1
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Lamm GHU, Zabelskii D, Balandin T, Gordeliy V, Wachtveitl J. Calcium-Sensitive Microbial Rhodopsin VirChR1: A Femtosecond to Second Photocycle Study. J Phys Chem Lett 2024; 15:5510-5516. [PMID: 38749015 DOI: 10.1021/acs.jpclett.4c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Viral rhodopsins are light-gated cation channels representing a novel class of microbial rhodopsins. For viral rhodopsin 1 subfamily members VirChR1 and OLPVR1, channel activity is abolished above a certain calcium concentration. Here we present a calcium-dependent spectroscopic analysis of VirChR1 on the femtosecond to second time scale. Unlike channelrhodopsin-2, VirChR1 possesses two intermediate states P1 and P2 on the ultrafast time scale, similar to J and K in ion-pumping rhodopsins. Subsequently, we observe multifaceted photocycle kinetics with up to seven intermediate states. Calcium predominantly affects the last photocycle steps, including the appearance of additional intermediates P6Ca and P7 representing the blocked channel. Furthermore, the photocycle of the counterion variant D80N is drastically altered, yielding intermediates with different spectra and kinetics compared to those of the wt. These findings demonstrate the central role of the counterion within the defined reaction sequence of microbial rhodopsins that ultimately defines the protein function.
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Affiliation(s)
- Gerrit H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | | | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- University Grenoble Alpes, CEA, CNRS, Institute de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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2
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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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3
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Bühl E, Resler T, Lam R, Asido M, Bamberg E, Schlesinger R, Bamann C, Heberle J, Wachtveitl J. Assessing the Role of R120 in the Gating of CrChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds. J Am Chem Soc 2023; 145:21832-21840. [PMID: 37773976 DOI: 10.1021/jacs.3c05399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The light-gated ion channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) is the most frequently used optogenetic tool in neurosciences. However, the precise molecular mechanism of the channel opening and the correlation among retinal isomerization, the photocycle, and the channel activity of the protein are missing. Here, we present electrophysiological and spectroscopic investigations on the R120H variant of CrChR2. R120 is a key residue in an extended network linking the retinal chromophore to several gates of the ion channel. We show that despite the deficient channel activity, the photocycle of the variant is intact. In a comparative study for R120H and the wild type, we resolve the vibrational changes in the spectral range of the retinal and amide I bands across the time range from femtoseconds to seconds. Analysis of the amide I mode reveals a significant impairment of the ultrafast protein response after retinal excitation. We conclude that channel opening in CrChR2 is prepared immediately after retinal excitation. Additionally, chromophore isomerization is essential for both photocycle and channel activities, although both processes can occur independently.
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Affiliation(s)
- Elena Bühl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Tom Resler
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Rebecca Lam
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
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4
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Wijesiri K, Gascón JA. Microsolvation Effects in the Spectral Tuning of Heliorhodopsin. J Phys Chem B 2022; 126:5803-5809. [PMID: 35894868 DOI: 10.1021/acs.jpcb.2c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heliorhodopsins (HeR) are a new category of heptahelical transmembrane photoactive proteins with a covalently linked all-trans retinal. The protonated Schiff base (PSB) nitrogen in the retinal is stabilized by a negatively charged counterion. It is well-known that stronger or weaker electrostatic interactions with the counterion cause a significant spectral blue- or red-shift, respectively, in both microbial and animal rhodopsins. In HeR, however, while Glu107 acts as the counterion, mutations of this residue are not directly correlated with a spectral shift. A molecular dynamics analysis revealed that a water cluster pocket produces a microsolvation effect on the Schiff base, compensating to various extents the replacement of the native counterion. Using a combination of molecular dynamics and quantum mechanical/molecular mechanics (QM/MM), we study this microsolvation effect on the electronic absorption of the retinylidene Schiff base chromophore of HeR.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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5
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Rodriguez-Rozada S, Wietek J, Tenedini F, Sauter K, Dhiman N, Hegemann P, Soba P, Wiegert JS. Aion is a bistable anion-conducting channelrhodopsin that provides temporally extended and reversible neuronal silencing. Commun Biol 2022; 5:687. [PMID: 35810216 PMCID: PMC9271052 DOI: 10.1038/s42003-022-03636-x] [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: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Optogenetic silencing allows to reveal the necessity of selected neuronal populations for various neurophysiological functions. These range from synaptic transmission and coordinated neuronal network activity to control of specific behaviors. An ideal single-component optogenetic silencing tool should be switchable between active and inactive states with precise timing while preserving its activity in the absence of light until switched to an inactive state. Although bistable anion-conducting channelrhodopsins (ACRs) were previously engineered to reach this goal, their conducting state lifetime was limited to only a few minutes and some ACRs were not fully switchable. Here we report Aion, a bistable ACR displaying a long-lasting open state with a spontaneous closing time constant close to 15 min. Moreover, Aion can be switched between the open and closed state with millisecond precision using blue and orange light, respectively. The long conducting state enables overnight silencing of neurons with minimal light exposure. We further generated trafficking-optimized versions of Aion, which show enhanced membrane localization and allow precisely timed, long-lasting all-optical control of nociceptive responses in larvae of Drosophila melanogaster. Thus, Aion is an optogenetic silencing tool for inhibition of neuronal activity over many hours which can be switched between an active and inactive state with millisecond precision. Aion is an anion-conducting, bistable channelrhodopsin that enables long-term silencing of neuronal networks, as demonstrated in organotypic hippocampal cultures and Drosophila melanogaster larvae.
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Affiliation(s)
- Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Jonas Wietek
- Institute for Biology, Experimental Biophysics, Humboldt University Berlin, D-10115, Berlin, Germany.,Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Federico Tenedini
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Kathrin Sauter
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.,Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Neena Dhiman
- LIMES Institute, Department of Molecular Brain Physiology and Behavior, University of Bonn, 53115, Bonn, Germany.,Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt University Berlin, D-10115, Berlin, Germany
| | - Peter Soba
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.,LIMES Institute, Department of Molecular Brain Physiology and Behavior, University of Bonn, 53115, Bonn, Germany.,Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
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6
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Liang R, Yu JK, Meisner J, Liu F, Martinez TJ. Electrostatic Control of Photoisomerization in Channelrhodopsin 2. J Am Chem Soc 2021; 143:5425-5437. [PMID: 33794085 DOI: 10.1021/jacs.1c00058] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.
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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
| | - Jimmy K Yu
- 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
- Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Jan Meisner
- 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 Martinez
- 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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7
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Abstract
Microbial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.
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8
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Tanaka T, Singh M, Shihoya W, Yamashita K, Kandori H, Nureki O. Structural basis for unique color tuning mechanism in heliorhodopsin. Biochem Biophys Res Commun 2020; 533:262-267. [PMID: 32951839 DOI: 10.1016/j.bbrc.2020.06.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Microbial rhodopsins comprise an opsin protein with seven transmembrane helices and a retinal as the chromophore. An all-trans retinal is covalently bonded to a lysine residue through the retinal Schiff base (RSB) and stabilized by a negatively charged counterion. The distance between the RSB and counterion is closely related to the light energy absorption. However, in heliorhodopsin-48C12 (HeR-48C12), while E107 acts as the counterion, E107D mutation exhibits an identical absorption spectrum to the wild-type, suggesting that the distance does not affect its absorption spectra. Here we present the 2.6 Å resolution crystal structure of the Thermoplasmatales archaeon HeR E108D mutant, which also has an identical absorption spectrum to the wild-type. The structure revealed that D108 does not form a hydrogen bond with the RSB, and its counterion interaction becomes weaker. Alternatively, the serine cluster, S78, S112, and S238 form a distinct interaction network around the RSB. The absorption spectra of the E to D and S to A double mutants suggested that S112 influences the spectral shift by compensating for the weaker counterion interaction. Our structural and spectral studies have revealed the unique spectral shift mechanism of HeR and clarified the physicochemical properties of HeRs.
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Affiliation(s)
- Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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9
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Channelrhodopsin-mediated optogenetics highlights a central role of depolarization-dependent plant proton pumps. Proc Natl Acad Sci U S A 2020; 117:20920-20925. [PMID: 32788371 PMCID: PMC7456130 DOI: 10.1073/pnas.2005626117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
People for centuries are puzzled how living creatures like plants sense their environment. Plants employ electrical signals to communicate a cue-dependent local status between plants cells and organs. As a first response to biotic and abiotic stresses, the membrane potential of plant cells depolarizes. Recovery from the depolarized state, repolarization, was proposed to involve ion channels and pumps. Here, we established channelrhodopsin (ChR2)-based optogenetics in plants and learned that the plant plasma membrane H+-ATPase represents the major driver of membrane potential repolarization control during plant electrical signaling, rather than voltage-dependent ion channels. In plants, environmental stressors trigger plasma membrane depolarizations. Being electrically interconnected via plasmodesmata, proper functional dissection of electrical signaling by electrophysiology is basically impossible. The green alga Chlamydomonas reinhardtii evolved blue light-excited channelrhodopsins (ChR1, 2) to navigate. When expressed in excitable nerve and muscle cells, ChRs can be used to control the membrane potential via illumination. In Arabidopsis plants, we used the algal ChR2-light switches as tools to stimulate plasmodesmata-interconnected photosynthetic cell networks by blue light and monitor the subsequent plasma membrane electrical responses. Blue-dependent stimulations of ChR2 expressing mesophyll cells, resting around −160 to −180 mV, reproducibly depolarized the membrane potential by 95 mV on average. Following excitation, mesophyll cells recovered their prestimulus potential not without transiently passing a hyperpolarization state. By combining optogenetics with voltage-sensing microelectrodes, we demonstrate that plant plasma membrane AHA-type H+-ATPase governs the gross repolarization process. AHA2 protein biochemistry and functional expression analysis in Xenopus oocytes indicates that the capacity of this H+ pump to recharge the membrane potential is rooted in its voltage- and pH-dependent functional anatomy. Thus, ChR2 optogenetics appears well suited to noninvasively expose plant cells to signal specific depolarization signatures. From the responses we learn about the molecular processes, plants employ to channel stress-associated membrane excitations into physiological responses.
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10
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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin. J Phys Chem B 2019; 123:4242-4250. [PMID: 30998011 PMCID: PMC6526469 DOI: 10.1021/acs.jpcb.9b01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Microbial rhodopsins
constitute a key protein family in optobiotechnological
applications such as optogenetics and voltage imaging. Spectral tuning
of rhodopsins into the deep-red and near-infrared spectral regions
is of great demand in such applications because more bathochromic
light into the near-infrared range penetrates deeper in living tissue.
Recently, retinal analogues have been successfully used in ion transporting
and fluorescent rhodopsins to achieve red-shifted absorption, activity,
and emission properties. Understanding their photochemical mechanism
is essential for further design of appropriate retinal analogues but
is yet only poorly understood for most retinal analogue pigments.
Here, we report the photoreaction dynamics of red-shifted analogue
pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto-
to submillisecond transient absorption spectroscopy. We found that
the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510
nm light illumination, which is comparable to the native retinal (A1)
in PR. On the other hand, the deprotonation of the A2 pigment Schiff
base was observed with a dominant time constant of 67 μs, which
is significantly slower than the A1 pigment. In the MOA2 pigment,
no isomerization or photoproduct formation was detected upon 520 nm
excitation, implying that all the excited molecules returned to the
initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very
slow excited state dynamics similar to the previously studied MMAR
pigment, but only very little photoproduct was formed. The low efficiency
of the photoproduct formation likely is the reason why DMAR analogue
pigments of PR showed very weak proton pumping activity.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands
| | - Sean Frehan
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Miroslav Kloz
- ELI-Beamlines , Institute of Physics , Na Slovance 2 , Praha 8 182 21 , Czech Republic
| | - Willem J de Grip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands.,Department of Biochemistry , Radboud University Medical Center , Nijmegen 6500 HB , The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
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11
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Dokukina I, Nenov A, Garavelli M, Marian CM, Weingart O. QM/MM Photodynamics of Retinal in the Channelrhodopsin Chimera C1C2 with OM3/MRCI. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Irina Dokukina
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Christel M. Marian
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
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12
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Singh M, Katayama K, Béjà O, Kandori H. Anion binding to mutants of the Schiff base counterion in heliorhodopsin 48C12. Phys Chem Chem Phys 2019; 21:23663-23671. [DOI: 10.1039/c9cp04102h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anion binds as the direct H-bonding acceptor of the Schiff base in E107A, while E107Q indirectly accommodates an anion.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Oded Béjà
- Faculty of Biology
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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13
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Bühl E, Eberhardt P, Bamann C, Bamberg E, Braun M, Wachtveitl J. Ultrafast Protein Response in Channelrhodopsin-2 Studied by Time-Resolved Infrared Spectroscopy. J Phys Chem Lett 2018; 9:7180-7184. [PMID: 30525663 DOI: 10.1021/acs.jpclett.8b03382] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ultrafast infrared transient absorption in the carbonyl vibrational region of protonated aspartate and glutamate residues in channelrhodopsin-2 from Chlamydomonas reinhardtii shows immediate protein response to retinal excitation. The observed difference bands are formed directly after the excitation on the subpicosecond time scale and were assigned to side chains in the retinal vicinity, such as D156 and E90. This finding implies an ultrafast and effective energy transfer from the retinal to its environment via hydrogen-bonded networks and reveals extraordinarily strong chromophore-protein coupling and intense interaction within the protein. Relevance to the protein function as an optically gated ion channel is discussed.
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Affiliation(s)
- Elena Bühl
- Institute of Physical and Theoretical Chemistry , Goethe University , Max von Laue-Straße 7 , 60438 Frankfurt am Main , Germany
| | - Peter Eberhardt
- Institute of Physical and Theoretical Chemistry , Goethe University , Max von Laue-Straße 7 , 60438 Frankfurt am Main , Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics , Max von Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics , Max von Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry , Goethe University , Max von Laue-Straße 7 , 60438 Frankfurt am Main , Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry , Goethe University , Max von Laue-Straße 7 , 60438 Frankfurt am Main , Germany
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14
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Singh M, Inoue K, Pushkarev A, Béjà O, Kandori H. Mutation Study of Heliorhodopsin 48C12. Biochemistry 2018; 57:5041-5049. [PMID: 30036039 DOI: 10.1021/acs.biochem.8b00637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rhodopsins are heptahelical transmembrane photoactive protein families: type 1 (microbial rhodopsins) and type 2 (animal rhodopsins). Both families share similar topologies and chromophore retinal, which is linked covalently as a protonated Schiff base to a Lys at the transmembrane 7 helix. Recently, through functional metagenomics analysis, we reported an unnoticed diverse family, heliorhodopsins (HeRs), which are abundant and distributed globally in archaea, bacteria, eukarya, and viruses. The sequence identity is <15% between HeRs and type 1 rhodopsins, so that many aspects of the molecular properties of HeRs remain unknown. Herein, to gain information about the residues responsible for the interaction with the chromophore, we applied Ala scanning to 30 candidate residues in HeR 48C12. As a result, 12 mutants showed no absorption change, eight exhibited a spectral blue-shift, six exhibited a spectral red-shift, and four did not form a pigment. R104, Y108, G145, and K241 play crucial roles in pigment formation. A combination of single mutants successfully engineered pigments absorbing at 523 nm (S112A/M141A) and 571 nm (H80A/S237A), covering more than ∼50 nm. These results provide fundamental knowledge about the molecular properties of HeRs.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
| | - Keiichi Inoue
- 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.,Frontier Research Institute for Material Science , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan.,PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Alina Pushkarev
- Faculty of Biology , Technion-Israel Institute of Technology , Haifa 32000 , Israel
| | - Oded Béjà
- Faculty of Biology , Technion-Israel Institute of Technology , Haifa 32000 , Israel
| | - 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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15
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Paul K, Sengupta P, Ark ED, Tu H, Zhao Y, Boppart SA. Coherent control of an opsin in living brain tissue. NATURE PHYSICS 2017; 13:1111-1116. [PMID: 29983725 PMCID: PMC6029863 DOI: 10.1038/nphys4257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Retinal-based opsins are light-sensitive proteins. The photoisomerization reaction of these proteins has been studied outside cellular environments using ultrashort tailored light pulses1-5. However, how living cell functions can be modulated via opsins by modifying fundamental nonlinear optical properties of light interacting with the retinal chromophore has remained largely unexplored. We report the use of chirped ultrashort near-infrared pulses to modulate light-evoked ionic current from Channelrhodopsin-2 (ChR2) in brain tissue, and consequently the firing pattern of neurons, by manipulating the phase of the spectral components of the light. These results confirm that quantum coherence of the retinal-based protein system, even in a living neuron, can influence its current output, and open up the possibilities of using designer-tailored pulses for controlling molecular dynamics of opsins in living tissue to selectively enhance or suppress neuronal function for adaptive feedback-loop applications in the future.
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Affiliation(s)
- Kush Paul
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Parijat Sengupta
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Eugene D Ark
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Haohua Tu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Youbo Zhao
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Stephen A Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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16
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Abstract
Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
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17
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Hontani Y, Broser M, Silapetere A, Krause BS, Hegemann P, Kennis JTM. The femtosecond-to-second photochemistry of red-shifted fast-closing anion channelrhodopsin PsACR1. Phys Chem Chem Phys 2017; 19:30402-30409. [DOI: 10.1039/c7cp06414d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Femtosecond-to-second complete photocycle model of anion channelrhodopsin PsACR1.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy
- Vrije Universiteit Amsterdam
- Amsterdam 1081 HV, De Boelelaan
- The Netherlands
| | - Matthias Broser
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Arita Silapetere
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Benjamin S. Krause
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Peter Hegemann
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy
- Vrije Universiteit Amsterdam
- Amsterdam 1081 HV, De Boelelaan
- The Netherlands
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18
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Optochemokine Tandem for Light-Control of Intracellular Ca2. PLoS One 2016; 11:e0165344. [PMID: 27768773 PMCID: PMC5074463 DOI: 10.1371/journal.pone.0165344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/10/2016] [Indexed: 01/13/2023] Open
Abstract
An optochemokine tandem was developed to control the release of calcium from endosomes into the cytosol by light and to analyze the internalization kinetics of G-protein coupled receptors (GPCRs) by electrophysiology. A previously constructed rhodopsin tandem was re-engineered to combine the light-gated Ca2+-permeable cation channel Channelrhodopsin-2(L132C), CatCh, with the chemokine receptor CXCR4 in a functional tandem protein tCXCR4/CatCh. The GPCR was used as a shuttle protein to displace CatCh from the plasma membrane into intracellular areas. As shown by patch-clamp measurements and confocal laser scanning microscopy, heterologously expressed tCXCR4/CatCh was internalized via the endocytic SDF1/CXCR4 signaling pathway. The kinetics of internalization could be followed electrophysiologically via the amplitude of the CatCh signal. The light-induced release of Ca2+ by tandem endosomes into the cytosol via CatCh was visualized using the Ca2+-sensitive dyes rhod2 and rhod2-AM showing an increase of intracellular Ca2+ in response to light.
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19
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Dampening Spontaneous Activity Improves the Light Sensitivity and Spatial Acuity of Optogenetic Retinal Prosthetic Responses. Sci Rep 2016; 6:33565. [PMID: 27650332 PMCID: PMC5030712 DOI: 10.1038/srep33565] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/19/2016] [Indexed: 01/19/2023] Open
Abstract
Retinitis pigmentosa is a progressive retinal dystrophy that causes irreversible visual impairment and blindness. Retinal prostheses currently represent the only clinically available vision-restoring treatment, but the quality of vision returned remains poor. Recently, it has been suggested that the pathological spontaneous hyperactivity present in dystrophic retinas may contribute to the poor quality of vision returned by retinal prosthetics by reducing the signal-to-noise ratio of prosthetic responses. Here, we investigated to what extent blocking this hyperactivity can improve optogenetic retinal prosthetic responses. We recorded activity from channelrhodopsin-expressing retinal ganglion cells in retinal wholemounts in a mouse model of retinitis pigmentosa. Sophisticated stimuli, inspired by those used in clinical visual assessment, were used to assess light sensitivity, contrast sensitivity and spatial acuity of optogenetic responses; in all cases these were improved after blocking spontaneous hyperactivity using meclofenamic acid, a gap junction blocker. Our results suggest that this approach significantly improves the quality of vision returned by retinal prosthetics, paving the way to novel clinical applications. Moreover, the improvements in sensitivity achieved by blocking spontaneous hyperactivity may extend the dynamic range of optogenetic retinal prostheses, allowing them to be used at lower light intensities such as those encountered in everyday life.
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20
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El-Tahawy MMT, Nenov A, Garavelli M. Photoelectrochromism in the Retinal Protonated Schiff Base Chromophore: Photoisomerization Speed and Selectivity under a Homogeneous Electric Field at Different Operational Regimes. J Chem Theory Comput 2016; 12:4460-75. [DOI: 10.1021/acs.jctc.6b00558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohsen M. T. El-Tahawy
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Chemistry
Department, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Artur Nenov
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Université
de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, Centre
Nationale de Recherche Scientifique, 46 allée d’Italie, 69007 Lyon Cedex 07, France
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21
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Affiliation(s)
- Franziska Schneider
- Experimental Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; , ,
| | - Christiane Grimm
- Experimental Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; , ,
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; , ,
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22
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Lórenz-Fonfría VA, Schultz BJ, Resler T, Schlesinger R, Bamann C, Bamberg E, Heberle J. Pre-gating conformational changes in the ChETA variant of channelrhodopsin-2 monitored by nanosecond IR spectroscopy. J Am Chem Soc 2015; 137:1850-61. [PMID: 25584873 DOI: 10.1021/ja5108595] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Light-gated ion permeation by channelrhodopsin-2 (ChR2) relies on the photoisomerization of the retinal chromophore and the subsequent photocycle, leading to the formation (on-gating) and decay (off-gating) of the conductive state. Here, we have analyzed the photocycle of a fast-cycling ChR2 variant (E123T mutation, also known as ChETA), by time-resolved UV/vis, step-scan FT-IR, and tunable quantum cascade laser IR spectroscopies with nanosecond resolution. Pre-gating conformational changes rise with a half-life of 200 ns, silent to UV/vis but detected by IR spectroscopy. They involve changes in the peptide backbone and in the H-bond of the side chain of the critical residue D156. Thus, the P1(500) intermediate must be separated into early and late states. Light-adapted ChR2 contains a mixture of all-trans and 13-cis retinal in a 70:30 ratio which are both photoactive. Analysis of ethylenic and fingerprint vibrations of retinal provides evidence that the 13-cis photocycle recovers in 1 ms. This recovery is faster than channel off-gating and most of the proton transfer reactions, implying that the 13-cis photocycle is of minor functional relevance for ChR2.
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Affiliation(s)
- Víctor A Lórenz-Fonfría
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
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23
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Ogren JI, Yi A, Mamaev S, Li H, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Comparison of the structural changes occurring during the primary phototransition of two different channelrhodopsins from Chlamydomonas algae. Biochemistry 2014; 54:377-88. [PMID: 25469620 PMCID: PMC4303311 DOI: 10.1021/bi501243y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Channelrhodopsins
(ChRs) from green flagellate algae function as
light-gated ion channels when expressed heterologously in mammalian
cells. Considerable interest has focused on understanding the molecular
mechanisms of ChRs to bioengineer their properties for specific optogenetic
applications such as elucidating the function of specific neurons
in brain circuits. While most studies have used channelrhodopsin-2
from Chlamydomonas reinhardtii (CrChR2), in this work low-temperature Fourier transform infrared-difference
spectroscopy is applied to study the conformational changes occurring
during the primary phototransition of the red-shifted ChR1 from Chlamydomonas augustae (CaChR1). Substitution
with isotope-labeled retinals or the retinal analogue A2, site-directed
mutagenesis, hydrogen–deuterium exchange, and H218O exchange were used to assign bands to the retinal
chromophore, protein, and internal water molecules. The primary phototransition
of CaChR1 at 80 K involves, in contrast to that of CrChR2, almost exclusively an all-trans to 13-cis isomerization of the retinal chromophore,
as in the primary phototransition of bacteriorhodopsin (BR). In addition,
significant differences are found for structural changes of the protein
and internal water(s) compared to those of CrChR2,
including the response of several Asp/Glu residues to retinal isomerization.
A negative amide II band is identified in the retinal ethylenic stretch
region of CaChR1, which reflects along with amide
I bands alterations in protein backbone structure early in the photocycle.
A decrease in the hydrogen bond strength of a weakly hydrogen bonded
internal water is detected in both CaChR1 and CrChR2, but the bands are much broader in CrChR2, indicating a more heterogeneous environment. Mutations involving
residues Glu169 and Asp299 (homologues of the Asp85 and Asp212 Schiff
base counterions, respectively, in BR) lead to the conclusion that
Asp299 is protonated during P1 formation and suggest that these residues
interact through a strong hydrogen bond that facilitates the transfer
of a proton from Glu169.
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Affiliation(s)
- John I Ogren
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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24
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Channelrhodopsin-2-XXL, a powerful optogenetic tool for low-light applications. Proc Natl Acad Sci U S A 2014; 111:13972-7. [PMID: 25201989 DOI: 10.1073/pnas.1408269111] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Channelrhodopsin-2 (ChR2) has provided a breakthrough for the optogenetic control of neuronal activity. In adult Drosophila melanogaster, however, its applications are severely constrained. This limitation in a powerful model system has curtailed unfolding the full potential of ChR2 for behavioral neuroscience. Here, we describe the D156C mutant, termed ChR2-XXL (extra high expression and long open state), which displays increased expression, improved subcellular localization, elevated retinal affinity, an extended open-state lifetime, and photocurrent amplitudes greatly exceeding those of all heretofore published ChR variants. As a result, neuronal activity could be efficiently evoked with ambient light and even without retinal supplementation. We validated the benefits of the variant in intact flies by eliciting simple and complex behaviors. We demonstrate efficient and prolonged photostimulation of monosynaptic transmission at the neuromuscular junction and reliable activation of a gustatory reflex pathway. Innate male courtship was triggered in male and female flies, and olfactory memories were written through light-induced associative training.
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25
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Mehler M, Scholz F, Ullrich SJ, Mao J, Braun M, Brown LJ, Brown RCD, Fiedler SA, Becker-Baldus J, Wachtveitl J, Glaubitz C. The EF loop in green proteorhodopsin affects conformation and photocycle dynamics. Biophys J 2014; 105:385-97. [PMID: 23870260 DOI: 10.1016/j.bpj.2013.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 11/20/2022] Open
Abstract
The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.
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Affiliation(s)
- Michaela Mehler
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Germany
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26
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Lórenz-Fonfría VA, Heberle J. Channelrhodopsin unchained: structure and mechanism of a light-gated cation channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:626-42. [PMID: 24212055 DOI: 10.1016/j.bbabio.2013.10.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/21/2013] [Accepted: 10/30/2013] [Indexed: 12/25/2022]
Abstract
The new and vibrant field of optogenetics was founded by the seminal discovery of channelrhodopsin, the first light-gated cation channel. Despite the numerous applications that have revolutionised neurophysiology, the functional mechanism is far from understood on the molecular level. An arsenal of biophysical techniques has been established in the last decades of research on microbial rhodopsins. However, application of these techniques is hampered by the duration and the complexity of the photoreaction of channelrhodopsin compared with other microbial rhodopsins. A particular interest in resolving the molecular mechanism lies in the structural changes that lead to channel opening and closure. Here, we review the current structural and mechanistic knowledge that has been accomplished by integrating the static structure provided by X-ray crystallography and electron microscopy with time-resolved spectroscopic and electrophysiological techniques. The dynamical reactions of the chromophore are effectively coupled to structural changes of the protein, as shown by ultrafast spectroscopy. The hierarchical sequence of structural changes in the protein backbone that spans the time range from 10(-12)s to 10(-3)s prepares the channel to open and, consequently, cations can pass. Proton transfer reactions that are associated with channel gating have been resolved. In particular, glutamate 253 and aspartic acid 156 were identified as proton acceptor and donor to the retinal Schiff base. The reprotonation of the latter is the critical determinant for channel closure. The proton pathway that eventually leads to proton pumping is also discussed. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Víctor A Lórenz-Fonfría
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany.
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27
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Neumann-Verhoefen MK, Neumann K, Bamann C, Radu I, Heberle J, Bamberg E, Wachtveitl J. Ultrafast Infrared Spectroscopy on Channelrhodopsin-2 Reveals Efficient Energy Transfer from the Retinal Chromophore to the Protein. J Am Chem Soc 2013; 135:6968-76. [DOI: 10.1021/ja400554y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mirka-Kristin Neumann-Verhoefen
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Karsten Neumann
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Ionela Radu
- Department
of Physics, Molecular
Biospectroscopy, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Experimental
Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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28
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Janke C, Scholz F, Becker-Baldus J, Glaubitz C, Wood PG, Bamberg E, Wachtveitl J, Bamann C. Photocycle and vectorial proton transfer in a rhodopsin from the eukaryote Oxyrrhis marina. Biochemistry 2013; 52:2750-63. [PMID: 23586665 DOI: 10.1021/bi301412n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Retinylidene photoreceptors are ubiquitously present in marine protists as first documented by the identification of green proteorhodopsin (GPR). We present a detailed investigation of a rhodopsin from the protist Oxyrrhis marina (OR1) with respect to its spectroscopic properties and to its vectorial proton transport. Despite its homology to GPR, OR1's features differ markedly in its pH dependence. Protonation of the proton acceptor starts at pH below 4 and is sensitive to the ionic conditions. The mutation of a conserved histidine H62 did not influence the pK(a) value in a similar manner as in other proteorhodopsins where the charged histidine interacts with the proton acceptor forming the so-called His-Asp cluster. Mutational and pH-induced effects were further reflected in the temporal behavior upon light excitation ranging from femtoseconds to seconds. The primary photodynamics exhibits a high sensitivity to the environment of the proton acceptor D100 that are correlated to the different initial states. The mutation of the H62 does not affect photoisomerization at neutral pH. This is in agreement with NMR data indicating the absence of the His-Asp cluster. The subsequent steps in the photocycle revealed protonation reactions at the Schiff base coupled to proton pumping even at low pH. The main electrogenic steps are associated with the reprotonation of the Schiff base and internal proton donor. Hence, OR1 shows a different theme of the His-Asp organization where the low pK(a) of the proton acceptor is not dominated by this interaction, but by other electrostatic factors.
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Affiliation(s)
- Christian Janke
- Max-Planck-Institut für Biophysik, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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Mandal AK, Ghosh S, Das AK, Mondal T, Bhattacharyya K. Effect of NaCl on ESPT‐Mediated FRET in a CTAC Micelle: A Femtosecond and FCS Study. Chemphyschem 2012; 14:788-96. [PMID: 23143825 DOI: 10.1002/cphc.201200669] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 02/01/2023]
Affiliation(s)
- Amit Kumar Mandal
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India), Fax: (+91) 33‐2473‐2805
| | - Shirsendu Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India), Fax: (+91) 33‐2473‐2805
| | - Atanu Kumar Das
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India), Fax: (+91) 33‐2473‐2805
| | - Tridib Mondal
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India), Fax: (+91) 33‐2473‐2805
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India), Fax: (+91) 33‐2473‐2805
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