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Prignano LA, Stevens MJ, Vanegas JM, Rempe SB, Dempski RE. Metadynamics simulations reveal mechanisms of Na+ and Ca2+ transport in two open states of the channelrhodopsin chimera, C1C2. PLoS One 2024; 19:e0309553. [PMID: 39241014 PMCID: PMC11379304 DOI: 10.1371/journal.pone.0309553] [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: 05/08/2024] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca2+ permeability vs. Na+ by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na+ and Ca2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.
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Affiliation(s)
- Lindsey A Prignano
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mark J Stevens
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Juan M Vanegas
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Robert E Dempski
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
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2
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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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3
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Sakai K, Shichida Y, Imamoto Y, Yamashita T. Creation of photocyclic vertebrate rhodopsin by single amino acid substitution. eLife 2022; 11:75979. [PMID: 35199641 PMCID: PMC8871353 DOI: 10.7554/elife.75979] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Opsins are universal photoreceptive proteins in animals and can be classified into three types based on their photoreaction properties. Upon light irradiation, vertebrate rhodopsin forms a metastable active state, which cannot revert back to the original dark state via either photoreaction or thermal reaction. By contrast, after photoreception, most opsins form a stable active state which can photoconvert back to the dark state. Moreover, we recently found a novel type of opsins whose activity is regulated by photocycling. However, the molecular mechanism underlying this diversification of opsins remains unknown. In this study, we showed that vertebrate rhodopsin acquired the photocyclic and photoreversible properties upon introduction of a single mutation at position 188. This revealed that the residue at position 188 contributes to the diversification of photoreaction properties of opsins by its regulation of the recovery from the active state to the original dark state.
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Affiliation(s)
- Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Research Organization for Science and technology, Ritsumeikan University, Kusatsu, Japan
| | - Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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4
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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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5
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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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6
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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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7
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De Meulenaere E, de Coene Y, Russier-Antoine I, Vanpraet L, Van den Haute C, Thevissen K, Baekelandt V, Bartic C, Hofkens J, Brevet PF, Clays K. Fluorescence-free First Hyperpolarizability Values of Fluorescent Proteins and Channel Rhodopsins. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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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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9
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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10
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Unifying photocycle model for light adaptation and temporal evolution of cation conductance in channelrhodopsin-2. Proc Natl Acad Sci U S A 2019; 116:9380-9389. [PMID: 31004059 PMCID: PMC6510988 DOI: 10.1073/pnas.1818707116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Although channelrhodopsin (ChR) is a widely applied light-activated ion channel, important properties such as light adaptation, photocurrent inactivation, and alteration of the ion selectivity during continuous illumination are not well understood from a molecular perspective. Herein, we address these open questions using single-turnover electrophysiology, time-resolved step-scan FTIR, and Raman spectroscopy of fully dark-adapted ChR2. This yields a unifying parallel photocycle model integrating now all so far controversial discussed data. In dark-adapted ChR2, the protonated retinal Schiff base chromophore (RSBH+) adopts an all-trans,C=N-anti conformation only. Upon light activation, a branching reaction into either a 13-cis,C=N-anti or a 13-cis,C=N-syn retinal conformation occurs. The anti-cycle features sequential H+ and Na+ conductance in a late M-like state and an N-like open-channel state. In contrast, the 13-cis,C=N-syn isomer represents a second closed-channel state identical to the long-lived P480 state, which has been previously assigned to a late intermediate in a single-photocycle model. Light excitation of P480 induces a parallel syn-photocycle with an open-channel state of small conductance and high proton selectivity. E90 becomes deprotonated in P480 and stays deprotonated in the C=N-syn cycle. Deprotonation of E90 and successive pore hydration are crucial for late proton conductance following light adaptation. Parallel anti- and syn-photocycles now explain inactivation and ion selectivity changes of ChR2 during continuous illumination, fostering the future rational design of optogenetic tools.
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11
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Luck M, Velázquez Escobar F, Glass K, Sabotke MI, Hagedorn R, Corellou F, Siebert F, Hildebrandt P, Hegemann P. Photoreactions of the Histidine Kinase Rhodopsin Ot-HKR from the Marine Picoalga Ostreococcus tauri. Biochemistry 2019; 58:1878-1891. [PMID: 30768260 DOI: 10.1021/acs.biochem.8b01200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tiny picoalga, Ostreococcus tauri, originating from the Thau Lagoon is a member of the marine phytoplankton. Because of its highly reduced genome and small cell size, while retaining the fundamental requirements of a eukaryotic photosynthetic cell, it became a popular model organism for studying photosynthesis or circadian clock-related processes. We analyzed the spectroscopic properties of the photoreceptor domain of the histidine kinase rhodopsin Ot-HKR that is suggested to be involved in the light-induced entrainment of the Ostreococcus circadian clock. We found that the rhodopsin, Ot-Rh, dark state absorbs maximally at 505 nm. Exposure to green-orange light led to the accumulation of a blue-shifted M-state-like absorbance form with a deprotonated Schiff base. This Ot-Rh P400 state had an unusually long lifetime of several minutes. A second long-living photoproduct with a red-shifted absorbance, P560, accumulated upon illumination with blue/UVA light. The resulting photochromicity of the rhodopsin is expected to be advantageous to its function as a molecular control element of the signal transducing HKR domains. The light intensity and the ratio of blue vs green light are reflected by the ratio of rhodopsin molecules in the long-living absorbance forms. Furthermore, dark-state absorbance and the photocycle kinetics vary with the salt content of the environment substantially. This observation is attributed to anion binding in the dark state and a transient anion release during the photocycle, indicating that the salinity affects the photoinduced processes.
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Affiliation(s)
- Meike Luck
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | | | - Kathrin Glass
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Mareike-Isabel Sabotke
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Rolf Hagedorn
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Florence Corellou
- Laboratoire d'Oceanographie Microbienne , Université Pierre et Marie Curie (Paris 6), Centre National de la Recherche Scientifique, Unité Mixte de Recherche , 7621 , Observatoire Oceanologique, Banyuls/mer , France
| | - Friedrich Siebert
- Institute of Chemistry, Technische Universität Berlin , Berlin 10623 , Germany.,Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik , Albert-Ludwigs-Universität Freiburg , Freiburg 79104 , Germany
| | - Peter Hildebrandt
- Institute of Chemistry, Technische Universität Berlin , Berlin 10623 , Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
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12
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Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V. Structural insights into ion conduction by channelrhodopsin 2. Science 2018; 358:358/6366/eaan8862. [PMID: 29170206 DOI: 10.1126/science.aan8862] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/30/2017] [Indexed: 11/02/2022]
Abstract
The light-gated ion channel channelrhodopsin 2 (ChR2) from Chlamydomonas reinhardtii is a major optogenetic tool. Photon absorption starts a well-characterized photocycle, but the structural basis for the regulation of channel opening remains unclear. We present high-resolution structures of ChR2 and the C128T mutant, which has a markedly increased open-state lifetime. The structure reveals two cavities on the intracellular side and two cavities on the extracellular side. They are connected by extended hydrogen-bonding networks involving water molecules and side-chain residues. Central is the retinal Schiff base that controls and synchronizes three gates that separate the cavities. Separate from this network is the DC gate that comprises a water-mediated bond between C128 and D156 and interacts directly with the retinal Schiff base. Comparison with the C128T structure reveals a direct connection of the DC gate to the central gate and suggests how the gating mechanism is affected by subtle tuning of the Schiff base's interactions.
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Affiliation(s)
- Oleksandr Volkov
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Kirill Kovalev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen, Aachen, Germany
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,ELI Beamlines, Institute of Physics, Czech Academy of Sciences, 18221 Prague, Czech Republic
| | | | | | - Roman Astashkin
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38027 Grenoble, France
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Georg Büldt
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany. .,Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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13
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Absorption and Emission Spectroscopic Investigation of Thermal Dynamics and Photo-Dynamics of the Rhodopsin Domain of the Rhodopsin-Guanylyl Cyclase from the Nematophagous Fungus Catenaria anguillulae. Int J Mol Sci 2017; 18:ijms18102099. [PMID: 28981475 PMCID: PMC5666781 DOI: 10.3390/ijms18102099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
The rhodopsin-guanylyl cyclase from the nematophagous fungus Catenaria anguillulae belongs to a recently discovered class of enzymerhodopsins and may find application as a tool in optogenetics. Here the rhodopsin domain CaRh of the rhodopsin-guanylyl cyclase from Catenaria anguillulae was studied by absorption and emission spectroscopic methods. The absorption cross-section spectrum and excitation wavelength dependent fluorescence quantum distributions of CaRh samples were determined (first absorption band in the green spectral region). The thermal stability of CaRh was studied by long-time attenuation measurements at room temperature (20.5 °C) and refrigerator temperature of 3.5 °C. The apparent melting temperature of CaRh was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 62 ± 2 °C). The photocycle dynamics of CaRh was investigated by sample excitation to the first inhomogeneous absorption band of the CaRhda dark-adapted state around 590 nm (long-wavelength tail), 530 nm (central region) and 470 nm (short-wavelength tail) and following the absorption spectra development during exposure and after exposure (time resolution 0.0125 s). The original protonated retinal Schiff base PRSBall-trans in CaRhda photo-converted reversibly to protonated retinal Schiff base PRSBall-trans,la1 with restructured surroundings (CaRhla₁ light-adapted state, slightly blue-shifted and broadened first absorption band, recovery to CaRhda with time constant of 0.8 s) and deprotonated retinal Schiff base RSB13-cis (CaRhla₂ light-adapted state, first absorption band in violet to near ultraviolet spectral region, recovery to CaRhda with time constant of 0.35 s). Long-time light exposure of light-adapted CaRhla₁ around 590, 530 and 470 nm caused low-efficient irreversible degradation to photoproducts CaRhprod. Schemes of the primary photocycle dynamics of CaRhda and the secondary photocycle dynamics of CaRhla1 are developed.
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14
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Kaufmann JCD, Krause BS, Grimm C, Ritter E, Hegemann P, Bartl FJ. Proton transfer reactions in the red light-activatable channelrhodopsin variant ReaChR and their relevance for its function. J Biol Chem 2017; 292:14205-14216. [PMID: 28659342 PMCID: PMC5572910 DOI: 10.1074/jbc.m117.779629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/27/2017] [Indexed: 11/06/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels widely used for activating selected cells in large cellular networks. ChR variants with a red-shifted absorption maximum, such as the modified Volvox carteri ChR1 red-activatable channelrhodopsin ("ReaChR," λmax = 527 nm), are of particular interest because longer wavelengths allow optical excitation of cells in deeper layers of organic tissue. In all ChRs investigated so far, proton transfer reactions and hydrogen bond changes are crucial for the formation of the ion-conducting pore and the selectivity for protons versus cations, such as Na+, K+, and Ca2+ (1). By using a combination of electrophysiological measurements and UV-visible and FTIR spectroscopy, we characterized the proton transfer events in the photocycle of ReaChR and describe their relevance for its function. 1) The central gate residue Glu130 (Glu90 in Chlamydomonas reinhardtii (Cr) ChR2) (i) undergoes a hydrogen bond change in D → K transition and (ii) deprotonates in K → M transition. Its negative charge in the open state is decisive for proton selectivity. 2) The counter-ion Asp293 (Asp253 in CrChR2) receives the retinal Schiff base proton during M-state formation. Starting from M, a photocycle branching occurs involving (i) a direct M → D transition and (ii) formation of late photointermediates N and O. 3) The DC pair residue Asp196 (Asp156 in CrChR2) deprotonates in N → O transition. Interestingly, the D196N mutation increases 15-syn-retinal at the expense of 15-anti, which is the predominant isomer in the wild type, and abolishes the peak current in electrophysiological measurements. This suggests that the peak current is formed by 15-anti species, whereas 15-syn species contribute only to the stationary current.
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Affiliation(s)
- Joel C D Kaufmann
- From the Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,.
| | | | | | | | | | - Franz J Bartl
- From the Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,; Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany.
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15
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Govorunova EG, Sineshchekov OA, Li H, Spudich JL. Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications. Annu Rev Biochem 2017; 86:845-872. [PMID: 28301742 PMCID: PMC5747503 DOI: 10.1146/annurev-biochem-101910-144233] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications. We review the currently known functions and present more in-depth assessment of three functionally and structurally distinct types discovered over the past two years: (a) anion channelrhodopsins (ACRs) from cryptophyte algae, which enable efficient optogenetic neural suppression; (b) cryptophyte cation channelrhodopsins (CCRs), structurally distinct from the green algae CCRs used extensively for neural activation and from cryptophyte ACRs; and
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Affiliation(s)
- Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
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16
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Yi A, Li H, Mamaeva N, Fernandez De Cordoba RE, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Structural Changes in an Anion Channelrhodopsin: Formation of the K and L Intermediates at 80 K. Biochemistry 2017; 56:2197-2208. [PMID: 28350445 DOI: 10.1021/acs.biochem.7b00002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A recently discovered natural family of light-gated anion channelrhodopsins (ACRs) from cryptophyte algae provides an effective means of optogenetically silencing neurons. The most extensively studied ACR is from Guillardia theta (GtACR1). Earlier studies of GtACR1 have established a correlation between formation of a blue-shifted L-like intermediate and the anion channel "open" state. To study structural changes of GtACR1 in the K and L intermediates of the photocycle, a combination of low-temperature Fourier transform infrared (FTIR) and ultraviolet-visible absorption difference spectroscopy was used along with stable-isotope retinal labeling and site-directed mutagenesis. In contrast to bacteriorhodopsin (BR) and other microbial rhodopsins, which form only a stable red-shifted K intermediate at 80 K, GtACR1 forms both stable K and L-like intermediates. Evidence includes the appearance of positive ethylenic and fingerprint vibrational bands characteristic of the L intermediate as well as a positive visible absorption band near 485 nm. FTIR difference bands in the carboxylic acid C═O stretching region indicate that several Asp/Glu residues undergo hydrogen bonding changes at 80 K. The Glu68 → Gln and Ser97 → Glu substitutions, residues located close to the retinylidene Schiff base, altered the K:L ratio and several of the FTIR bands in the carboxylic acid region. In the case of the Ser97 → Glu substitution, a significant red-shift of the absorption wavelength of the K and L intermediates occurs. Sequence comparisons suggest that L formation in GtACR1 at 80 K is due in part to the substitution of the highly conserved Leu or Ile at position 93 in helix 3 (BR sequence) with the homologous Met105 in GtACR1.
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Affiliation(s)
- Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - 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, Texas 77030, United States
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Roberto E Fernandez De Cordoba
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Johan Lugtenburg
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - 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, Texas 77030, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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17
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Krause BS, Grimm C, Kaufmann JCD, Schneider F, Sakmar TP, Bartl FJ, Hegemann P. Complex Photochemistry within the Green-Absorbing Channelrhodopsin ReaChR. Biophys J 2017; 112:1166-1175. [PMID: 28355544 PMCID: PMC5374998 DOI: 10.1016/j.bpj.2017.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/29/2016] [Accepted: 02/01/2017] [Indexed: 11/26/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-activated ion channels widely employed for photostimulation of excitable cells. This study focuses on ReaChR, a chimeric ChR variant with optimal properties for optogenetic applications. We combined electrophysiological recordings with infrared and UV-visible spectroscopic measurements to investigate photocurrents and photochemical properties of ReaChR. Our data imply that ReaChR is green-light activated (λmax = 532 nm) with a non-rhodopsin-like action spectrum peaking at 610 nm for stationary photocurrents. This unusual spectral feature is associated with photoconversion of a previously unknown light-sensitive, blue-shifted photocycle intermediate L (λmax = 495 nm), which is accumulated under continuous illumination. To explain the complex photochemical reactions, we propose a symmetrical two-cycle-model based on the two C15=N isomers of the retinal cofactor with either syn- or anti-configuration, each comprising six consecutive states D, K, L, M, N, and O. Ion conduction involves two states per cycle, the late M- (M2) with a deprotonated retinal Schiff base and the consecutive green-absorbing N-state that both equilibrate via reversible reprotonation. In our model, a fraction of the deprotonated M-intermediate of the anti-cycle may be photoconverted-as the L-state-back to its inherent dark state, or to its M-state pendant (M') of the syn-cycle. The latter reaction pathway requires a C13=C14, C15=N double-isomerization of the retinal chromophore, whereas the intracircular photoconversion of M back to D involves only one C13=C14 double-bond isomerization.
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Affiliation(s)
- Benjamin S Krause
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Christiane Grimm
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Joel C D Kaufmann
- Institute for Medical Physics and Biophysics, Charité Berlin, Berlin, Germany
| | - Franziska Schneider
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, Rockefeller University, New York, New York
| | - Franz J Bartl
- Institute for Medical Physics and Biophysics, Charité Berlin, Berlin, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
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18
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Zamani A, Sakuragi S, Ishizuka T, Yawo H. Kinetic characteristics of chimeric channelrhodopsins implicate the molecular identity involved in desensitization. Biophys Physicobiol 2017; 14:13-22. [PMID: 28409086 PMCID: PMC5289414 DOI: 10.2142/biophysico.14.0_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/29/2016] [Indexed: 12/01/2022] Open
Abstract
Channelrhodopsin (ChR)-1 and ChR2 were the first-identified members of ChRs which are a growing subfamily of microbial-type rhodopsins. Light absorption drives the generation of a photocurrent in cell membranes expressing ChR2. However, the photocurrent amplitude attenuates and becomes steady-state during prolonged irradiation. This process, called desensitization or inactivation, has been attributed to the accumulation of intermediates less conductive to cations. Here we provided evidence that the dark-adapted (DA) photocurrent before desensitization is kinetically different from the light-adapted (LA) one after desensitization, that is, the deceleration of both basal-to-conductive and conductive-to-basal transitions. When the kinetics were compared between the DA and LA photocurrents for the ChR1/2 chimeras, the transmembrane helices, TM1 and TM2, were the determinants of both basal-to-conductive and conductive-to-basal transitions, whereas TM4 may contribute to the basal-to-conductive transitions and TM5 may contribute to the conductive-to-basal transitions, respectively. The fact that the desensitization-dependent decrease of the basal-to-conductive and conductive-to-basal transitions was facilitated by the TM1 exchange from ChR2 to ChR1 and reversed by the further TM2 exchange suggests that the conformation change for the channel gating is predominantly regulated by the interaction between TM1 and TM2. Although the exchange of TM1 from ChR2 to ChR1 showed no obvious influence on the spectral sensitivity, this exchange significantly induced the desensitization-dependent blue shift. Therefore, the TM1 and 2 are the main structures involved in two features of the desensitization, the stabilization of protein conformation and the charge distribution around the retinal-Schiff base (RSB+).
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Affiliation(s)
- Alemeh Zamani
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi 980-8577, Japan
| | - Shigeo Sakuragi
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi 980-8577, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi 980-8577, Japan
| | - Hiromu Yawo
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi 980-8577, Japan.,Center for Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
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19
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Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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20
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Volz P, Krause N, Balke J, Schneider C, Walter M, Schneider F, Schlesinger R, Alexiev U. Light and pH-induced Changes in Structure and Accessibility of Transmembrane Helix B and Its Immediate Environment in Channelrhodopsin-2. J Biol Chem 2016; 291:17382-93. [PMID: 27268055 DOI: 10.1074/jbc.m115.711200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Indexed: 11/06/2022] Open
Abstract
A variant of the cation channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) was selectively labeled at position Cys-79 at the end of the first cytoplasmic loop and the beginning of transmembrane helix B with the fluorescent dye fluorescein (acetamidofluorescein). We utilized (i) time-resolved fluorescence anisotropy experiments to monitor the structural dynamics at the cytoplasmic surface close to the inner gate in the dark and after illumination in the open channel state and (ii) time-resolved fluorescence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4. The light-induced increase in final anisotropy for acetamidofluorescein bound to the channel variant with a prolonged conducting state clearly shows that the formation of the open channel state is associated with a large conformational change at the cytoplasmic surface, consistent with an outward tilt of helix B. Furthermore, results from solute accessibility studies of the cytoplasmic end of helix B suggest a pH-dependent structural heterogeneity that appears below pH 7. At pH 7.4 conformational homogeneity was observed, whereas at pH 6.0 two protein fractions exist, including one in which residue 79 is buried. This inaccessible fraction amounts to 66% in nanodiscs and 82% in micelles. Knowledge about pH-dependent structural heterogeneity may be important for CrChR2 applications in optogenetics.
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Affiliation(s)
- Pierre Volz
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Nils Krause
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Jens Balke
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Constantin Schneider
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Maria Walter
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Franziska Schneider
- the Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Ramona Schlesinger
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Ulrike Alexiev
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
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21
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Guo Y, Beyle FE, Bold BM, Watanabe HC, Koslowski A, Thiel W, Hegemann P, Marazzi M, Elstner M. Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant. Chem Sci 2016; 7:3879-3891. [PMID: 30155032 PMCID: PMC6013792 DOI: 10.1039/c6sc00468g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
We show by extensive ground state and absorption spectra simulations that the channelrhodopsin-2 active site samples three different hydrogen-bonding patterns.
In spite of considerable interest, the active site of channelrhodopsin still lacks a detailed atomistic description, the understanding of which could strongly enhance the development of novel optogenetics tools. We present a computational study combining different state-of-the-art techniques, including hybrid quantum mechanics/molecular mechanics schemes and high-level quantum chemical methods, to properly describe the hydrogen-bonding pattern between the retinal chromophore and its counterions in channelrhodopsin-2 Wild-Type and C128T mutant. Especially, we show by extensive ground state dynamics that the active site, containing a glutamic acid (E123) and a water molecule, is highly dynamic, sampling three different hydrogen-bonding patterns. This results in a broad absorption spectrum that is representative of the different structural motifs found. A comparison with bacteriorhodopsin, characterized by a pentagonal hydrogen-bonded active site structure, elucidates their different absorption properties.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Franziska E Beyle
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Beatrix M Bold
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Hiroshi C Watanabe
- Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Peter Hegemann
- Institute of Biology , Experimental Biophysics , Humboldt-Universität , Invalidenstraße 42 , D-10115 Berlin , Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Marcus Elstner
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
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22
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Abstract
After the discovery of Channelrhodopsin, a light-gated ion channel, only a few people saw the diverse range of applications for such a protein. Now, more than 10 years later Channelrhodopsins have become widely accepted as the ultimate tool to control the membrane potential of excitable cells via illumination. The demand for more application-specific Channelrhodopsin variants started a race between protein engineers to design improved variants. Even though many engineered variants have undisputable advantages compared to wild-type variants, many users are alienated by the tremendous amount of new variants and their perplexing names. Here, we review new variants whose efficacy has already been proven in neurophysiological experiments, or variants which are likely to extend the optogenetic toolbox. Variants are described based on their mechanistic and operational properties in terms of expression, kinetics, ion selectivity, and wavelength responsivity.
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Affiliation(s)
- Jonas Wietek
- Experimental Biophysics, Humboldt University Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Matthias Prigge
- Department of Neurobiology, Weizmann Institute of Science, Herzel 234, 76100, Rehovot, Israel.
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23
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Conversion of a light-driven proton pump into a light-gated ion channel. Sci Rep 2015; 5:16450. [PMID: 26597707 PMCID: PMC4657025 DOI: 10.1038/srep16450] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022] Open
Abstract
Interest in microbial rhodopsins with ion pumping activity has been revitalized in the context of optogenetics, where light-driven ion pumps are used for cell hyperpolarization and voltage sensing. We identified an opsin-encoding gene (CsR) in the genome of the arctic alga Coccomyxa subellipsoidea C-169 that can produce large photocurrents in Xenopus oocytes. We used this property to analyze the function of individual residues in proton pumping. Modification of the highly conserved proton shuttling residue R83 or its interaction partner Y57 strongly reduced pumping power. Moreover, this mutation converted CsR at moderate electrochemical load into an operational proton channel with inward or outward rectification depending on the amino acid substitution. Together with molecular dynamics simulations, these data demonstrate that CsR-R83 and its interacting partner Y57 in conjunction with water molecules forms a proton shuttle that blocks passive proton flux during the dark-state but promotes proton movement uphill upon illumination.
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24
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Bruun S, Stoeppler D, Keidel A, Kuhlmann U, Luck M, Diehl A, Geiger MA, Woodmansee D, Trauner D, Hegemann P, Oschkinat H, Hildebrandt P, Stehfest K. Light-Dark Adaptation of Channelrhodopsin Involves Photoconversion between the all-trans and 13-cis Retinal Isomers. Biochemistry 2015; 54:5389-400. [PMID: 26237332 DOI: 10.1021/acs.biochem.5b00597] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Channelrhodopsins (ChR) are light-gated ion channels of green algae that are widely used to probe the function of neuronal cells with light. Most ChRs show a substantial reduction in photocurrents during illumination, a process named "light adaptation". The main objective of this spectroscopic study was to elucidate the molecular processes associated with light-dark adaptation. Here we show by liquid and solid-state nuclear magnetic resonance spectroscopy that the retinal chromophore of fully dark-adapted ChR is exclusively in an all-trans configuration. Resonance Raman (RR) spectroscopy, however, revealed that already low light intensities establish a photostationary equilibrium between all-trans,15-anti and 13-cis,15-syn configurations at a ratio of 3:1. The underlying photoreactions involve simultaneous isomerization of the C(13)═C(14) and C(15)═N bonds. Both isomers of this DAapp state may run through photoinduced reaction cycles initiated by photoisomerization of only the C(13)═C(14) bond. RR spectroscopic experiments further demonstrated that photoinduced conversion of the apparent dark-adapted (DAapp) state to the photocycle intermediates P500 and P390 is distinctly more efficient for the all-trans isomer than for the 13-cis isomer, possibly because of different chromophore-water interactions. Our data demonstrating two complementary photocycles of the DAapp isomers are fully consistent with the existence of two conducting states that vary in quantitative relation during light-dark adaptation, as suggested previously by electrical measurements.
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Affiliation(s)
- Sara Bruun
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Daniel Stoeppler
- Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Anke Keidel
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Uwe Kuhlmann
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Meike Luck
- Humboldt-Universität zu Berlin , Institut für Biologie, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Anne Diehl
- Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Michel-Andreas Geiger
- Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - David Woodmansee
- Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstraße 5-13, 81377 München, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstraße 5-13, 81377 München, Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin , Institut für Biologie, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Katja Stehfest
- Humboldt-Universität zu Berlin , Institut für Biologie, Invalidenstrasse 42, D-10115 Berlin, Germany
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25
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Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2015. [PMID: 26216996 DOI: 10.1073/pnas.1507713112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Channelrhodopsin-2 from Chlamydomonas reinhardtii is a light-gated ion channel. Over recent years, this ion channel has attracted considerable interest because of its unparalleled role in optogenetic applications. However, despite considerable efforts, an understanding of how molecular events during the photocycle, including the retinal trans-cis isomerization and the deprotonation/reprotonation of the Schiff base, are coupled to the channel-opening mechanism remains elusive. To elucidate this question, changes of conformation and configuration of several photocycle and conducting/nonconducting states need to be determined at atomic resolution. Here, we show that such data can be obtained by solid-state NMR enhanced by dynamic nuclear polarization applied to (15)N-labeled channelrhodopsin-2 carrying 14,15-(13)C2 retinal reconstituted into lipid bilayers. In its dark state, a pure all-trans retinal conformation with a stretched C14-C15 bond and a significant out-of-plane twist of the H-C14-C15-H dihedral angle could be observed. Using a combination of illumination, freezing, and thermal relaxation procedures, a number of intermediate states was generated and analyzed by DNP-enhanced solid-state NMR. Three distinct intermediates could be analyzed with high structural resolution: the early [Formula: see text] K-like state, the slowly decaying late intermediate [Formula: see text], and a third intermediate populated only under continuous illumination conditions. Our data provide novel insight into the photoactive site of channelrhodopsin-2 during the photocycle. They further show that DNP-enhanced solid-state NMR fills the gap for challenging membrane proteins between functional studies and X-ray-based structure analysis, which is required for resolving molecular mechanisms.
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26
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Stensitzki T, Muders V, Schlesinger R, Heberle J, Heyne K. The primary photoreaction of channelrhodopsin-1: wavelength dependent photoreactions induced by ground-state heterogeneity. Front Mol Biosci 2015; 2:41. [PMID: 26258130 PMCID: PMC4510425 DOI: 10.3389/fmolb.2015.00041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/06/2015] [Indexed: 12/31/2022] Open
Abstract
The primary photodynamics of channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by VIS-pump supercontinuum probe experiments from femtoseconds to 100 picoseconds. In contrast to reported experiments on channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2), we found a clear dependence of the photoreaction dynamics on varying the excitation wavelength. Upon excitation at 500 and at 550 nm we detected different bleaching bands, and spectrally distinct photoproduct absorptions in the first picoseconds. We assign the former to the ground-state heterogeneity of a mixture of 13-cis and all-trans retinal maximally absorbing around 480 and 540 nm, respectively. At 550 nm, all-trans retinal of the ground state is almost exclusively excited. Here, we found a fast all-trans to 13-cis isomerization process to a hot and spectrally broad P1 photoproduct with a time constant of (100 ± 50) fs, followed by photoproduct relaxation with time constants of (500 ± 100) fs and (5 ± 1) ps. The remaining fraction relaxes back to the parent ground state with time constants of (500 ± 100) fs and (5 ± 1) ps. Upon excitation at 500 nm a mixture of both chromophore conformations is excited, resulting in overlapping reaction dynamics with additional time constants of <300 fs, (1.8 ± 0.3) ps and (90 ± 25) ps. A new photoproduct Q is formed absorbing at around 600 nm. Strong coherent oscillatory signals were found pertaining up to several picoseconds. We determined low frequency modes around 200 cm−1, similar to those reported for bacteriorhodopsin.
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Affiliation(s)
- Till Stensitzki
- Institute of Experimental Physics, Free University Berlin Berlin, Germany
| | - Vera Muders
- Institute of Experimental Physics, Free University Berlin Berlin, Germany
| | - Ramona Schlesinger
- Institute of Experimental Physics, Free University Berlin Berlin, Germany
| | - Joachim Heberle
- Institute of Experimental Physics, Free University Berlin Berlin, Germany
| | - Karsten Heyne
- Institute of Experimental Physics, Free University Berlin Berlin, Germany
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Ritter E, Puskar L, Bartl FJ, Aziz EF, Hegemann P, Schade U. Time-resolved infrared spectroscopic techniques as applied to channelrhodopsin. Front Mol Biosci 2015. [PMID: 26217670 PMCID: PMC4493399 DOI: 10.3389/fmolb.2015.00038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Among optogenetic tools, channelrhodopsins, the light gated ion channels of the plasma membrane from green algae, play the most important role. Properties like channel selectivity, timing parameters or color can be influenced by the exchange of selected amino acids. Although widely used, in the field of neurosciences for example, there is still little known about their photocycles and the mechanism of ion channel gating and conductance. One of the preferred methods for these studies is infrared spectroscopy since it allows observation of proteins and their function at a molecular level and in near-native environment. The absorption of a photon in channelrhodopsin leads to retinal isomerization within femtoseconds, the conductive states are reached in the microsecond time scale and the return into the fully dark-adapted state may take more than minutes. To be able to cover all these time regimes, a range of different spectroscopical approaches are necessary. This mini-review focuses on time-resolved applications of the infrared technique to study channelrhodopsins and other light triggered proteins. We will discuss the approaches with respect to their suitability to the investigation of channelrhodopsin and related proteins.
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Affiliation(s)
- Eglof Ritter
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ljiljana Puskar
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
| | - Franz J Bartl
- Institut für medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Emad F Aziz
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany ; Fachbereich Physik, Freie Universität Berlin Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ulrich Schade
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
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Takemoto M, Kato HE, Koyama M, Ito J, Kamiya M, Hayashi S, Maturana AD, Deisseroth K, Ishitani R, Nureki O. Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening. PLoS One 2015; 10:e0131094. [PMID: 26114863 PMCID: PMC4482709 DOI: 10.1371/journal.pone.0131094] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/28/2015] [Indexed: 11/25/2022] Open
Abstract
Channelrhodopsin (ChR) is a light-gated cation channel that responds to blue light. Since ChR can be readily expressed in specific neurons to precisely control their activities by light, it has become a powerful tool in neuroscience. Although the recently solved crystal structure of a chimeric ChR, C1C2, provided the structural basis for ChR, our understanding of the molecular mechanism of ChR still remains limited. Here we performed electrophysiological analyses and all-atom molecular dynamics (MD) simulations, to investigate the importance of the intracellular and central constrictions of the ion conducting pore observed in the crystal structure of C1C2. Our electrophysiological analysis revealed that two glutamate residues, Glu122 and Glu129, in the intracellular and central constrictions, respectively, should be deprotonated in the photocycle. The simulation results suggested that the deprotonation of Glu129 in the central constriction leads to ion leakage in the ground state, and implied that the protonation of Glu129 is important for preventing ion leakage in the ground state. Moreover, we modeled the 13-cis retinal bound; i.e., activated C1C2, and performed MD simulations to investigate the conformational changes in the early stage of the photocycle. Our simulations suggested that retinal photoisomerization induces the conformational change toward channel opening, including the movements of TM6, TM7 and TM2. These insights into the dynamics of the ground states and the early photocycle stages enhance our understanding of the channel function of ChR.
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Affiliation(s)
- Mizuki Takemoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Hideaki E. Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Michio Koyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Jumpei Ito
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464–8601, Japan
| | - Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606–8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606–8502, Japan
| | - Andrés D. Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464–8601, Japan
| | - Karl Deisseroth
- Department of Bioengineering and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States of America
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
- * E-mail: (ON); (RI)
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
- * E-mail: (ON); (RI)
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29
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Venkatachalam V, Cohen AE. Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J 2015; 107:1554-63. [PMID: 25296307 DOI: 10.1016/j.bpj.2014.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/02/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
To study the impact of neural activity on cellular physiology, one would like to combine precise control of firing patterns with highly sensitive probes of cellular physiology. Light-gated ion channels, e.g., Channelrhodopsin-2, enable precise control of firing patterns; green fluorescent protein-based reporters, e.g., the GCaMP6f Ca(2+) reporter, enable highly sensitive probing of cellular physiology. However, for most actuator-reporter combinations, spectral overlap prevents straightforward combination within a single cell. Here we explore multiwavelength control of channelrhodopsins to circumvent this limitation. The "stoplight" technique described in this article uses channelrhodopsin variants that are opened by blue light and closed by orange light. Cells are illuminated with constant blue light to excite fluorescence of a green fluorescent protein-based reporter. Modulated illumination with orange light negatively regulates activation of the channelrhodopsin. We performed detailed photophysical characterization and kinetic modeling of four candidate stoplight channelrhodopsins. The variant with the highest contrast, sdChR(C138S,E154A), enabled all-optical measurements of activity-induced calcium transients in cultured rat hippocampal neurons, although cell-to-cell variation in expression levels presents a challenge for quantification.
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Affiliation(s)
- Veena Venkatachalam
- Biophysics Program, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland.
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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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Szundi I, Li H, Chen E, Bogomolni R, Spudich JL, Kliger DS. Platymonas subcordiformis Channelrhodopsin-2 Function: I. THE PHOTOCHEMICAL REACTION CYCLE. J Biol Chem 2015; 290:16573-84. [PMID: 25971972 DOI: 10.1074/jbc.m114.631614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 11/06/2022] Open
Abstract
The photocycle kinetics of Platymonas subcordiformis channelrhodopsin-2 (PsChR2), among the most highly efficient light-gated cation channels and the most blue-shifted channelrhodopsin, was studied by time-resolved absorption spectroscopy in the 340-650-nm range and in the 100-ns to 3-s time window. Global exponential fitting of the time dependence of spectral changes revealed six lifetimes: 0.60 μs, 5.3 μs, 170 μs, 1.4 ms, 6.7 ms, and 1.4 s. The sequential intermediates derived for a single unidirectional cycle scheme based on these lifetimes were found to contain mixtures of K, L, M, O, and P molecular states, named in analogy to photointermediates in the bacteriorhodopsin photocycle. The photochemistry is described by the superposition of two independent parallel photocycles. The analysis revealed that 30% of the photoexcited receptor molecules followed Cycle 1 through the K, M, O, and P states, whereas 70% followed Cycle 2 through the K, L, M, and O states. The recovered state, R, is spectrally close, but not identical, to the dark state on the seconds time scale. The two-cycle model of this high efficiency channelrhodopsin-2 (ChR) opens new perspectives in understanding the mechanism of channelrhodopsin function.
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Affiliation(s)
- Istvan Szundi
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064 and
| | - Hai Li
- the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030
| | - Eefei Chen
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064 and
| | - Roberto Bogomolni
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064 and
| | - John L Spudich
- the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030
| | - David S Kliger
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064 and
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Szundi I, Bogomolni R, Kliger DS. Platymonas subcordiformis Channelrhodopsin-2 (PsChR2) Function: II. RELATIONSHIP OF THE PHOTOCHEMICAL REACTION CYCLE TO CHANNEL CURRENTS. J Biol Chem 2015; 290:16585-94. [PMID: 25971978 DOI: 10.1074/jbc.m115.653071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 11/06/2022] Open
Abstract
Channelrhodopsins, such as the algal phototaxis receptor Platymonas subcordiformis channelrhodopsin-2 (PsChR2), are light-gated cation channels used as optogenetic tools for photocontrol of membrane potential in living cells. Channelrhodopsin (ChR)-mediated photocurrent responses are complex and poorly understood, exhibiting alterations in peak current amplitude, extents and kinetics of inactivation, and kinetics of the recovery of the prestimulus dark current that are sensitive to duration and frequency of photostimuli. From the analysis of time-resolved optical absorption data, presented in the accompanying article, we derived a two-cycle model that describes the photocycles of PsChR2. Here, we applied the model to evaluate the transient currents produced by PsChR2 expressed in HEK293 cells under both fast laser excitation and step-like continuous illumination. Interpretation of the photocurrents in terms of the photocycle kinetics indicates that the O states in both cycles are responsible for the channel current and fit the current transients under the different illumination regimes. The peak and plateau currents in response to a single light step, a train of light pulses, and a light step superimposed on a continuous light background observed for ChR2 proteins are explained in terms of contributions from the two parallel photocycles. The analysis shows that the peak current desensitization and recovery phenomena are inherent properties of the photocycles. The light dependence of desensitization is reproduced and explained by the time evolution of the concentration transients in response to step-like illumination. Our data show that photocycle kinetic parameters are sufficient to explain the complex dependence of photocurrent responses to photostimuli.
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Affiliation(s)
- Istvan Szundi
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
| | - Roberto Bogomolni
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
| | - David S Kliger
- From the Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
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Hososhima S, Sakai S, Ishizuka T, Yawo H. Kinetic evaluation of photosensitivity in bi-stable variants of chimeric channelrhodopsins. PLoS One 2015; 10:e0119558. [PMID: 25789474 PMCID: PMC4366085 DOI: 10.1371/journal.pone.0119558] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/14/2015] [Indexed: 11/30/2022] Open
Abstract
Channelrhodopsin-1 and 2 (ChR1 and ChR2) form cation channels that are gated by light through an unknown mechanism. We tested the DC-gate hypothesis that C167 and D195 are involved in the stabilization of the cation-permeable state of ChRWR/C1C2 which consists of TM1-5 of ChR1 and TM6-7 of ChR2 and ChRFR which consists of TM1-2 of ChR1 and TM3-7 of ChR2. The cation permeable state of each ChRWR and ChRFR was markedly prolonged in the order of several tens of seconds when either C167 or D195 position was mutated to alanine (A). Therefore, the DC-gate function was conserved among these chimeric ChRs. We next investigated the kinetic properties of the ON/OFF response of these bi-stable ChR mutants as they are important in designing the photostimulation protocols for the optogenetic manipulation of neuronal activities. The turning-on rate constant of each photocurrent followed a linear relationship to 0–0.12 mWmm−2 of blue LED light or to 0–0.33 mWmm−2 of cyan LED light. Each photocurrent of bi-stable ChR was shut off to the non-conducting state by yellow or orange LED light in a manner dependent on the irradiance. As the magnitude of the photocurrent was mostly determined by the turning-on rate constant and the irradiation time, the minimal irradiance that effectively evoked an action potential (threshold irradiance) was decreased with time only if the neuron, which expresses bi-stable ChRs, has a certain large membrane time constant (eg. τm > 20 ms). On the other hand, in another group of neurons, the threshold irradiance was not dependent on the irradiation time. Based on these quantitative data, we would propose that these bi-stable ChRs would be most suitable for enhancing the intrinsic activity of excitatory pyramidal neurons at a minimal magnitude of irradiance.
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Affiliation(s)
- Shoko Hososhima
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
- Core Research of Evolutional Science & Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Seiichiro Sakai
- Core Research of Evolutional Science & Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- Laboratory for Local Neuronal Circuits, Brain Science Institute, RIKEN, Wako, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
- Core Research of Evolutional Science & Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Hiromu Yawo
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
- Core Research of Evolutional Science & Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- Center for Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- * E-mail:
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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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Jeschke M, Moser T. Considering optogenetic stimulation for cochlear implants. Hear Res 2015; 322:224-34. [PMID: 25601298 DOI: 10.1016/j.heares.2015.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/09/2014] [Accepted: 01/08/2015] [Indexed: 02/04/2023]
Abstract
Electrical cochlear implants are by far the most successful neuroprostheses and have been implanted in over 300,000 people worldwide. Cochlear implants enable open speech comprehension in most patients but are limited in providing music appreciation and speech understanding in noisy environments. This is generally considered to be due to low frequency resolution as a consequence of wide current spread from stimulation contacts. Accordingly, the number of independently usable stimulation channels is limited to less than a dozen. As light can be conveniently focused, optical stimulation might provide an alternative approach to cochlear implants with increased number of independent stimulation channels. Here, we focus on summarizing recent work on optogenetic stimulation as one way to develop optical cochlear implants. We conclude that proof of principle has been presented for optogenetic stimulation of the cochlea and central auditory neurons in rodents as well as for the technical realization of flexible μLED-based multichannel cochlear implants. Still, much remains to be done in order to advance the technique for auditory research and even more for eventual clinical translation. This article is part of a Special Issue entitled <Lasker Award>.
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Affiliation(s)
- Marcus Jeschke
- Institute for Auditory Neuroscience, University Medical Center Goettingen, Goettingen, Germany; Auditory Neuroscience Group, German Primate Center, Goettingen, Germany.
| | - Tobias Moser
- Institute for Auditory Neuroscience, University Medical Center Goettingen, Goettingen, Germany; Auditory Neuroscience Group, German Primate Center, Goettingen, Germany; Bernstein Focus for Neurotechnology, University of Göttingen, Goettingen, Germany; Collaborative Research Center 889, University of Goettingen Medical Center, Goettingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University of Goettingen, Goettingen, Germany.
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Li H, Govorunova EG, Sineshchekov OA, Spudich JL. Role of a helix B lysine residue in the photoactive site in channelrhodopsins. Biophys J 2014; 106:1607-17. [PMID: 24739160 DOI: 10.1016/j.bpj.2014.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/20/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022] Open
Abstract
In most studied microbial rhodopsins two conserved carboxylic acid residues (the homologs of Asp-85 and Asp-212 in bacteriorhodopsin) and an arginine residue (the homolog of Arg-82) form a complex counterion to the protonated retinylidene Schiff base, and neutralization of the negatively charged carboxylates causes red shifts of the absorption maximum. In contrast, the corresponding neutralizing mutations in some relatively low-efficiency channelrhodopsins (ChRs) result in blue shifts. These ChRs do not contain a lysine residue in the second helix, conserved in higher efficiency ChRs (Lys-132 in the crystallized ChR chimera). By action spectroscopy of photoinduced channel currents in HEK293 cells and absorption spectroscopy of detergent-purified pigments, we found that in tested ChRs the Lys-132 homolog controls the direction of spectral shifts in the mutants of the photoactive site carboxylic acid residues. Analysis of double mutants shows that red spectral shifts occur when this Lys is present, whether naturally or by mutagenesis, and blue shifts occur when it is replaced with a neutral residue. A neutralizing mutation of the Lys-132 homolog alone caused a red spectral shift in high-efficiency ChRs, whereas its introduction into low-efficiency ChR1 from Chlamydomonas augustae (CaChR1) caused a blue shift. Taking into account that the effective charge of the carboxylic acid residues is a key factor in microbial rhodopsin spectral tuning, these findings suggest that the Lys-132 homolog modulates their pKa values. On the other hand, mutation of the Arg-82 homolog that fulfills this role in bacteriorhodopsin caused minimal spectral changes in the tested ChRs. Titration revealed that the pKa of the Asp-85 homolog in CaChR1 lies in the alkaline region unlike in most studied microbial rhodopsins, but is substantially decreased by introduction of a Lys-132 homolog or neutralizing mutation of the Asp-212 homolog. In the three ChRs tested the Lys-132 homolog also alters channel current kinetics.
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Affiliation(s)
- Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas.
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Müller M, Bamann C, Bamberg E, Kühlbrandt W. Light-induced helix movements in channelrhodopsin-2. J Mol Biol 2014; 427:341-9. [PMID: 25451024 DOI: 10.1016/j.jmb.2014.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/10/2014] [Accepted: 11/02/2014] [Indexed: 11/26/2022]
Abstract
Channelrhodopsin-2 (ChR2) is a cation-selective light-gated channel from Chlamydomonas reinhardtii (Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, et al. Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci USA 2003;100:13940-5), which has become a powerful tool in optogenetics. Two-dimensional crystals of the slow photocycling C128T ChR2 mutant were exposed to 473 nm light and rapidly frozen to trap the open state. Projection difference maps at 6Å resolution show the location, extent and direction of light-induced conformational changes in ChR2 during the transition from the closed state to the ion-conducting open state. Difference peaks indicate that transmembrane helices (TMHs) TMH2, TMH6 and TMH7 reorient or rearrange during the photocycle. No major differences were found near TMH3 and TMH4 at the dimer interface. While conformational changes in TMH6 and TMH7 are known from other microbial-type rhodopsins, our results indicate that TMH2 has a key role in light-induced channel opening and closing in ChR2.
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Affiliation(s)
- Maria Müller
- Max Planck Institute of Biophysics Department of Structural Biology, Max von Laue Strasse 3, 60438 Frankfurt, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics Department of Biophysical Chemistry, Max von Laue Strasse 3, 60438 Frankfurt, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics Department of Biophysical Chemistry, Max von Laue Strasse 3, 60438 Frankfurt, Germany
| | - Werner Kühlbrandt
- Max Planck Institute of Biophysics Department of Structural Biology, Max von Laue Strasse 3, 60438 Frankfurt, Germany.
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Muders V, Kerruth S, Lórenz-Fonfría VA, Bamann C, Heberle J, Schlesinger R. Resonance Raman and FTIR spectroscopic characterization of the closed and open states of channelrhodopsin-1. FEBS Lett 2014; 588:2301-6. [PMID: 24859039 DOI: 10.1016/j.febslet.2014.05.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 11/17/2022]
Abstract
Channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) is a light-activated cation channel, which is a promising optogenetic tool. We show by resonance Raman spectroscopy and retinal extraction followed by high pressure liquid chromatography (HPLC) that the isomeric ratio of all-trans to 13-cis of solubilized channelrhodopsin-1 is with 70:30 identical to channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Critical frequency shifts in the retinal vibrations are identified in the Raman spectrum upon transition to the open (conductive P2(380)) state. Fourier transform infrared spectroscopy (FTIR) spectra indicate different structures of the open states in the two channelrhodopsins as reflected by the amide I bands and the protonation pattern of acidic amino acids.
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Affiliation(s)
- Vera Muders
- Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Silke Kerruth
- Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Christian Bamann
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, 60438 Frankfurt/Main, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
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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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Structural differences between the closed and open states of channelrhodopsin-2 as observed by EPR spectroscopy. FEBS Lett 2013; 587:3309-13. [DOI: 10.1016/j.febslet.2013.08.043] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/13/2013] [Accepted: 08/29/2013] [Indexed: 11/21/2022]
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Grote M, Engelhard M, Hegemann P. Of ion pumps, sensors and channels - perspectives on microbial rhodopsins between science and history. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:533-45. [PMID: 23994288 DOI: 10.1016/j.bbabio.2013.08.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 10/26/2022]
Abstract
We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl⁻ into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. 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)
- Mathias Grote
- Institut für Philosophie, Literatur-, Wissenschafts- und Technikgeschichte, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Martin Engelhard
- Max Planck Institut für Molekulare Physiologie, Otto Hahn Str. 11, 44227 Dortmund, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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