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Aoyama M, Katayama K, Kandori H. Unique hydrogen-bonding network in a viral channelrhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149148. [PMID: 38906314 DOI: 10.1016/j.bbabio.2024.149148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Channelrhodopsins (CRs) are used as key tools in optogenetics, and novel CRs, either found from nature or engineered by mutation, have greatly contributed to the development of optogenetics. Recently CRs were discovered from viruses, and crystal structure of a viral CR, OLPVR1, reported a very similar water-containing hydrogen-bonding network near the retinal Schiff base to that of a light-driven proton-pump bacteriorhodopsin (BR). In both OLPVR1 and BR, nearly planar pentagonal cluster structures are comprised of five oxygen atoms, three oxygens from water molecules and two oxygens from the Schiff base counterions. The planar pentagonal cluster stabilizes a quadrupole, two positive charges at the Schiff base and an arginine, and two negative charges at the counterions, and thus plays important roles in light-gated channel function of OLPVR1 and light-driven proton pump function of BR. Despite similar pentagonal cluster structures, present FTIR analysis revealed different hydrogen-bonding networks between OLPVR1 and BR. The hydrogen bond between the protonated Schiff base and a water is stronger in OLPVR1 than in BR, and internal water molecules donate hydrogen bonds much weaker in OLPVR1 than in BR. In OLPVR1, the bridged water molecule between the Schiff base and counterions forms hydrogen bonds to D76 and D200 equally, while the hydrogen-bonding interaction is much stronger to D85 than to D212 in BR. The present interpretation is supported by the mutation results, where D76 and D200 equally work as the Schiff base counterions in OLPVR1, but D85 is the primary counterion in BR. This work reports highly sensitive hydrogen-bonding network in the Schiff base region, which would be closely related to each function through light-induced alterations of the network.
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Affiliation(s)
- Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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2
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Yu H, Song L, Duan X, Zhu D, Li N, Pan R, Xu R, Yu X, Ye F, Jiang X, Ye H, Pan Z, Wei S, Jiang Z. Optogenetics in taste research: A decade of enlightenment. Oral Dis 2024; 30:903-913. [PMID: 36620868 DOI: 10.1111/odi.14498] [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: 07/28/2022] [Revised: 12/03/2022] [Accepted: 01/05/2023] [Indexed: 01/10/2023]
Abstract
The electrophysiological function of the tongue involves complicated activities in taste sense, producing the perceptions of salty, sweet, bitter, and sour. However, therapies and prevention of taste loss arising from dysfunction in electrophysiological activity require further fundamental research. Optogenetics has revolutionized neuroscience and brought the study of sensory system to a higher level in taste. The year 2022 marks a decade of developments of optogenetics in taste since this technology was adopted from neuroscience and applied to the taste research. This review summarizes a decade of advances that define near-term translation with optogenetic tools, and newly-discovered mechanisms with the applications of these tools. The main limitations and opportunities for optogenetics in taste research are also discussed.
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Affiliation(s)
- Hanshu Yu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Luyao Song
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangyao Duan
- Zhejiang University School of Medicine, Hangzhou, China
| | - Danji Zhu
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, Zhejiang Provincial Clinical Research Centre for Oral Diseases, Cancer Centre of Zhejiang University, Stomatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Na Li
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, Zhejiang Provincial Clinical Research Centre for Oral Diseases, Cancer Centre of Zhejiang University, Stomatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Runxin Pan
- Zhejiang University School of Medicine, Hangzhou, China
| | - Rui Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xinying Yu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Fengkai Ye
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xinrui Jiang
- Zhejiang University School of Medicine, Hangzhou, China
| | - Han Ye
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zikang Pan
- Zhejiang University School of Medicine, Hangzhou, China
| | - Sixing Wei
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiwei Jiang
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, Zhejiang Provincial Clinical Research Centre for Oral Diseases, Cancer Centre of Zhejiang University, Stomatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Kaziannis S, Broser M, van Stokkum IHM, Dostal J, Busse W, Munhoven A, Bernardo C, Kloz M, Hegemann P, Kennis JTM. Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction. Proc Natl Acad Sci U S A 2024; 121:e2318996121. [PMID: 38478688 PMCID: PMC10962995 DOI: 10.1073/pnas.2318996121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.
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Affiliation(s)
- Spyridon Kaziannis
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
- Department of Physics, University of Ioannina, IoanninaGr-45110, Greece
| | - Matthias Broser
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Ivo H. M. van Stokkum
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Jakub Dostal
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Wayne Busse
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Arno Munhoven
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Cesar Bernardo
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Peter Hegemann
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
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Fischer P, Schiewer E, Broser M, Busse W, Spreen A, Grosse M, Hegemann P, Bartl F. The Functionality of the DC Pair in a Rhodopsin Guanylyl Cyclase from Catenaria anguillulae. J Mol Biol 2024; 436:168375. [PMID: 38092286 DOI: 10.1016/j.jmb.2023.168375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
Rhodopsin guanylyl cyclases (RGCs) belong to the class of enzymerhodopsins catalyzing the transition from GTP into the second messenger cGMP, whereas light-regulation of enzyme activity is mediated by a membrane-bound microbial rhodopsin domain, that holds the catalytic center inactive in the dark. Structural determinants for activation of the rhodopsin moiety eventually leading to catalytic activity are largely unknown. Here, we investigate the mechanistic role of the D283-C259 (DC) pair that is hydrogen bonded via a water molecule as a crucial functional motif in the homodimeric C. anguillulae RGC. Based on a structural model of the DC pair in the retinal binding pocket obtained by MD simulation, we analyzed formation and kinetics of early and late photocycle intermediates of the rhodopsin domain wild type and specific DC pair mutants by combined UV-Vis and FTIR spectroscopy at ambient and cryo-temperatures. By assigning specific infrared bands to S-H vibrations of C259 we are able to show that the DC pair residues are tightly coupled. We show that deprotonation of D283 occurs already in the inactive L state as a prerequisite for M state formation, whereas structural changes of C259 occur in the active M state and early cryo-trapped intermediates. We propose a comprehensive molecular model for formation of the M state that activates the catalytic moiety. It involves light induced changes in bond strength and hydrogen bonding of the DC pair residues from the early J state to the active M state and explains the retarding effect of C259 mutants.
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Affiliation(s)
- Paul Fischer
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Enrico Schiewer
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Wayne Busse
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Anika Spreen
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Max Grosse
- Institut für Biologie, Biophysikalische Chemie, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
| | - Franz Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt Universität zu Berlin, Invalidenstr, 42, 10115 Berlin, Germany.
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Pyari G, Bansal H, Roy S. Optogenetically mediated large volume suppression and synchronized excitation of human ventricular cardiomyocytes. Pflugers Arch 2023; 475:1479-1503. [PMID: 37415050 DOI: 10.1007/s00424-023-02831-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023]
Abstract
A major challenge in cardiac optogenetics is to have minimally invasive large volume excitation and suppression for effective cardioversion and treatment of tachycardia. It is important to study the effect of light attenuation on the electrical activity of cells in in vivo cardiac optogenetic experiments. In this computational study, we present a detailed analysis of the effect of light attenuation in different channelrhodopsins (ChRs)-expressing human ventricular cardiomyocytes. The study shows that sustained illumination from the myocardium surface used for suppression, simultaneously results in spurious excitation in deeper tissue regions. Tissue depths of suppressed and excited regions have been determined for different opsin expression levels. It is shown that increasing the expression level by 5-fold enhances the depth of suppressed tissue from 2.24 to 3.73 mm with ChR2(H134R) (ChR2 with a single point mutation at position H134), 3.78 to 5.12 mm with GtACR1 (anion-conducting ChR from cryptophyte algae Guillardia theta) and 6.63 to 9.31 mm with ChRmine (a marine opsin gene from Tiarina fusus). Light attenuation also results in desynchrony in action potentials in different tissue regions under pulsed illumination. It is further shown that gradient-opsin expression not only enables suppression up to the same level of tissue depth but also enables synchronized excitation under pulsed illumination. The study is important for the effective treatment of tachycardia and cardiac pacing and for extending the scale of cardiac optogenetics.
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Affiliation(s)
- Gur Pyari
- Department of Physics and Computer Science, Dayalbagh Educational Institute, Agra, 282005, India
| | - Himanshu Bansal
- Department of Physics and Computer Science, Dayalbagh Educational Institute, Agra, 282005, India
| | - Sukhdev Roy
- Department of Physics and Computer Science, Dayalbagh Educational Institute, Agra, 282005, India.
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Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. Sequential absorption of two photons creates a bistable form of RubyACR responsible for its strong desensitization. Proc Natl Acad Sci U S A 2023; 120:e2301521120. [PMID: 37186849 PMCID: PMC10214203 DOI: 10.1073/pnas.2301521120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Channelrhodopsins with red-shifted absorption, rare in nature, are highly desired for optogenetics because light of longer wavelengths more deeply penetrates biological tissue. RubyACRs (Anion ChannelRhodopsins), a group of four closely related anion-conducting channelrhodopsins from thraustochytrid protists, are the most red-shifted channelrhodopsins known with absorption maxima up to 610 nm. Their photocurrents are large, as is typical of blue- and green-absorbing ACRs, but they rapidly decrease during continuous illumination (desensitization) and extremely slowly recover in the dark. Here, we show that long-lasting desensitization of RubyACRs results from photochemistry not observed in any previously studied channelrhodopsins. Absorption of a second photon by a photocycle intermediate with maximal absorption at 640 nm (P640) renders RubyACR bistable (i.e., very slowly interconvertible between two spectrally distinct forms). The photocycle of this bistable form involves long-lived nonconducting states (Llong and Mlong), formation of which is the reason for long-lasting desensitization of RubyACR photocurrents. Both Llong and Mlong are photoactive and convert to the initial unphotolyzed state upon blue or ultraviolet (UV) illumination, respectively. We show that desensitization of RubyACRs can be reduced or even eliminated by using ns laser flashes, trains of short light pulses instead of continuous illumination to avoid formation of Llong and Mlong, or by application of pulses of blue light between pulses of red light to photoconvert Llong to the initial unphotolyzed state.
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Affiliation(s)
- Oleg A. Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Elena G. Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Hai Li
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Yumei Wang
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - John L. Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
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Shibata K, Oda K, Nishizawa T, Hazama Y, Ono R, Takaramoto S, Bagherzadeh R, Yawo H, Nureki O, Inoue K, Akiyama H. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. J Am Chem Soc 2023; 145:10779-10789. [PMID: 37129501 DOI: 10.1021/jacs.3c01879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.
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Affiliation(s)
- Keisei Shibata
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Kazumasa Oda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Yuji Hazama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Ryohei Ono
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Shunki Takaramoto
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hidefumi Akiyama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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van Wyk M, Kleinlogel S. A visual opsin from jellyfish enables precise temporal control of G protein signalling. Nat Commun 2023; 14:2450. [PMID: 37117224 PMCID: PMC10147646 DOI: 10.1038/s41467-023-38231-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
Phototransduction is mediated by distinct types of G protein cascades in different animal taxa: bilateral invertebrates typically utilise the Gαq pathway whereas vertebrates typically utilise the Gαt(i/o) pathway. By contrast, photoreceptors in jellyfish (Cnidaria) utilise the Gαs intracellular pathway, similar to olfactory transduction in mammals1. How this habitually slow pathway has adapted to support dynamic vision in jellyfish remains unknown. Here we study a light-sensing protein (rhodopsin) from the box jellyfish Carybdea rastonii and uncover a mechanism that dramatically speeds up phototransduction: an uninterrupted G protein-coupled receptor - G protein complex. Unlike known G protein-coupled receptors (GPCRs), this rhodopsin constitutively binds a single downstream Gαs partner to enable G-protein activation and inactivation within tens of milliseconds. We use this GPCR in a viral gene therapy to restore light responses in blind mice.
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Affiliation(s)
- Michiel van Wyk
- Department of Biomedical Research, University of Bern, Bern, Switzerland.
- Institute of Physiology, University of Bern, Bern, Switzerland.
| | - Sonja Kleinlogel
- Department of Biomedical Research, University of Bern, Bern, Switzerland.
- Institute of Physiology, University of Bern, Bern, Switzerland.
- Roche Pharma and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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Xin Q, Zhang W, Yuan S. The Mechanism of the Channel Opening in Channelrhodopsin-2: A Molecular Dynamics Simulation. Int J Mol Sci 2023; 24:ijms24065667. [PMID: 36982741 PMCID: PMC10057421 DOI: 10.3390/ijms24065667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
Channelrhodopsin-2 (ChR2) has been one of the most important objects in the study of optogenetics. The retinal chromophore molecule absorbs photons and undergoes an isomerization reaction, which triggers the photocycle, resulting in a series of conformational changes. In this study, a series of intermediate structures (including D470, P500, P390-early, P390-late, and P520 states) of ChR2 in the photocycle were modeled, and molecular dynamics (MD) simulations were performed to elucidate the mechanism of ion channel opening of ChR2. The maximum absorption wavelength of these intermediates calculated by time-dependent density function theory (TD-DFT) is in general agreement with the experimental values, the distribution of water density gradually increases in the process of photocycle, and the radius of the ion channel is larger than 6 Å. All these results indicate that our structural models of the intermediates are reasonable. The evolution of protonation state of E90 during the photocycle is explained. E90 will deprotonate when the P390-early transforms into P390-late, in which the two conformations of P390-early and P390-late obtained from the simulations are consistent with the experimental descriptions. To validate the conductive P520 state, the potential mean force (PMF) of Na+ ions passing through the P520 intermediate was calculated by using steered molecular dynamics (SMD) simulation combined with umbrella sampling. The result shows that the Na+ ions passing through the channel with a very low energy barrier, especially in the central gate, is almost barrierless. This indicates that the channel is open in the P520 state.
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Gating and ion selectivity of Channelrhodopsins are critical for photo-activated orientation of Chlamydomonas as shown by in vivo point mutation. Nat Commun 2022; 13:7253. [PMID: 36433995 PMCID: PMC9700795 DOI: 10.1038/s41467-022-35018-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 11/26/2022] Open
Abstract
The green unicellular alga Chlamydomonas reinhardtii with two photoreceptors called channelrhodopsins is a model organism that gave birth to a new scientific field of biomedical studies, optogenetics. Although channelrhodopsins are helping to decipher the activity of the human brain, their functionality has never been extensively studied in the organism of origin, mainly due to the difficulties connected to reverse genetic interventions. In this study, we present a CRISPR-Cas9-based technique that enables a precise in vivo exchange of single amino acids in a selected gene. To shed light on the function of channelrhodopsins ChR1 (C1) and ChR2 (C2) in vivo, we deleted both channelrhodopsins independently in the wild-type strain and introduced point mutations in the remaining channel, causing modified photocycle kinetics and ion selectivity. The mutated strains, ΔC1C2-E123T, ΔC1C2-E90R and ΔC1C2-E90Q, showed about 100-fold decrease in photosensitivity, a reduced photophobic response and faster light adaptation rates due to accelerated photocycle kinetics and reduced Ca2+ conductance. Moreover, the ΔC1C2-E90Q with an additionally reduced H+ permeability produced an electrical response only in the presence of Na+ ions, highlighting a contribution and importance of H+ conductance to photocurrents in the wild-type algae. Finally, in the ΔC1C2-E90R strain with the channelrhodopsin selectivity converted to anions, no photo-responses were detected. We conclude that the precise photocycle kinetics and the particular ion selectivity of channelrhodopsins are the key parameters for efficient phototaxis in low light conditions.
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11
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Hososhima S, Mizutori R, Abe-Yoshizumi R, Rozenberg A, Shigemura S, Pushkarev A, Konno M, Katayama K, Inoue K, Tsunoda SP, Béjà O, Kandori H. Proton-transporting heliorhodopsins from marine giant viruses. eLife 2022; 11:78416. [PMID: 36065640 PMCID: PMC9448325 DOI: 10.7554/elife.78416] [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: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here, we report that a viral HeR from Emiliania huxleyi virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a PAG of the Schiff base, and mutations at these positions converted the protein into an outward proton pump. Three environmental viral HeRs from the same group as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of E. huxleyi contain one HeR that is related to the viral HeRs, while its viruses EhV-201 and EhV-202 contain two and three HeRs, respectively. Except for V2HeR3 from EhV-202, none of these proteins exhibit ion transport activity. Thus, when expressed in the E. huxleyi cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tool, similarly to type-1 microbial rhodopsins.
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Affiliation(s)
- Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Ritsu Mizutori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | | | - Shunta Shigemura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | | | - Masae Konno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
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12
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Govorunova EG, Sineshchekov OA, Brown LS, Spudich JL. Biophysical characterization of light-gated ion channels using planar automated patch clamp. Front Mol Neurosci 2022; 15:976910. [PMID: 36017077 PMCID: PMC9396214 DOI: 10.3389/fnmol.2022.976910] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 01/09/2023] Open
Abstract
Channelrhodopsins (ChRs) are proteins that guide phototaxis in protists and exhibit light-gated channel conductance when their genes are heterologously expressed in mammalian cells. ChRs are widely used as molecular tools to control neurons and cardiomyocytes with light (optogenetics). Cation- and anion-selective ChRs (CCRs and ACRs, respectively) enable stimulation and inhibition of neuronal activity by depolarization and hyperpolarization of the membrane, respectively. More than 400 natural ChR variants have been identified so far, and high-throughput polynucleotide sequencing projects add many more each year. However, electrophysiological characterization of new ChRs lags behind because it is mostly done by time-consuming manual patch clamp (MPC). Here we report using a high-throughput automated patch clamp (APC) platform, SyncroPatch 384i from Nanion Technologies, for ChR research. We find that this instrument can be used for determination of the light intensity dependence and current-voltage relationships in ChRs and discuss its advantages and limitations.
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Affiliation(s)
- Elena G. Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Oleg A. Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Leonid S. Brown
- Biophysics Interdepartmental Group, Department of Physics, University of Guelph, Guelph, ON, Canada
| | - John L. Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
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13
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Emiliani V, Entcheva E, Hedrich R, Hegemann P, Konrad KR, Lüscher C, Mahn M, Pan ZH, Sims RR, Vierock J, Yizhar O. Optogenetics for light control of biological systems. NATURE REVIEWS. METHODS PRIMERS 2022; 2:55. [PMID: 37933248 PMCID: PMC10627578 DOI: 10.1038/s43586-022-00136-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 11/08/2023]
Abstract
Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.
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Affiliation(s)
- Valentina Emiliani
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, USA
| | - Rainer Hedrich
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kai R. Konrad
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Lüscher
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Department of Clinical Neurosciences, Geneva University Hospital, Geneva, Switzerland
| | - Mathias Mahn
- Department of Neurobiology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zhuo-Hua Pan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ruth R. Sims
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Neuroscience Research Center, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Ofer Yizhar
- Departments of Brain Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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14
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Abstract
Optogenetic actuators enable highly precise spatiotemporal interrogation of biological processes at levels ranging from the subcellular to cells, circuits and behaving organisms. Although their application in neuroscience has traditionally focused on the control of spiking activity at the somatodendritic level, the scope of optogenetic modulators for direct manipulation of presynaptic functions is growing. Presynaptically localized opsins combined with light stimulation at the terminals allow light-mediated neurotransmitter release, presynaptic inhibition, induction of synaptic plasticity and specific manipulation of individual components of the presynaptic machinery. Here, we describe presynaptic applications of optogenetic tools in the context of the unique cell biology of axonal terminals, discuss their potential shortcomings and outline future directions for this rapidly developing research area.
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15
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Govorunova EG, Gou Y, Sineshchekov OA, Li H, Lu X, Wang Y, Brown LS, St-Pierre F, Xue M, Spudich JL. Kalium channelrhodopsins are natural light-gated potassium channels that mediate optogenetic inhibition. Nat Neurosci 2022; 25:967-974. [PMID: 35726059 PMCID: PMC9854242 DOI: 10.1038/s41593-022-01094-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 05/12/2022] [Indexed: 02/02/2023]
Abstract
Channelrhodopsins are used widely for optical control of neurons, in which they generate photoinduced proton, sodium or chloride influx. Potassium (K+) is central to neuron electrophysiology, yet no natural K+-selective light-gated channel has been identified. Here, we report kalium channelrhodopsins (KCRs) from Hyphochytrium catenoides. Previously known gated potassium channels are mainly ligand- or voltage-gated and share a conserved K+-selectivity filter. KCRs differ in that they are light-gated and have independently evolved an alternative K+ selectivity mechanism. The KCRs are potent, highly selective of K+ over Na+, and open in less than 1 ms following photoactivation. The permeability ratio PK/PNa of 23 makes H. catenoides KCR1 (HcKCR1) a powerful hyperpolarizing tool to suppress excitable cell firing upon illumination, demonstrated here in mouse cortical neurons. HcKCR1 enables optogenetic control of K+ gradients, which is promising for the study and potential treatment of potassium channelopathies such as epilepsy, Parkinson's disease and long-QT syndrome and other cardiac arrhythmias.
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Affiliation(s)
- Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Yueyang Gou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- The Cain Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Yumei Wang
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Mingshan Xue
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- The Cain Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
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16
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Ramamonjy A, Dervaux J, Brunet P. Nonlinear Phototaxis and Instabilities in Suspensions of Light-Seeking Algae. PHYSICAL REVIEW LETTERS 2022; 128:258101. [PMID: 35802423 DOI: 10.1103/physrevlett.128.258101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
The mechanism by which living organisms seek optimal light conditions-phototaxis-is a fundamental process for motile photosynthetic microbes. It is involved in a broad array of natural processes and applications from bloom formation to the production of high-value chemicals in photobioreactors. Here, we show that a population of the model alga Chlamydomonas reinhardtii exhibits a highly sensitive nonlinear response to light and demonstrate that the self-organization of cells in a heterogeneous environment becomes unstable as the result of a coupling between bioconvective flows and phototaxis.
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Affiliation(s)
- Aina Ramamonjy
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS and Université de Paris, 75013 Paris, France
| | - Julien Dervaux
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS and Université de Paris, 75013 Paris, France
| | - Philippe Brunet
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS and Université de Paris, 75013 Paris, France
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17
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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18
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Capone M, Zanetti-Polzi L, Leonzi I, Spreti N, Daidone I. Evidence for a high pK a of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach. J Biomol Struct Dyn 2022:1-8. [PMID: 35593533 DOI: 10.1080/07391102.2022.2077834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Candida antarctica Lipase B (CALB) is a paradigm for the family of lipases. At pH 7, the optimal pH for catalysis, the protonation state of an aspartic acid of the active site (Asp134) could not be conclusively assigned. In fact, the pKa estimate provided by a widely used computational tool, namely PropKa, that predicts pKa values of ionizable groups in proteins based on the crystallographic structure, is only slightly above 7 (pKa = 7.25). This, along with the lack of an experimental evaluation, makes the assignment of its protonation state at neutral pH challenging. Here, we calculate the pKa of Asp134 by means of a fully atomistic multiscale computational approach based on classical molecular dynamics (MD) simulation and the perturbed matrix method (PMM), namely the MD-PMM approach. MD-PMM is able to take into account the dynamics of the system and, at the same time, to treat the deprotonation step at the quantum level. The calculations provide a pKa value of 8.9 ± 1.1, hence suggesting that Asp134 in CALB should be protonated at neutral, and even at slightly basic, pH.
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Affiliation(s)
- Matteo Capone
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Ilenia Leonzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
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19
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Bansal H, Pyari G, Roy S. Co-expressing fast channelrhodopsin with step-function opsin overcomes spike failure due to photocurrent desensitization in optogenetics: a theoretical study. J Neural Eng 2022; 19. [PMID: 35320791 DOI: 10.1088/1741-2552/ac6061] [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: 12/13/2021] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
Objective A fundamental challenge in optogenetics is to elicit long-term high-fidelity neuronal spiking with negligible heating. Fast channelrhodopsins (ChRs) require higher irradiances and cause spike failure due to photocurrent desensitization under sustained illumination, whereas, more light-sensitive step-function opsins (SFOs) exhibit prolonged depolarization with insufficient photocurrent and fast response for high-fidelity spiking. Approach We present a novel method to overcome this fundamental limitation by co-expressing fast ChRs with SFOs. A detailed theoretical analysis of ChETA co-expressed with different SFOs, namely ChR2(C128A), ChR2(C128S), SSFO and SOUL, expressing hippocampal neurons has been carried out by formulating their accurate theoretical models. Main results ChETA-SFO-expressing hippocampal neurons show a more stable photocurrent that overcomes spike failure. Spiking fidelity in these neurons can be sustained even at lower irradiances of subsequent pulses (77 % of initial pulse intensity in ChETA-ChR2(C128A)-expressing neurons) or by using red-shifted light pulses at appropriate intervals. High-fidelity spiking up to 60 Hz can be evoked in ChR2-C128S-ChETA-expressing neurons, which cannot be attained with only SFOs. Significance The present study provides important insights about photostimulation protocols for bi-stable switching of neurons. This new approach provides a means for sustained low-power, high-frequency, and high-fidelity optogenetic switching of neurons, necessary to study various neural functions and neurodegenerative disorders and enhance the utility of optogenetics for biomedical applications.
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Affiliation(s)
- Himanshu Bansal
- Department of Physics and Computer science, Dayalbagh Educational Institute Faculty of Science, AGRA, Agra, UP, 282005, INDIA
| | - Gur Pyari
- Department of Physics & Computer Science, Dayalbagh Educational Institute Faculty of Science, Faculty of Science, Dayalbagh, Agra-282 005, Agra, Uttar Pradesh, 282005, INDIA
| | - Sukhdev Roy
- Department of Physics & Computer Science, Dayalbagh Educational Institute Faculty of Science, Faculty of Science, Dayalbagh, Agra-282 005, Agra, Uttar Pradesh, 282005, INDIA
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20
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Zhang L, Wang K, Ning S, Pedersen PA, Duelli AS, Gourdon PE. Isolation and Crystallization of the D156C form of Optogenetic ChR2. Cells 2022; 11:cells11050895. [PMID: 35269517 PMCID: PMC8909857 DOI: 10.3390/cells11050895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels that are receiving increasing attention as optogenetic tools. Despite extensive efforts to gain understanding of how these channels function, the molecular events linking light absorption of the retinal cofactor to channel opening remain elusive. While dark-state structures of ChR2 or chimeric proteins have demonstrated the architecture of non-conducting states, there is a need for open- and desensitized-state structures to uncover the mechanistic principles underlying channel activity. To facilitate comprehensive structural studies of ChR2 in non-closed states, we report a production and purification procedure of the D156C form of ChR2, which displays prolonged channel opening compared to the wild type. We demonstrate considerable yields (0.45 mg/g fermenter cell culture) of recombinantly produced protein using S. cerevisiae, which is purified to high homogeneity both as opsin (retinal-free) and as functional ChR2 with added retinal. We also develop conditions that enable the growth of ChR2 crystals that scatter X-rays to 6 Å, and identify a molecular replacement solution that suggests that the packing is different from published structures. Consequently, our cost-effective production and purification pipeline opens the way for downstream structural studies of different ChR2 states, which may provide a foundation for further adaptation of this protein for optogenetic applications.
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Affiliation(s)
- Liying Zhang
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Shuo Ning
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China;
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark;
| | - Annette Susanne Duelli
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Pontus Emanuel Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden
- Correspondence: ; Tel.: +45-50339990
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21
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Pallikaras V, Carter F, Velazquez-Martinez DN, Arvanitogiannis A, Shizgal P. The trade-off between pulse duration and power in optical excitation of midbrain dopamine neurons approximates Bloch's law. Behav Brain Res 2022; 419:113702. [PMID: 34864162 DOI: 10.1016/j.bbr.2021.113702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022]
Abstract
Optogenetic experiments reveal functional roles of specific neurons. However, functional inferences have been limited by widespread adoption of a restricted set of stimulation parameters. Broader exploration of the parameter space can deepen insight into the mapping between selective neural activity and behavior. In this way, characteristics of the activated neural circuit, such as temporal integration, can be inferred. Our objective was to determine whether an equal-energy principle accounts for the interaction of pulse duration and optical power in optogenetic excitation. Six male TH::Cre rats worked for optogenetic (ChannelRhodopsin-2) stimulation of VTA dopamine neurons. We used a within-subject design to describe the trade-off between pulse duration and optical power in determining reward seeking. Parameters were customized for each subject based on behavioral effectiveness. Within a useful range of powers (~12.6-31.6 mW) the product of optical power and pulse duration required to produce a given level of reward seeking was roughly constant. Such reciprocity is consistent with Bloch's law, which posits an equal-energy principle of temporal summation over short durations in human vision. The trade-off between pulse duration and power broke down at higher powers. Thus, optical power and duration can be adjusted reciprocally for brief durations and lower powers, and power can be substituted for pulse duration to scale the region of excitation in behavioral optogenetic experiments. The findings demonstrate the utility of within-subject and trade-off designs in optogenetics and of parameter adjustment based on functional endpoints instead of physical properties of the stimulation.
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Affiliation(s)
- Vasilios Pallikaras
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, 7141 Sherbrooke St W., Montreal, QC H4B 1R6, Canada
| | - Francis Carter
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, 7141 Sherbrooke St W., Montreal, QC H4B 1R6, Canada
| | - David Natanael Velazquez-Martinez
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, 7141 Sherbrooke St W., Montreal, QC H4B 1R6, Canada
| | - Andreas Arvanitogiannis
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, 7141 Sherbrooke St W., Montreal, QC H4B 1R6, Canada
| | - Peter Shizgal
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, 7141 Sherbrooke St W., Montreal, QC H4B 1R6, Canada.
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22
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Govorunova EG, Sineshchekov OA, Spudich JL. Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships. Front Cell Neurosci 2022; 15:800313. [PMID: 35140589 PMCID: PMC8818676 DOI: 10.3389/fncel.2021.800313] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) from phototactic algae have become widely used as genetically encoded molecular tools to control cell membrane potential with light. Recent advances in polynucleotide sequencing, especially in environmental samples, have led to identification of hundreds of channelrhodopsin homologs in many phylogenetic lineages, including non-photosynthetic protists. Only a few CCRs and ACRs have been characterized in detail, but there are indications that ion channel function has evolved within the rhodopsin superfamily by convergent routes. The diversity of channelrhodopsins provides an exceptional platform for the study of structure-function evolution in membrane proteins. Here we review the current state of channelrhodopsin research and outline perspectives for its further development.
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23
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Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol 2022; 2501:1-52. [PMID: 35857221 DOI: 10.1007/978-1-0716-2329-9_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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24
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Xin Q, Cheng J, Wang H, Zhang W, Lu H, Zhou J, Lo GV, Dou Y, Yuan S. Modeling the syn-cycle in the light activated opening of the channelrhodopsin-2 ion channel. RSC Adv 2022; 12:6515-6524. [PMID: 35424642 PMCID: PMC8981705 DOI: 10.1039/d1ra08521b] [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: 11/21/2021] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
The ion channel of channelrhodopsin-2 (ChR2) is activated by absorbing light. The light stimulates retinal to isomerize to start the photocycle. There are two pathways for photocycles, which are caused by isomerization of the retinal from all-trans, 15-anti to 13-cis, 15-anti in the dark-adapted state (anti-cycle) and from 13-cis, 15-syn to all-trans, 15-syn in the light-adapted state (syn-cycle). In this work, the structure of the syn-cycle intermediate and mechanism of channel opening were studied by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Due to the lack of crystal structure of intermediates in the syn-cycle of ChR2, the intermediate models were constructed from the homologous intermediates in the anti-cycle. The isomerization of retinal was shown to cause the central gate (CG) hydrogen bond network to rearrange, cutting the link between TM2 and TM7. TM2 is moved by the intrahelical hydrogen bond of E90 and K93, and induced the intracellular gate (ICG) to expand. The ion penetration pathway between TM1, TM2, TM3 and TM7 in the P500* state was observed by MD simulations. However, this channel is not fully opened compared with the homologous P500 state in the anti-cycle. In addition, the protons on Schiff bases were found to be unable to form hydrogen bonds with the counter residues (E123 and D253) in the P500* state, preventing an evolution of the P500* state to a P390-like state in the syn-cycle. Modelling the syn-cycle is a series of operations on the ChR2 crystal structure (PDB ID: 6EID). By replacement and isomerization, we obtained P500* and P480 intermediates. A feasible explanation that no P390* was observed in experiment was inferred.![]()
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Affiliation(s)
- Qi Xin
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Jie Cheng
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Hongwei Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, Australia
| | - Wenying Zhang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Hong Lu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Junpeng Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Glenn V. Lo
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, LA 70310, USA
| | - Yusheng Dou
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, LA 70310, USA
| | - Shuai Yuan
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
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25
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Lin S, Du Y, Xia Y, Xie Y, Xiao L, Wang G. Advances in optogenetic studies of depressive-like behaviors and underlying neural circuit mechanisms. Front Psychiatry 2022; 13:950910. [PMID: 36159933 PMCID: PMC9492959 DOI: 10.3389/fpsyt.2022.950910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUNDS The neural circuit mechanisms underlying depression remain unclear. Recently optogenetics has gradually gained recognition as a novel technique to regulate the activity of neurons with light stimulation. Scientists are now transferring their focus to the function of brain regions and neural circuits in the pathogenic progress of depression. Deciphering the circuitry mechanism of depressive-like behaviors may help us better understand the symptomatology of depression. However, few studies have summarized current progress on optogenetic researches into the neural circuit mechanisms of depressive-like behaviors. AIMS This review aimed to introduce fundamental characteristics and methodologies of optogenetics, as well as how this technique achieves specific neuronal control with spatial and temporal accuracy. We mainly summarized recent progress in neural circuit discoveries in depressive-like behaviors using optogenetics and exhibited the potential of optogenetics as a tool to investigate the mechanism and possible optimization underlying antidepressant treatment such as ketamine and deep brain stimulation. METHODS A systematic review of the literature published in English mainly from 2010 to the present in databases was performed. The selected literature is then categorized and summarized according to their neural circuits and depressive-like behaviors. CONCLUSIONS Many important discoveries have been made utilizing optogenetics. These findings support optogenetics as a powerful and potential tool for studying depression. And our comprehension to the etiology of depression and other psychiatric disorders will also be more thorough with this rapidly developing technique in the near future.
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Affiliation(s)
- Shanshan Lin
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiwei Du
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yujie Xia
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yumeng Xie
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ling Xiao
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Gaohua Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
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26
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Abstract
Optogenetics has revolutionized not only neuroscience but also had an impact on muscle physiology and cell biology. Rhodopsin-based optogenetics started with the discovery of the light-gated cation channels, called channelrhodopsins. Together with the light-driven ion pumps, these channels allow light-mediated control of electrically excitable cells in culture tissue and living animals. They can be activated (depolarized) or silenced (hyperpolarized) by light with incomparably high spatiotemporal resolution. Optogenetics allows the light manipulation of cells under electrode-free conditions in a minimally invasive manner. Through modern genetic techniques, virus-induced transduction can be performed with extremely high cell specificity in tissue and living animals, allowing completely new approaches for analyzing neural networks, behavior studies, and investigations of neurodegenerative diseases. First clinical trials for the optogenetic recovery of vision are underway.This chapter provides a comprehensive description of the structure and function of the different light-gated channels and some new light-activated ion pumps. Some of them already play an essential role in optogenetics while others are supposed to become important tools for more specialized applications in the future.At the moment, a large number of publications are available concerning intrinsic mechanisms of microbial rhodopsins. Mostly they describe CrChR2 and its variants, as CrChR2 is still the most prominent optogenetic tool. Therefore, many biophysically and biochemically oriented groups contributed to the overwhelming mass of information on this unique ion channel's molecular mechanism. In this context, the function of new optogenetic tools is discussed, which is essential for rational optimization of the optogenetic approach for an eventual biomedical application. The comparison of the effectivity of ion pumps versus ion channels is discussed as well.Applications of rhodopsins-based optogenetic tools are also discussed in the chapter. Because of the enormous number of these applications in neuroscience, only exemplary studies on cell culture neural tissue, muscle physiology, and remote control of animal behavior are presented.
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Affiliation(s)
- Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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27
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Córdova C, Lozano C, Rodríguez B, Marchant I, Zúñiga R, Ochova P, Olivero P, González-Arriagada WA. Optogenetic control of cancer cell survival in ChR2-transfected HeLa cells. Int J Exp Pathol 2021; 102:242-248. [PMID: 34791724 DOI: 10.1111/iep.12426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/13/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Optogenetics is a molecular biological technique involving transfection of cells with photosensitive proteins and the subsequent study of their biological effects. The aim of this study was to evaluate the effect of blue light on the survival of HeLa cells, transfected with channelrhodopsin-2 (ChR2). HeLa wild-type cells were transfected with a plasmid that contained the gene for ChR2. Transfection and channel function were evaluated by real-time polymerase chain reaction (RT-PCR), fluorescence imaging using green fluorescent protein (GFP) and flow cytometry for intracellular calcium changes using a Fura Red probe. We developed a platform for optogenetic stimulation for use within the cell culture incubator. Different stimulation procedures using blue light (467 nm) were applied for up to 24 h. Cell survival was determined by flow cytometry using propidium iodide and rhodamine probes. Change in cell survival showed a statistically significant (p < 0.05) inverse association with the frequency and time of application of the light stimulus. This change seemed to be associated with the ChR2 cis-trans-isomerization cycle. Cell death was associated with high concentrations of calcium in the cytoplasm and stimulation intervals less than the period of isomerization. It is possible to transfect HeLa cells with ChR2 and control their survival under blue light stimulation. We suggest that this practice should be considered in the future development of optogenetic systems in biological or biomedical research.
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Affiliation(s)
- Claudio Córdova
- Laboratorio de Estructura y Función Celular, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Carlo Lozano
- Servicio de Anatomía Patológica, Carlos Van Buren Hospital, Valparaíso, Chile
| | - Belén Rodríguez
- Laboratorio de Estructura y Función Celular, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Ivanny Marchant
- Laboratorio de Estructura y Función Celular, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso, Chile.,Centro de Investigación Interoperativo en Ciencias Odontológicas y Médicas, Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Rodrigo Zúñiga
- Servicio de Anatomía Patológica, Carlos Van Buren Hospital, Valparaíso, Chile
| | - Paola Ochova
- Servicio de Anatomía Patológica, Carlos Van Buren Hospital, Valparaíso, Chile
| | - Pablo Olivero
- Laboratorio de Estructura y Función Celular, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso, Chile.,Centro de Investigación Interoperativo en Ciencias Odontológicas y Médicas, Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Wilfredo Alejandro González-Arriagada
- Oral and Maxillofacial Pathology, Facultad de Odontología, Universidad de Los Andes, Las Condes, Chile.,Centro de Investigación e Innovación Biomédica, Universidad de Los Andes, Las Condes, Chile
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28
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Fischer P, Mukherjee S, Schiewer E, Broser M, Bartl F, Hegemann P. The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy. eLife 2021; 10:e71384. [PMID: 34665128 PMCID: PMC8575461 DOI: 10.7554/elife.71384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases, and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here, we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus Catenaria anguillulae, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.
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Affiliation(s)
- Paul Fischer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Shatanik Mukherjee
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Franz Bartl
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
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29
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Ördög B, Teplenin A, De Coster T, Bart CI, Dekker SO, Zhang J, Ypey DL, de Vries AAF, Pijnappels DA. The Effects of Repetitive Use and Pathological Remodeling on Channelrhodopsin Function in Cardiomyocytes. Front Physiol 2021; 12:710020. [PMID: 34539432 PMCID: PMC8448166 DOI: 10.3389/fphys.2021.710020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Aim: Channelrhodopsins (ChRs) are a large family of light-gated ion channels with distinct properties, which is of great importance in the selection of a ChR variant for a given application. However, data to guide such selection for cardiac optogenetic applications are lacking. Therefore, we investigated the functioning of different ChR variants in normal and pathological hypertrophic cardiomyocytes subjected to various illumination protocols. Methods and Results: Isolated neonatal rat ventricular cardiomyocytes (NRVMs) were transduced with lentiviral vectors to express one of the following ChR variants: H134R, CatCh, ReaChR, or GtACR1. NRVMs were treated with phenylephrine (PE) to induce pathological hypertrophy (PE group) or left untreated [control (CTL) group]. In these groups, ChR currents displayed unique and significantly different properties for each ChR variant on activation by a single 1-s light pulse (1 mW/mm2: 470, 565, or 617 nm). The concomitant membrane potential (Vm) responses also showed a ChR variant-specific profile, with GtACR1 causing a slight increase in average Vm during illumination (Vplateau: −38 mV) as compared with a Vplateau > −20 mV for the other ChR variants. On repetitive activation at increasing frequencies (10-ms pulses at 1–10 Hz for 30 s), peak currents, which are important for cardiac pacing, decreased with increasing activation frequencies by 17–78% (p < 0.05), while plateau currents, which are critical for arrhythmia termination, decreased by 10–75% (p < 0.05), both in a variant-specific manner. In contrast, the corresponding Vplateau remained largely stable. Importantly, current properties and Vm responses were not statistically different between the PE and CTL groups, irrespective of the variant used (p > 0.05). Conclusion: Our data show that ChR variants function equally well in cell culture models of healthy and pathologically hypertrophic myocardium but show strong, variant-specific use-dependence. This use-dependent nature of ChR function should be taken into account during the design of cardiac optogenetic studies and the interpretation of the experimental findings thereof.
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Affiliation(s)
- Balázs Ördög
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Alexander Teplenin
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Tim De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Cindy I Bart
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Sven O Dekker
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Juan Zhang
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Dirk L Ypey
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Antoine A F de Vries
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Daniël A Pijnappels
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
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30
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Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity.
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31
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Becker‐Baldus J, Leeder A, Brown LJ, Brown RCD, Bamann C, Glaubitz C. The Desensitized Channelrhodopsin‐2 Photointermediate Contains 13 ‐
cis
, 15 ‐
syn
Retinal Schiff Base. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Johanna Becker‐Baldus
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Alexander Leeder
- Department of Chemistry University of Southampton Southampton SO17 1BJ UK
| | - Lynda J. Brown
- Department of Chemistry University of Southampton Southampton SO17 1BJ UK
| | | | - Christian Bamann
- Max-Planck-Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
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32
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Becker-Baldus J, Leeder A, Brown LJ, Brown RCD, Bamann C, Glaubitz C. The Desensitized Channelrhodopsin-2 Photointermediate Contains 13 -cis, 15 -syn Retinal Schiff Base. Angew Chem Int Ed Engl 2021; 60:16442-16447. [PMID: 33973334 PMCID: PMC8362212 DOI: 10.1002/anie.202015797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/18/2021] [Indexed: 11/13/2022]
Abstract
Channelrhodopsin‐2 (ChR2) is a light‐gated cation channel and was used to lay the foundations of optogenetics. Its dark state X‐ray structure has been determined in 2017 for the wild‐type, which is the prototype for all other ChR variants. However, the mechanistic understanding of the channel function is still incomplete in terms of structural changes after photon absorption by the retinal chromophore and in the framework of functional models. Hence, detailed information needs to be collected on the dark state as well as on the different photointermediates. For ChR2 detailed knowledge on the chromophore configuration in the different states is still missing and a consensus has not been achieved. Using DNP‐enhanced solid‐state MAS NMR spectroscopy on proteoliposome samples, we unambiguously determined the chromophore configuration in the desensitized state, and we show that this state occurs towards the end of the photocycle.
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Affiliation(s)
- Johanna Becker-Baldus
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Alexander Leeder
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Lynda J Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Richard C D Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Christian Bamann
- Max-Planck-Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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33
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Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. J Chem Phys 2021; 154:084105. [PMID: 33639764 DOI: 10.1063/5.0038913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.
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Affiliation(s)
- Sandra M V Pinto
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100 L'Aquila, Italy
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34
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Schoeters R, Tarnaud T, Martens L, Joseph W, Raedt R, Tanghe E. Double Two-State Opsin Model With Autonomous Parameter Inference. Front Comput Neurosci 2021; 15:688331. [PMID: 34220478 PMCID: PMC8243001 DOI: 10.3389/fncom.2021.688331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Optogenetics has a lot of potential to become an effective neuromodulative therapy for clinical applications. Selecting the correct opsin is crucial to have an optimal optogenetic tool. With computational modeling, the neuronal response to the current dynamics of an opsin can be extensively and systematically tested. Unlike electrical stimulation where the effect is directly defined by the applied field, the stimulation in optogenetics is indirect, depending on the selected opsin's non-linear kinetics. With the continuous expansion of opsin possibilities, computational studies are difficult due to the need for an accurate model of the selected opsin first. To this end, we propose a double two-state opsin model as alternative to the conventional three and four state Markov models used for opsin modeling. Furthermore, we provide a fitting procedure, which allows for autonomous model fitting starting from a vast parameter space. With this procedure, we successfully fitted two distinctive opsins (ChR2(H134R) and MerMAID). Both models are able to represent the experimental data with great accuracy and were obtained within an acceptable time frame. This is due to the absence of differential equations in the fitting procedure, with an enormous reduction in computational cost as result. The performance of the proposed model with a fit to ChR2(H134R) was tested, by comparing the neural response in a regular spiking neuron to the response obtained with the non-instantaneous, four state Markov model (4SB), derived by Williams et al. (2013). Finally, a computational speed gain was observed with the proposed model in a regular spiking and sparse Pyramidal-Interneuron-Network-Gamma (sPING) network simulation with respect to the 4SB-model, due to the former having two differential equations less. Consequently, the proposed model allows for computationally efficient optogenetic neurostimulation and with the proposed fitting procedure will be valuable for further research in the field of optogenetics.
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Affiliation(s)
- Ruben Schoeters
- WAVES, Department of Information Technology (INTEC), Ghent University/IMEC, Ghent, Belgium
| | - Thomas Tarnaud
- WAVES, Department of Information Technology (INTEC), Ghent University/IMEC, Ghent, Belgium
| | - Luc Martens
- WAVES, Department of Information Technology (INTEC), Ghent University/IMEC, Ghent, Belgium
| | - Wout Joseph
- WAVES, Department of Information Technology (INTEC), Ghent University/IMEC, Ghent, Belgium
| | - Robrecht Raedt
- 4BRAIN, Department of Neurology, Institute for Neuroscience, Ghent University, Ghent, Belgium
| | - Emmeric Tanghe
- WAVES, Department of Information Technology (INTEC), Ghent University/IMEC, Ghent, Belgium
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35
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Dreier MA, Althoff P, Norahan MJ, Tennigkeit SA, El-Mashtoly SF, Lübben M, Kötting C, Rudack T, Gerwert K. Time-resolved spectroscopic and electrophysiological data reveal insights in the gating mechanism of anion channelrhodopsin. Commun Biol 2021; 4:578. [PMID: 33990694 PMCID: PMC8121809 DOI: 10.1038/s42003-021-02101-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/12/2021] [Indexed: 02/04/2023] Open
Abstract
Channelrhodopsins are widely used in optogenetic applications. High photocurrents and low current inactivation levels are desirable. Two parallel photocycles evoked by different retinal conformations cause cation-conducting channelrhodopsin-2 (CrChR2) inactivation: one with efficient conductivity; one with low conductivity. Given the longer half-life of the low conducting photocycle intermediates, which accumulate under continuous illumination, resulting in a largely reduced photocurrent. Here, we demonstrate that for channelrhodopsin-1 of the cryptophyte Guillardia theta (GtACR1), the highly conducting C = N-anti-photocycle was the sole operating cycle using time-resolved step-scan FTIR spectroscopy. The correlation between our spectroscopic measurements and previously reported electrophysiological data provides insights into molecular gating mechanisms and their role in the characteristic high photocurrents. The mechanistic importance of the central constriction site amino acid Glu-68 is also shown. We propose that canceling out the poorly conducting photocycle avoids the inactivation observed in CrChR2, and anticipate that this discovery will advance the development of optimized optogenetic tools.
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Affiliation(s)
- Max-Aylmer Dreier
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Philipp Althoff
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Mohamad Javad Norahan
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Stefan Alexander Tennigkeit
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Samir F El-Mashtoly
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Mathias Lübben
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Carsten Kötting
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany.
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.
| | - Klaus Gerwert
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, Bochum, Germany.
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.
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36
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Oda K, Nomura T, Nakane T, Yamashita K, Inoue K, Ito S, Vierock J, Hirata K, Maturana AD, Katayama K, Ikuta T, Ishigami I, Izume T, Umeda R, Eguma R, Oishi S, Kasuya G, Kato T, Kusakizako T, Shihoya W, Shimada H, Takatsuji T, Takemoto M, Taniguchi R, Tomita A, Nakamura R, Fukuda M, Miyauchi H, Lee Y, Nango E, Tanaka R, Tanaka T, Sugahara M, Kimura T, Shimamura T, Fujiwara T, Yamanaka Y, Owada S, Joti Y, Tono K, Ishitani R, Hayashi S, Kandori H, Hegemann P, Iwata S, Kubo M, Nishizawa T, Nureki O. Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. eLife 2021; 10:62389. [PMID: 33752801 PMCID: PMC7987342 DOI: 10.7554/elife.62389] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/15/2021] [Indexed: 01/17/2023] Open
Abstract
Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore.
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Affiliation(s)
- Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keiichi Inoue
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Johannes Vierock
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kunio Hirata
- RIKEN SPring-8 Center, Hyogo, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
| | - Andrés D Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kota Katayama
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Tatsuya Ikuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Itsuki Ishigami
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tamaki Izume
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rie Umeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryuun Eguma
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satomi Oishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Go Kasuya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takafumi Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Takatsuji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mizuki Takemoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Reiya Taniguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryoki Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hirotake Miyauchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yongchan Lee
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takaaki Fujiwara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuaki Yamanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hideki Kandori
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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37
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Cheng J, Zhang W, Zhou S, Ran X, Shang Y, Lo GV, Dou Y, Yuan S. The effect on ion channel of different protonation states of E90 in channelrhodopsin-2: a molecular dynamics simulation. RSC Adv 2021; 11:14542-14551. [PMID: 35424009 PMCID: PMC8697799 DOI: 10.1039/d1ra01879e] [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: 03/10/2021] [Accepted: 04/13/2021] [Indexed: 11/21/2022] Open
Abstract
Channelrhodopsin-2 (ChR2) is a cationic channel protein that has been extensively studied in optogenetics. The ion channel is opened via a series of proton transfers and H-bond changes during the photocycle but the detailed mechanism is still unknown. Molecular dynamics (MD) simulations with enhanced sampling were performed on the dark-adapted state (i.e., D470) and two photocycle intermediates (P1500 and P2390) to study the proton transfer path of the Schiff base and the subsequent conformational changes. The results suggest there are two possible proton transfer pathways from the Schiff base to proton acceptors (i.e., E123 or D253), depending on the protonation of E90. If E90 is protonated in the P1500 state, the proton on the Schiff base will transfer to E123. The polyene chain of 13-cis retinal tilts and opens the channel that detours the blocking central gate (CG) and forms a narrow channel through the transmembrane helices (TM) 2, 3, 6 and 7. In contrast, if E90 deprotonates after retinal isomerization, the primary proton acceptor is D253, and an almost-open channel through TM1, 2, 3 and 7 is generated. The channel diameter is very close to the experimental value. The potential mean force (PMF) suggests that the free energy is extremely low for ions passing through this channel. With E90 protonated, the proton acceptor of RSBH+ is E123 with a narrow channel along TM3; while with E90 deprotonated, proton transfer from RSBH+ to D253 generates an approximately open channel along TM2.![]()
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Affiliation(s)
- Jie Cheng
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Wenying Zhang
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Shuangyan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Xu Ran
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Yiwen Shang
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Glenn V. Lo
- Department of Chemistry and Physical Sciences
- Nicholls State University
- Thibodaux
- USA
| | - Yusheng Dou
- Department of Chemistry and Physical Sciences
- Nicholls State University
- Thibodaux
- USA
| | - Shuai Yuan
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
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38
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Nagasaka Y, Hososhima S, Kubo N, Nagata T, Kandori H, Inoue K, Yawo H. Gate-keeper of ion transport-a highly conserved helix-3 tryptophan in a channelrhodopsin chimera, C1C2/ChRWR. Biophys Physicobiol 2020; 17:59-70. [PMID: 33173715 PMCID: PMC7593130 DOI: 10.2142/biophysico.bsj-2020007] [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: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/01/2022] Open
Abstract
Microbial rhodopsin is a large family of membrane proteins having seven transmembrane helices (TM1-7) with an all-trans retinal (ATR) chromophore that is covalently bound to Lys in the TM7. The Trp residue in the middle of TM3, which is homologous to W86 of bacteriorhodopsin (BR), is highly conserved among microbial rhodopsins with various light-driven functions. However, the significance of this Trp for the ion transport function of microbial rhodopsins has long remained unknown. Here, we replaced the W163 (BR W86 counterpart) of a channelrhodopsin (ChR), C1C2/ChRWR, which is a chimera between ChR1 and 2, with a smaller aromatic residue, Phe to verify its role in the ion transport. Under whole-cell patch clamp recordings from the ND7/23 cells that were transfected with the DNA plasmid coding human codon optimized C1C2/ChRWR (hWR) or its W163F mutant (hWR-W163F), the photocurrents were evoked by a pulsatile light at 475 nm. The ion-transporting activity of hWR was strongly altered by the W163F mutation in 3 points: (1) the H+ leak at positive membrane potential (Vm) and its light-adaptation, (2) the attenuation of cation channel activity and (3) the manifestation of outward H+ pump activity. All of these results strongly suggest that W163 has a role in stabilizing the structure involved in the gating-on and -off of the cation channel, the role of “gate keeper”. We can attribute the attenuation of cation channel activity to the incomplete gating-on and the H+ leak to the incomplete gating-off.
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Affiliation(s)
- Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Naoko Kubo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Physiology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO) , Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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39
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Zabelskii D, Alekseev A, Kovalev K, Rankovic V, Balandin T, Soloviov D, Bratanov D, Savelyeva E, Podolyak E, Volkov D, Vaganova S, Astashkin R, Chizhov I, Yutin N, Rulev M, Popov A, Eria-Oliveira AS, Rokitskaya T, Mager T, Antonenko Y, Rosselli R, Armeev G, Shaitan K, Vivaudou M, Büldt G, Rogachev A, Rodriguez-Valera F, Kirpichnikov M, Moser T, Offenhäusser A, Willbold D, Koonin E, Bamberg E, Gordeliy V. Viral rhodopsins 1 are an unique family of light-gated cation channels. Nat Commun 2020; 11:5707. [PMID: 33177509 PMCID: PMC7659345 DOI: 10.1038/s41467-020-19457-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na+/K+-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca2+ permeability. Nucleocytoplasmic Large DNA Viruses (NCLDV) that infect algae encode two distinct families of microbial rhodopsins. Here, the authors characterise two proteins form the viral rhodopsin group 1 OLPVR1 and VirChR1, present the 1.4 Å crystal structure of OLPVR1 and show that viral rhodopsins 1 are light-gated cation channels.
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Affiliation(s)
- Dmitrii Zabelskii
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Kirill Kovalev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vladan Rankovic
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dmytro Soloviov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv, 03680, Ukraine
| | - Dmitry Bratanov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ekaterina Savelyeva
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany.,Laboratory of Functional Materials and Devices for Nanoelectronics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Center of Shared Research Facilities, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Podolyak
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Svetlana Vaganova
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Natalia Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maksim Rulev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,European Synchrotron Radiation Facility, Grenoble, France
| | | | - Ana-Sofia Eria-Oliveira
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Tatiana Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Mager
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Yuri Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain.,Department of Marine Microbiology and Biogeochemistry, Royal Netherland Institute for Sea Research (NIOZ), and Utrecht University, Den Burg, The Netherlands
| | - Grigoriy Armeev
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Konstantin Shaitan
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Michel Vivaudou
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Mikhail Kirpichnikov
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,M. M. Shemyakin-Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Andreas Offenhäusser
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ernst Bamberg
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany. .,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany. .,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
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40
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Charge Transport by Light-Activated Rhodopsins Determined by Electrophysiological Recordings. Methods Mol Biol 2020. [PMID: 32865739 DOI: 10.1007/978-1-0716-0830-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Electrophysiological experiments are required to determine the ion transport properties of light-activated currents from microbial rhodopsin expressing cells. The recordings set the quantitative basis for correlation with spectroscopic data and for understanding of channel gating, ion transport vectoriality, or ion selectivity. This chapter focuses on voltage-clamp recordings of channelrhodopsin-2-expressing cells, and it will describe different illumination protocols that reveal the kinetic properties of gating. While the opening and closing reaction is determined from a single turnover upon a short laser flash, desensitization of the light-gated currents is studied under continuous illumination. Recovery from the desensitized state is probed after prolonged illumination with a subsequent light activation upon different dark intervals. Compiling the experimental data will define a minimum number of states in kinetic schemes used to describe the light-gated currents in channelrhodopsins, and emphasis will be given on how to correlate the results with the different time-resolved spectroscopic experiments.
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41
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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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42
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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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43
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Xu X, Mee T, Jia X. New era of optogenetics: from the central to peripheral nervous system. Crit Rev Biochem Mol Biol 2020; 55:1-16. [PMID: 32070147 DOI: 10.1080/10409238.2020.1726279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Optogenetics has recently gained recognition as a biological technique to control the activity of cells using light stimulation. Many studies have applied optogenetics to cell lines in the central nervous system because it has the potential to elucidate neural circuits, treat neurological diseases and promote nerve regeneration. There have been fewer studies on the application of optogenetics in the peripheral nervous system. This review introduces the basic principles and approaches of optogenetics and summarizes the physiology and mechanism of opsins and how the technology enables bidirectional control of unique cell lines with superior spatial and temporal accuracy. Further, this review explores and discusses the therapeutic potential for the development of optogenetics and its capacity to revolutionize treatment for refractory epilepsy, depression, pain, and other nervous system disorders, with a focus on neural regeneration, especially in the peripheral nervous system. Additionally, this review synthesizes the latest preclinical research on optogenetic stimulation, including studies on non-human primates, summarizes the challenges, and highlights future perspectives. The potential of optogenetic stimulation to optimize therapy for peripheral nerve injuries (PNIs) is also highlighted. Optogenetic technology has already generated exciting, preliminary evidence, supporting its role in applications to several neurological diseases, including PNIs.
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Affiliation(s)
- Xiang Xu
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas Mee
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaofeng Jia
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Orthopedics, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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44
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Ritter E, Puskar L, Kim SY, Park JH, Hofmann KP, Bartl F, Hegemann P, Schade U. Féry Infrared Spectrometer for Single-Shot Analysis of Protein Dynamics. J Phys Chem Lett 2019; 10:7672-7677. [PMID: 31763851 DOI: 10.1021/acs.jpclett.9b03099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current submillisecond time-resolved broad-band infrared spectroscopy, one of the most frequently used techniques for studying structure-function relationships in life sciences, is typically limited to fast-cycling reactions that can be repeated thousands of times with high frequency. Notably, a majority of chemical and biological processes do not comply with this requirement. For example, the activation of vertebrate rhodopsin, a prototype of many protein receptors in biological organisms that mediate basic functions of life, including vision, smell, and taste, is irreversible. Here we present a dispersive single-shot Féry spectrometer setup that extends such spectroscopy to irreversible and slow-cycling systems by exploiting the unique properties of brilliant synchrotron infrared light combined with an advanced focal plane detector array embedded in a dispersive optical concept. We demonstrate our single-shot method on microbial actinorhodopsin with a slow photocycle and on vertebrate rhodopsin with irreversible activation.
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Affiliation(s)
- Eglof Ritter
- Humboldt-Universität zu Berlin , Experimentelle Biophysik , 10115 Berlin , Germany
- Humboldt-Universität zu Berlin , Biophysikalische Chemie , 10115 Berlin , Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum Berlin für Materialien und Energie , 12498 Berlin , Germany
| | - So Young Kim
- Chonbuk National University , Division of Biotechnology, Advanced Institute of Environment and Bioscience , 54596 Iksan , Republic of Korea
| | - Jung Hee Park
- Chonbuk National University , Division of Biotechnology, Advanced Institute of Environment and Bioscience , 54596 Iksan , Republic of Korea
| | | | - Franz Bartl
- Humboldt-Universität zu Berlin , Biophysikalische Chemie , 10115 Berlin , Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin , Experimentelle Biophysik , 10115 Berlin , Germany
| | - Ulrich Schade
- Helmholtz-Zentrum Berlin für Materialien und Energie , 12498 Berlin , Germany
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45
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Abstract
We previously reported a cation channelrhodopsin, Gt_CCR4, which is one of the 44 types of microbial rhodopsins from a cryptophyte flagellate, Guillardia theta. Due to the modest homology of amino acid sequences with a chlorophyte channelrhodopsin such as Cr_ChR2 from Chlamydomonas reinhardtii, it has been proposed that a family of cryptophyte channelrhodopsin, including Gt_CCR4, has a distinct molecular mechanism for channel gating and ion permeation. In this study, we compared the photocurrent properties, cation selectivity and kinetics between well-known Cr_ChR2 and Gt_CCR4 by a conventional path clamp method. Large and stable light-induced cation conduction by Gt_CCR4 at the maximum absorbing wavelength (530 nm) was observed with only small inactivation (15%), whereas the photocurrent of Cr_ChR2 exhibited significant inactivation (50%) and desensitization. The light sensitivity of Gt_CCR4 was higher (EC50 = 0.13 mW/mm2) than that of Cr_ChR2 (EC50 = 0.80 mW/mm2) while the channel open life time (photocycle speed) was in the same range as that of Cr_ChR2 (25~30 ms for Gt_CCR4 and 10~15 ms for Cr_ChR2). This observation implies that Gt_CCR4 enables optical neuronal spiking with weak light in high temporal resolution when applied in neuroscience. Furthermore, we demonstrated high Na+ selectivity of Gt_CCR4 in which the selectivity ratio for Na+ was 37-fold larger than that for Cr_ChR2, which primarily conducts H+. On the other hand, Gt_CCR4 conducted almost no H+ and no Ca2+ under physiological conditions. These results suggest that ion selectivity in Gt_CCR4 is distinct from that in Cr_ChR2. In addition, a unique red-absorbing and stable intermediate in the photocycle was observed, indicating a photochromic property of Gt_CCR4.
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46
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Oppermann J, Fischer P, Silapetere A, Liepe B, Rodriguez-Rozada S, Flores-Uribe J, Schiewer E, Keidel A, Vierock J, Kaufmann J, Broser M, Luck M, Bartl F, Hildebrandt P, Wiegert JS, Béjà O, Hegemann P, Wietek J. MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nat Commun 2019; 10:3315. [PMID: 31346176 PMCID: PMC6658528 DOI: 10.1038/s41467-019-11322-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. Here we describe a metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of optogenetic tools from metagenomic databases and enhance general understanding of ChR function.
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Affiliation(s)
- Johannes Oppermann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Paul Fischer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Arita Silapetere
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Bernhard Liepe
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - José Flores-Uribe
- Technion-Israel Institute of Technology, 32000, Haifa, Israel
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Anke Keidel
- Institute for Chemistry, Physical Chemistry/Biophysical Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Joel Kaufmann
- Institute for Biology, Biophysical Chemistry, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Meike Luck
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Franz Bartl
- Institute for Biology, Biophysical Chemistry, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Peter Hildebrandt
- Institute for Chemistry, Physical Chemistry/Biophysical Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Oded Béjà
- Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany.
| | - Jonas Wietek
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany.
- Department of Neurobiology, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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47
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Liang R, Liu F, Martínez TJ. Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2. J Phys Chem Lett 2019; 10:2862-2868. [PMID: 31083920 DOI: 10.1021/acs.jpclett.9b00701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn-Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the "aborted bicycle-pedal" mechanism. In addition, RPSB photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which could trigger subsequent channel opening and ion conduction.
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Affiliation(s)
- Ruibin Liang
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Fang Liu
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
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