1
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Söllner J, Derler I. Genetic code expansion, an emerging tool in the Ca 2+ ion channel field. J Physiol 2024; 602:3297-3313. [PMID: 38695316 DOI: 10.1113/jp285840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 07/17/2024] Open
Abstract
Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.
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Affiliation(s)
- Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
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2
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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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3
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Sereikaitė V, Jensen TMT, Bartling CRO, Jemth P, Pless SA, Strømgaard K. Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations. Chembiochem 2018; 19:2136-2145. [PMID: 30073762 DOI: 10.1002/cbic.201800350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/09/2023]
Abstract
All proteins contain characteristic backbones formed of consecutive amide bonds, which can engage in hydrogen bonds. However, the importance of these is not easily addressed by conventional technologies that only allow for side-chain substitutions. By contrast, technologies such as nonsense suppression mutagenesis and protein ligation allow for manipulation of the protein backbone. In particular, replacing the backbone amide groups with ester groups, that is, amide-to-ester mutations, is a powerful tool to examine backbone-mediated hydrogen bonds. In this minireview, we showcase examples of how amide-to-ester mutations can be used to uncover pivotal roles of backbone-mediated hydrogen bonds in protein recognition, folding, function, and structure.
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Affiliation(s)
- Vita Sereikaitė
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Thomas M T Jensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Christian R O Bartling
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 75123, Uppsala, Sweden
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
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4
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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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5
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Crystal structure of a human neuronal nAChR extracellular domain in pentameric assembly: Ligand-bound α2 homopentamer. Proc Natl Acad Sci U S A 2016; 113:9635-40. [PMID: 27493220 DOI: 10.1073/pnas.1602619113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study we report the X-ray crystal structure of the extracellular domain (ECD) of the human neuronal α2 nicotinic acetylcholine receptor (nAChR) subunit in complex with the agonist epibatidine at 3.2 Å. Interestingly, α2 was crystallized as a pentamer, revealing the intersubunit interactions in a wild type neuronal nAChR ECD and the full ligand binding pocket conferred by two adjacent α subunits. The pentameric assembly presents the conserved structural scaffold observed in homologous proteins, as well as distinctive features, providing unique structural information of the binding site between principal and complementary faces. Structure-guided mutagenesis and electrophysiological data confirmed the presence of the α2(+)/α2(-) binding site on the heteromeric low sensitivity α2β2 nAChR and validated the functional importance of specific residues in α2 and β2 nAChR subunits. Given the pathological importance of the α2 nAChR subunit and the high sequence identity with α4 (78%) and other neuronal nAChR subunits, our findings offer valuable information for modeling several nAChRs and ultimately for structure-based design of subtype specific drugs against the nAChR associated diseases.
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6
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Wilkins ME, Caley A, Gielen MC, Harvey RJ, Smart TG. Murine startle mutant Nmf11 affects the structural stability of the glycine receptor and increases deactivation. J Physiol 2016; 594:3589-607. [PMID: 27028707 PMCID: PMC4929309 DOI: 10.1113/jp272122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/21/2016] [Indexed: 11/10/2022] Open
Abstract
Key points Hyperekplexia or startle disease is a serious neurological condition affecting newborn children and usually involves dysfunctional glycinergic neurotransmission. Glycine receptors (GlyRs) are major mediators of inhibition in the spinal cord and brainstem. A missense mutation, replacing asparagine (N) with lysine (K), at position 46 in the GlyR α1 subunit induced hyperekplexia following a reduction in the potency of the transmitter glycine; this resulted from a rapid deactivation of the agonist current at mutant GlyRs. These effects of N46K were rescued by mutating a juxtaposed residue, N61 on binding Loop D, suggesting these two asparagines may interact. Asparagine 46 is considered to be important for the structural stability of the subunit interface and glycine binding site, and its mutation represents a new mechanism by which GlyR dysfunction induces startle disease.
Abstract Dysfunctional glycinergic inhibitory transmission underlies the debilitating neurological condition, hyperekplexia, which is characterised by exaggerated startle reflexes, muscle hypertonia and apnoea. Here we investigated the N46K missense mutation in the GlyR α1 subunit gene found in the ethylnitrosourea (ENU) murine mutant, Nmf11, which causes reduced body size, evoked tremor, seizures, muscle stiffness, and morbidity by postnatal day 21. Introducing the N46K mutation into recombinant GlyR α1 homomeric receptors, expressed in HEK cells, reduced the potencies of glycine, β‐alanine and taurine by 9‐, 6‐ and 3‐fold respectively, and that of the competitive antagonist strychnine by 15‐fold. Replacing N46 with hydrophobic, charged or polar residues revealed that the amide moiety of asparagine was crucial for GlyR activation. Co‐mutating N61, located on a neighbouring β loop to N46, rescued the wild‐type phenotype depending on the amino acid charge. Single‐channel recording identified that burst length for the N46K mutant was reduced and fast agonist application revealed faster glycine deactivation times for the N46K mutant compared with the WT receptor. Overall, these data are consistent with N46 ensuring correct alignment of the α1 subunit interface by interaction with juxtaposed residues to preserve the structural integrity of the glycine binding site. This represents a new mechanism by which GlyR dysfunction induces startle disease. Hyperekplexia or startle disease is a serious neurological condition affecting newborn children and usually involves dysfunctional glycinergic neurotransmission. Glycine receptors (GlyRs) are major mediators of inhibition in the spinal cord and brainstem. A missense mutation, replacing asparagine (N) with lysine (K), at position 46 in the GlyR α1 subunit induced hyperekplexia following a reduction in the potency of the transmitter glycine; this resulted from a rapid deactivation of the agonist current at mutant GlyRs. These effects of N46K were rescued by mutating a juxtaposed residue, N61 on binding Loop D, suggesting these two asparagines may interact. Asparagine 46 is considered to be important for the structural stability of the subunit interface and glycine binding site, and its mutation represents a new mechanism by which GlyR dysfunction induces startle disease.
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Affiliation(s)
- Megan E Wilkins
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alex Caley
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marc C Gielen
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Robert J Harvey
- Department of Pharmacology, UCL School of Pharmacy, 29-39, Brunswick Square, London, WC1N 1AX, UK
| | - Trevor G Smart
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
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7
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Yoluk Ö, Lindahl E, Andersson M. Conformational gating dynamics in the GluCl anion-selective chloride channel. ACS Chem Neurosci 2015; 6:1459-67. [PMID: 25992588 DOI: 10.1021/acschemneuro.5b00111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cys-loop receptors are central to propagation of signals in the nervous system. The gating of the membrane-spanning pore is triggered by structural rearrangements in the agonist-binding site, located some 50 Å away from the pore. A sequential conformational change, propagating from the ligand-binding site to the pore, has been proposed to govern gating in all Cys-loop receptors. Here, we identify structural and dynamic components of the conformational gating in the eukaryotic glutamate-gated chloride channel (GluCl) by means of molecular dynamics (MD) simulations with and without the l-glutamate agonist bound. A significant increase in pore opening and accompanying hydration is observed in the presence of glutamate. Potential of mean force calculations reveal that the barrier for ion passage drops from 15 kcal/mol to 5-10 kcal/mol with the agonist bound. This appears to be explained by agonist binding that leads to significant changes in the intersubunit hydrogen-bonding pattern, which induce a slight tilt of the extracellular domain relative to the transmembrane domain in the simulations. This rearrangement is subtle, but correspond to the direction of the quaternary twist observed as a key difference between open and closed X-ray structures. While the full reversible gating is still a much slower process, the observed structural dynamics sheds new light on the early stages of how the agonist influences the extracellular domain, how the extracellular domain interacts with the transmembrane domain, and how changes in the transmembrane domain alter the free energy of ion passage.
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Affiliation(s)
- Özge Yoluk
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Erik Lindahl
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Magnus Andersson
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
- Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
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8
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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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9
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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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10
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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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11
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Lynagh T, Pless SA. Principles of agonist recognition in Cys-loop receptors. Front Physiol 2014; 5:160. [PMID: 24795655 PMCID: PMC4006026 DOI: 10.3389/fphys.2014.00160] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/04/2014] [Indexed: 12/22/2022] Open
Abstract
Cys-loop receptors are ligand-gated ion channels that are activated by a structurally diverse array of neurotransmitters, including acetylcholine, serotonin, glycine, and GABA. After the term "chemoreceptor" emerged over 100 years ago, there was some wait until affinity labeling, molecular cloning, functional studies, and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically diverse as glycine and serotonin has been subject to intense research over the last three decades. This review outlines the functional diversity and current structural understanding of agonist-binding sites, including those of invertebrate Cys-loop receptors. Together, this provides a framework to understand the atomic determinants involved in how these valuable therapeutic targets recognize and bind their ligands.
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Affiliation(s)
| | - Stephan A. Pless
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of CopenhagenCopenhagen, Denmark
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12
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Atkinson A, Graton J, Le Questel JY. Insights into a highly conserved network of hydrogen bonds in the agonist binding site of nicotinic acetylcholine receptors: a structural and theoretical study. Proteins 2014; 82:2303-17. [PMID: 24752960 DOI: 10.1002/prot.24589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 11/07/2022]
Abstract
Structural and theoretical studies on the geometrical features of a hydrogen-bond network occurring in the binding site of nicotinic acetylcholine receptors (nAChRs) and composed of interconnected WxPD (Trp-x-Pro-Asp) and SWyz (Ser-Trp-yz) sequences from loops A and B, respectively, have been carried out. Multiple sequence alignments using as template the sequence of the apoform of Aplysia californica acetylcholine binding protein (Ac-AChBP) show the strict conservation of serine and tryptophan residues of the loop B SWyz sequence. Considering a sample of 19 high resolution AChBP structures, the strong conformational preferences of the key tryptophan residue has been pointing out, whatever the form, free or bounded, of AChBP. The geometry of the motif hydrogen-bond network has been characterized through the analyses of seven distances. The robustness of the various hydrogen-bond interactions is pointed out, the one involving the aspartate carboxylate group and the serine residue being the shortest of the network. The role of a cooperative effect involving a NH(His145)…OH (Ser142) hydrogen bond is highlighted. Density functional theory calculations on several simplified models based on the motif hydrogen-bond network allow probing the importance of the various hydrogen-bond interactions. The removal of the Ser142 hydroxyl group induces strong structural rearrangements, in agreement with the structural observations. Molecular electrostatic potential calculations on model systems highlight the importance of a cooperative effect in the whole hydrogen-bond network. More precisely, the key role of the Ser142 hydroxyl group, involved in several hydrogen bonds, is underlined.
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Affiliation(s)
- Alexandre Atkinson
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, Nantes, F-44322, France
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13
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Ihara M, Shimazu N, Utsunomiya M, Akamatsu M, Sattelle DB, Matsuda K. A single amino acid polymorphism in the Drosophila melanogaster Dα1 (ALS) subunit enhances neonicotinoid efficacy at Dα1-chicken β2 hybrid nicotinic acetylcholine receptor expressed in Xenopus laevis oocytes. Biosci Biotechnol Biochem 2014; 78:543-9. [DOI: 10.1080/09168451.2014.891928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Abstract
Polymorphisms are sometimes observed in native insect nicotinic acetylcholine receptor (nAChR) subunits, which are important insecticide targets, yet little is known of their impact on insecticide actions. Here we investigated the effects of a polymorphism involving the substitution of histidine108 by leucine in the Drosophila melanogaster Dα1 subunit on the agonist actions of the neurotransmitter acetylcholine (ACh) and two commercial neonicotinoid insecticides (imidacloprid and clothianidin). There was no significant impact of the H108L substitution on either the ACh EC50, the concentration leading to a half maximal ACh response, or the maximum current amplitude in response at 10 μM ACh, of the Dα1-chicken β2 nAChR expressed in Xenopus laevis oocytes. However, the response amplitudes to imidacloprid and clothianidin were significantly enhanced, indicating a role of His108 in the selective interactions of Dα1 with these neonicotinoids.
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Affiliation(s)
- Makoto Ihara
- Faculty of Agriculture, Department of Applied Biological Chemistry, Kinki University, Nara, Japan
| | - Naoya Shimazu
- Faculty of Agriculture, Department of Applied Biological Chemistry, Kinki University, Nara, Japan
| | - Mai Utsunomiya
- Faculty of Agriculture, Department of Applied Biological Chemistry, Kinki University, Nara, Japan
| | - Miki Akamatsu
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - David B Sattelle
- The Wolfson Institute for Biomedical Research, Department of Medicine, University College London, London, UK
| | - Kazuhiko Matsuda
- Faculty of Agriculture, Department of Applied Biological Chemistry, Kinki University, Nara, Japan
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14
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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
![]()
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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15
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Matthews ML, Chang WC, Layne AP, Miles LA, Krebs C, Bollinger JM. Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase. Nat Chem Biol 2014; 10:209-15. [PMID: 24463698 PMCID: PMC4076429 DOI: 10.1038/nchembio.1438] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 12/10/2013] [Indexed: 12/14/2022]
Abstract
Iron-dependent halogenases employ cis-halo-Fe(IV)-oxo (haloferryl) complexes to functionalize unactivated aliphatic carbon centers, a capability elusive to synthetic chemists. Halogenation requires (1) coordination of a halide anion (Cl− or Br−) to the enzyme's Fe(II) cofactor; (2) coupled activation of O2 and decarboxylation of α-ketoglutarate to generate the haloferryl intermediate; (3) abstraction of hydrogen (H•) from the substrate by the ferryl oxo group; and (4) transfer of the cis halogen as Cl• or Br• to the substrate radical. This enzymatic solution to an unsolved chemical challenge is potentially generalizable to installation of other functional groups, provided that the corresponding anions can support the four requisite steps. We show here that the wild-type halogenase SyrB2 can indeed direct aliphatic nitration and azidation reactions by the same chemical logic. The discovery and enhancement by mutagenesis of these previously unknown reaction types suggests unrecognized or untapped versatility in ferryl-mediated enzymatic C–H-bond activation.
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Affiliation(s)
- Megan L Matthews
- 1] Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA. [2]
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew P Layne
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Linde A Miles
- 1] Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA. [2]
| | - Carsten Krebs
- 1] Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA. [2] Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - J Martin Bollinger
- 1] Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA. [2] Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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16
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Francis BR. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 2013; 77:134-58. [PMID: 23743924 DOI: 10.1007/s00239-013-9567-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022]
Abstract
Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071-3944, USA,
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17
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Merski M, Shoichet BK. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. J Med Chem 2013; 56:2874-84. [PMID: 23473072 PMCID: PMC3624796 DOI: 10.1021/jm301823g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Simplified
model binding sites allow one to isolate entangled terms
in molecular energy functions. Here, we investigate the effects on
ligand recognition of the introduction of a histidine into a hydrophobic
cavity in lysozyme. We docked 656040 molecules and tested 26 highly
and nine poorly ranked. Twenty-one highly ranked molecules bound and
five were false positives, while three poorly ranked molecules were
false negatives. In the 16 X-ray complexes now known, the docking
predictions overlaid well with the crystallographic results. Although
ligand enrichment was high, the false negatives, the false positives,
and the inability to rank order illuminated weaknesses in our scoring,
particularly overweighed apolar and underweighted polar terms. Adjusting
these led to new problems, reflecting the entangled nature of docking
scoring functions. Changes in ligand affinity relative to other lysozyme
cavities speak to the subtleties of molecular recognition even in
these simple sites and to their relevance for testing different models
of recognition.
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Affiliation(s)
- Matthew Merski
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
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18
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Physostigmine and galanthamine bind in the presence of agonist at the canonical and noncanonical subunit interfaces of a nicotinic acetylcholine receptor. J Neurosci 2013; 33:485-94. [PMID: 23303929 DOI: 10.1523/jneurosci.3483-12.2013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Galanthamine and physostigmine are clinically used cholinomimetics that both inhibit acetylcholinesterase and also interact directly with and potentiate nAChRs. As with most nAChR-positive allosteric modulators, the location and number of their binding site(s) within nAChRs are unknown. In this study, we use the intrinsic photoreactivities of [(3)H]physostigmine and [(3)H]galanthamine upon irradiation at 312 nm to directly identify amino acids contributing to their binding sites in the Torpedo californica nAChR. Protein sequencing of fragments isolated from proteolytic digests of [(3)H]physostigmine- or [(3)H]galanthamine-photolabeled nAChR establish that, in the presence of agonist (carbamylcholine), both drugs photolabeled amino acids on the complementary (non-α) surface of the transmitter binding sites (γTyr-111/γTyr-117/δTyr172). They also photolabeled δTyr-212 at the δ-β subunit interface and γTyr-105 in the vestibule of the ion channel, with photolabeling of both residues enhanced in the presence of agonist. Furthermore, [(3)H]physostigmine photolabeling of γTyr-111, γTyr-117, δTyr-212, and γTyr-105 was inhibited in the presence of nonradioactive galanthamine. The locations of the photolabeled amino acids in the nAChR structure and the results of computational docking studies provide evidence that, in the presence of agonist, physostigmine and galanthamine bind to at least three distinct sites in the nAChR extracellular domain: at the α-γ interface (1) in the entry to the transmitter binding site and (2) in the vestibule of the ion channel near the level of the transmitter binding site, and at the δ-β interface (3) in a location equivalent to the benzodiazepine binding site in GABA(A) receptors.
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19
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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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20
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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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21
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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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22
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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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23
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Abstract
Since the discovery of the major excitatory and inhibitory neurotransmitters and their receptors in the brain, many have deliberated over their likely structures and how these may relate to function. This was initially satisfied by the determination of the first amino acid sequences of the Cys-loop receptors that recognized acetylcholine, serotonin, GABA, and glycine, followed later by similar determinations for the glutamate receptors, comprising non-NMDA and NMDA subtypes. The last decade has seen a rapid advance resulting in the first structures of Cys-loop receptors, related bacterial and molluscan homologs, and glutamate receptors, determined down to atomic resolution. This now provides a basis for determining not just the complete structures of these important receptor classes, but also for understanding how various domains and residues interact during agonist binding, receptor activation, and channel opening, including allosteric modulation. This article reviews our current understanding of these mechanisms for the Cys-loop and glutamate receptor families.
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Affiliation(s)
- Trevor G Smart
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom.
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24
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Pless SA, Leung AWY, Galpin JD, Ahern CA. Contributions of conserved residues at the gating interface of glycine receptors. J Biol Chem 2011; 286:35129-36. [PMID: 21835920 DOI: 10.1074/jbc.m111.269027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Glycine receptors (GlyRs) are chloride channels that mediate fast inhibitory neurotransmission and are members of the pentameric ligand-gated ion channel (pLGIC) family. The interface between the ligand binding domain and the transmembrane domain of pLGICs has been proposed to be crucial for channel gating and is lined by a number of charged and aromatic side chains that are highly conserved among different pLGICs. However, little is known about specific interactions between these residues that are likely to be important for gating in α1 GlyRs. Here we use the introduction of cysteine pairs and the in vivo nonsense suppression method to incorporate unnatural amino acids to probe the electrostatic and hydrophobic contributions of five highly conserved side chains near the interface, Glu-53, Phe-145, Asp-148, Phe-187, and Arg-218. Our results suggest a salt bridge between Asp-148 in loop 7 and Arg-218 in the pre-M1 domain that is crucial for channel gating. We further propose that Phe-145 and Phe-187 play important roles in stabilizing this interaction by providing a hydrophobic environment. In contrast to the equivalent residues in loop 2 of other pLGICs, the negative charge at Glu-53 α1 GlyRs is not crucial for normal channel function. These findings help decipher the GlyR gating pathway and show that distinct residue interaction patterns exist in different pLGICs. Furthermore, a salt bridge between Asp-148 and Arg-218 would provide a possible mechanistic explanation for the pathophysiologically relevant hyperekplexia, or startle disease, mutant Arg-218 → Gln.
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Affiliation(s)
- Stephan A Pless
- Department of Anesthesiology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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25
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Contributions of counter-charge in a potassium channel voltage-sensor domain. Nat Chem Biol 2011; 7:617-23. [PMID: 21785425 PMCID: PMC4933587 DOI: 10.1038/nchembio.622] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 05/11/2011] [Indexed: 12/24/2022]
Abstract
Voltage-sensor domains couple membrane potential to conformational changes in voltage-gated ion channels and phosphatases. Highly co-evolved acidic and aromatic side-chains assist the transfer of cationic side-chains across the transmembrane electric field during voltage-sensing. We investigated the functional contribution of negative electrostatic potentials from these residues to channel gating and voltage-sensing with unnatural amino acid mutagenesis, electrophysiology, voltage-clamp fluorometry and ab initio calculations. The data show that neutralization of two conserved acidic side-chains in transmembrane segments S2 and S3, Glu293 and Asp316 in Shaker potassium channels, have little functional effect on conductance-voltage relationships, although Glu293 appears to catalyze S4 movement. Our results suggest that neither Glu293 nor Asp316 engages in electrostatic state-dependent charge-charge interactions with S4, likely because they occupy, and possibly help create, a water-filled vestibule.
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26
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Purohit P, Auerbach A. Glycine hinges with opposing actions at the acetylcholine receptor-channel transmitter binding site. Mol Pharmacol 2010; 79:351-9. [PMID: 21115636 DOI: 10.1124/mol.110.068767] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The extent to which agonists activate synaptic receptor-channels depends on both the intrinsic tendency of the unliganded receptor to open and the amount of agonist binding energy realized in the channel-opening process. We examined mutations of the nicotinic acetylcholine receptor transmitter binding site (α subunit loop B) with regard to both of these parameters. αGly147 is an "activation" hinge where backbone flexibility maintains high values for intrinsic gating, the affinity of the resting conformation for agonists and net ligand binding energy. αGly153 is a "deactivation" hinge that maintains low values for these parameters. αTrp149 (between these two glycines) serves mainly to provide ligand binding energy for gating. We propose that a concerted motion of the two glycine hinges (plus other structural elements at the binding site) positions αTrp149 so that it provides physiologically optimal binding and gating function at the nerve-muscle synapse.
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Affiliation(s)
- Prasad Purohit
- Department of Physiology and Biophysics, SUNY at Buffalo, Buffalo, NY 14214, USA
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27
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Roose JL, Yocum CF, Popelkova H. Function of PsbO, the Photosystem II Manganese-Stabilizing Protein: Probing the Role of Aspartic Acid 157. Biochemistry 2010; 49:6042-51. [DOI: 10.1021/bi100303f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Johnna L. Roose
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Charles F. Yocum
- Department of Molecular, Cellular, and Developmental Biology
- Department of Chemistry
| | - Hana Popelkova
- Department of Molecular, Cellular, and Developmental Biology
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28
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Disruption of an intersubunit electrostatic bond is a critical step in glycine receptor activation. Proc Natl Acad Sci U S A 2010; 107:7987-92. [PMID: 20385800 DOI: 10.1073/pnas.1001845107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proper regulation of neurotransmission requires that ligand-activated ion channels remain closed until agonist binds. How channels then open remains poorly understood. Glycine receptor (GlyR) gating is initiated by agonist binding at interfaces between adjacent subunits in the extracellular domain. Aspartate-97, located at the alpha1 GlyR interface, is a conserved residue in the cys-loop receptor superfamily. The mutation of D97 to arginine (D97R) causes spontaneous channel opening, with open and closed dwell times similar to those of maximally activated WT GlyR. Using a model of the N-terminal domain of the alpha1 GlyR, we hypothesized that an arginine-119 residue was forming intersubunit electrostatic bonds with D97. The D97R/R119E charge reversal restored this interaction, stabilizing channels in their closed states. Cysteine substitution shows that this link occurs between adjacent subunits. This intersubunit electrostatic interaction among GlyR subunits thus contributes to the stabilization of the closed channel state, and its disruption represents a critical step in GlyR activation.
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29
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Miller PS, Smart TG. Binding, activation and modulation of Cys-loop receptors. Trends Pharmacol Sci 2010; 31:161-74. [PMID: 20096941 DOI: 10.1016/j.tips.2009.12.005] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022]
Abstract
It is over forty years since the major neurotransmitters and their protein receptors were identified, and over twenty years since determination of the first amino-acid sequences of the Cys-loop receptors that recognize acetylcholine, serotonin, GABA and glycine. The last decade has seen the first structures of these proteins (and related bacterial and molluscan homologues) determined to atomic resolution. Hopefully over the next decade, more detailed molecular structures of entire Cys-loop receptors in drug-bound and drug-free conformations will become available. These, together with functional studies, will provide a clear picture of how these receptors participate in neurotransmission and how structural variations between receptor subtypes impart their unique characteristics. This insight should facilitate the design of novel and improved therapeutics to treat neurological disorders. This review considers our current understanding about the processes of agonist binding, receptor activation and channel opening, as well as allosteric modulation of the Cys-loop receptor family.
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Affiliation(s)
- Paul S Miller
- Department of Neuroscience, Physiology & Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
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30
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Rucktooa P, Smit AB, Sixma TK. Insight in nAChR subtype selectivity from AChBP crystal structures. Biochem Pharmacol 2009; 78:777-87. [DOI: 10.1016/j.bcp.2009.06.098] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 06/19/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
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31
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Huang X, Zheng F, Zhan CG. Modeling differential binding of alpha4beta2 nicotinic acetylcholine receptor with agonists and antagonists. J Am Chem Soc 2009; 130:16691-6. [PMID: 19554732 DOI: 10.1021/ja8055326] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three-dimensional structures of both the open- and closed-channel states of alpha4beta2 receptor have been modeled and used to study their binding with representative agonists and antagonists. The obtained binding structures and free energies consistently reveal that antagonists bind more favorably with the closed-channel state and agonists bind more favorably with the open-channel state. The computational insights have led us to propose a computational strategy and protocol predicting whether a receptor ligand is an agonist or antagonist. Using the computational protocol, one only needs to calculate the relative binding free energies for a ligand binding with the open- and closed-channel structures. The ligand is predicted to be an agonist if the binding free energy calculated for the ligand binding with the open-channel state is significantly lower than that for its binding with the closed-channel state. If the binding free energy of a ligand with the open-channel state is higher than that with the closed-channel, the ligand is predicted to be an antagonist. The binding free energies calculated for all of the ligands binding with their most favorable channel states of the receptor are all close to the corresponding experimentally derived binding free energies. The new computational insights obtained and novel computational strategy and protocol proposed in this study are expected to be valuable in structure-based rational design of novel agonists/antagonists of nAChRs as therapeutic agents.
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Affiliation(s)
- Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street, Lexington, Kentucky 40536, USA
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32
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Srivastava S, Hamouda AK, Pandhare A, Duddempudi PK, Sanghvi M, Cohen JB, Blanton MP. [(3)H]Epibatidine photolabels non-equivalent amino acids in the agonist binding site of Torpedo and alpha4beta2 nicotinic acetylcholine receptors. J Biol Chem 2009; 284:24939-47. [PMID: 19620239 DOI: 10.1074/jbc.m109.019083] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptor (nAChR) agonists, such as epibatidine and its molecular derivatives, are potential therapeutic agents for a variety of neurological disorders. In order to identify determinants for subtype-selective agonist binding, it is important to determine whether an agonist binds in a common orientation in different nAChR subtypes. To compare the mode of binding of epibatidine in a muscle and a neuronal nAChR, we photolabeled Torpedo alpha(2)betagammadelta and expressed human alpha4beta2 nAChRs with [(3)H]epibatidine and identified by Edman degradation the photolabeled amino acids. Irradiation at 254 nm resulted in photolabeling of alphaTyr(198) in agonist binding site Segment C of the principal (+) face in both alpha subunits and of gammaLeu(109) and gammaTyr(117) in Segment E of the complementary (-) face, with no labeling detected in the delta subunit. For affinity-purified alpha4beta2 nAChRs, [(3)H]epibatidine photolabeled alpha4Tyr(195) (equivalent to Torpedo alphaTyr(190)) in Segment C as well as beta2Val(111) and beta2Ser(113) in Segment E (equivalent to Torpedo gammaLeu(109) and gammaTyr(111), respectively). Consideration of the location of the photolabeled amino acids in homology models of the nAChRs based upon the acetylcholine-binding protein structure and the results of ligand docking simulations suggests that epibatidine binds in a single preferred orientation within the alpha-gamma transmitter binding site, whereas it binds in two distinct orientations in the alpha4beta2 nAChR.
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Affiliation(s)
- Shouryadeep Srivastava
- Department of Pharmacology and Neuroscience and the Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
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33
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Kim EA, Jung KC, Sohn UD, Im C. Quantitative Structure Activity Relationship between Diazabicyclo[4.2.0]octanes Derivatives and Nicotinic Acetylcholine Receptor Agonists. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2009; 13:55-59. [PMID: 19885027 PMCID: PMC2766720 DOI: 10.4196/kjpp.2009.13.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Three dimensional quantitative structure activity relationship between diazabicyclo[4.2.0]octanes and nicotinic acetylcholine receptor (halpha4beta2 and halpha3beta4) agonists was studied using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). From 11 CoMFA and CoMSIA models, CoMSIA with steric and electrostatic fields gave the best predictive models (q(2)=0.926 and 0.945, r(2) (ncv)=0.983 and 0.988). This study can be used to develop potent halpha4beta2 receptor agonists with low activity on halpha3beta4 subtype.
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Affiliation(s)
- Eun Ae Kim
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea
| | | | - Uy Dong Sohn
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea
| | - Chaeuk Im
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea
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34
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Gleitsman KR, Kedrowski SMA, Lester HA, Dougherty DA. An intersubunit hydrogen bond in the nicotinic acetylcholine receptor that contributes to channel gating. J Biol Chem 2008; 283:35638-43. [PMID: 18952603 PMCID: PMC2602911 DOI: 10.1074/jbc.m807226200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/21/2008] [Indexed: 11/06/2022] Open
Abstract
The muscle nicotinic acetylcholine receptor is a large, allosteric, ligand-gated ion channel with the subunit composition alpha2betagammadelta. Although much is now known about the structure of the binding site, relatively little is understood about how the binding event is communicated to the channel gate, causing the pore to open. Here we identify a key hydrogen bond near the binding site that is involved in the gating pathway. Using mutant cycle analysis with the novel unnatural residue alpha-hydroxyserine, we find that the backbone N-H of alphaSer-191 in loop C makes a hydrogen bond to an anionic side chain of the complementary subunit upon agonist binding. However, the anionic partner is not the glutamate predicted by the crystal structures of the homologous acetylcholine-binding protein. Instead, the hydrogen-bonding partner is the extensively researched aspartate gammaAsp-174/deltaAsp-180, which had originally been identified as a key binding residue for cationic agonists.
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Affiliation(s)
- Kristin Rule Gleitsman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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35
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Tantama M, Licht S. Use of calculated cation-pi binding energies to predict relative strengths of nicotinic acetylcholine receptor agonists. ACS Chem Biol 2008; 3:693-702. [PMID: 19032090 DOI: 10.1021/cb800189y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Agonists and antagonists of the nicotinic acetylcholine receptor (nAChR) are used to treat nicotine addiction, neuromuscular disorders, and neurological diseases. In designing small molecule therapeutics with the nAChR as a target, it is useful to identify chemical parameters that correlate with ability to activate the receptor. Previous studies have shown that cation-pi interactions at the transmitter binding sites of the nAChR are important for receptor activation by strong agonists such as acetylcholine. We hypothesized that a calculated estimate of cation-pi binding ability could be used to predict the efficiency for channel opening (i.e., the gating efficiency) associated with activation of the acetylcholine receptor by a series of structurally related organic cations. We demonstrate that the calculated cation-pi energy is strongly correlated with gating efficiency but only weakly correlated with closed-state binding affinity. Our results suggest that cation-pi interactions contribute significantly to the open-state affinity of these cations and that the calculated cation-pi energy will be a useful parameter for designing nAChR agonists and antagonists.
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Affiliation(s)
- Mathew Tantama
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 16, Room 573B, Cambridge, Massachusetts 02139
| | - Stuart Licht
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 16, Room 573B, Cambridge, Massachusetts 02139
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Mapping a molecular link between allosteric inhibition and activation of the glycine receptor. Nat Struct Mol Biol 2008; 15:1084-93. [PMID: 18806798 DOI: 10.1038/nsmb.1492] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Accepted: 08/27/2008] [Indexed: 11/08/2022]
Abstract
Cys-loop ligand-gated ion channels mediate rapid neurotransmission throughout the central nervous system. They possess agonist recognition sites and allosteric sites where modulators regulate ion channel function. Using strychnine-sensitive glycine receptors, we identified a scaffold of hydrophobic residues enabling allosteric communication between glycine-agonist binding loops A and D, and the Zn(2+)-inhibition site. Mutating these hydrophobic residues disrupted Zn(2+) inhibition, generating novel Zn(2+)-activated receptors and spontaneous channel activity. Homology modeling and electrophysiology revealed that these phenomena are caused by disruption to three residues on the '-' loop face of the Zn(2+)-inhibition site, and to D84 and D86, on a neighboring beta3 strand, forming a Zn(2+)-activation site. We provide a new view for the activation of a Cys-loop receptor where, following agonist binding, the hydrophobic core and interfacial loops reorganize in a concerted fashion to induce downstream gating.
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Price KL, Bower KS, Thompson AJ, Lester HA, Dougherty DA, Lummis SCR. A hydrogen bond in loop A is critical for the binding and function of the 5-HT3 receptor. Biochemistry 2008; 47:6370-7. [PMID: 18498149 PMCID: PMC2649372 DOI: 10.1021/bi800222n] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding sites of Cys-loop receptors are formed from at least six loops (A-F). Here we have used mutagenesis, radioligand binding, voltage clamp electrophysiology, and homology modeling to probe the role of two residues in loop A of the 5-HT3 receptor: Asn128 and Glu129. The data show that substitution of Asn128, with a range of alternative natural and unnatural amino acids, changed the EC50 (from approximately 10-fold more potent to approximately 10-fold less potent than that of the wild type), increased the maximal peak current for mCPBG compared to 5-HT (R max) 2-19-fold, and decreased n H, indicating this residue is involved in receptor gating; we propose Asn128 faces away from the binding pocket and plays a role in facilitating transitions between conformational states. Substitutions of Glu129 resulted in functional receptors only when the residue could accept a hydrogen bond, but with both these and other substitutions, no [(3)H]granisetron binding could be detected, indicating a role in ligand binding. We propose that Glu129 faces into the binding pocket, where, through its ability to hydrogen bond, it plays a critical role in ligand binding. Thus, the data support a modified model of the 5-HT3 receptor binding site and show that loop A plays a critical role in both the ligand binding and function of this receptor.
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Affiliation(s)
- Kerry L Price
- Department of Biochemistry, University of Cambridge, UK
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Wells GB. Structural answers and persistent questions about how nicotinic receptors work. FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2008; 13:5479-510. [PMID: 18508600 PMCID: PMC2430769 DOI: 10.2741/3094] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The electron diffraction structure of nicotinic acetylcholine receptor (nAChR) from Torpedo marmorata and the X-ray crystallographic structure of acetylcholine binding protein (AChBP) are providing new answers to persistent questions about how nAChRs function as biophysical machines and as participants in cellular and systems physiology. New high-resolution information about nAChR structures might come from advances in crystallography and NMR, from extracellular domain nAChRs as high fidelity models, and from prokaryotic nicotinoid proteins. At the level of biophysics, structures of different nAChRs with different pharmacological profiles and kinetics will help describe how agonists and antagonists bind to orthosteric binding sites, how allosteric modulators affect function by binding outside these sites, how nAChRs control ion flow, and how large cytoplasmic domains affect function. At the level of cellular and systems physiology, structures of nAChRs will help characterize interactions with other cellular components, including lipids and trafficking and signaling proteins, and contribute to understanding the roles of nAChRs in addiction, neurodegeneration, and mental illness. Understanding nAChRs at an atomic level will be important for designing interventions for these pathologies.
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Affiliation(s)
- Gregg B Wells
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA.
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Abstract
The challenges to obtaining chemical-scale information on the molecules of neuroscience are considerable. Most targets are complex integral membrane proteins that are not amenable to direct structural characterization. However, by combining the tools of organic synthesis, molecular biology, and electrophysiology, rational and systematic structure-function studies can be performed in what we have termed physical organic chemistry on the brain. Using these tools, we have probed hydrophobic effects, hydrogen bonding, cation-pi interactions, and conformational changes associated with channel gating. The insights gained provide important guidance for drug discovery efforts targeting ion channels and neuroreceptors and mechanistic insights for the complex proteins of neuroscience.
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Affiliation(s)
- Dennis A Dougherty
- Division of Chemistry and Chemical Engineering California Institute of Technology, Pasadena, CA 91125, USA.
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Wang J, Lester HA, Dougherty DA. Establishing an ion pair interaction in the homomeric rho1 gamma-aminobutyric acid type A receptor that contributes to the gating pathway. J Biol Chem 2007; 282:26210-6. [PMID: 17606618 DOI: 10.1074/jbc.m702314200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
gamma-Aminobutyric acid type A (GABA(A)) receptors are members of the Cys-loop superfamily of ligand-gated ion channels. Upon agonist binding, the receptor undergoes a structural transition from the closed to the open state, but the mechanism of gating is not well understood. Here we utilized a combination of conventional mutagenesis and the high precision methodology of unnatural amino acid incorporation to study the gating interface of the human homopentameric rho1 GABA(A) receptor. We have identified an ion pair interaction between two conserved charged residues, Glu(92) in loop 2 of the extracellular domain and Arg(258) in the pre-M1 region. We hypothesize that the salt bridge exists in the closed state by kinetic measurements and free energy analysis. Several other charged residues at the gating interface are not critical to receptor function, supporting previous conclusions that it is the global charge pattern of the gating interface that controls receptor function in the Cys-loop superfamily.
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Affiliation(s)
- Jinti Wang
- Division of Chemistry and Chemical Engineering and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Maloney DJ, Ghanem N, Zhou J, Hecht SM. Positional assignment of differentially substituted bisaminoacylated pdCpAs. Org Biomol Chem 2007; 5:3135-8. [PMID: 17878972 DOI: 10.1039/b708786a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis and NMR analysis of a 2'-O-alanyl, 3'-O-[1-(13)C]valyl-pdCpA derivative has permitted the definitive assignment of the positions of acylation of tandemly activated pdCpAs, and the bisaminoacylated transfer RNAs derived therefrom.
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Affiliation(s)
- David J Maloney
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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