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Palmisano VF, Anguita-Ortiz N, Faraji S, Nogueira JJ. Voltage-Gated Ion Channels: Structure, Pharmacology and Photopharmacology. Chemphyschem 2024; 25:e202400162. [PMID: 38649320 DOI: 10.1002/cphc.202400162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
Voltage-gated ion channels are transmembrane proteins responsible for the generation and propagation of action potentials in excitable cells. Over the last decade, advancements have enabled the elucidation of crystal structures of ion channels. This progress in structural understanding, particularly in identifying the binding sites of local anesthetics, opens avenues for the design of novel compounds capable of modulating ion conduction. However, many traditional drugs lack selectivity and come with adverse side effects. The emergence of photopharmacology has provided an orthogonal way of controlling the activity of compounds, enabling the regulation of ion conduction with light. In this review, we explore the central pore region of voltage-gated sodium and potassium channels, providing insights from both structural and pharmacological perspectives. We discuss the different binding modes of synthetic compounds that can physically occlude the pore and, therefore, block ion conduction. Moreover, we examine recent advances in the photopharmacology of voltage-gated ion channels, introducing molecular approaches aimed at controlling their activity by using photosensitive drugs.
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Affiliation(s)
- Vito F Palmisano
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Nuria Anguita-Ortiz
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Shirin Faraji
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
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2
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Cholasseri R, De S. Deciphering the shape selective conformational equilibrium of E- and Z-locked azobenzene-tetraethylammonium ion in regulating photo-switchable K +-ion channel blocking. Phys Chem Chem Phys 2024; 26:19161-19175. [PMID: 38973424 DOI: 10.1039/d4cp01604a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
The search for photo-switchable optopharmacological agents that can block ion channels has been a prevalent area owing to its prime advantages of reversibility and specificity over the traditional blockers. However, the quest for a higher blocking ability shown by a less stable photo-isomer to perfectly suit the requirement of the optopharmacological agents is still ongoing. To date, only a marginal improvement in terms of blocking ability is observed by the less stable E-isomer of para-substituted locked azobenzene with TEA (LAB-TEA) for the K+-ion channel. Thus, rationalization of the limitation for achieving high activity by the E-isomer is rather essential to aid the improvement of the efficiency of photoswitchable blocker drugs. Herein, we report a molecular-level analysis on the mechanism of blocking by E- and Z-LAB-TEA with the bacterial KcsA K+-ion channel using Molecular Dynamics (MD) simulation and Quantum Mechanical (QM) calculations. The positively charged TEA fragment engages in stronger electrostatic interactions, while the neutral LAB fragment engages in weaker dispersive interactions. The binding free energy calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) for E-LAB-TEA (-22.3 kcal mol-1) shows less thermodynamic preference for binding with K+-ion channels than Z-LAB-TEA (-21.6 kcal mol-1) corroborating the experimental observation. The correlation between the structure and the binding ability of E- and Z-isomers of LAB-TEA indicates that the channel gate is narrow and acts as a bottleneck for the entry of the binder molecule inside the large cavity. Upon irradiation, the Z-isomer converts into a less stable but long and planar E-isomer (ΔE of photoisomerism = 7.0 kcal mol-1, at SA2-CASPT2(6,4)/6-31+G(d)//CASSCF(6,4)/6-31+G(d)), which is structurally more suitable to fit into the narrow channel gate rather than the curved and non-planar Z-LAB-TEA. Thus, a reduction in the ionic current is observed owing to the preferential entry and subsequent blocking by E-LAB-TEA. Discontinuing the irradiation leads to conversion to the Z-isomer, the curved nature of which hinders its spontaneous release outside the cavity, thereby contributing only a small increase in the ionic current.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala, 673 601, India
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut University P. O, Malappuram, Kerala, 673 635, India.
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3
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Saponaro A, Krumbach JH, Chaves-Sanjuan A, Sharifzadeh AS, Porro A, Castelli R, Hamacher K, Bolognesi M, DiFrancesco D, Clarke OB, Thiel G, Moroni A. Structural determinants of ivabradine block of the open pore of HCN4. Proc Natl Acad Sci U S A 2024; 121:e2402259121. [PMID: 38917012 PMCID: PMC11228525 DOI: 10.1073/pnas.2402259121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
HCN1-4 channels are the molecular determinants of the If/Ih current that crucially regulates cardiac and neuronal cell excitability. HCN dysfunctions lead to sinoatrial block (HCN4), epilepsy (HCN1), and chronic pain (HCN2), widespread medical conditions awaiting subtype-specific treatments. Here, we address the problem by solving the cryo-EM structure of HCN4 in complex with ivabradine, to date the only HCN-specific drug on the market. Our data show ivabradine bound inside the open pore at 3 Å resolution. The structure unambiguously proves that Y507 and I511 on S6 are the molecular determinants of ivabradine binding to the inner cavity, while F510, pointing outside the pore, indirectly contributes to the block by controlling Y507. Cysteine 479, unique to the HCN selectivity filter (SF), accelerates the kinetics of block. Molecular dynamics simulations further reveal that ivabradine blocks the permeating ion inside the SF by electrostatic repulsion, a mechanism previously proposed for quaternary ammonium ions.
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Affiliation(s)
- Andrea Saponaro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Jan H Krumbach
- Department of Physics, Technische Universität Darmstadt, Darmstadt 64289, Germany
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | | | | | - Alessandro Porro
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Roberta Castelli
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Kay Hamacher
- Department of Physics, Technische Universität Darmstadt, Darmstadt 64289, Germany
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | | | - Dario DiFrancesco
- Department of Biosciences, University of Milan, Milan 20133, Italy
- Institute of Biophysics-Milan, Consiglio Nazionale delle Ricerche, Milan 20133, Italy
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032
| | - Gerhard Thiel
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan 20133, Italy
- Institute of Biophysics-Milan, Consiglio Nazionale delle Ricerche, Milan 20133, Italy
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4
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Fan C, Flood E, Sukomon N, Agarwal S, Allen TW, Nimigean CM. Calcium-gated potassium channel blockade via membrane-facing fenestrations. Nat Chem Biol 2024; 20:52-61. [PMID: 37653172 PMCID: PMC10847966 DOI: 10.1038/s41589-023-01406-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
- Schrödinger, Inc., New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shubhangi Agarwal
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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5
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Iwamoto M, Morito M, Oiki S, Nishitani Y, Yamamoto D, Matsumori N. Cardiolipin binding enhances KcsA channel gating via both its specific and dianion-monoanion interchangeable sites. iScience 2023; 26:108471. [PMID: 38077151 PMCID: PMC10709135 DOI: 10.1016/j.isci.2023.108471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/29/2023] [Accepted: 11/13/2023] [Indexed: 01/17/2024] Open
Abstract
KcsA is a potassium channel with a plethora of structural and functional information, but its activity in the KcsA-producing actinomycete membranes remains elusive. To determine lipid species involved in channel-modulation, a surface plasmon resonance (SPR)-based methodology, characterized by immobilization of membrane proteins under a membrane environment, was applied. Dianionic cardiolipin (CL) showed extremely higher affinity for KcsA than monoanionic lipids. The SPR experiments further demonstrated that CL bound not only to the N-terminal M0 helix, a lipid-sensor domain, but to the M0 helix-deleted mutant. In contrast, monoanionic lipids interacted primarily with the M0 helix. This indicates the presence of an alternative CL-binding site, plausibly in the transmembrane domain. Single-channel recordings demonstrated that CL enhanced channel opening in an M0-independent manner. Taken together, the action of monoanionic lipids is exclusively mediated by the M0 helix, while CL binds both the M0 helix and its specific site, further enhancing the channel activity.
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Affiliation(s)
- Masayuki Iwamoto
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Masayuki Morito
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
| | - Shigetoshi Oiki
- Biomedial Imaging Research Center, University of Fukui, Fukui 910-1193, Japan
| | - Yudai Nishitani
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Daisuke Yamamoto
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
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6
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Gabriel TS, Hansen UP, Urban M, Drexler N, Winterstein T, Rauh O, Thiel G, Kast SM, Schroeder I. Asymmetric Interplay Between K + and Blocker and Atomistic Parameters From Physiological Experiments Quantify K + Channel Blocker Release. Front Physiol 2021; 12:737834. [PMID: 34777005 PMCID: PMC8586521 DOI: 10.3389/fphys.2021.737834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022] Open
Abstract
Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels.
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Affiliation(s)
- Tobias S Gabriel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin Urban
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Nils Drexler
- Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Tobias Winterstein
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
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7
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Mechanisms underlying drug-mediated regulation of membrane protein function. Proc Natl Acad Sci U S A 2021; 118:2113229118. [PMID: 34753824 DOI: 10.1073/pnas.2113229118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
The hydrophobic coupling between membrane proteins and their host lipid bilayer provides a mechanism by which bilayer-modifying drugs may alter protein function. Drug regulation of membrane protein function thus may be mediated by both direct interactions with the protein and drug-induced alterations of bilayer properties, in which the latter will alter the energetics of protein conformational changes. To tease apart these mechanisms, we examine how the prototypical, proton-gated bacterial potassium channel KcsA is regulated by bilayer-modifying drugs using a fluorescence-based approach to quantify changes in both KcsA function and lipid bilayer properties (using gramicidin channels as probes). All tested drugs inhibited KcsA activity, and the changes in the different gating steps varied with bilayer thickness, suggesting a coupling to the bilayer. Examining the correlations between changes in KcsA gating steps and bilayer properties reveals that drug-induced regulation of membrane protein function indeed involves bilayer-mediated mechanisms. Both direct, either specific or nonspecific, binding and bilayer-mediated mechanisms therefore are likely to be important whenever there is overlap between the concentration ranges at which a drug alters membrane protein function and bilayer properties. Because changes in bilayer properties will impact many diverse membrane proteins, they may cause indiscriminate changes in protein function.
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8
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Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs. Int J Mol Sci 2021; 22:ijms22158143. [PMID: 34360907 PMCID: PMC8348670 DOI: 10.3390/ijms22158143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/01/2022] Open
Abstract
The superfamily of P-loop channels includes various potassium channels, voltage-gated sodium and calcium channels, transient receptor potential channels, and ionotropic glutamate receptors. Despite huge structural and functional diversity of the channels, their pore-forming domain has a conserved folding. In the past two decades, scores of atomic-scale structures of P-loop channels with medically important drugs in the inner pore have been published. High structural diversity of these complexes complicates the comparative analysis of these structures. Here we 3D-aligned structures of drug-bound P-loop channels, compared their geometric characteristics, and analyzed the energetics of ligand-channel interactions. In the superimposed structures drugs occupy most of the sterically available space in the inner pore and subunit/repeat interfaces. Cationic groups of some drugs occupy vacant binding sites of permeant ions in the inner pore and selectivity-filter region. Various electroneutral drugs, lipids, and detergent molecules are seen in the interfaces between subunits/repeats. In many structures the drugs strongly interact with lipid and detergent molecules, but physiological relevance of such interactions is unclear. Some eukaryotic sodium and calcium channels have state-dependent or drug-induced π-bulges in the inner helices, which would be difficult to predict. The drug-induced π-bulges may represent a novel mechanism of gating modulation.
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9
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Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
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10
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Giudici AM, Díaz-García C, Renart ML, Coutinho A, Prieto M, González-Ros JM, Poveda JA. Tetraoctylammonium, a Long Chain Quaternary Ammonium Blocker, Promotes a Noncollapsed, Resting-Like Inactivated State in KcsA. Int J Mol Sci 2021; 22:ijms22020490. [PMID: 33419017 PMCID: PMC7825302 DOI: 10.3390/ijms22020490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023] Open
Abstract
Alkylammonium salts have been used extensively to study the structure and function of potassium channels. Here, we use the hydrophobic tetraoctylammonium (TOA+) to shed light on the structure of the inactivated state of KcsA, a tetrameric prokaryotic potassium channel that serves as a model to its homologous eukaryotic counterparts. By the combined use of a thermal denaturation assay and the analysis of homo-Förster resonance energy transfer in a mutant channel containing a single tryptophan (W67) per subunit, we found that TOA+ binds the channel cavity with high affinity, either with the inner gate open or closed. Moreover, TOA+ bound at the cavity allosterically shifts the equilibrium of the channel's selectivity filter conformation from conductive to an inactivated-like form. The inactivated TOA+-KcsA complex exhibits a loss in the affinity towards permeant K+ at pH 7.0, when the channel is in its closed state, but maintains the two sets of K+ binding sites and the W67-W67 intersubunit distances characteristic of the selectivity filter in the channel resting state. Thus, the TOA+-bound state differs clearly from the collapsed channel state described by X-ray crystallography and claimed to represent the inactivated form of KcsA.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Clara Díaz-García
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Ana Coutinho
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
- Departamento de Química e Bioquímica, Faculty of Sciences, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
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11
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Tikhonov DB, Lin L, Yang DSC, Yuchi Z, Zhorov BS. Phenylalkylamines in calcium channels: computational analysis of experimental structures. J Comput Aided Mol Des 2020; 34:1157-1169. [PMID: 32648151 DOI: 10.1007/s10822-020-00330-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
Experimental 3D structures of calcium channels with phenylalkylamines (PAAs) provide basis for further analysis of atomic mechanisms of these important cardiovascular drugs. In the crystal structure of the engineered calcium channel CavAb with Br-verapamil and in the cryo-EM structure of the Cav1.1 channel with verapamil, the ligands bind in the inner pore. However, there are significant differences between these structures. In the crystal structure the ligand ammonium group is much closer to the ion in the selectivity-filter region Site 3, which is most proximal to the inner pore, than in the cryo-EM structure. Here we used Monte Carlo energy minimizations to dock PAAs in calcium channels. Our computations suggest that in the crystal structure Site 3 is occupied by a water molecule rather than by a calcium ion. Analysis of the published electron density map does not rule out this possibility. In the cryo-EM structures the ammonium group of verapamil is shifted from the calcium ion in Site 3 either along the pore axis, towards the cytoplasm or away from the axis. Our unbiased docking reproduced these binding modes. However, in the cryo-EM structures detergent and lipid molecules interact with verapamil. When we removed these molecules, the nitrile group of verapamil bound to the calcium ion in Site 3. Models of Cav1.2 with different PAAs suggest similar binding modes and direct contacts of the ligands electronegative atoms with the calcium ion in Site 3. Such interactions explain paradoxes in structure-activity relationships of PAAs.
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Affiliation(s)
- Denis B Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russian Federation.
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Daniel S C Yang
- Almazov National Medical Research Centre, St. Petersburg, Russia, 197341
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
| | - Boris S Zhorov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russian Federation.
- Almazov National Medical Research Centre, St. Petersburg, Russia, 197341.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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12
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Domingo R, van der Westhuyzen R, Hamann AR, Mostert KJ, Barnard L, Paquet T, Tjhin ET, Saliba KJ, van Otterlo WAL, Strauss E. Overcoming synthetic challenges in targeting coenzyme A biosynthesis with the antimicrobial natural product CJ-15,801. MEDCHEMCOMM 2019; 10:2118-2125. [PMID: 32206243 DOI: 10.1039/c9md00312f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/16/2019] [Indexed: 11/21/2022]
Abstract
The biosynthesis of the essential metabolic cofactor coenzyme A (CoA) has been receiving increasing attention as a new target that shows potential to counter the rising resistance to established antimicrobials. In particular, phosphopantothenoylcysteine synthetase (PPCS)-the second CoA biosynthesis enzyme that is found as part of the bifunctional CoaBC protein in bacteria, but is monofunctional in eukaryotes-has been validated as a target through extensive genetic knockdown studies in Mycobacterium tuberculosis. Moreover, it has been identified as the molecular target of the fungal natural product CJ-15,801 that shows selective activity against Staphylococcus aureus and the malaria parasite Plasmodium falciparum. As such, CJ-15,801 and 4'-phospho-CJ-15,801 (its metabolically active form) are excellent tool compounds for use in the development of new antimicrobial PPCS inhibitors. Unfortunately, further study and analysis of CJ-15,801 is currently being hampered by several unique challenges posed by its synthesis. In this study we describe how these challenges were overcome by using a robust palladium-catalyzed coupling to form the key N-acyl vinylogous carbamate moiety with retention of stereochemistry, and by extensive investigation of protecting groups suited to the labile functional group combinations contained in this molecule. We also demonstrate that using TBAF for deprotection causes undesired off-target effects related to the presence of residual tertiary ammonium salts. Finally, we provide a new method for the chemoenzymatic preparation of 4'-phospho-CJ-15,801 on multi-milligram scale, after showing that chemical synthesis of the molecule is not practical. Taken together, the results of this study advances our pursuit to discover new antimicrobials that specifically target CoA biosynthesis and/or utilization.
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Affiliation(s)
- Riyad Domingo
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Renier van der Westhuyzen
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Anton R Hamann
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Konrad J Mostert
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Leanne Barnard
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Tanya Paquet
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
| | - Erick T Tjhin
- Research School of Biology , The Australian National University , Canberra , ACT , Australia
| | - Kevin J Saliba
- Research School of Biology , The Australian National University , Canberra , ACT , Australia.,Medical School , The Australian National University , Canberra , ACT , Australia
| | - Willem A L van Otterlo
- Department of Chemistry and Polymer Science , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa
| | - Erick Strauss
- Department of Biochemistry , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa .
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13
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Diffracted X-ray tracking method for recording single-molecule protein motions. Biochim Biophys Acta Gen Subj 2019; 1864:129361. [PMID: 31077793 DOI: 10.1016/j.bbagen.2019.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Proteins change their conformation depending on function. Although a vast number of static pictures of proteins have been accumulated, information regarding their dynamics in function is limited. Diffracted X-ray tracking (DXT) is a good candidate to obtain the missing data. SCOPE OF REVIEW A gold nanocrystal was attached to the target protein as a probe and the motion of the X-ray diffraction spots from the crystal corresponded to the motion of the target. Although it has advantages of high temporal (sub-millisecond) and spatial (approximately 0.1°) resolutions, it is not extensively utilized. This review focused on its effective application from a user's perspective. We also present an example with the KcsA channel and the status of recent developments to show the future possibilities of the method. MAJOR CONCLUSIONS DXT is a powerful method to investigate intramolecular structural changes. For instance, in the KcsA channel, the method revealed a wave of conformational changes transmitted from the gate region to the end of the molecule. The method is continuously being developed, and users can choose an appropriate measurement system depending on the condition of their sample. GENERAL SIGNIFICANCE Revealing the protein structural changes with respect to function is an important frontier. The most distinctive feature of the DXT method is that both high temporal and spatial resolutions are achievable, and it is possible to track the motions of multiple molecules at the same time. This feature is an advantage for screening molecules associated with the target proteins (e.g., ligands and medicines).
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14
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Conformational plasticity in the KcsA potassium channel pore helix revealed by homo-FRET studies. Sci Rep 2019; 9:6215. [PMID: 30996281 PMCID: PMC6470172 DOI: 10.1038/s41598-019-42405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
Potassium channels selectivity filter (SF) conformation is modulated by several factors, including ion-protein and protein-protein interactions. Here, we investigate the SF dynamics of a single Trp mutant of the potassium channel KcsA (W67) using polarized time-resolved fluorescence measurements. For the first time, an analytical framework is reported to analyze the homo-Förster resonance energy transfer (homo-FRET) within a symmetric tetrameric protein with a square geometry. We found that in the closed state (pH 7), the W67-W67 intersubunit distances become shorter as the average ion occupancy of the SF increases according to cation type and concentration. The hypothesis that the inactivated SF at pH 4 is structurally similar to its collapsed state, detected at low K+, pH 7, was ruled out, emphasizing the critical role played by the S2 binding site in the inactivation process of KcsA. This homo-FRET approach provides complementary information to X-ray crystallography in which the protein conformational dynamics is usually compromised.
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15
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Rinné S, Kiper AK, Vowinkel KS, Ramírez D, Schewe M, Bedoya M, Aser D, Gensler I, Netter MF, Stansfeld PJ, Baukrowitz T, Gonzalez W, Decher N. The molecular basis for an allosteric inhibition of K +-flux gating in K 2P channels. eLife 2019; 8:39476. [PMID: 30803485 PMCID: PMC6391080 DOI: 10.7554/elife.39476] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 02/06/2019] [Indexed: 01/05/2023] Open
Abstract
Two-pore-domain potassium (K2P) channels are key regulators of many physiological and pathophysiological processes and thus emerged as promising drug targets. As for other potassium channels, there is a lack of selective blockers, since drugs preferentially bind to a conserved binding site located in the central cavity. Thus, there is a high medical need to identify novel drug-binding sites outside the conserved lipophilic central cavity and to identify new allosteric mechanisms of channel inhibition. Here, we identified a novel binding site and allosteric inhibition mechanism, disrupting the recently proposed K+-flux gating mechanism of K2P channels, which results in an unusual voltage-dependent block of leak channels belonging to the TASK subfamily. The new binding site and allosteric mechanism of inhibition provide structural and mechanistic insights into the gating of TASK channels and the basis for the drug design of a new class of potent blockers targeting specific types of K2P channels.
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Affiliation(s)
- Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Kirsty S Vowinkel
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Talca, Chile
| | - Marcus Schewe
- Institute of Physiology, University of Kiel, Kiel, Germany
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - Diana Aser
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Isabella Gensler
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Michael F Netter
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Phillip J Stansfeld
- Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
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16
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Abstract
Voltage-gated sodium (Na+) channels are expressed in virtually all electrically excitable tissues and are essential for muscle contraction and the conduction of impulses within the peripheral and central nervous systems. Genetic disorders that disrupt the function of these channels produce an array of Na+ channelopathies resulting in neuronal impairment, chronic pain, neuromuscular pathologies, and cardiac arrhythmias. Because of their importance to the conduction of electrical signals, Na+ channels are the target of a wide variety of local anesthetic, antiarrhythmic, anticonvulsant, and antidepressant drugs. The voltage-gated family of Na+ channels is composed of α-subunits that encode for the voltage sensor domains and the Na+-selective permeation pore. In vivo, Na+ channel α-subunits are associated with one or more accessory β-subunits (β1-β4) that regulate gating properties, trafficking, and cell-surface expression of the channels. The permeation pore of Na+ channels is divided in two parts: the outer mouth of the pore is the site of the ion selectivity filter, while the inner cytoplasmic pore serves as the channel activation gate. The cytoplasmic lining of the permeation pore is formed by the S6 segments that include highly conserved aromatic amino acids important for drug binding. These residues are believed to undergo voltage-dependent conformational changes that alter drug binding as the channels cycle through the closed, open, and inactivated states. The purpose of this chapter is to broadly review the mechanisms of Na+ channel gating and the models used to describe drug binding and Na+ channel inhibition.
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Affiliation(s)
- M E O'Leary
- Cooper Medical School of Rowan University, Camden, NJ, USA
| | - M Chahine
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, QC, Canada.
- Department of Medicine, Université Laval, Quebec City, QC, Canada.
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17
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Renart ML, Montoya E, Giudici AM, Poveda JA, Fernández AM, Morales A, González-Ros JM. Selective exclusion and selective binding both contribute to ion selectivity in KcsA, a model potassium channel. J Biol Chem 2017; 292:15552-15560. [PMID: 28778926 DOI: 10.1074/jbc.m117.795807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/17/2017] [Indexed: 11/06/2022] Open
Abstract
The selectivity filter in potassium channels, a main component of the ion permeation pathway, configures a stack of binding sites (sites S1-S4) to which K+ and other cations may bind. Specific ion binding to such sites induces changes in the filter conformation, which play a key role in defining both selectivity and permeation. Here, using the potassium channel KcsA as a model, we contribute new evidence to reinforce this assertion. First, ion binding to KcsA blocked by tetrabutylammonium at the most cytoplasmic site in the selectivity filter (S4) suggests that such a site, when in the nonconductive filter conformation, has a higher affinity for cation binding than the most extracellular S1 site. This filter asymmetry, along with differences in intracellular and extracellular concentrations of K+versus Na+ under physiological conditions, should strengthen selection of the permeant K+ by the channel. Second, we used different K+ concentrations to shift the equilibrium between nonconductive and conductive states of the selectivity filter in which to test competitive binding of Na+ These experiments disclosed a marked decrease in the affinity of Na+ to bind the channel when the conformational equilibrium shifts toward the conductive state. This finding suggested that in addition to the selective binding of K+ and other permeant species over Na+, there is a selective exclusion of nonpermeant species from binding the channel filter, once it reaches a fully conductive conformation. We conclude that selective binding and selective exclusion of permeant and nonpermeant cations, respectively, are important determinants of ion channel selectivity.
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Affiliation(s)
- M Lourdes Renart
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
| | - Estefanía Montoya
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
| | - A Marcela Giudici
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
| | - José A Poveda
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
| | - Asia M Fernández
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
| | - Andrés Morales
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain
| | - José M González-Ros
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain and
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18
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Ahmed L, Rasulev B, Kar S, Krupa P, Mozolewska MA, Leszczynski J. Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose. NANOSCALE 2017; 9:10263-10276. [PMID: 28696446 DOI: 10.1039/c7nr00770a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. Here we explore their characteristics that could make them prospective leads for known disease-related proteins. High-throughput virtual screening supported by comprehensive multi-software protein-ligand docking simulation and cheminformatics approaches has been applied in investigation of interactions of 1117 proteins with a 169 fullerene nanoparticles decorated with different small molecules. Moreover, obtained docking results were confirmed by the series of unrestricted all-atom molecular dynamics (MD) simulations. Hydrophobicity of fullerene core along with hydrophilic interaction of side chains plays a key role in binding with the studied proteins. We identified a series of nanoparticles that can lead to development of robust drugs for target proteins and another series that can behave as a highly toxic agent. The structure-activity relationship analysis revealed two significant molecular properties responsible for the binding score values. The application of carefully selected computational techniques and described outcome of the study facilitate development of functional fullerene nanoparticles for drug-like and drug delivery applications.
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Affiliation(s)
- Lucky Ahmed
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA. and Center for Computationally Assisted Science and Technology (CCAST), North Dakota State University, 1805 NDSU Research Park Dr, PO Box 6050, Fargo, ND 58108, USA and Department of Coatings and Polymer Materials, North Dakota State University, NDSU Dept. 2760, PO Box 6050, Fargo, ND 58108, USA
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warszaw, 01-248, Poland
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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19
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Mourot A, Herold C, Kienzler MA, Kramer RH. Understanding and improving photo-control of ion channels in nociceptors with azobenzene photo-switches. Br J Pharmacol 2017. [PMID: 28635081 DOI: 10.1111/bph.13923] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND PURPOSE The photo-isomerizable local anaesthetic, quaternary ammonium-azobenzene-quaternary ammonium (QAQ), provides rapid, optical control over pain signalling without involving genetic modification. In darkness or in green light, trans-QAQ blocks voltage-gated K+ and Na+ channels and silences action potentials in pain-sensing neurons. Upon photo-isomerization to cis with near UV light, QAQ blockade is rapidly relieved, restoring neuronal activity. However, the molecular mechanism of cis and trans QAQ blockade is not known. Moreover, the absorption spectrum of QAQ requires UV light for photo-control, precluding use deep inside neural tissue. EXPERIMENTAL APPROACH Electrophysiology and molecular modelling were used to characterize the binding of cis and trans QAQ to voltage-gated K+ channels and to develop quaternary ammonium-ethylamine-azobenzene-quaternary ammonium (QENAQ), a red-shifted QAQ derivative controlled with visible light. KEY RESULTS trans QAQ was sixfold more potent than cis QAQ, in blocking current through Shaker K+ channels. Both isomers were use-dependent, open channel blockers, binding from the cytoplasmic side, but only trans QAQ block was slightly voltage dependent. QENAQ also blocked native K+ and Na+ channels preferentially in the trans state. QENAQ was photo-isomerized to cis with blue light and spontaneously reverted to trans within seconds in darkness, enabling rapid photo-control of action potentials in sensory neurons. CONCLUSIONS AND IMPLICATIONS Light-switchable local anaesthetics provide a means to non-invasively photo-control pain signalling with high selectivity and fast kinetics. Understanding the mode of action of QAQ and related compounds will help to design of drugs with improved photo-pharmacological properties. LINKED ARTICLES This article is part of a themed section on Recent Advances in Targeting Ion Channels to Treat Chronic Pain. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.12/issuetoc.
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Affiliation(s)
- Alexandre Mourot
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS-IBPS), Paris, France
| | - Christian Herold
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.,Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | | | - Richard H Kramer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
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20
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Unambiguous observation of blocked states reveals altered, blocker-induced, cardiac ryanodine receptor gating. Sci Rep 2016; 6:34452. [PMID: 27703263 PMCID: PMC5050499 DOI: 10.1038/srep34452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/12/2016] [Indexed: 11/08/2022] Open
Abstract
The flow of ions through membrane channels is precisely regulated by gates. The architecture and function of these elements have been studied extensively, shedding light on the mechanisms underlying gating. Recent investigations have focused on ion occupancy of the channel’s selectivity filter and its ability to alter gating, with most studies involving prokaryotic K+ channels. Some studies used large quaternary ammonium blocker molecules to examine the effects of altered ionic flux on gating. However, the absence of blocking events that are visibly distinct from closing events in K+ channels makes unambiguous interpretation of data from single channel recordings difficult. In this study, the large K+ conductance of the RyR2 channel permits direct observation of blocking events as distinct subconductance states and for the first time demonstrates the differential effects of blocker molecules on channel gating. This experimental platform provides valuable insights into mechanisms of blocker-induced modulation of ion channel gating.
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21
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Armacost KA, Goh GB, Brooks CL. Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations. J Chem Theory Comput 2016; 11:1267-77. [PMID: 26579773 DOI: 10.1021/ct500894k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Traditional free energy calculation methods are well-known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multisite λ-dynamics (BP-REX MSλD), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MSλD and the original MSλD are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved λ-space sampling is observed for the BP-REX MSλD simulations, yielding a 2-5-fold increase in the number of transitions between substituents compared to traditional MSλD. We also demonstrate the efficacy of varying the value of c, the parameter that controls the ruggedness of the landscape mediating the sampling of λ-states, based on the flexibility of the fragment. Finally, we developed a protocol for maximizing the transition frequency between fragments. This protocol reduces the "kinetic barrier" for alchemically transforming fragments by grouping and ordering based on volume. These findings are applied to a challenging test set involving a series of geldanamycin-based inhibitors of heat shock protein 90 (Hsp90). Even though the perturbations span volume changes by as large as 60 Å(3), the values for the free energy change achieve an average unsigned error (AUE) of 1.5 kcal/mol relative to experimental Kd measurements with a reasonable correlation (R = 0.56). Our results suggest that the BP-REX MSλD algorithm is a highly efficient and scalable free energy method, which when utilized will enable routine calculations on the order of hundreds of compounds using only a few simulations.
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Affiliation(s)
- Kira A Armacost
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Garrett B Goh
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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22
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Modeling interactions between blocking and permeant cations in the NavMs channel. Eur J Pharmacol 2016; 780:188-93. [PMID: 27020546 DOI: 10.1016/j.ejphar.2016.03.048] [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: 12/21/2015] [Revised: 03/19/2016] [Accepted: 03/24/2016] [Indexed: 02/01/2023]
Abstract
Mechanisms of sodium channel block by local anesthetics (LAs) are still a matter of intensive studies. In the absence of high-resolution structures of eukaryotic channels, atomic details of LA-channel interactions are analyzed using homology modeling. LAs are predicted to access the closed channel through a sidewalk (fenestration) between the channel repeats, bind in a horizontal orientation, and leave its aromatic moiety in the interface. Recent X-ray structure of a bacterial sodium channel NavMs with a cationic molecule Pl1, which is structurally similar to LAs, has confirmed this theoretical prediction and demonstrated a reduced selectivity filter occupancy by the permeant ions in the Pl1-bound channel. However, the nature of the antagonism between LAs and permeant ions is still unclear. Here we used the NavMs structure and Monte Carlo energy minimizations to model Pl1 binding. Our computations predict that Pl1 can displace permeant ion(s) from the selectivity filter by both steric and electrostatic mechanisms. We hypothesize that the electrostatic mechanism is more general, because it is applicable to many LAs and related drugs, which lack a moiety capable to enter the selectivity filter and sterically displace the permeant ion. The electrostatic mechanism is also consistent with the data that various cationic blockers of potassium channels bind in the inner pore without entering the selectivity filter.
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23
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Kuzmenkov AI, Grishin EV, Vassilevski AA. Diversity of Potassium Channel Ligands: Focus on Scorpion Toxins. BIOCHEMISTRY (MOSCOW) 2016; 80:1764-99. [DOI: 10.1134/s0006297915130118] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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Linder T, Saxena P, Timin E, Hering S, Stary-Weinzinger A. Structural Insights into Trapping and Dissociation of Small Molecules in K+ Channels. J Chem Inf Model 2014; 54:3218-28. [DOI: 10.1021/ci500353r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobias Linder
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Priyanka Saxena
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Eugen Timin
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Steffen Hering
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Anna Stary-Weinzinger
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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25
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Lenaeus MJ, Burdette D, Wagner T, Focia PJ, Gross A. Structures of KcsA in complex with symmetrical quaternary ammonium compounds reveal a hydrophobic binding site. Biochemistry 2014; 53:5365-73. [PMID: 25093676 PMCID: PMC4139162 DOI: 10.1021/bi500525s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Potassium channels allow for the
passive movement of potassium
ions across the cell membrane and are instrumental in controlling
the membrane potential in all cell types. Quaternary ammonium (QA)
compounds block potassium channels and have long been used to study
the functional and structural properties of these channels. Here we
describe the interaction between three symmetrical hydrophobic QAs
and the prokaryotic potassium channel KcsA. The structures demonstrate
the presence of a hydrophobic pocket between the inner helices of
KcsA and provide insight into the binding site and blocking mechanism
of hydrophobic QAs. The structures also reveal a structurally hidden
pathway between the central cavity and the outside membrane environment
reminiscent of the lateral fenestration observed in sodium channels
that can be accessed through small conformational changes in the pore
wall. We propose that the hydrophobic binding pocket stabilizes the
alkyl chains of long-chain QA molecules and may play a key role in
hydrophobic drug binding in general.
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Affiliation(s)
- Michael J Lenaeus
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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26
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Weiß K, Neef A, Van Q, Kramer S, Gregor I, Enderlein J. Quantifying the diffusion of membrane proteins and peptides in black lipid membranes with 2-focus fluorescence correlation spectroscopy. Biophys J 2014; 105:455-62. [PMID: 23870266 DOI: 10.1016/j.bpj.2013.06.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022] Open
Abstract
Protein diffusion in lipid membranes is a key aspect of many cellular signaling processes. To quantitatively describe protein diffusion in membranes, several competing theoretical models have been proposed. Among these, the Saffman-Delbrück model is the most famous. This model predicts a logarithmic dependence of a protein's diffusion coefficient on its inverse hydrodynamic radius (D ∝ ln 1/R) for small radius values. For large radius values, it converges toward a D ∝ 1/R scaling. Recently, however, experimental data indicate a Stokes-Einstein-like behavior (D ∝ 1/R) of membrane protein diffusion at small protein radii. In this study, we investigate protein diffusion in black lipid membranes using dual-focus fluorescence correlation spectroscopy. This technique yields highly accurate diffusion coefficients for lipid and protein diffusion in membranes. We find that despite its simplicity, the Saffman-Delbrück model is able to describe protein diffusion extremely well and a Stokes-Einstein-like behavior can be ruled out.
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Affiliation(s)
- Kerstin Weiß
- III. Institute of Physics, Georg-August-University Göttingen, Göttingen, Germany
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27
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Dempsey CE, Wright D, Colenso CK, Sessions RB, Hancox JC. Assessing hERG pore models as templates for drug docking using published experimental constraints: the inactivated state in the context of drug block. J Chem Inf Model 2014; 54:601-12. [PMID: 24471705 PMCID: PMC3977586 DOI: 10.1021/ci400707h] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
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Many
structurally and therapeutically diverse drugs interact with
the human heart K+ channel hERG by binding within the K+ permeation pathway of the open channel, leading to drug-induced
‘long QT syndrome’. Drug binding to hERG is often stabilized
by inactivation gating. In the absence of a crystal structure, hERG
pore homology models have been used to characterize drug interactions.
Here we assess potentially inactivated states of the bacterial K+ channel, KcsA, as templates for inactivated state hERG pore
models in the context of drug binding using computational docking.
Although Flexidock and GOLD docking produced low energy score poses
in the models tested, each method selected a MthK K+ channel-based
model over models based on the putative inactivated state KcsA structures
for each of the 9 drugs tested. The variety of docking poses found
indicates that an optimal arrangement for drug binding of aromatic
side chains in the hERG pore can be achieved in several different
configurations. This plasticity of the drug “binding site”
is likely to be a feature of the hERG inactivated state. The results
demonstrate that experimental data on specific drug interactions can
be used as structural constraints to assess and refine hERG homology
models.
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Affiliation(s)
- Christopher E Dempsey
- School of Biochemistry, Medical Sciences Building, University of Bristol , University Walk, Bristol BS8 1TD, U.K
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28
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Tikhonov DB, Zhorov BS. Homology modeling of Kv1.5 channel block by cationic and electroneutral ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:978-87. [PMID: 24316168 DOI: 10.1016/j.bbamem.2013.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/12/2013] [Accepted: 11/26/2013] [Indexed: 01/05/2023]
Abstract
The inner pore of potassium channels is targeted by many ligands of intriguingly different chemical structures. Previous studies revealed common and diverse characteristics of action of ligands including cooperativity of ligand binding, voltage- and use-dependencies, and patterns of ligand-sensing residues. Not all these data are rationalized in published models of ligand-channel complexes. Here we have used energy calculations with experimentally defined constraints to dock flecainide, ICAGEN-4, benzocaine, vernakalant, and AVE0118 into the inner pore of Kv1.5 channel. We arrived at ligand-binding models that suggest possible explanations for different values of the Hill coefficient, different voltage dependencies of ligands action, and effects of mutations of residues in subunit interfaces. Two concepts were crucial to build the models. First, the inner-pore block of a potassium channel requires a cationic "blocking particle". A ligand, which lacks a positively charged group, blocks the channel in a complex with a permeant ion. Second, hydrophobic moieties of a flexible ligand have a tendency to bind in hydrophobic subunit interfaces.
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Affiliation(s)
- Denis B Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Boris S Zhorov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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29
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Gray NW, Zhorov BS, Moczydlowski EG. Interaction of local anesthetics with the K (+) channel pore domain: KcsA as a model for drug-dependent tetramer stability. Channels (Austin) 2013; 7:182-93. [PMID: 23545989 DOI: 10.4161/chan.24455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Local anesthetics and related drugs block ionic currents of Na (+) , K (+) and Ca ( 2+) conducted across the cell membrane by voltage-dependent ion channels. Many of these drugs bind in the permeation pathway, occlude the pore and stop ion movement. However channel-blocking drugs have also been associated with decreased membrane stability of certain tetrameric K (+) channels, similar to the destabilization of channel function observed at low extracellular K (+) concentration. Such drug-dependent stability may result from electrostatic repulsion of K (+) from the selectivity filter by a cationic drug molecule bound in the central cavity of the channel. In this study we used the pore domain of the KcsA K (+) channel protein to test this hypothesis experimentally with a biochemical assay of tetramer stability and theoretically by computational simulation of local anesthetic docking to the central cavity. We find that two common local anesthetics, lidocaine and tetracaine, promote thermal dissociation of the KcsA tetramer in a K (+) -dependent fashion. Docking simulations of these drugs with open, open-inactivated and closed crystal structures of KcsA yield many energetically favorable drug-channel complexes characterized by nonbonded attraction to pore-lining residues and electrostatic repulsion of K (+) . The results suggest that binding of cationic drugs to the inner cavity can reduce tetramer stability of K (+) channels.
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Affiliation(s)
- Noel W Gray
- Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
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30
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Zhorov BS, Tikhonov DB. Ligand action on sodium, potassium, and calcium channels: role of permeant ions. Trends Pharmacol Sci 2013; 34:154-61. [PMID: 23375737 DOI: 10.1016/j.tips.2013.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/04/2013] [Accepted: 01/07/2013] [Indexed: 12/22/2022]
Abstract
Ion channels are targets for many naturally occurring toxins and small-molecule drugs. Despite great progress in the X-ray crystallography of ion channels, we still do not have a complete understanding of the atomistic mechanisms of channel modulation by ligands. In particular, the importance of the simultaneous interaction of permeant ions with the ligand and the channel protein has not been the focus of much attention. Considering these interactions often allows one to rationalize the highly diverse experimental data within the framework of relatively simple structural models. This has been illustrated in earlier studies on the action of local anesthetics, sodium channel activators, as well as blockers of potassium and calcium channels. Here, we discuss the available data with a view to understanding the use-, voltage-, and current carrying cation-dependence of the ligand action, paradoxes in structure--activity relationships, and effects of mutations in these ion channels.
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Affiliation(s)
- Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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31
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The voltage-dependent gate in MthK potassium channels is located at the selectivity filter. Nat Struct Mol Biol 2012; 20:159-66. [PMID: 23262489 PMCID: PMC3565016 DOI: 10.1038/nsmb.2473] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/21/2012] [Indexed: 12/18/2022]
Abstract
Understanding how ion channels open and close their pores is crucial for understanding their physiological roles. We used intracellular quaternary ammonium blockers to locate the voltage-dependent gate in MthK potassium channels from Methanobacterium thermoautotrophicum with electrophysiology and X-ray crystallography. Blockers bind in an aqueous cavity between two putative gates, an intracellular gate and the selectivity filter. Thus, these blockers directly probe gate location: an intracellular gate will prevent binding when closed, whereas a selectivity filter gate will always allow binding. A kinetic analysis of tetrabutylammonium block of single MthK channels combined with X-ray crystallographic analysis of the pore with tetrabutylantimony unequivocally determined that the voltage-dependent gate, like the C-type inactivation gate in eukaryotic channels, is located at the selectivity filter. State-dependent binding kinetics suggests that MthK inactivation leads to conformational changes within the cavity and intracellular pore entrance.
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32
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Mason SA, Viero C, Euden J, Bannister M, West D, Chen SRW, Williams AJ. The contribution of hydrophobic residues in the pore-forming region of the ryanodine receptor channel to block by large tetraalkylammonium cations and Shaker B inactivation peptides. ACTA ACUST UNITED AC 2012; 140:325-39. [PMID: 22930804 PMCID: PMC3434103 DOI: 10.1085/jgp.201210851] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although no high-resolution structural information is available for the ryanodine receptor (RyR) channel pore-forming region (PFR), molecular modeling has revealed broad structural similarities between this region and the equivalent region of K+ channels. This study predicts that, as is the case in K+ channels, RyR has a cytosolic vestibule lined with predominantly hydrophobic residues of transmembrane helices (TM10). In K+ channels, this vestibule is the binding site for blocking tetraalkylammonium (TAA) cations and Shaker B inactivation peptides (ShBPs), which are stabilized by hydrophobic interactions involving specific residues of the lining helices. We have tested the hypothesis that the cytosolic vestibule of RyR fulfils a similar role and that TAAs and ShBPs are stabilized by hydrophobic interactions with residues of TM10. Both TAAs and ShBPs block RyR from the cytosolic side of the channel. By varying the composition of TAAs and ShBPs, we demonstrate that the affinity of both species is determined by their hydrophobicity, with variations reflecting alterations in the dissociation rate of the bound blockers. We investigated the role of TM10 residues of RyR by monitoring block by TAAs and ShBPs in channels in which the hydrophobicity of individual TM10 residues was lowered by alanine substitution. Although substitutions changed the kinetics of TAA interaction, they produced no significant changes in ShBP kinetics, indicating the absence of specific hydrophobic sites of interactions between RyR and these peptides. Our investigations (a) provide significant new information on both the mechanisms and structural components of the RyR PFR involved in block by TAAs and ShBPs, (b) highlight important differences in the mechanisms and structures determining TAA and ShBP block in RyR and K+ channels, and (c) demonstrate that although the PFRs of these channels contain analogous structural components, significant differences in structure determine the distinct ion-handling properties of the two species of channel.
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Affiliation(s)
- Sammy A Mason
- Institute of Molecular and Experimental Medicine, Wales Heart Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, Wales, UK
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33
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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34
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Smithers N, Bolivar JH, Lee AG, East JM. Characterizing the fatty acid binding site in the cavity of potassium channel KcsA. Biochemistry 2012; 51:7996-8002. [PMID: 22971149 PMCID: PMC3466778 DOI: 10.1021/bi3009196] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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We show that interactions of fatty acids with the central
cavity of potassium channel KcsA can be characterized using the fluorescence
probe 11-dansylaminoundecanoic acid (Dauda). The fluorescence emission
spectrum of Dauda bound to KcsA in bilayers of dioleoylphosphatidylcholine
contains three components, which can be attributed to KcsA-bound and
lipid-bound Dauda together with unbound Dauda. The binding of Dauda
to KcsA was characterized by a dissociation constant of 0.47 ±
0.10 μM with 0.94 ± 0.06 binding site per KcsA tetramer.
Displacement of KcsA-bound Dauda by the tetrabutylammonium (TBA) ion
confirmed that the Dauda binding site was in the central cavity of
KcsA. Dissociation constants for a range of fatty acids were determined
by displacement of Dauda: binding of fatty acids increased in strength
with an increasing chain length from C14 to C20 but then decreased
in strength from C20 to C22. Increasing the number of double bonds
in the chain from one to four had little effect on binding, dissociation
constants for oleic acid and arachidonic acid, for example, being
2.9 ± 0.2 and 3.0 ± 0.4 μM, respectively. Binding
of TBA to KcsA was very slow, whereas binding of Dauda was fast, suggesting
that TBA can enter the cavity only through an open channel whereas
Dauda can bind to the closed channel, presumably entering the cavity
via the lipid bilayer.
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Affiliation(s)
- Natalie Smithers
- Centre for Biological Sciences, Life Sciences Building, University of Southampton , Southampton SO17 1BJ, UK
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35
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Bolivar JH, Smithers N, East JM, Marsh D, Lee AG. Multiple binding sites for fatty acids on the potassium channel KcsA. Biochemistry 2012; 51:2889-98. [PMID: 22409348 PMCID: PMC3336937 DOI: 10.1021/bi300153v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions of fatty acids with the potassium channel KcsA were studied using Trp fluorescence quenching and electron paramagnetic resonance (EPR) techniques. The brominated analogue of oleic acid was shown to bind to annular sites on KcsA and to the nonannular sites at each protein-protein interface in the homotetrameric structure with binding constants relative to dioleoylphosphatidylcholine of 0.67 ± 0.04 and 0.87 ± 0.08, respectively. Mutation of the two Arg residues close to the nonannular binding sites had no effect on fatty acid binding. EPR studies with a spin-labeled analogue of stearic acid detected a high-affinity binding site for the fatty acid with strong immobilization. Fluorescence quenching studies with the spin-labeled analogue showed that the binding site detected in the EPR experiments could not be one of the annular or nonannular binding sites. Instead, it is proposed that the EPR studies detect binding to the central hydrophobic cavity of the channel, with a binding constant in the range of ~0.1-1 μM.
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Affiliation(s)
- Juan H Bolivar
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton SO17 1BJ, UK
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36
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Structural correlates of selectivity and inactivation in potassium channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:272-85. [PMID: 21958666 DOI: 10.1016/j.bbamem.2011.09.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 09/07/2011] [Accepted: 09/09/2011] [Indexed: 12/23/2022]
Abstract
Potassium channels are involved in a tremendously diverse range of physiological applications requiring distinctly different functional properties. Not surprisingly, the amino acid sequences for these proteins are diverse as well, except for the region that has been ordained the "selectivity filter". The goal of this review is to examine our current understanding of the role of the selectivity filter and regions adjacent to it in specifying selectivity as well as its role in gating/inactivation and possible mechanisms by which these processes are coupled. Our working hypothesis is that an amino acid network behind the filter modulates selectivity in channels with the same signature sequence while at the same time affecting channel inactivation properties. This article is part of a Special Issue entitled: Membrane protein structure and function.
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37
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Lieberman RL, Culver JA, Entzminger KC, Pai JC, Maynard JA. Crystallization chaperone strategies for membrane proteins. Methods 2011; 55:293-302. [PMID: 21854852 DOI: 10.1016/j.ymeth.2011.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 10/17/2022] Open
Abstract
From G protein-coupled receptors to ion channels, membrane proteins represent over half of known drug targets. Yet, structure-based drug discovery is hampered by the dearth of available three-dimensional models for this large category of proteins. Other than efforts to improve membrane protein expression and stability, current strategies to improve the ability of membrane proteins to crystallize involve examining many orthologs and DNA constructs, testing the effects of different detergents for purification and crystallization, creating a lipidic environment during crystallization, and cocrystallizing with covalent or non-covalent soluble protein chaperones with an intrinsic high propensity to crystallize. In this review, we focus on this last category, highlighting successes of crystallization chaperones in membrane protein structure determination and recent developments in crystal chaperone engineering, including molecular display to enhance chaperone crystallizability, and end with a novel generic approach in development to target any membrane protein of interest.
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Affiliation(s)
- Raquel L Lieberman
- School of Chemistry and Biochemistry, Institute for Bioscience and Bioengineering, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA.
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38
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Streit AK, Netter MF, Kempf F, Walecki M, Rinné S, Bollepalli MK, Preisig-Müller R, Renigunta V, Daut J, Baukrowitz T, Sansom MSP, Stansfeld PJ, Decher N. A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore. J Biol Chem 2011; 286:13977-84. [PMID: 21362619 PMCID: PMC3077598 DOI: 10.1074/jbc.m111.227884] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two-pore domain potassium (K(2P)) channels play a key role in setting the membrane potential of excitable cells. Despite their role as putative targets for drugs and general anesthetics, little is known about the structure and the drug binding site of K(2P) channels. We describe A1899 as a potent and highly selective blocker of the K(2P) channel TASK-1. As A1899 acts as an open-channel blocker and binds to residues forming the wall of the central cavity, the drug was used to further our understanding of the channel pore. Using alanine mutagenesis screens, we have identified residues in both pore loops, the M2 and M4 segments, and the halothane response element to form the drug binding site of TASK-1. Our experimental data were used to validate a K(2P) open-pore homology model of TASK-1, providing structural insights for future rational design of drugs targeting K(2P) channels.
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Affiliation(s)
- Anne K Streit
- Institute for Physiology and Pathophysiology, Vegetative Physiology Group, University of Marburg, 35037 Marburg, Germany
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39
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Madeja M, Steffen W, Mesic I, Garic B, Zhorov BS. Overlapping binding sites of structurally different antiarrhythmics flecainide and propafenone in the subunit interface of potassium channel Kv2.1. J Biol Chem 2010; 285:33898-905. [PMID: 20709754 DOI: 10.1074/jbc.m110.159897] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kv2.1 channels, which are expressed in brain, heart, pancreas, and other organs and tissues, are important targets for drug design. Flecainide and propafenone are known to block Kv2.1 channels more potently than other Kv channels. Here, we sought to explore structural determinants of this selectivity. We demonstrated that flecainide reduced the K(+) currents through Kv2.1 channels expressed in Xenopus laevis oocytes in a voltage- and time-dependent manner. By systematically exchanging various segments of Kv2.1 with those from Kv1.2, we determined flecainide-sensing residues in the P-helix and inner helix S6. These residues are not exposed to the inner pore, a conventional binding region of open channel blockers. The flecainide-sensing residues also contribute to propafenone binding, suggesting overlapping receptors for the drugs. Indeed, propafenone and flecainide compete for binding in Kv2.1. We further used Monte Carlo-energy minimizations to map the receptors of the drugs. Flecainide docking in the Kv1.2-based homology model of Kv2.1 predicts the ligand ammonium group in the central cavity and the benzamide moiety in a niche between S6 and the P-helix. Propafenone also binds in the niche. Its carbonyl group accepts an H-bond from the P-helix, the amino group donates an H-bond to the P-loop turn, whereas the propyl group protrudes in the pore and blocks the access to the selectivity filter. Thus, besides the binding region in the central cavity, certain K(+) channel ligands can expand in the subunit interface whose residues are less conserved between K(+) channels and hence may be targets for design of highly desirable subtype-specific K(+) channel drugs.
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Affiliation(s)
- Michael Madeja
- Institute of Physiology, University of Münster, Münster, Germany.
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40
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Zimin PI, Garic B, Bodendiek SB, Mahieux C, Wulff H, Zhorov BS. Potassium channel block by a tripartite complex of two cationophilic ligands and a potassium ion. Mol Pharmacol 2010; 78:588-99. [PMID: 20601455 DOI: 10.1124/mol.110.064014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Voltage-gated potassium channels (Kv) are targets for drugs of large chemical diversity. Although hydrophobic cations block Kv channels with Hill coefficients of 1, uncharged electron-rich (cationophilic) molecules often display Hill coefficients of 2. The mechanism of the latter block is unknown. Using a combination of computational and experimental approaches, we mapped the receptor for the immunosuppressant PAP-1 (5-(4-phenoxybutoxy)psoralen), a high-affinity blocker of Kv1.3 channels in lymphocytes. Ligand-docking using Monte Carlo minimizations suggested a model in which two cationophilic PAP-1 molecules coordinate a K(+) ion in the pore with their coumarin moieties, whereas the hydrophobic phenoxyalkoxy side chains extend into the intrasubunit interfaces between helices S5 and S6. We tested the model by generating 58 point mutants involving residues in and around the predicted receptor and then determined their biophysical properties and sensitivity to PAP-1 by whole-cell patch-clamp. The model correctly predicted the key PAP-1-sensing residues in the outer helix, the P-loop, and the inner helix and explained the Hill coefficient of 2 by demonstrating that the Kv1.3 pore can accommodate two or even four PAP-1 molecules. The model further explained the voltage-dependence of block by PAP-1 and its thousand-fold selectivity for Kv1.3 over non-Kv1 channels. The 23- to 125-fold selectivity of PAP-1 for Kv1.3 over other Kv1 channels is probably due to its preferential affinity to the C-type inactivated state, in which cessation of K(+) flux stabilizes the tripartite PAP-1:K(+):PAP-1 complex in the pore. Our study provides a new concept for potassium channel block by cationophilic ligands.
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Affiliation(s)
- Pavel I Zimin
- Department of Pharmacology, University of California, Davis, California, USA
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41
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Denning EJ, Woolf TB. Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins 2010; 78:1105-19. [PMID: 19950367 DOI: 10.1002/prot.22632] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The growing dataset of K(+) channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homology models for the molecular conformations of K(+) channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro-Val-Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K(+) channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter-S5-S6 subunit motions, and lastly the large-scale domain rearrangements.
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Affiliation(s)
- Elizabeth J Denning
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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42
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Jerng HH, Dougherty K, Covarrubias M, Pfaffinger PJ. A novel N-terminal motif of dipeptidyl peptidase-like proteins produces rapid inactivation of KV4.2 channels by a pore-blocking mechanism. Channels (Austin) 2009; 3:448-61. [PMID: 19901547 DOI: 10.4161/chan.3.6.10216] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The somatodendritic subthreshold A-type K(+) current in neurons (I(SA)) depends on its kinetic and voltage-dependent properties to regulate membrane excitability, action potential repetitive firing, and signal integration. Key functional properties of the K(V)4 channel complex underlying I(SA) are determined by dipeptidyl peptidase-like proteins known as dipeptidyl peptidase 6 (DPP6) and dipeptidyl peptidase 10 (DPP10). Among the multiple known DPP10 isoforms with alternative N-terminal sequences, DPP10a confers exceptionally fast inactivation to K(V)4.2 channels. To elucidate the molecular basis of this fast inactivation, we investigated the structure-function relationship of the DPP10a N-terminal region and its interaction with the K(V)4.2 channel. Here, we show that DPP10a shares a conserved N-terminal sequence (MNQTA) with DPP6a (aka DPP6-E), which also induces fast inactivation. Deletion of the NQTA sequence in DPP10a eliminates this dramatic fast inactivation, and perfusion of MNQTA peptide to the cytoplasmic face of inside-out patches inhibits the K(V)4.2 current. DPP10a-induced fast inactivation exhibits competitive interactions with internally applied tetraethylammonium (TEA), and elevating the external K(+) concentration accelerates recovery from DPP10a-mediated fast inactivation. These results suggest that fast inactivation induced by DPP10a or DPP6a is mediated by a common N-terminal inactivation motif via a pore-blocking mechanism. This mechanism may offer an attractive target for novel pharmacological interventions directed at impairing I(SA) inactivation and reducing neuronal excitability.
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Affiliation(s)
- Henry H Jerng
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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43
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Cheng RCK, Tikhonov DB, Zhorov BS. Structural model for phenylalkylamine binding to L-type calcium channels. J Biol Chem 2009; 284:28332-28342. [PMID: 19700404 DOI: 10.1074/jbc.m109.027326] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phenylalkylamines (PAAs), a major class of L-type calcium channel (LTCC) blockers, have two aromatic rings connected by a flexible chain with a nitrile substituent. Structural aspects of ligand-channel interactions remain unclear. We have built a KvAP-based model of LTCC and used Monte Carlo energy minimizations to dock devapamil, verapamil, gallopamil, and other PAAs. The PAA-LTCC models have the following common features: (i) the meta-methoxy group in ring A, which is proximal to the nitrile group, accepts an H-bond from a PAA-sensing Tyr_IIIS6; (ii) the meta-methoxy group in ring B accepts an H-bond from a PAA-sensing Tyr_IVS6; (iii) the ammonium group is stabilized at the focus of P-helices; and (iv) the nitrile group binds to a Ca(2+) ion coordinated by the selectivity filter glutamates in repeats III and IV. The latter feature can explain Ca(2+) potentiation of PAA action and the presence of an electronegative atom at a similar position of potent PAA analogs. Tyr substitution of a Thr in IIIS5 is known to enhance action of devapamil and verapamil. Our models predict that the para-methoxy group in ring A of devapamil and verapamil accepts an H-bond from this engineered Tyr. The model explains structure-activity relationships of PAAs, effects of LTCC mutations on PAA potency, data on PAA access to LTCC, and Ca(2+) potentiation of PAA action. Common and class-specific aspects of action of PAAs, dihydropyridines, and benzothiazepines are discussed in view of the repeat interface concept.
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Affiliation(s)
- Ricky C K Cheng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Denis B Tikhonov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada; Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg 194223, Russia
| | - Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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44
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Zachariae U, Giordanetto F, Leach AG. Side Chain Flexibilities in the Human Ether-a-go-go Related Gene Potassium Channel (hERG) Together with Matched-Pair Binding Studies Suggest a New Binding Mode for Channel Blockers. J Med Chem 2009; 52:4266-76. [DOI: 10.1021/jm900002x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ulrich Zachariae
- Physical and Computational Chemistry, AstraZeneca, Mereside, Alderley Park, Macclesfield SK11 4TG, U.K
| | | | - Andrew G. Leach
- Physical and Computational Chemistry, AstraZeneca, Mereside, Alderley Park, Macclesfield SK11 4TG, U.K
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45
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Tikhonov DB, Zhorov BS. Structural model for dihydropyridine binding to L-type calcium channels. J Biol Chem 2009; 284:19006-17. [PMID: 19416978 DOI: 10.1074/jbc.m109.011296] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
1,4-Dihydropyridines (DHPs) constitute a major class of ligands for L-type Ca(2+) channels (LTCC). The DHPs have a boat-like, six-membered ring with an NH group at the stern, an aromatic moiety at the bow, and substituents at the port and starboard sides. Various DHPs exhibit antagonistic or agonistic activities, which were previously explained as stabilization or destabilization, respectively, of the closed activation gate by the portside substituents. Here we report a novel structural model in which agonist and antagonist activities are determined by different parts of the DHP molecule and have different mechanisms. In our model, which is based on Monte Carlo minimizations of DHP-LTCC complexes, the DHP moieties at the stern, bow, and starboard form H-bonds with side chains of the key DHP-sensing residues Tyr_IIIS6, Tyr_IVS6, and Gln_IIIS5, respectively. We propose that these H-bonds, which are common for agonists and antagonists, stabilize the LTCC conformation with the open activation gate. This explains why both agonists and antagonists increase probability of the long lasting channel openings and why even partial disruption of the contacts eliminates the agonistic action. In our model, the portside approaches the selectivity filter. Hydrophobic portside of antagonists may induce long lasting channel closings by destabilizing Ca(2+) binding to the selectivity filter glutamates. Agonists have either hydrophilic substituents or a hydrogen atom at their portside, and thus lack this destabilizing effect. The predicted orientation of the DHP core allows accommodation of long substituents in the domain interface or in the inner pore. Our model may be useful for developing novel clinically relevant LTCC blockers.
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Affiliation(s)
- Denis B Tikhonov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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46
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Imai YN, Ryu S, Oiki S. Docking Model of Drug Binding to the Human Ether-à-go-go Potassium Channel Guided by Tandem Dimer Mutant Patch-Clamp Data: A Synergic Approach. J Med Chem 2009; 52:1630-8. [DOI: 10.1021/jm801236n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yumi N. Imai
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Sunghi Ryu
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Shigetoshi Oiki
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
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47
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Santos JS, Grigoriev SM, Montal M. Molecular template for a voltage sensor in a novel K+ channel. III. Functional reconstitution of a sensorless pore module from a prokaryotic Kv channel. ACTA ACUST UNITED AC 2009; 132:651-66. [PMID: 19029373 PMCID: PMC2585861 DOI: 10.1085/jgp.200810077] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
KvLm is a prokaryotic voltage-gated K+ (Kv) channel from Listeria monocytogenes. The sequence of the voltage-sensing module (transmembrane segments S1-S4) of KvLm is atypical in that it contains only three of the eight conserved charged residues known to be deterministic for voltage sensing in eukaryotic Kv's. In contrast, the pore module (PM), including the S4-S5 linker and cytoplasmic tail (linker-S5-P-S6-C-terminus) of KvLm, is highly conserved. Here, the full-length (FL)-KvLm and the KvLm-PM only proteins were expressed, purified, and reconstituted into giant liposomes. The properties of the reconstituted FL-KvLm mirror well the characteristics of the heterologously expressed channel in Escherichia coli spheroplasts: a right-shifted voltage of activation, micromolar tetrabutylammonium-blocking affinity, and a single-channel conductance comparable to that of eukaryotic Kv's. Conversely, ionic currents through the PM recapitulate both the conductance and blocking properties of the FL-KvLm, yet the KvLm-PM exhibits only rudimentary voltage dependence. Given that the KvLm-PM displays many of the conduction properties of FL-KvLm and of other eukaryotic Kv's, including strict ion selectivity, we conclude that self-assembly of the PM subunits in lipid bilayers, in the absence of the voltage-sensing module, generates a conductive oligomer akin to that of the native KvLm, and that the structural independence of voltage sensing and PMs observed in eukaryotic Kv channels was initially implemented by nature in the design of prokaryotic Kv channels. Collectively, the results indicate that this robust functional module will prove valuable as a molecular template for coupling new sensors and to elucidate PM residue–specific contributions to Kv conduction properties.
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Affiliation(s)
- Jose S Santos
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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48
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Jara-Oseguera A, Llorente I, Rosenbaum T, Islas LD. Properties of the inner pore region of TRPV1 channels revealed by block with quaternary ammoniums. ACTA ACUST UNITED AC 2009; 132:547-62. [PMID: 18955595 PMCID: PMC2571972 DOI: 10.1085/jgp.200810051] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transient receptor potential vanilloid 1 (TRPV1) nonselective cationic channel is a polymodal receptor that activates in response to a wide variety of stimuli. To date, little structural information about this channel is available. Here, we used quaternary ammonium ions (QAs) of different sizes in an effort to gain some insight into the nature and dimensions of the pore of TRPV1. We found that all four QAs used, tetraethylammonium (TEA), tetrapropylammonium (TPrA), tetrabutylammonium, and tetrapentylammonium, block the TRPV1 channel from the intracellular face of the channel in a voltage-dependent manner, and that block by these molecules occurs with different kinetics, with the bigger molecules becoming slower blockers. We also found that TPrA and the larger QAs can only block the channel in the open state, and that they interfere with the channel's activation gate upon closing, which is observed as a slowing of tail current kinetics. TEA does not interfere with the activation gate, indicating that this molecule can reside in its blocking site even when the channel is closed. The dependence of the rate constants on the size of the blocker suggests a size of around 10 A for the inner pore of TRPV1 channels.
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Affiliation(s)
- Andrés Jara-Oseguera
- Departamento de Fisiología, Facultad de Medicina, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, D.F., 04510, México
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Pavlov E, Britvina T, McArthur JR, Ma Q, Sierralta I, Zamponi GW, French RJ. Trans-channel interactions in batrachotoxin-modified skeletal muscle sodium channels: voltage-dependent block by cytoplasmic amines, and the influence of mu-conotoxin GIIIA derivatives and permeant ions. Biophys J 2008; 95:4277-88. [PMID: 18658222 PMCID: PMC2567948 DOI: 10.1529/biophysj.108.138297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 07/09/2008] [Indexed: 01/22/2023] Open
Abstract
External mu-conotoxins and internal amine blockers inhibit each other's block of voltage-gated sodium channels. We explore the basis of this interaction by measuring the shifts in voltage-dependence of channel inhibition by internal amines induced by two mu-conotoxin derivatives with different charge distributions and net charges. Charge changes on the toxin were made at residue 13, which is thought to penetrate most deeply into the channel, making it likely to have the strongest individual interaction with an internal charged ligand. When an R13Q or R13E molecule was bound to the channel, the voltage dependence of diethylammonium (DEA)-block shifted toward more depolarized potentials (23 mV for R13Q, and 16 mV for R13E). An electrostatic model of the repulsion between DEA and the toxin simulated these data, with a distance between residue 13 of the mu-conotoxin and the DEA-binding site of approximately 15 A. Surprisingly, for tetrapropylammonium, the shifts were only 9 mV for R13Q, and 7 mV for R13E. The smaller shifts associated with R13E, the toxin with a smaller net charge, are generally consistent with an electrostatic interaction. However, the smaller shifts observed for tetrapropylammonium than for DEA suggest that other factors must be involved. Two observations indicate that the coupling of permeant ion occupancy of the channel to blocker binding may contribute to the overall amine-toxin interaction: 1), R13Q binding decreases the apparent affinity of sodium for the conducting pore by approximately 4-fold; and 2), increasing external [Na(+)] decreases block by DEA at constant voltage. Thus, even though a number of studies suggest that sodium channels are occupied by no more than one ion most of the time, measurable coupling occurs between permeant ions and toxin or amine blockers. Such interactions likely determine, in part, the strength of trans-channel, amine-conotoxin interactions.
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Affiliation(s)
- Evgeny Pavlov
- Department of Physiology and Biophysics, University of Calgary, Calgary, Alberta, Canada
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50
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Syeda R, Holden MA, Hwang WL, Bayley H. Screening Blockers Against a Potassium Channel with a Droplet Interface Bilayer Array. J Am Chem Soc 2008; 130:15543-8. [DOI: 10.1021/ja804968g] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruhma Syeda
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Matthew A. Holden
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - William L. Hwang
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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