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Chatelain FC, Gilbert N, Bichet D, Jauch A, Feliciangeli S, Lesage F, Bignucolo O. Mechanistic basis of the dynamic response of TWIK1 ionic selectivity to pH. Nat Commun 2024; 15:3849. [PMID: 38719838 PMCID: PMC11079055 DOI: 10.1038/s41467-024-48067-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Highly selective for K+ at neutral pH, the TWIK1 channel becomes permeable to Na+ upon acidification. Using molecular dynamics simulations, we identify a network of residues involved in this unique property. Between the open and closed states previously observed by electron microscopy, molecular dynamics simulations show that the channel undergoes conformational changes between pH 7.5-6 involving residues His122, Glu235, Lys246 and Phe109. A complex network of interactions surrounding the selectivity filter at high pH transforms into a simple set of stronger interactions at low pH. In particular, His122 protonated by acidification moves away from Lys246 and engages in a salt bridge with Glu235. In addition, stacking interactions between Phe109 and His122, which stabilize the selectivity filter in its K+-selective state at high pH, disappear upon acidification. This leads to dissociation of the Phe109 aromatic side chain from this network, resulting in the Na+-permeable conformation of the channel.
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Affiliation(s)
- Franck C Chatelain
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Nicolas Gilbert
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Delphine Bichet
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Annaïse Jauch
- Immunodeficiency Laboratory, Department of Biomedicine, Basel, Switzerland
| | - Sylvain Feliciangeli
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Florian Lesage
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France.
- Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France.
| | - Olivier Bignucolo
- Université Côte d'Azur, Centre national de la recherche scientifique, Institut national de la santé et de la recherche médicale, Institut de pharmacologie moléculaire et cellulaire, 06560, Valbonne, France
- Swiss Institute of Bioinformatics, Basel, Switzerland
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2
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Turney TS, Li V, Brohawn SG. Structural Basis for pH-gating of the K + channel TWIK1 at the selectivity filter. Nat Commun 2022; 13:3232. [PMID: 35680900 PMCID: PMC9184524 DOI: 10.1038/s41467-022-30853-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/20/2022] [Indexed: 11/11/2022] Open
Abstract
TWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K+ channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays unique properties among K2Ps including low basal activity and inhibition by extracellular protons through incompletely understood mechanisms. Here, we present cryo-EM structures of TWIK1 in lipid nanodiscs at high and low pH that reveal a previously undescribed gating mechanism at the K+ selectivity filter. At high pH, TWIK1 adopts an open conformation. At low pH, protonation of an extracellular histidine results in a cascade of conformational changes that close the channel by sealing the top of the selectivity filter, displacing the helical cap to block extracellular ion access pathways, and opening gaps for lipid block of the intracellular cavity. These data provide a mechanistic understanding for extracellular pH-gating of TWIK1 and illustrate how diverse mechanisms have evolved to gate the selectivity filter of K+ channels.
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Affiliation(s)
- Toby S Turney
- Biophysics Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, 94720, USA
| | - Vivian Li
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, 94720, USA
| | - Stephen G Brohawn
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA.
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, 94720, USA.
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3
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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Heath GR, Lin YC, Matin TR, Scheuring S. Structural dynamics of channels and transporters by high-speed atomic force microscopy. Methods Enzymol 2021; 652:127-159. [PMID: 34059280 DOI: 10.1016/bs.mie.2021.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Channels and transporters are vital for transmembrane transport of ions and solutes, and also of larger compounds such as lipids and macromolecules. Therefore, they are crucial in many biological processes such as sensing, signal transduction, and the regulation of the distribution of molecules. Dysfunctions of these membrane proteins are associated to numerous diseases, and their interaction with drugs is critical in medicine. Understanding the behavior of channels and transporters requires structural and dynamic information to decipher the molecular mechanisms underlying their function. High-Speed Atomic Force Microscopy (HS-AFM) now allows the study of single transmembrane channels and transporters in action under physiological conditions, i.e., at ambient temperature and pressure, in physiological buffer and in a membrane, and in a most direct, label-free manner. In this chapter, we discuss the HS-AFM sample preparation, application, and data analysis protocols to study the structural and conformational dynamics of membrane-embedded channels and transporters.
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Affiliation(s)
- George R Heath
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - Yi-Chih Lin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Tina R Matin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States; Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, United States.
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Lewis A, McCrossan ZA, Manville RW, Popa MO, Cuello LG, Goldstein SAN. TOK channels use the two gates in classical K + channels to achieve outward rectification. FASEB J 2020; 34:8902-8919. [PMID: 32519783 DOI: 10.1096/fj.202000545r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/11/2022]
Abstract
TOKs are outwardly rectifying K+ channels in fungi with two pore-loops and eight transmembrane spans. Here, we describe the TOKs from four pathogens that cause the majority of life-threatening fungal infections in humans. These TOKs pass large currents only in the outward direction like the canonical isolate from Saccharomyces cerevisiae (ScTOK), and distinct from other K+ channels. ScTOK, AfTOK1 (Aspergillus fumigatus), and H99TOK (Cryptococcus neoformans grubii) are K+ -selective and pass current above the K+ reversal potential. CaTOK (Candida albicans) and CnTOK (Cryptococcus neoformans neoformans) pass both K+ and Na+ and conduct above a reversal potential reflecting the mixed permeability of their selectivity filter. Mutations in CaTOK and ScTOK at sites homologous to those that open the internal gates in classical K+ channels are shown to produce inward TOK currents. A favored model for outward rectification is proposed whereby the reversal potential determines ion occupancy, and thus, conductivity, of the selectivity filter gate that is coupled to an imperfectly restrictive internal gate, permitting the filter to sample ion concentrations on both sides of the membrane.
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Affiliation(s)
- Anthony Lewis
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Zoe A McCrossan
- NIHR Evaluation, Trials and Studies Coordinating Centre (NETSCC), University of Southampton, Southampton, UK
| | - Rían W Manville
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - M Oana Popa
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Luis G Cuello
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Steve A N Goldstein
- Departments of Physiology & Biophysics and Pediatrics, School of Medicine, Samueli College of Health Sciences, University of California, Irvine, Irvine, CA, USA
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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Nematian-Ardestani E, Abd-Wahab F, Chatelain FC, Sun H, Schewe M, Baukrowitz T, Tucker SJ. Selectivity filter instability dominates the low intrinsic activity of the TWIK-1 K2P K + channel. J Biol Chem 2019; 295:610-618. [PMID: 31806709 DOI: 10.1074/jbc.ra119.010612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/04/2019] [Indexed: 12/24/2022] Open
Abstract
Two-pore domain K+ (K2P) channels have many important physiological functions. However, the functional properties of the TWIK-1 (K2P1.1/KCNK1) K2P channel remain poorly characterized because heterologous expression of this ion channel yields only very low levels of functional activity. Several underlying reasons have been proposed, including TWIK-1 retention in intracellular organelles, inhibition by posttranslational sumoylation, a hydrophobic barrier within the pore, and a low open probability of the selectivity filter (SF) gate. By evaluating these potential mechanisms, we found that the latter dominates the low intrinsic functional activity of TWIK-1. Investigating this further, we observed that the low activity of the SF gate appears to arise from the inefficiency of K+ in stabilizing an active (i.e. conductive) SF conformation. In contrast, other permeant ion species, such as Rb+, NH4 +, and Cs+, strongly promoted a pH-dependent activated conformation. Furthermore, many K2P channels are activated by membrane depolarization via an SF-mediated gating mechanism, but we found here that only very strong nonphysiological depolarization produces voltage-dependent activation of heterologously expressed TWIK-1. Remarkably, we also observed that TWIK-1 Rb+ currents are potently inhibited by intracellular K+ (IC50 = 2.8 mm). We conclude that TWIK-1 displays unique SF gating properties among the family of K2P channels. In particular, the apparent instability of the conductive conformation of the TWIK-1 SF in the presence of K+ appears to dominate the low levels of intrinsic functional activity observed when the channel is expressed at the cell surface.
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Affiliation(s)
- Ehsan Nematian-Ardestani
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Firdaus Abd-Wahab
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Franck C Chatelain
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Labex ICST, 06560 Valbonne, France
| | - Han Sun
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Marcus Schewe
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Thomas Baukrowitz
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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8
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Nematian-ardestani E, Abd-wahab MF, Chatelain FC, Sun H, Schewe M, Baukrowitz T, Tucker SJ. Selectivity filter instability dominates the low intrinsic activity of the TWIK-1 K2P K + Channel.. [DOI: 10.1101/735704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
ABSTRACTTwo-pore domain (K2P) K+ channels have many important physiological functions. However, the functional properties of the TWIK-1 (K2P1.1/KCNK1) K2P channel remain poorly characterized because heterologous expression of this ion channel yields only very low levels of functional activity. Several underlying reasons have been proposed, including TWIK-1 retention in intracellular organelles, inhibition by post-translational sumoylation, a hydrophobic barrier within the pore, and a low open probability of the selectivity filter (SF) gate. By evaluating these various potential mechanisms, we found that the latter dominates the low intrinsic functional activity of TWIK-1. Investigating the underlying mechanism, we observed that the low activity of the SF gate appears to arise from the inefficiency of K+ in stabilizing an active (i.e. conductive) SF conformation. In contrast, other permeant ion species, such as Rb+, NH4+, and Cs+, strongly promoted a pH-dependent activated conformation. Furthermore, many K2P channels are activated by membrane depolarization via a SF-mediated gating mechanism, but we found here that only very strong, non-physiological depolarization produces voltage-dependent activation of heterologously expressed TWIK-1. Remarkably, we also observed that TWIK-1 Rb+ currents are potently inhibited by intracellular K+ (IC50 = 2.8 mM). We conclude that TWIK-1 displays unique SF gating properties among the family of K2P channels. In particular, the apparent instability of the conductive conformation of the TWIK-1 SF in the presence of K+ appears to dominate the low levels of intrinsic functional activity observed when the channel is expressed at the cell surface.
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9
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Heath GR, Scheuring S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr Opin Struct Biol 2019; 57:93-102. [PMID: 30878714 DOI: 10.1016/j.sbi.2019.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
Recent advances in high-speed atomic force microscopy (HS-AFM) have made it possible to study the conformational dynamics of single unlabeled transmembrane channels and transporters. Improving environmental control with the integration of a non-disturbing buffer exchange system, which in turn allows the gradual change of conditions during HS-AFM operation, has provided a breakthrough toward the performance of structural titration experiments. Further advancements in temporal resolution with the use of line scanning and height spectroscopy techniques show how high-speed atomic force microscopy can measure millisecond to microsecond dynamics, pushing this method beyond current spatial and temporal limits offered by less direct techniques.
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Affiliation(s)
- George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA.
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Kimura T, Lorenz-Fonfria VA, Douki S, Motoki H, Ishitani R, Nureki O, Higashi M, Furutani Y. Vibrational and Molecular Properties of Mg2+ Binding and Ion Selectivity in the Magnesium Channel MgtE. J Phys Chem B 2018; 122:9681-9696. [DOI: 10.1021/acs.jpcb.8b07967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tetsunari Kimura
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Victor A. Lorenz-Fonfria
- Institute of Molecular Science (ICMol), Universitat de València, Catedràtic José Beltrán Martínez 2, 46980 Paterna, Spain
- Department of Biochemistry and Molecular Biology, Universitat de València, Carrer Doctor Moliner 50, 46100 Burjassot, Spain
| | - Shintaro Douki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideyoshi Motoki
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami, Okinawa 903-0213, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami, Okinawa 903-0213, Japan
| | - Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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