
- Division of Chemistry & Chemical Engineering and ‡Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Henry A. Lester
- Division of Chemistry & Chemical Engineering and ‡Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry & Chemical Engineering and ‡Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
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32
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Dougherty DA, Van Arnam EB. In vivo incorporation of non-canonical amino acids by using the chemical aminoacylation strategy: a broadly applicable mechanistic tool. Chembiochem 2014; 15:1710-20. [PMID: 24990307 DOI: 10.1002/cbic.201402080] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 01/05/2023]
Abstract
We describe a strategy for incorporating non-canonical amino acids site-specifically into proteins expressed in living cells, involving organic synthesis to chemically aminoacylate a suppressor tRNA, protein expression in Xenopus oocytes, and monitoring protein function, primarily by electrophysiology. With this protocol, a very wide range of non-canonical amino acids can be employed, allowing both systematic structure-function studies and the incorporation of reactive functionalities. Here, we present an overview of the methodology and examples meant to illustrate the versatility and power of the method as a tool for investigating protein structure and function.
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Affiliation(s)
- Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (USA).
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33
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Marotta C, Rreza I, Lester HA, Dougherty DA. Selective ligand behaviors provide new insights into agonist activation of nicotinic acetylcholine receptors. ACS Chem Biol 2014; 9:1153-9. [PMID: 24564429 PMCID: PMC4033646 DOI: 10.1021/cb400937d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/24/2014] [Indexed: 12/29/2022]
Abstract
Nicotinic acetylcholine receptors are a diverse set of ion channels that are essential to everyday brain function. Contemporary research studies selective activation of individual subtypes of receptors, with the hope of increasing our understanding of behavioral responses and neurodegenerative diseases. Here, we aim to expand current binding models to help explain the specificity seen among three activators of α4β2 receptors: sazetidine-A, cytisine, and NS9283. Through mutational analysis, we can interchange the activation profiles of the stoichiometry-selective compounds sazetidine-A and cytisine. In addition, mutations render NS9283--currently identified as a positive allosteric modulator--into an agonist. These results lead to two conclusions: (1) occupation at each primary face of an α subunit is needed to activate the channel and (2) the complementary face of the adjacent subunit dictates the binding ability of the agonist.
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34
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Van Arnam EB, Dougherty DA. Functional probes of drug-receptor interactions implicated by structural studies: Cys-loop receptors provide a fertile testing ground. J Med Chem 2014; 57:6289-300. [PMID: 24568098 PMCID: PMC4136689 DOI: 10.1021/jm500023m] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Structures
of integral membrane receptors provide valuable models
for drug–receptor interactions across many important classes
of drug targets and have become much more widely available in recent
years. However, it remains to be determined to what extent these images
are relevant to human receptors in their biological context and how
subtle issues such as subtype selectivity can be informed by them.
The high precision structural modifications enabled by unnatural amino
acid mutagenesis on mammalian receptors expressed in vertebrate cells
allow detailed tests of predictions from structural studies. Using
the Cys-loop superfamily of ligand-gated ion channels, we show that
functional studies lead to detailed binding models that, at times,
are significantly at odds with the structural studies on related invertebrate
proteins. Importantly, broad variations in binding interactions are
seen for very closely related receptor subtypes and for varying drugs
at a given binding site. These studies highlight the essential interplay
between structural studies and functional studies that can guide efforts
to develop new pharmaceuticals.
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Affiliation(s)
- Ethan B Van Arnam
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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35
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Marotta CB, Dilworth CN, Lester HA, Dougherty DA. Probing the non-canonical interface for agonist interaction with an α5 containing nicotinic acetylcholine receptor. Neuropharmacology 2014; 77:342-9. [PMID: 24144909 PMCID: PMC3934363 DOI: 10.1016/j.neuropharm.2013.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 11/18/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) containing the α5 subunit are of interest because genome-wide association studies and candidate gene studies have identified polymorphisms in the α5 gene that are linked to an increased risk for nicotine dependence, lung cancer, and/or alcohol addiction. To probe the functional impact of an α5 subunit on nAChRs, a method to prepare a homogeneous population of α5-containing receptors must be developed. Here we use a gain of function (9') mutation to isolate populations of α5-containing nAChRs for characterization by electrophysiology. We find that the α5 subunit modulates nAChR rectification when co-assembled with α4 and β2 subunits. We also probe the α5-α4 interface for possible ligand-binding interactions. We find that mutations expected to ablate an agonist-binding site involving the α5 subunit have no impact on receptor function. The most straightforward interpretation of this observation is that agonists do not bind at the α5-α4 interface, in contrast to what has recently been demonstrated for the α4-α4 interface in related receptors. In addition, our mutational results suggest that the α5 subunit does not replace the α4 or β2 subunits and is relegated to occupying only the auxiliary position of the pentameric receptor.
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Affiliation(s)
- Christopher B Marotta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA
| | - Crystal N Dilworth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
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36
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Pless SA, Niciforovic AP, Galpin JD, Nunez JJ, Kurata HT, Ahern CA. A novel mechanism for fine-tuning open-state stability in a voltage-gated potassium channel. Nat Commun 2013; 4:1784. [PMID: 23653196 PMCID: PMC3644096 DOI: 10.1038/ncomms2761] [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: 07/25/2012] [Accepted: 03/18/2013] [Indexed: 12/23/2022] Open
Abstract
Voltage-gated potassium channels elicit membrane hyperpolarization through voltage-sensor domains that regulate the conductive status of the pore domain. To better understand the inherent basis for the open-closed equilibrium in these channels, we undertook an atomistic scan using synthetic fluorinated derivatives of aromatic residues previously implicated in the gating of Shaker potassium channels. Here we show that stepwise dispersion of the negative electrostatic surface potential of only one site, Phe481, stabilizes the channel open state. Furthermore, these data suggest that this apparent stabilization is the consequence of the amelioration of an inherently repulsive open-state interaction between the partial negative charge on the face of Phe481 and a highly co-evolved acidic side chain, Glu395, and this interaction is potentially modulated through the Tyr485 hydroxyl. We propose that the intrinsic open-state destabilization via aromatic repulsion represents a new mechanism by which ion channels, and likely other proteins, fine-tune conformational equilibria. Voltage-gated potassium channels cycle between closed and open states through poorly-defined transitions. Pless and colleagues incorporate artificial amino acids into Shaker potassium channels and find that that the negative electrostatic surface potential of Phe481, destabilizes the channel open state.
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Affiliation(s)
- Stephan A Pless
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia, Canada V6T 1Z3
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37
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Van Arnam EB, Blythe EE, Lester HA, Dougherty DA. An unusual pattern of ligand-receptor interactions for the α7 nicotinic acetylcholine receptor, with implications for the binding of varenicline. Mol Pharmacol 2013; 84:201-7. [PMID: 23680636 DOI: 10.1124/mol.113.085795] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor shows broad pharmacology, complicating the development of subtype-specific nicotinic receptor agonists. Here we use unnatural amino acid mutagenesis to characterize binding to α7 by the smoking cessation drug varenicline (Chantix; Pfizer, Groton, CT), an α4β2-targeted agonist that shows full efficacy and modest potency at the α7 receptor. We find that unlike binding to its target receptor, varenicline does not form a cation-π interaction with TrpB, further supporting a unique binding mode for the cationic amine of nicotinic agonists at the α7 receptor. We also evaluate binding to the complementary face of the receptor's binding site by varenicline, the endogenous agonist acetylcholine, and the potent nicotine analog epibatidine. Interestingly, we find no evidence for functionally important interactions involving backbone NH and CO groups thought to bind the canonical agonist hydrogen bond acceptor of the nicotinic pharmacophore, perhaps reflecting a lesser importance of this pharmacophore element for α7 binding. We also show that the Trp55 and Leu119 side chains of the binding site's complementary face are important for the binding of the larger agonists epibatidine and varenicline, but dispensable for binding of the smaller, endogenous agonist acetylcholine.
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Affiliation(s)
- Ethan B Van Arnam
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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38
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Krueger AT, Imperiali B. Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology. Chembiochem 2013; 14:788-99. [DOI: 10.1002/cbic.201300079] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/16/2022]
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39
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Wong HE, Irwin JA, Kwon I. Halogenation generates effective modulators of amyloid-Beta aggregation and neurotoxicity. PLoS One 2013; 8:e57288. [PMID: 23468958 PMCID: PMC3585355 DOI: 10.1371/journal.pone.0057288] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Halogenation of organic compounds plays diverse roles in biochemistry, including selective chemical modification of proteins and improved oral absorption/blood-brain barrier permeability of drug candidates. Moreover, halogenation of aromatic molecules greatly affects aromatic interaction-mediated self-assembly processes, including amyloid fibril formation. Perturbation of the aromatic interaction caused by halogenation of peptide building blocks is known to affect the morphology and other physical properties of the fibrillar structure. Consequently, in this article, we investigated the ability of halogenated ligands to modulate the self-assembly of amyloidogenic peptide/protein. As a model system, we chose amyloid-beta peptide (Aβ), which is implicated in Alzheimer’s disease, and a novel modulator of Aβ aggregation, erythrosine B (ERB). Considering that four halogen atoms are attached to the xanthene benzoate group in ERB, we hypothesized that halogenation of the xanthene benzoate plays a critical role in modulating Aβ aggregation and cytotoxicity. Therefore, we evaluated the modulating capacities of four ERB analogs containing different types and numbers of halogen atoms as well as fluorescein as a negative control. We found that fluorescein is not an effective modulator of Aβ aggregation and cytotoxicity. However, halogenation of either the xanthenes or benzoate ring of fluorescein substantially enhanced the inhibitory capacity on Aβ aggregation. Such Aβ aggregation inhibition by ERB analogs except rose bengal correlated well to the inhibition of Aβ cytotoxicity. To our knowledge, this is the first report demonstrating that halogenation of aromatic rings substantially enhance inhibitory capacities of small molecules on Aβ-associated neurotoxicity via Aβ aggregation modulation.
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Affiliation(s)
- H. Edward Wong
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, Unites States of America
| | - Jacob A. Irwin
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, Unites States of America
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, Unites States of America
- Institutes on Aging, University of Virginia, Charlottesville, Virginia, Unites States of America
- * E-mail:
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40
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Blum AP, Van Arnam EB, German LA, Lester HA, Dougherty DA. Binding interactions with the complementary subunit of nicotinic receptors. J Biol Chem 2013; 288:6991-7. [PMID: 23349463 DOI: 10.1074/jbc.m112.439968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The agonist-binding site of nicotinic acetylcholine receptors (nAChRs) spans an interface between two subunits of the pentameric receptor. The principal component of this binding site is contributed by an α subunit, and it binds the cationic moiety of the nicotinic pharmacophore. The other part of the pharmacophore, a hydrogen bond acceptor, has recently been shown to bind to the complementary non-α subunit via the backbone NH of a conserved Leu. This interaction was predicted by studies of ACh-binding proteins and confirmed by functional studies of the neuronal (CNS) nAChR, α4β2. The ACh-binding protein structures further suggested that the hydrogen bond to the backbone NH is mediated by a water molecule and that a second hydrogen bonding interaction occurs between the water molecule and the backbone CO of a conserved Asn, also on the non-α subunit. Here, we provide new insights into the nature of the interactions between the hydrogen bond acceptor of nicotinic agonists and the complementary subunit backbone. We studied both the nAChR of the neuromuscular junction (muscle-type) and a neuronal subtype, (α4)2(β4)3. In the muscle-type receptor, both ACh and nicotine showed a strong interaction with the Leu NH, but the potent nicotine analog epibatidine did not. This interaction was much attenuated in the α4β4 receptor. Surprisingly, we found no evidence for a functionally significant interaction with the backbone carbonyl of the relevant Asn in either receptor with an array of agonists.
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Affiliation(s)
- Angela P Blum
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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41
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Pless SA, Ahern CA. Unnatural Amino Acids as Probes of Ligand-Receptor Interactions and Their Conformational Consequences. Annu Rev Pharmacol Toxicol 2013; 53:211-29. [DOI: 10.1146/annurev-pharmtox-011112-140343] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephan A. Pless
- Department of Anesthesiology, Pharmacology and Therapeutics and Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Christopher A. Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242;
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42
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Abstract
Ion channels, as membrane proteins, are the sensors of the cell. They act as the first line of communication with the world beyond the plasma membrane and transduce changes in the external and internal environments into unique electrical signals to shape the responses of excitable cells. Because of their importance in cellular communication, ion channels have been intensively studied at the structural and functional levels. Here, we summarize the diverse approaches, including molecular and cellular, chemical, optical, biophysical, and computational, used to probe the structural and functional rearrangements that occur during channel activation (or sensitization), inactivation (or desensitization), and various forms of modulation. The emerging insights into the structure and function of ion channels by multidisciplinary approaches allow the development of new pharmacotherapies as well as new tools useful in controlling cellular activity.
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Affiliation(s)
- Wei-Guang Li
- Neuroscience Division, Department of Biochemistry and Molecular Cell Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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43
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Ashby JA, McGonigle IV, Price KL, Cohen N, Comitani F, Dougherty DA, Molteni C, Lummis SCR. GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study. Biophys J 2012. [PMID: 23200041 DOI: 10.1016/j.bpj.2012.10.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptors using computational and electrophysiological techniques. A homology model of the extracellular domain of RDL was generated and GABA docked into the binding site. Molecular dynamics simulations predicted critical GABA binding interactions with aromatic residues F206, Y254, and Y109 and hydrophilic residues E204, S176, R111, R166, S176, and T251. These residues were mutated, expressed in Xenopus oocytes, and their functions assessed using electrophysiology. The data support the binding mechanism provided by the simulations, which predict that GABA forms many interactions with binding site residues, the most significant of which are cation-π interactions with F206 and Y254, H-bonds with E204, S205, R111, S176, T251, and ionic interactions with R111 and E204. These findings clarify the roles of a range of residues in binding GABA in the RDL receptor, and also show that molecular dynamics simulations are a useful tool to identify specific interactions in Cys-loop receptors.
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44
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Duffy NH, Lester HA, Dougherty DA. Ondansetron and granisetron binding orientation in the 5-HT(3) receptor determined by unnatural amino acid mutagenesis. ACS Chem Biol 2012; 7:1738-45. [PMID: 22873819 DOI: 10.1021/cb300246j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The serotonin type 3 receptor (5-HT(3)R) is a ligand-gated ion channel found in the central and peripheral nervous systems. The 5-HT(3)R is a therapeutic target, and the clinically available drugs ondansetron and granisetron inhibit receptor activity. Their inhibitory action is through competitive binding to the native ligand binding site, although the binding orientation of the drugs at the receptor has been a matter of debate. Here we heterologously express mouse 5-HT(3)A receptors in Xenopus oocytes and use unnatural amino acid mutagenesis to establish a cation-π interaction for both ondansetron and granisetron to tryptophan 183 in the ligand binding pocket. This cation-π interaction establishes a binding orientation for both ondansetron and granisetron within the binding pocket.
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Affiliation(s)
- Noah H. Duffy
- Division
of Chemistry and Chemical Engineering and ‡Division of Biology, California Institute of Technology,
Pasadena, California 91125, United States
| | - Henry A. Lester
- Division
of Chemistry and Chemical Engineering and ‡Division of Biology, California Institute of Technology,
Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division
of Chemistry and Chemical Engineering and ‡Division of Biology, California Institute of Technology,
Pasadena, California 91125, United States
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45
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Miles TF, Bower KS, Lester HA, Dougherty DA. A coupled array of noncovalent interactions impacts the function of the 5-HT3A serotonin receptor in an agonist-specific way. ACS Chem Neurosci 2012; 3:753-60. [PMID: 23077719 DOI: 10.1021/cn3000586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/20/2012] [Indexed: 11/28/2022] Open
Abstract
The serotonin type 3A (5-HT(3)A) receptor is a Cys-loop (pentameric) neurotransmitter-gated ion channel found in the central and peripheral nervous systems and implicated in numerous diseases. In previous studies with the endogenous agonist serotonin, we identified two interactions critical for receptor function: a cation-π interaction with W183 in loop B (TrpB) and a hydrogen bond to E129 in loop A. Here we employ mutant cycle analyses utilizing conventional and unnatural amino acid mutagenesis to demonstrate that a third residue, D124 of loop A, forms two functionally important hydrogen bonds to the backbone of loop B. We also show that these three interactions, the cation-π interaction, the backbone hydrogen bonds, and the E129 hydrogen bond, are tightly coupled to each other, suggesting they function as a single unit. We also identify key functional differences between serotonin and the competitive partial agonist m-chlorophenyl biguanide (mCPBG) at these residues. mCPBG displays no cation-π at TrpB and extreme sensitivity to the positioning of E129, on which it is reliant for initiation of channel gating.
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Affiliation(s)
- Timothy F. Miles
- Division
of Biology and ‡Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
91125, United States
| | - Kiowa S. Bower
- Division
of Biology and ‡Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
91125, United States
| | - Henry A. Lester
- Division
of Biology and ‡Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
91125, United States
| | - Dennis A. Dougherty
- Division
of Biology and ‡Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
91125, United States
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46
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Lemoine D, Jiang R, Taly A, Chataigneau T, Specht A, Grutter T. Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem Rev 2012; 112:6285-318. [PMID: 22988962 DOI: 10.1021/cr3000829] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Damien Lemoine
- Laboratoire de Biophysicochimie des Récepteurs Canaux, UMR 7199 CNRS, Conception et Application de Molécules Bioactives, Faculté de Pharmacie, Université de Strasbourg , 67400 Illkirch, France
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47
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Daeffler KNM, Lester HA, Dougherty DA. Functionally important aromatic-aromatic and sulfur-π interactions in the D2 dopamine receptor. J Am Chem Soc 2012; 134:14890-6. [PMID: 22897614 PMCID: PMC3461201 DOI: 10.1021/ja304560x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recently published crystal structure of the D3 dopamine receptor shows a tightly packed region of aromatic residues on helices 5 and 6 in the space bridging the binding site and what is thought to be the origin of intracellular helical motion. This highly conserved region also makes contacts with residues on helix 3, and here we use double mutant cycle analysis and unnatural amino acid mutagenesis to probe the functional role of several residues in this region of the closely related D2 dopamine receptor. Of the eight mutant pairs examined, all show significant functional coupling (Ω > 2), with the largest coupling coefficients observed between residues on different helices, C3.36/W6.48, T3.37/S5.46, and F5.47/F6.52. Additionally, three aromatic residues examined, F5.47, Y5.48, and F5.51, show consistent trends upon progressive fluorination of the aromatic side chain. These trends are indicative of a functionally important electrostatic interaction with the face of the aromatic residue examined, which is likely attributed to aromatic-aromatic interactions between residues in this microdomain. We also propose that the previously determined fluorination trend at W6.48 is likely due to a sulfur-π interaction with the side chain of C3.36. We conclude that these residues form a tightly packed structural microdomain that connects helices 3, 5, and 6, thus forming a barrier that prevents dopamine from binding further toward the intracellular surface. Upon activation, these residues likely do not change their relative conformation, but rather act to translate agonist binding at the extracellular surface into the large intracellular movements that characterize receptor activation.
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Affiliation(s)
- Kristina N.-M. Daeffler
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Henry A. Lester
- Division of Biology, California Institute of Technology, Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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48
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Tavares XDS, Blum AP, Nakamura DT, Puskar NL, Shanata JAP, Lester HA, Dougherty DA. Variations in binding among several agonists at two stoichiometries of the neuronal, α4β2 nicotinic receptor. J Am Chem Soc 2012; 134:11474-80. [PMID: 22716019 DOI: 10.1021/ja3011379] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Drug-receptor binding interactions of four agonists, ACh, nicotine, and the smoking cessation compounds varenicline (Chantix) and cytisine (Tabex), have been evaluated at both the 2:3 and 3:2 stoichiometries of the α4β2 nicotinic acetylcholine receptor (nAChR). Previous studies have established that unnatural amino acid mutagenesis can probe three key binding interactions at the nAChR: a cation-π interaction, and two hydrogen-bonding interactions to the protein backbone of the receptor. We find that all drugs make a cation-π interaction to TrpB of the receptor. All drugs except ACh, which lacks an N(+)H group, make a hydrogen bond to a backbone carbonyl, and ACh and nicotine behave similarly in acting as a hydrogen-bond acceptor. However, varenicline is not a hydrogen-bond acceptor to the backbone NH that interacts strongly with the other three compounds considered. In addition, we see interesting variations in hydrogen bonding interactions with cytisine that provide a rationalization for the stoichiometry selectivity seen with this compound.
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Affiliation(s)
- Ximena Da Silva Tavares
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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49
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Abstract
The synapse is a localized neurohumoral contact between a neuron and an effector cell and may be considered the quantum of fast intercellular communication. Analogously, the postsynaptic neurotransmitter receptor may be considered the quantum of fast chemical to electrical transduction. Our understanding of postsynaptic receptors began to develop about a hundred years ago with the demonstration that electrical stimulation of the vagus nerve released acetylcholine and slowed the heart beat. During the past 50 years, advances in understanding postsynaptic receptors increased at a rapid pace, owing largely to studies of the acetylcholine receptor (AChR) at the motor endplate. The endplate AChR belongs to a large superfamily of neurotransmitter receptors, called Cys-loop receptors, and has served as an exemplar receptor for probing fundamental structures and mechanisms that underlie fast synaptic transmission in the central and peripheral nervous systems. Recent studies provide an increasingly detailed picture of the structure of the AChR and the symphony of molecular motions that underpin its remarkably fast and efficient chemoelectrical transduction.
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Affiliation(s)
- Steven M Sine
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
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Puskar NL, Lester HA, Dougherty DA. Probing the effects of residues located outside the agonist binding site on drug-receptor selectivity in the nicotinic receptor. ACS Chem Biol 2012; 7:841-6. [PMID: 22296725 DOI: 10.1021/cb200448j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nicotinic acetylcholine receptors (nAChRs) are a family of closely related but pharmacologically distinct neurotransmitter-gated ion channels. They are therapeutic targets for a wide range of neurological disorders, and a key issue in drug development is selective targeting among the more than 20 subtypes of nAChRs that are known. The present work evaluates a proposed hydrogen bonding interaction involving a residue known as the "loop B glycine" that distinguishes receptors that are highly responsive to ACh and nicotine from those that are much less so. We have performed structure-function studies on the loop B site, including unnatural amino acid mutagenesis, in three different nAChR subtypes and found that the correlation between agonist potency and this residue is strong. Low potency receptor subtypes have a glycine at this key site, and mutation to a residue with a side chain converts a low potency receptor to a high potency receptor. Innately high potency receptors have a lysine at the loop B site and show a decrease in potency for the reverse mutation (i.e., introducing a glycine). This residue lies outside of the agonist binding site, and studies of other residues at the agonist binding site show that the details of how changes at the loop B glycine site impact agonist potency vary for differing receptor subtypes. This suggests a model in which the loop B residue influences the global shape of the agonist binding site rather than modulating any specific interaction.
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Affiliation(s)
- Nyssa L. Puskar
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, 164-30, Pasadena, California 91125, United States
| | - Henry A. Lester
- Division of Biology, California Institute of Technology, 156-29, Pasadena
, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, 164-30, Pasadena, California 91125, United States
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