1
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Bühl E, Resler T, Lam R, Asido M, Bamberg E, Schlesinger R, Bamann C, Heberle J, Wachtveitl J. Assessing the Role of R120 in the Gating of CrChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds. J Am Chem Soc 2023; 145:21832-21840. [PMID: 37773976 DOI: 10.1021/jacs.3c05399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The light-gated ion channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) is the most frequently used optogenetic tool in neurosciences. However, the precise molecular mechanism of the channel opening and the correlation among retinal isomerization, the photocycle, and the channel activity of the protein are missing. Here, we present electrophysiological and spectroscopic investigations on the R120H variant of CrChR2. R120 is a key residue in an extended network linking the retinal chromophore to several gates of the ion channel. We show that despite the deficient channel activity, the photocycle of the variant is intact. In a comparative study for R120H and the wild type, we resolve the vibrational changes in the spectral range of the retinal and amide I bands across the time range from femtoseconds to seconds. Analysis of the amide I mode reveals a significant impairment of the ultrafast protein response after retinal excitation. We conclude that channel opening in CrChR2 is prepared immediately after retinal excitation. Additionally, chromophore isomerization is essential for both photocycle and channel activities, although both processes can occur independently.
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Affiliation(s)
- Elena Bühl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Tom Resler
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Rebecca Lam
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
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2
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Shibata K, Oda K, Nishizawa T, Hazama Y, Ono R, Takaramoto S, Bagherzadeh R, Yawo H, Nureki O, Inoue K, Akiyama H. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. J Am Chem Soc 2023; 145:10779-10789. [PMID: 37129501 DOI: 10.1021/jacs.3c01879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.
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Affiliation(s)
- Keisei Shibata
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Kazumasa Oda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Yuji Hazama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Ryohei Ono
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Shunki Takaramoto
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hidefumi Akiyama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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3
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Sugiura M, Ishikawa K, Katayama K, Sumii Y, Abe-Yoshizumi R, Tsunoda SP, Furutani Y, Shibata N, Brown LS, Kandori H. Unusual Photoisomerization Pathway in a Near-Infrared Light Absorbing Enzymerhodopsin. J Phys Chem Lett 2022; 13:9539-9543. [PMID: 36201035 DOI: 10.1021/acs.jpclett.2c02334] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial and animal rhodopsins possess retinal chromophores which capture light and normally photoisomerize from all-trans to 13-cis and from 11-cis to all-trans-retinal, respectively. Here, we show that a near-infrared light-absorbing enzymerhodopsin from Obelidium mucronatum (OmNeoR) contains the all-trans form in the dark but isomerizes into the 7-cis form upon illumination. The photoproduct (λmax = 372 nm; P372) possesses a deprotonated Schiff base, and the system exhibits a bistable nature. The photochemistry of OmNeoR was arrested at <270 K, indicating the presence of a potential barrier in the excited state. Formation of P372 is accompanied by protonation changes of protonated carboxylic acids and peptide backbone changes of an α-helix. Photoisomerization from the all-trans to 7-cis retinal conformation rarely occurs in any solvent and protein environments; thus, the present study reports on a novel photochemistry mediated by a microbial rhodopsin, leading from the all-trans to 7-cis form selectively.
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Affiliation(s)
- Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kazuki Ishikawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Sumii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Norio Shibata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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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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Becker‐Baldus J, Leeder A, Brown LJ, Brown RCD, Bamann C, Glaubitz C. The Desensitized Channelrhodopsin‐2 Photointermediate Contains 13 ‐
cis
, 15 ‐
syn
Retinal Schiff Base. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Johanna Becker‐Baldus
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Alexander Leeder
- Department of Chemistry University of Southampton Southampton SO17 1BJ UK
| | - Lynda J. Brown
- Department of Chemistry University of Southampton Southampton SO17 1BJ UK
| | | | - Christian Bamann
- Max-Planck-Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
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6
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Becker-Baldus J, Leeder A, Brown LJ, Brown RCD, Bamann C, Glaubitz C. The Desensitized Channelrhodopsin-2 Photointermediate Contains 13 -cis, 15 -syn Retinal Schiff Base. Angew Chem Int Ed Engl 2021; 60:16442-16447. [PMID: 33973334 PMCID: PMC8362212 DOI: 10.1002/anie.202015797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/18/2021] [Indexed: 11/13/2022]
Abstract
Channelrhodopsin‐2 (ChR2) is a light‐gated cation channel and was used to lay the foundations of optogenetics. Its dark state X‐ray structure has been determined in 2017 for the wild‐type, which is the prototype for all other ChR variants. However, the mechanistic understanding of the channel function is still incomplete in terms of structural changes after photon absorption by the retinal chromophore and in the framework of functional models. Hence, detailed information needs to be collected on the dark state as well as on the different photointermediates. For ChR2 detailed knowledge on the chromophore configuration in the different states is still missing and a consensus has not been achieved. Using DNP‐enhanced solid‐state MAS NMR spectroscopy on proteoliposome samples, we unambiguously determined the chromophore configuration in the desensitized state, and we show that this state occurs towards the end of the photocycle.
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Affiliation(s)
- Johanna Becker-Baldus
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Alexander Leeder
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Lynda J Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Richard C D Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Christian Bamann
- Max-Planck-Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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7
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Kaufmann JCD, Krause BS, Adam S, Ritter E, Schapiro I, Hegemann P, Bartl FJ. Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR. Biophys J 2020; 119:705-716. [PMID: 32697975 DOI: 10.1016/j.bpj.2020.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022] Open
Abstract
The function of photoreceptors relies on efficient transfer of absorbed light energy from the chromophore to the protein to drive conformational changes that ultimately generate an output signal. In retinal-binding proteins, mainly two mechanisms exist to store the photon energy after photoisomerization: 1) conformational distortion of the prosthetic group retinal, and 2) charge separation between the protonated retinal Schiff base (RSBH+) and its counterion complex. Accordingly, energy transfer to the protein is achieved by chromophore relaxation and/or reduction of the charge separation in the RSBH+-counterion complex. Combining FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the widely used, red-activatable Volvox carteri channelrhodopsin-1 derivate ReaChR that energy storage and transfer into the protein depends on the protonation state of glutamic acid E163 (Ci1), one of the counterions of the RSBH+. Ci1 retains a pKa of 7.6 so that both its protonated and deprotonated forms equilibrate at physiological conditions. Protonation of Ci1 leads to a rigid hydrogen-bonding network in the active-site region. This stabilizes the distorted conformation of the retinal after photoactivation and decelerates energy transfer into the protein by impairing the release of the strain energy. In contrast, with deprotonated Ci1 or removal of the Ci1 glutamate side chain, the hydrogen-bonded system is less rigid, and energy transfer by chromophore relaxation is accelerated. Based on the hydrogen out-of-plane (HOOP) band decay kinetics, we determined the activation energy for these processes in dependence of the Ci1 protonation state.
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Affiliation(s)
- Joel C D Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité Berlin, Berlin, Germany
| | - Benjamin S Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eglof Ritter
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Franz J Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany.
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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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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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10
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Atomistic Insight into the Role of Threonine 127 in the Functional Mechanism of Channelrhodopsin-2. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9224905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Channelrhodopsins (ChRs) belong to the unique class of light-gated ion channels. The structure of channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) has been resolved, but the mechanistic link between light-induced isomerization of the chromophore retinal and channel gating remains elusive. Replacements of residues C128 and D156 (DC gate) resulted in drastic effects in channel closure. T127 is localized close to the retinal Schiff base and links the DC gate to the Schiff base. The homologous residue in bacteriorhodopsin (T89) has been shown to be crucial for the visible absorption maximum and dark–light adaptation, suggesting an interaction with the retinylidene chromophore, but the replacement had little effect on photocycle kinetics and proton pumping activity. Here, we show that the T127A and T127S variants of CrChR2 leave the visible absorption maximum unaffected. We inferred from hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and resonance Raman spectroscopy that the hydroxylic side chain of T127 is hydrogen-bonded to E123 and the latter is hydrogen-bonded to the retinal Schiff base. The C=N–H vibration of the Schiff base in the T127A variant was 1674 cm−1, the highest among all rhodopsins reported to date. We also found heterogeneity in the Schiff base ground state vibrational properties due to different rotamer conformations of E123. The photoreaction of T127A is characterized by a long-lived P2380 state during which the Schiff base is deprotonated. The conservative replacement of T127S hardly affected the photocycle kinetics. Thus, we inferred that the hydroxyl group at position 127 is part of the proton transfer pathway from D156 to the Schiff base during rise of the P3530 intermediate. This finding provides molecular reasons for the evolutionary conservation of the chemically homologous residues threonine, serine, and cysteine at this position in all channelrhodopsins known so far.
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11
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Oppermann J, Fischer P, Silapetere A, Liepe B, Rodriguez-Rozada S, Flores-Uribe J, Schiewer E, Keidel A, Vierock J, Kaufmann J, Broser M, Luck M, Bartl F, Hildebrandt P, Wiegert JS, Béjà O, Hegemann P, Wietek J. MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nat Commun 2019; 10:3315. [PMID: 31346176 PMCID: PMC6658528 DOI: 10.1038/s41467-019-11322-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. Here we describe a metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of optogenetic tools from metagenomic databases and enhance general understanding of ChR function.
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Affiliation(s)
- Johannes Oppermann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Paul Fischer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Arita Silapetere
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Bernhard Liepe
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - José Flores-Uribe
- Technion-Israel Institute of Technology, 32000, Haifa, Israel
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Anke Keidel
- Institute for Chemistry, Physical Chemistry/Biophysical Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Joel Kaufmann
- Institute for Biology, Biophysical Chemistry, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Meike Luck
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Franz Bartl
- Institute for Biology, Biophysical Chemistry, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Peter Hildebrandt
- Institute for Chemistry, Physical Chemistry/Biophysical Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Oded Béjà
- Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany.
| | - Jonas Wietek
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany.
- Department of Neurobiology, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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12
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Saita M, Pranga-Sellnau F, Resler T, Schlesinger R, Heberle J, Lorenz-Fonfria VA. Photoexcitation of the P4480 State Induces a Secondary Photocycle That Potentially Desensitizes Channelrhodopsin-2. J Am Chem Soc 2018; 140:9899-9903. [DOI: 10.1021/jacs.8b03931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Mattia Saita
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Franziska Pranga-Sellnau
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Tom Resler
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Victor A. Lorenz-Fonfria
- Institute of Molecular Science, Universitat de València, 46980 Paterna, Spain
- Department of Biochemistry and Molecular Biology, Universitat de València, 46100 Burjassot, Spain
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13
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Ding X, Sun C, Cui H, Chen S, Gao Y, Yang Y, Wang J, He X, Iuga D, Tian F, Watts A, Zhao X. Functional roles of tyrosine 185 during the bacteriorhodopsin photocycle as revealed by in situ spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1006-1014. [PMID: 29800547 DOI: 10.1016/j.bbabio.2018.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/15/2018] [Accepted: 05/20/2018] [Indexed: 01/22/2023]
Abstract
Tyrosine 185 (Y185), one of the aromatic residues within the retinal (Ret) chromophore binding pocket in helix F of bacteriorhodopsin (bR), is highly conserved among the microbial rhodopsin family proteins. Many studies have investigated the functions of Y185, but its underlying mechanism during the bR photocycle remains unclear. To address this research gap, in situ two-dimensional (2D) magic-angle spinning (MAS) solid-state NMR (ssNMR) of specifically labelled bR, combined with light-induced transient absorption change measurements, dynamic light scattering (DLS) measurements, titration analysis and site-directed mutagenesis, was used to elucidate the functional roles of Y185 during the bR photocycle in the native membrane environment. Different interaction modes were identified between Y185 and the Ret chromophore in the dark-adapted (inactive) state and M (active) state, indicating that Y185 may serve as a rotamer switch maintaining the protein dynamics, and plays an important role in the efficient proton-pumping mechanism in the bR purple membrane.
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Affiliation(s)
- Xiaoyan Ding
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, PA 17033-0850, USA
| | - Chao Sun
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Haolin Cui
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Sijin Chen
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Yujiao Gao
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Yanan Yang
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Juan Wang
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Xiao He
- Shang Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, PR China
| | - Dinu Iuga
- The UK 850 MHz Solid-State NMR Facility, Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, PA 17033-0850, USA.
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Xin Zhao
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China.
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14
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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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15
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Abstract
Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. In a 4-µs MM simulation of a dark-adapted ChR2 dimer, water entered the vestibules of the closed channel. Retinal all-trans to 13-cis isomerization, simulated with metadynamics, triggered a major restructuring of the charge cluster forming the channel gate. On a microsecond time scale, water penetrated the gate to form a membrane-spanning preopen pore between helices H1, H2, H3, and H7. This influx of water into an ion-impermeable preopen pore is consistent with time-resolved infrared spectroscopy and electrophysiology experiments. In the retinal 13-cis state, D253 emerged as the proton acceptor of the Schiff base. Upon proton transfer from the Schiff base to D253, modeled by QM/MM simulations, we obtained an early-M/P2390-like intermediate. Rapid rotation of the unprotonated Schiff base toward the cytosolic side effectively prevents its reprotonation from the extracellular side. From MM and QM simulations, we gained detailed insight into the mechanism of ChR2 photoactivation and early events in pore formation. By rearranging the network of charges and hydrogen bonds forming the gate, water emerges as a key player in light-driven ChR2 channel opening.
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Affiliation(s)
- Albert Ardevol
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
- Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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16
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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17
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Guo Y, Wolff FE, Schapiro I, Elstner M, Marazzi M. Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2. Phys Chem Chem Phys 2018; 20:27501-27509. [DOI: 10.1039/c8cp05210g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Franziska E. Wolff
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research
- Institute of Chemistry
- Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Marcus Elstner
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
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18
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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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19
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Urmann D, Lorenz C, Linker SM, Braun M, Wachtveitl J, Bamann C. Photochemical Properties of the Red-shifted Channelrhodopsin Chrimson. Photochem Photobiol 2017; 93:782-795. [DOI: 10.1111/php.12741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/02/2017] [Indexed: 01/03/2023]
Affiliation(s)
- David Urmann
- Institute of Physical and Theoretical Chemistry; Johann Wolfgang Goethe University Frankfurt; Frankfurt am Main Germany
| | - Charlotte Lorenz
- Department of Biophysical Chemistry; Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Stephanie M. Linker
- Department of Biophysical Chemistry; Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry; Johann Wolfgang Goethe University Frankfurt; Frankfurt am Main Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Johann Wolfgang Goethe University Frankfurt; Frankfurt am Main Germany
| | - Christian Bamann
- Department of Biophysical Chemistry; Max Planck Institute of Biophysics; Frankfurt am Main Germany
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20
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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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21
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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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22
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Niho A, Yoshizawa S, Tsukamoto T, Kurihara M, Tahara S, Nakajima Y, Mizuno M, Kuramochi H, Tahara T, Mizutani Y, Sudo Y. Demonstration of a Light-Driven SO42– Transporter and Its Spectroscopic Characteristics. J Am Chem Soc 2017; 139:4376-4389. [DOI: 10.1021/jacs.6b12139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akiko Niho
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Marie Kurihara
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shinya Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yu Nakajima
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hikaru Kuramochi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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23
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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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24
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Ding X, Wang H, Peng B, Cui H, Gao Y, Iuga D, Judge PJ, Li G, Watts A, Zhao X. Mediation mechanism of tyrosine 185 on the retinal isomerization equilibrium and the proton release channel in the seven-transmembrane receptor bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1786-1795. [DOI: 10.1016/j.bbabio.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 01/17/2023]
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25
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Chen H, Zhu H, Liu P, Li L. A study on the conformational space of the all-trans retinal deprotonated Schiff base. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Yi A, Mamaeva N, Li H, Spudich JL, Rothschild KJ. Resonance Raman Study of an Anion Channelrhodopsin: Effects of Mutations near the Retinylidene Schiff Base. Biochemistry 2016; 55:2371-80. [PMID: 27039989 DOI: 10.1021/acs.biochem.6b00104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optogenetics relies on the expression of specific microbial rhodopsins in the neuronal plasma membrane. Most notably, this includes channelrhodopsins, which when heterologously expressed in neurons function as light-gated cation channels. Recently, a new class of microbial rhodopsins, termed anion channel rhodopsins (ACRs), has been discovered. These proteins function as efficient light-activated channels strictly selective for anions. They exclude the flow of protons and other cations and cause hyperpolarization of the membrane potential in neurons by allowing the inward flow of chloride ions. In this study, confocal near-infrared resonance Raman spectroscopy (RRS) along with hydrogen/deuterium exchange, retinal analogue substitution, and site-directed mutagenesis were used to study the retinal structure as well as its interactions with the protein in the unphotolyzed state of an ACR from Guillardia theta (GtACR1). These measurements reveal that (i) the retinal chromophore exists as an all-trans configuration with a protonated Schiff base (PSB) very similar to that of bacteriorhodopsin (BR), (ii) the chromophore RRS spectrum is insensitive to changes in pH from 3 to 11, whereas above this pH the Schiff base (SB) is deprotonated, (iii) when Ser97, the homologue to Asp85 in BR, is replaced with a Glu, it remains in a neutral form (i.e., as a carboxylic acid) but is deprotonated at higher pH to form a blue-shifted species, (iv) Asp234, the homologue of the protonated retinylidene SB counterion Asp212 in BR, does not serve as the primary counteranion for the protonated SB, and (v) substitution of Glu68 with an Gln increases the pH at which SB deprotonation is observed. These results suggest that Glu68 and Asp234 located near the SB exist in a neutral state in unphotolyzed GtACR1 and indicate that other unidentified negative charges stabilize the protonated state of the GtACR1 SB.
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Affiliation(s)
- Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Natalia Mamaeva
- 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
| | - 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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27
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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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28
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Ji ZG, Wang H. ChR2 transgenic animals in peripheral sensory system: Sensing light as various sensations. Life Sci 2016; 150:95-102. [PMID: 26903290 DOI: 10.1016/j.lfs.2016.02.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/31/2015] [Accepted: 02/13/2016] [Indexed: 12/28/2022]
Abstract
Since the introduction of Channelrhodopsin-2 (ChR2) to neuroscience, optogenetics technology was developed, making it possible to activate specific neurons or circuits with spatial and temporal precision. Various ChR2 transgenic animal models have been generated and are playing important roles in revealing the mechanisms of neural activities, mapping neural circuits, controlling the behaviors of animals as well as exploring new strategy for treating the neurological diseases in both central and peripheral nervous system. An animal including humans senses environments through Aristotle's five senses (sight, hearing, smell, taste and touch). Usually, each sense is associated with a kind of sensory organ (eyes, ears, nose, tongue and skin). Is it possible that one could hear light, smell light, taste light and touch light? When ChR2 is targeted to different peripheral sensory neurons by viral vectors or generating ChR2 transgenic animals, the animals can sense the light as various sensations such as hearing, touch, pain, smell and taste. In this review, we focus on ChR2 transgenic animals in the peripheral nervous system. Firstly the working principle of ChR2 as an optogenetic actuator is simply described. Then the current transgenic animal lines where ChR2 was expressed in peripheral sensory neurons are presented and the findings obtained by these animal models are reviewed.
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Affiliation(s)
- Zhi-Gang Ji
- The Department of Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Hongxia Wang
- The Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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29
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Koua FHM, Kandori H. Light-induced structural changes during early photo-intermediates of the eubacterial Cl−pump Fulvimarina rhodopsin observed by FTIR difference spectroscopy. RSC Adv 2016. [DOI: 10.1039/c5ra19363j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fulvimarina pelagirhodopsin (FR) is a member of inward eubacterial light-activated Cl−translocating rhodopsins (ClR) that were found recently in marine bacteria.
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Affiliation(s)
| | - Hideki Kandori
- OptoBioTechnology Research Center
- Nagoya Institute of Technology
- 466-8555 Nagoya
- Japan
- Department of Frontier Materials
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30
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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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31
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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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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: 9] [Impact Index Per Article: 1.0] [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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33
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Resler T, Schultz BJ, Lórenz-Fonfría VA, Schlesinger R, Heberle J. Kinetic and vibrational isotope effects of proton transfer reactions in channelrhodopsin-2. Biophys J 2015; 109:287-97. [PMID: 26200864 PMCID: PMC4621815 DOI: 10.1016/j.bpj.2015.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-gated cation channels. After blue-light excitation, the protein undergoes a photocycle with different intermediates. Here, we have recorded transient absorbance changes of ChR2 from Chlamydomonas reinhardtii in the visible and infrared regions with nanosecond time resolution, the latter being accomplished using tunable quantum cascade lasers. Because proton transfer reactions play a key role in channel gating, we determined vibrational as well as kinetic isotope effects (VIEs and KIEs) of carboxylic groups of various key aspartic and glutamic acid residues by monitoring their C=O stretching vibrations in H2O and in D2O. D156 exhibits a substantial KIE (>2) in its deprotonation and reprotonation, which substantiates its role as the internal proton donor to the retinal Schiff base. The unusual VIE of D156, upshifted from 1736 cm(-1) to 1738 cm(-1) in D2O, was scrutinized by studying the D156E variant. The C=O stretch of E156 shifted down by 8 cm(-1) in D2O, providing evidence for the accessibility of the carboxylic group. The C=O stretching band of E90 exhibits a VIE of 9 cm(-1) and a KIE of ∼2 for the de- and the reprotonation reactions during the lifetime of the late desensitized state. The KIE of 1 determined in the time range from 20 ns to 5 ms is incompatible with early deprotonation of E90.
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Affiliation(s)
- Tom Resler
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | | | | | - Ramona Schlesinger
- Genetic Biophysics at Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany.
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34
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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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35
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Ogren JI, Yi A, Mamaev S, Li H, Spudich JL, Rothschild KJ. Proton transfers in a channelrhodopsin-1 studied by Fourier transform infrared (FTIR) difference spectroscopy and site-directed mutagenesis. J Biol Chem 2015; 290:12719-30. [PMID: 25802337 DOI: 10.1074/jbc.m114.634840] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Channelrhodopsin-1 from the alga Chlamydomonas augustae (CaChR1) is a low-efficiency light-activated cation channel that exhibits properties useful for optogenetic applications such as a slow light inactivation and a red-shifted visible absorption maximum as compared with the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Previously, both resonance Raman and low-temperature FTIR difference spectroscopy revealed that unlike CrChR2, CaChR1 under our conditions exhibits an almost pure all-trans retinal composition in the unphotolyzed ground state and undergoes an all-trans to 13-cis isomerization during the primary phototransition typical of other microbial rhodopsins such as bacteriorhodopsin (BR). Here, we apply static and rapid-scan FTIR difference spectroscopy along with site-directed mutagenesis to characterize the proton transfer events occurring upon the formation of the long-lived conducting P2 (380) state of CaChR1. Assignment of carboxylic C=O stretch bands indicates that Asp-299 (homolog to Asp-212 in BR) becomes protonated and Asp-169 (homolog to Asp-85 in BR) undergoes a net change in hydrogen bonding relative to the unphotolyzed ground state of CaChR1. These data along with earlier FTIR measurements on the CaChR1 → P1 transition are consistent with a two-step proton relay mechanism that transfers a proton from Glu-169 to Asp-299 during the primary phototransition and from the Schiff base to Glu-169 during P2 (380) formation. The unusual charge neutrality of both Schiff base counterions in the P2 (380) conducting state suggests that these residues may function as part of a cation selective filter in the open channel state of CaChR1 as well as other low-efficiency ChRs.
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Affiliation(s)
- John I Ogren
- From the Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts 02215 and
| | - Adrian Yi
- From the Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts 02215 and
| | - Sergey Mamaev
- From the Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts 02215 and
| | - Hai Li
- the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center, Houston, Texas 77030
| | - John L Spudich
- the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center, Houston, Texas 77030
| | - Kenneth J Rothschild
- From the Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts 02215 and
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36
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Inoue K, Tsukamoto T, Shimono K, Suzuki Y, Miyauchi S, Hayashi S, Kandori H, Sudo Y. Converting a Light-Driven Proton Pump into a Light-Gated Proton Channel. J Am Chem Soc 2015; 137:3291-9. [DOI: 10.1021/ja511788f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Keiichi Inoue
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Tsukamoto
- Division
of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry,
and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazumi Shimono
- Faculty
of Pharmaceutical Sciences, Toho University, Funabashi 274-8510, Japan
| | - Yuto Suzuki
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Seiji Miyauchi
- Faculty
of Pharmaceutical Sciences, Toho University, Funabashi 274-8510, Japan
| | - Shigehiko Hayashi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuki Sudo
- Division
of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry,
and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
- Japan Science and Technology Agency, CREST, K’s Gobancho, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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37
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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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38
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Dokukina I, Weingart O. Spectral properties and isomerisation path of retinal in C1C2 channelrhodopsin. Phys Chem Chem Phys 2015; 17:25142-50. [DOI: 10.1039/c5cp02650d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed torsion profiles along the reactive coordinate in S1reveal a two-path deactivation mechanism for retinal in C1C2 channelrhodopsin.
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Affiliation(s)
- I. Dokukina
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - O. Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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39
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Ogren JI, Yi A, Mamaev S, Li H, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Comparison of the structural changes occurring during the primary phototransition of two different channelrhodopsins from Chlamydomonas algae. Biochemistry 2014; 54:377-88. [PMID: 25469620 PMCID: PMC4303311 DOI: 10.1021/bi501243y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Channelrhodopsins
(ChRs) from green flagellate algae function as
light-gated ion channels when expressed heterologously in mammalian
cells. Considerable interest has focused on understanding the molecular
mechanisms of ChRs to bioengineer their properties for specific optogenetic
applications such as elucidating the function of specific neurons
in brain circuits. While most studies have used channelrhodopsin-2
from Chlamydomonas reinhardtii (CrChR2), in this work low-temperature Fourier transform infrared-difference
spectroscopy is applied to study the conformational changes occurring
during the primary phototransition of the red-shifted ChR1 from Chlamydomonas augustae (CaChR1). Substitution
with isotope-labeled retinals or the retinal analogue A2, site-directed
mutagenesis, hydrogen–deuterium exchange, and H218O exchange were used to assign bands to the retinal
chromophore, protein, and internal water molecules. The primary phototransition
of CaChR1 at 80 K involves, in contrast to that of CrChR2, almost exclusively an all-trans to 13-cis isomerization of the retinal chromophore,
as in the primary phototransition of bacteriorhodopsin (BR). In addition,
significant differences are found for structural changes of the protein
and internal water(s) compared to those of CrChR2,
including the response of several Asp/Glu residues to retinal isomerization.
A negative amide II band is identified in the retinal ethylenic stretch
region of CaChR1, which reflects along with amide
I bands alterations in protein backbone structure early in the photocycle.
A decrease in the hydrogen bond strength of a weakly hydrogen bonded
internal water is detected in both CaChR1 and CrChR2, but the bands are much broader in CrChR2, indicating a more heterogeneous environment. Mutations involving
residues Glu169 and Asp299 (homologues of the Asp85 and Asp212 Schiff
base counterions, respectively, in BR) lead to the conclusion that
Asp299 is protonated during P1 formation and suggest that these residues
interact through a strong hydrogen bond that facilitates the transfer
of a proton from Glu169.
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Affiliation(s)
- John I Ogren
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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40
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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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41
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Rozin R, Wand A, Jung KH, Ruhman S, Sheves M. pH Dependence of Anabaena Sensory Rhodopsin: Retinal Isomer Composition, Rate of Dark Adaptation, and Photochemistry. J Phys Chem B 2014; 118:8995-9006. [DOI: 10.1021/jp504688y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rinat Rozin
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amir Wand
- Institute
of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Sanford Ruhman
- Institute
of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Mordechai Sheves
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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42
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Ogren JI, Mamaev S, Russano D, Li H, Spudich JL, Rothschild KJ. Retinal chromophore structure and Schiff base interactions in red-shifted channelrhodopsin-1 from Chlamydomonas augustae. Biochemistry 2014; 53:3961-70. [PMID: 24869998 PMCID: PMC4072394 DOI: 10.1021/bi500445c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Channelrhodopsins (ChRs), which form
a distinct branch of the microbial
rhodopsin family, control phototaxis in green algae. Because ChRs
can be expressed and function in neuronal membranes as light-gated
cation channels, they have rapidly become an important optogenetic
tool in neurobiology. While channelrhodopsin-2 from the unicellular
alga Chlamydomonas reinhardtii (CrChR2) is the most commonly used and extensively studied optogenetic
ChR, little is known about the properties of the diverse group of
other ChRs. In this study, near-infrared confocal resonance Raman
spectroscopy along with hydrogen–deuterium exchange and site-directed
mutagenesis were used to study the structure of red-shifted ChR1 from Chlamydomonas augustae (CaChR1). These
measurements reveal that (i) CaChR1 has an all-trans-retinal structure similar to those of the light-driven
proton pump bacteriorhodopsin (BR) and sensory rhodopsin II but different
from that of the mixed retinal composition of CrChR2,
(ii) lowering the pH from 7 to 2 or substituting neutral residues
for Glu169 or Asp299 does not significantly shift the ethylenic stretch
frequency more than 1–2 cm–1 in contrast
to BR in which a downshift of 7–9 cm–1 occurs
reflecting neutralization of the Asp85 counterion, and (iii) the CaChR1 protonated Schiff base (SB) has stronger hydrogen
bonding than BR. A model is proposed to explain these results whereby
at pH 7 the predominant counterion to the SB is Asp299 (the homologue
to Asp212 in BR) while Glu169 (the homologue to Asp85 in BR) exists
in a neutral state. We observe an unusual constancy of the resonance
Raman spectra over the broad range from pH 9 to 2 and discuss its
implications. These results are in accord with recent visible absorption
and current measurements of CaChR1 [Sineshchekov,
O. A., et al. (2013) Intramolecular proton transfer in channelrhodopsins. Biophys. J. 104, 807–817; Li, H., et al. (2014) Role
of a helix B lysine residue in the photoactive site in channelrhodopsins. Biophys. J. 106, 1607–1617].
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Affiliation(s)
- John I Ogren
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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43
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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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44
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Ito S, Kato HE, Taniguchi R, Iwata T, Nureki O, Kandori H. Water-containing hydrogen-bonding network in the active center of channelrhodopsin. J Am Chem Soc 2014; 136:3475-82. [PMID: 24512107 DOI: 10.1021/ja410836g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2-6 water vibrations) and animal (6-8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel.
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Affiliation(s)
- Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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45
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 785] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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46
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Del Val C, Royuela-Flor J, Milenkovic S, Bondar AN. Channelrhodopsins: a bioinformatics perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:643-55. [PMID: 24252597 DOI: 10.1016/j.bbabio.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 12/28/2022]
Abstract
Channelrhodopsins are microbial-type rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs its dynamics and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications. Here we use bioinformatics methods to derive accurate alignments of channelrhodopsin sequences, assess the sequence conservation patterns and find conserved motifs in channelrhodopsins, and use homology modeling to construct three-dimensional structural models of channelrhodopsins. The analyses reveal that helices C and D of channelrhodopsins contain Cys, Ser, and Thr groups that can engage in both intra- and inter-helical hydrogen bonds. We propose that these polar groups participate in inter-helical hydrogen-bonding clusters important for the protein conformational dynamics and for the local water interactions. 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)
- Coral Del Val
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain.
| | - José Royuela-Flor
- Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany
| | - Stefan Milenkovic
- Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany.
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47
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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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48
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Govorunova EG, Sineshchekov OA, Li H, Janz R, Spudich JL. Characterization of a highly efficient blue-shifted channelrhodopsin from the marine alga Platymonas subcordiformis. J Biol Chem 2013; 288:29911-22. [PMID: 23995841 DOI: 10.1074/jbc.m113.505495] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Rhodopsin photosensors of phototactic algae act as light-gated cation channels when expressed in animal cells. These proteins (channelrhodopsins) are extensively used for millisecond scale photocontrol of cellular functions (optogenetics). We report characterization of PsChR, one of the phototaxis receptors in the alga Platymonas (Tetraselmis) subcordiformis. PsChR exhibited ∼3-fold higher unitary conductance and greater relative permeability for Na(+) ions, as compared with the most frequently used channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Photocurrents generated by PsChR in HEK293 cells showed lesser inactivation and faster peak recovery than those by CrChR2. Their maximal spectral sensitivity was at 445 nm, making PsChR the most blue-shifted channelrhodopsin so far identified. The λmax of detergent-purified PsChR was 437 nm at neutral pH and exhibited red shifts (pKa values at 6.6 and 3.8) upon acidification. The purified pigment undergoes a photocycle with a prominent red-shifted intermediate whose formation and decay kinetics match the kinetics of channel opening and closing. The rise and decay of an M-like intermediate prior to formation of this putative conductive state were faster than in CrChR2. PsChR mediated sufficient light-induced membrane depolarization in cultured hippocampal neurons to trigger reliable repetitive spiking at the upper threshold frequency of the neurons. At low frequencies spiking probability decreases less with PsChR than with CrChR2 because of the faster recovery of the former. Its blue-shifted absorption enables optogenetics at wavelengths even below 400 nm. A combination of characteristics makes PsChR important for further research on structure-function relationships in ChRs and potentially useful for optogenetics, especially for combinatorial applications when short wavelength excitation is required.
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Affiliation(s)
- Elena G Govorunova
- From the Department of Biochemistry & Molecular Biology, Center for Membrane Biology and
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49
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Watanabe HC, Welke K, Sindhikara DJ, Hegemann P, Elstner M. Towards an Understanding of Channelrhodopsin Function: Simulations Lead to Novel Insights of the Channel Mechanism. J Mol Biol 2013; 425:1795-814. [DOI: 10.1016/j.jmb.2013.01.033] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/24/2013] [Accepted: 01/28/2013] [Indexed: 01/25/2023]
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50
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Neumann-Verhoefen MK, Neumann K, Bamann C, Radu I, Heberle J, Bamberg E, Wachtveitl J. Ultrafast Infrared Spectroscopy on Channelrhodopsin-2 Reveals Efficient Energy Transfer from the Retinal Chromophore to the Protein. J Am Chem Soc 2013; 135:6968-76. [DOI: 10.1021/ja400554y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mirka-Kristin Neumann-Verhoefen
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Karsten Neumann
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Ionela Radu
- Department
of Physics, Molecular
Biospectroscopy, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Experimental
Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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