1
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Oldemeyer S, La Greca M, Langner P, Lê Công KL, Schlesinger R, Heberle J. Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells. J Am Chem Soc 2024; 146:19118-19127. [PMID: 38950551 DOI: 10.1021/jacs.4c03891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.
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Affiliation(s)
- Sabine Oldemeyer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Mariafrancesca La Greca
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Karoline-Luisa Lê Công
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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2
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Temperini ME, Polito R, Intze A, Gillibert R, Berkmann F, Baldassarre L, Giliberti V, Ortolani M. A mid-infrared laser microscope for the time-resolved study of light-induced protein conformational changes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:064102. [PMID: 37862502 DOI: 10.1063/5.0136676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/26/2023] [Indexed: 10/22/2023]
Abstract
We have developed a confocal laser microscope operating in the mid-infrared range for the study of light-sensitive proteins, such as rhodopsins. The microscope features a co-aligned infrared and visible illumination path for the selective excitation and probing of proteins located in the IR focus only. An external-cavity tunable quantum cascade laser provides a wavelength tuning range (5.80-6.35 µm or 1570-1724 cm-1) suitable for studying protein conformational changes as a function of time delay after visible light excitation with a pulsed LED. Using cryogen-free detectors, the relative changes in the infrared absorption of rhodopsin thin films around 10-4 have been observed with a time resolution down to 30 ms. The measured full-width at half maximum of the Airy disk at λ = 6.08 µm in transmission mode with a confocal arrangement of apertures is 6.6 µm or 1.1λ. Dark-adapted sample replacement at the beginning of each photocycle is then enabled by exchanging the illuminated thin-film location with the microscope mapping stage synchronized to data acquisition and LED excitation and by averaging hundreds of time traces acquired in different nearby locations within a homogeneous film area. We demonstrate that this instrument provides crucial advantages for time-resolved IR studies of rhodopsin thin films with a slow photocycle. Time-resolved studies of inhomogeneous samples may also be possible with the presented instrument.
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Affiliation(s)
- Maria Eleonora Temperini
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Raffaella Polito
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Antonia Intze
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Raymond Gillibert
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Fritz Berkmann
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Leonetta Baldassarre
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Valeria Giliberti
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Michele Ortolani
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
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3
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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4
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Walter M, Schlesinger R. Nanodisc Reconstitution of Channelrhodopsins Heterologously Expressed in Pichia pastoris for Biophysical Investigations. Methods Mol Biol 2021; 2191:29-48. [PMID: 32865737 DOI: 10.1007/978-1-0716-0830-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
For a successful characterization of channelrhodopsins with biophysical methods like FTIR, Raman, EPR and NMR spectroscopy and X-ray crystallography, large amounts of purified protein are requested. For proteins of eukaryotic origin, which are poorly expressing in bacterial systems or not at all, the yeast Pichia pastoris represents a promising alternative for overexpression. Here we describe the methods for cloning, overexpression and mutagenesis as well as the purification procedures for channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2), channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) and the scaffold protein MSP1D1 for reconstitution of the membrane proteins into nanodiscs. Finally, protocols are provided to study CaChR1 by FTIR difference spectroscopy and by time-resolved UV/Vis spectroscopy.
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Affiliation(s)
- Maria Walter
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany.
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5
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Wang R, Mu L, Bao Y, Lin H, Ji T, Shi Y, Zhu J, Wu W. Holistically Engineered Polymer-Polymer and Polymer-Ion Interactions in Biocompatible Polyvinyl Alcohol Blends for High-Performance Triboelectric Devices in Self-Powered Wearable Cardiovascular Monitorings. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002878. [PMID: 32596980 DOI: 10.1002/adma.202002878] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/11/2020] [Indexed: 05/08/2023]
Abstract
The capability of sensor systems to efficiently scavenge their operational power from stray, weak environmental energies through sustainable pathways could enable viable schemes for self-powered health diagnostics and therapeutics. Triboelectric nanogenerators (TENG) can effectively transform the otherwise wasted environmental, mechanical energy into electrical power. Recent advances in TENGs have resulted in a significant boost in output performance. However, obstacles hindering the development of efficient triboelectric devices based on biocompatible materials continue to prevail. Being one of the most widely used polymers for biomedical applications, polyvinyl alcohol (PVA) presents exciting opportunities for biocompatible, wearable TENGs. Here, the holistic engineering and systematic characterization of the impact of molecular and ionic fillers on PVA blends' triboelectric performance is presented for the first time. Triboelectric devices built with optimized PVA-gelatin composite films exhibit stable and robust triboelectricity outputs. Such wearable devices can detect the imperceptible skin deformation induced by the human pulse and capture the cardiovascular information encoded in the pulse signals with high fidelity. The gained fundamental understanding and demonstrated capabilities enable the rational design and holistic engineering of novel materials for more capable biocompatible triboelectric devices that can continuously monitor vital physiological signals for self-powered health diagnostics and therapeutics.
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Affiliation(s)
- Ruoxing Wang
- School of Industrial Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Flex Laboratory, Purdue University, West Lafayette, IN, 47907, USA
| | - Liwen Mu
- Intelligent Composites Laboratory, Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
- Division of Machine Elements, Luleå University of Technology, Luleå, 97187, Sweden
| | - Yukai Bao
- School of Industrial Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Han Lin
- Intelligent Composites Laboratory, Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Tuo Ji
- Intelligent Composites Laboratory, Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Yijun Shi
- Division of Machine Elements, Luleå University of Technology, Luleå, 97187, Sweden
| | - Jiahua Zhu
- Intelligent Composites Laboratory, Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Wenzhuo Wu
- School of Industrial Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
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6
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Tomida S, Ito S, Mato T, Furutani Y, Inoue K, Kandori H. Infrared spectroscopic analysis on structural changes around the protonated Schiff base upon retinal isomerization in light-driven sodium pump KR2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148190. [DOI: 10.1016/j.bbabio.2020.148190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/30/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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7
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Inoue K, Tsunoda SP, Singh M, Tomida S, Hososhima S, Konno M, Nakamura R, Watanabe H, Bulzu PA, Banciu HL, Andrei AŞ, Uchihashi T, Ghai R, Béjà O, Kandori H. Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H + pumps. SCIENCE ADVANCES 2020; 6:eaaz2441. [PMID: 32300653 PMCID: PMC7148096 DOI: 10.1126/sciadv.aaz2441] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/17/2020] [Indexed: 05/05/2023]
Abstract
Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H+ pump. The mutation of a cytoplasmic glutamate inhibited inward H+ transport, suggesting that it functions as a cytoplasmic H+ acceptor. The function, trimeric structure, and H+ transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H+ pumping microbial rhodopsins, implying that they evolved convergently. The inward H+ pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- 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
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Corresponding author. (K.I.); (H.K.)
| | - 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
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Masae Konno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ryoko Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan
| | - Paul-Adrian Bulzu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Horia L. Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- Corresponding author. (K.I.); (H.K.)
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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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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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Senger M, Eichmann V, Laun K, Duan J, Wittkamp F, Knör G, Apfel UP, Happe T, Winkler M, Heberle J, Stripp ST. How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer. J Am Chem Soc 2019; 141:17394-17403. [PMID: 31580662 PMCID: PMC6823627 DOI: 10.1021/jacs.9b09225] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Hydrogenases are metalloenzymes that
catalyze the conversion of
protons and molecular hydrogen, H2. [FeFe]-hydrogenases
show particularly high rates of hydrogen turnover and have inspired
numerous compounds for biomimetic H2 production. Two decades
of research on the active site cofactor of [FeFe]-hydrogenases have
put forward multiple models of the catalytic proceedings. In comparison,
our understanding of proton transfer is poor. Previously, residues
were identified forming a hydrogen-bonding network between active
site cofactor and bulk solvent; however, the exact mechanism of catalytic
proton transfer remained inconclusive. Here, we employ in
situ infrared difference spectroscopy on the [FeFe]-hydrogenase
from Chlamydomonas reinhardtii evaluating dynamic
changes in the hydrogen-bonding network upon photoreduction. While
proton transfer appears to be impaired in the oxidized state (Hox), the presented data support continuous proton transfer
in the reduced state (Hred). Our analysis allows for
a direct, molecular unique assignment to individual amino acid residues.
We found that transient protonation changes of glutamic acid residue
E141 and, most notably, arginine R148 facilitate bidirectional proton
transfer in [FeFe]-hydrogenases.
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Affiliation(s)
- Moritz Senger
- Experimental Molecular Biophysics, Department of Physics , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Viktor Eichmann
- Experimental Molecular Biophysics, Department of Physics , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Konstantin Laun
- Experimental Molecular Biophysics, Department of Physics , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | | | | | - Günther Knör
- Institute of Inorganic Chemistry , Johannes Kepler Universität Linz , Altenberger Straße 69 , 4040 Linz , Austria
| | | | | | | | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Sven Timo Stripp
- Experimental Molecular Biophysics, Department of Physics , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
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11
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Unifying photocycle model for light adaptation and temporal evolution of cation conductance in channelrhodopsin-2. Proc Natl Acad Sci U S A 2019; 116:9380-9389. [PMID: 31004059 PMCID: PMC6510988 DOI: 10.1073/pnas.1818707116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Although channelrhodopsin (ChR) is a widely applied light-activated ion channel, important properties such as light adaptation, photocurrent inactivation, and alteration of the ion selectivity during continuous illumination are not well understood from a molecular perspective. Herein, we address these open questions using single-turnover electrophysiology, time-resolved step-scan FTIR, and Raman spectroscopy of fully dark-adapted ChR2. This yields a unifying parallel photocycle model integrating now all so far controversial discussed data. In dark-adapted ChR2, the protonated retinal Schiff base chromophore (RSBH+) adopts an all-trans,C=N-anti conformation only. Upon light activation, a branching reaction into either a 13-cis,C=N-anti or a 13-cis,C=N-syn retinal conformation occurs. The anti-cycle features sequential H+ and Na+ conductance in a late M-like state and an N-like open-channel state. In contrast, the 13-cis,C=N-syn isomer represents a second closed-channel state identical to the long-lived P480 state, which has been previously assigned to a late intermediate in a single-photocycle model. Light excitation of P480 induces a parallel syn-photocycle with an open-channel state of small conductance and high proton selectivity. E90 becomes deprotonated in P480 and stays deprotonated in the C=N-syn cycle. Deprotonation of E90 and successive pore hydration are crucial for late proton conductance following light adaptation. Parallel anti- and syn-photocycles now explain inactivation and ion selectivity changes of ChR2 during continuous illumination, fostering the future rational design of optogenetic tools.
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Watari M, Ikuta T, Yamada D, Shihoya W, Yoshida K, Tsunoda SP, Nureki O, Kandori H. Spectroscopic study of the transmembrane domain of a rhodopsin-phosphodiesterase fusion protein from a unicellular eukaryote. J Biol Chem 2019; 294:3432-3443. [PMID: 30622140 DOI: 10.1074/jbc.ra118.006277] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/31/2018] [Indexed: 02/02/2023] Open
Abstract
The choanoflagellate Salpingoeca rosetta contains a chimeric rhodopsin protein composed of an N-terminal rhodopsin (Rh) domain and a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain. The Rh-PDE enzyme light-dependently decreases the concentrations of cyclic nucleotides such as cGMP and cAMP. Photoexcitation of purified full-length Rh-PDE yields an "M" intermediate with a deprotonated Schiff base, and its recovery is much faster than that of the enzyme domain. To gain structural and mechanistic insights into the Rh domain, here we expressed and purified the transmembrane domain of Rh-PDE, Rh-PDE(TMD), and analyzed it with transient absorption, light-induced difference UV-visible, and FTIR spectroscopy methods. These analyses revealed that the "K" intermediate forms within 0.005 ms and converts into the M intermediate with a time constant of 4 ms, with the latter returning to the original state within 4 s. FTIR spectroscopy revealed that all-trans to 13-cis photoisomerization occurs as the primary event during which chromophore distortion is located at the middle of the polyene chain, allowing the Schiff base to form a stronger hydrogen bond. We also noted that the peptide backbone of the α-helix becomes deformed upon M intermediate formation. Results from site-directed mutagenesis suggested that Glu-164 is protonated and that Asp-292 acts as the only Schiff base counterion in Rh-PDE. A strong reduction of enzymatic activity in a D292N variant, but not in an E164Q variant, indicated an important catalytic role of the negative charge at Asp-292. Our findings provide further mechanistic insights into rhodopsin-mediated, light-dependent regulation of second-messenger levels in eukaryotic microbes.
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Affiliation(s)
- Masahito Watari
- From the Department of Life Science and Applied Chemistry and
| | - Tatsuya Ikuta
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Daichi Yamada
- From the Department of Life Science and Applied Chemistry and
| | - Wataru Shihoya
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Kazuho Yoshida
- From the Department of Life Science and Applied Chemistry and
| | - Satoshi P Tsunoda
- From the Department of Life Science and Applied Chemistry and.,the 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
| | - Osamu Nureki
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Hideki Kandori
- From the Department of Life Science and Applied Chemistry and .,the OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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13
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Adam S, Bondar AN. Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin. PLoS One 2018; 13:e0201298. [PMID: 30086158 PMCID: PMC6080761 DOI: 10.1371/journal.pone.0201298] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Channelrhodopsins are light-sensitive ion channels whose reaction cycles involve conformation-coupled transfer of protons. Understanding how channelrhodopsins work is important for applications in optogenetics, where light activation of these proteins triggers changes in the transmembrane potential across excitable membranes. A fundamental open question is how the protein environment ensures that unproductive proton transfer from the retinal Schiff base to the nearby carboxylate counterion is avoided in the resting state of the channel. To address this question, we performed combined quantum mechanical/molecular mechanical proton transfer calculations with explicit treatment of the surrounding lipid membrane. The free energy profiles computed for proton transfer to the counterion, either via a direct jump or mediated by a water molecule, demonstrate that, when retinal is all-trans, water and protein electrostatic interactions largely favour the protonated retinal Schiff base state. We identified a conserved lysine group as an essential structural element for the proton transfer energetics in channelrhodopsins.
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Affiliation(s)
- Suliman Adam
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
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14
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Ito S, Kandori H, Lorenz-Fonfria VA. Potential Second-Harmonic Ghost Bands in Fourier Transform Infrared (FT-IR) Difference Spectroscopy of Proteins. APPLIED SPECTROSCOPY 2018; 72:956-963. [PMID: 29350538 DOI: 10.1177/0003702818757521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fourier transform infrared (FT-IR) difference absorption spectroscopy is a common method for studying the structural and dynamical aspects behind protein function. In particular, the 2800-1800 cm-1 spectral range has been used to obtain information about internal (deuterated) water molecules, as well as site-specific details about cysteine residues and chemically modified and artificial amino acids. Here, we report on the presence of ghost bands in cryogenic light-induced FT-IR difference spectra of the protein bacteriorhodopsin. The presence of these ghost bands can be particularly problematic in the 2800-1900 cm-1 region, showing intensities similar to O-D vibrations from water molecules. We demonstrate that they arise from second harmonics from genuine chromophore bands located in the 1400-850 cm-1 region, generated by double-modulation artifacts caused from reflections of the IR beam at the sample and at the cryostat windows back to the interferometer (inter-reflections). The second-harmonic ghost bands can be physically removed by placing an optical filter of suitable cutoff in the beam path, but at the cost of losing part of the multiplexing advantage of FT-IR spectroscopy. We explored alternatives to the use of optical filters. Tilting the cryostat windows was effective in reducing the intensity of the second harmonic artifacts but tilting the sample windows was not, presumably by their close proximity to the focal point of the IR beam. We also introduce a simple numerical post-processing approach that can partially, but not fully, correct for second-harmonic ghost bands in FT-IR difference spectra.
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Affiliation(s)
- Shota Ito
- 1 Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- 1 Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- 2 OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Victor A Lorenz-Fonfria
- 3 Institute of Molecular Science (ICMol), Universitat de València, Paterna, Spain
- 4 Department of Biochemistry and Molecular Biology, Universitat de València, Burjassot, Spain
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15
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Senger M, Mebs S, Duan J, Shulenina O, Laun K, Kertess L, Wittkamp F, Apfel UP, Happe T, Winkler M, Haumann M, Stripp ST. Protonation/reduction dynamics at the [4Fe-4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases. Phys Chem Chem Phys 2018; 20:3128-3140. [PMID: 28884175 DOI: 10.1039/c7cp04757f] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The [FeFe]-hydrogenases of bacteria and algae are the most efficient hydrogen conversion catalysts in nature. Their active-site cofactor (H-cluster) comprises a [4Fe-4S] cluster linked to a unique diiron site that binds three carbon monoxide (CO) and two cyanide (CN-) ligands. Understanding microbial hydrogen conversion requires elucidation of the interplay of proton and electron transfer events at the H-cluster. We performed real-time spectroscopy on [FeFe]-hydrogenase protein films under controlled variation of atmospheric gas composition, sample pH, and reductant concentration. Attenuated total reflection Fourier-transform infrared spectroscopy was used to monitor shifts of the CO/CN- vibrational bands in response to redox and protonation changes. Three different [FeFe]-hydrogenases and several protein and cofactor variants were compared, including element and isotopic exchange studies. A protonated equivalent (HoxH) of the oxidized state (Hox) was found, which preferentially accumulated at acidic pH and under reducing conditions. We show that the one-electron reduced state Hred' represents an intrinsically protonated species. Interestingly, the formation of HoxH and Hred' was independent of the established proton pathway to the diiron site. Quantum chemical calculations of the respective CO/CN- infrared band patterns favored a cysteine ligand of the [4Fe-4S] cluster as the protonation site in HoxH and Hred'. We propose that proton-coupled electron transfer facilitates reduction of the [4Fe-4S] cluster and prevents premature formation of a hydride at the catalytic diiron site. Our findings imply that protonation events both at the [4Fe-4S] cluster and at the diiron site of the H-cluster are important in the hydrogen conversion reaction of [FeFe]-hydrogenases.
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Affiliation(s)
- Moritz Senger
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, 14195 Berlin, Germany.
| | - Stefan Mebs
- Department of Physics, Biophysics of Metalloenzymes, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany.
| | - Olga Shulenina
- Faculty of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Konstantin Laun
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, 14195 Berlin, Germany.
| | - Leonie Kertess
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany.
| | - Florian Wittkamp
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany.
| | - Martin Winkler
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany.
| | - Michael Haumann
- Department of Physics, Biophysics of Metalloenzymes, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, 14195 Berlin, Germany.
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16
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Schultz BJ, Mohrmann H, Lorenz-Fonfria VA, Heberle J. Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:666-674. [PMID: 28110813 DOI: 10.1016/j.saa.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm-1) and on the CO rebinding reaction of myoglobin (1960-1840cm-1), at a spectral resolution of 1cm-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10-4 are detected in single-shot experiments at t>1μs, and of 5×10-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H2O).
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Affiliation(s)
- Bernd-Joachim Schultz
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hendrik Mohrmann
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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17
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Kaneko A, Inoue K, Kojima K, Kandori H, Sudo Y. Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering. Biophys Rev 2017; 9:861-876. [PMID: 29178082 DOI: 10.1007/s12551-017-0335-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Technological progress has enabled the successful application of functional conversion to a variety of biological molecules, such as nucleotides and proteins. Such studies have revealed the functionally essential elements of these engineered molecules, which are difficult to characterize at the level of an individual molecule. The functional conversion of biological molecules has also provided a strategy for their rational and atomistic design. The engineered molecules can be used in studies to improve our understanding of their biological functions and to develop protein-based tools. In this review, we introduce the functional conversion of membrane-embedded photoreceptive retinylidene proteins (also called rhodopsins) and discuss these proteins mainly on the basis of results obtained from our own studies. This information provides insights into the molecular mechanism of light-induced protein functions and their use in optogenetics, a technology which involves the use of light to control biological activities.
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Affiliation(s)
- Akimasa Kaneko
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - 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
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, 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
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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18
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Bertoldo JB, Rodrigues T, Dunsmore L, Aprile FA, Marques MC, Rosado LA, Boutureira O, Steinbrecher TB, Sherman W, Corzana F, Terenzi H, Bernardes GJL. A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases. Chem 2017; 3:665-677. [PMID: 29094109 PMCID: PMC5656095 DOI: 10.1016/j.chempr.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) strains highlights the need to develop more efficacious and potent drugs. However, this goal is dependent on a comprehensive understanding of Mtb virulence protein effectors at the molecular level. Here, we used a post-expression cysteine (Cys)-to-dehydrolanine (Dha) chemical editing strategy to identify a water-mediated motif that modulates accessibility of the protein tyrosine phosphatase A (PtpA) catalytic pocket. Importantly, this water-mediated Cys-Cys non-covalent motif is also present in the phosphatase SptpA from Staphylococcus aureus, which suggests a potentially preserved structural feature among bacterial tyrosine phosphatases. The identification of this structural water provides insight into the known resistance of Mtb PtpA to the oxidative conditions that prevail within an infected host macrophage. This strategy could be applied to extend the understanding of the dynamics and function(s) of proteins in their native state and ultimately aid in the design of small-molecule modulators.
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Affiliation(s)
- Jean B Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marta C Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Leonardo A Rosado
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Omar Boutureira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York, NY 10036, USA
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
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19
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Yamauchi Y, Konno M, Ito S, Tsunoda SP, Inoue K, Kandori H. Molecular properties of a DTD channelrhodopsin from Guillardia theta. Biophys Physicobiol 2017. [PMID: 28630812 PMCID: PMC5468465 DOI: 10.2142/biophysico.14.0_57] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Microbial rhodopsins are membrane proteins found widely in archaea, eubacteria and eukaryotes (fungal and algal species). They have various functions, such as light-driven ion pumps, light-gated ion channels, light sensors and light-activated enzymes. A light-driven proton pump bacteriorhodopsin (BR) contains a DTD motif at positions 85, 89, and 96, which is unique to archaeal proton pumps. Recently, channelrhodopsins (ChRs) containing the DTD motif, whose sequential identity is ~20% similar to BR and to cation ChRs in Chlamydomonas reinhardtii (CrCCRs), were found. While extensive studies on ChRs have been performed with CrCCR2, the molecular properties of DTD ChRs remain an intrigue. In this paper, we studied a DTD rhodopsin from G. theta (GtCCR4) using electrophysiological measurements, flash photolysis, and low-temperature difference FTIR spectroscopy. Electrophysiological measurements clearly showed that GtCCR4 functions as a light-gated cation channel, similar to other G. theta DTD ChRs (GtCCR1-3). Light-driven proton pump activity was also suggested for GtCCR4. Both electrophysiological and flash photolysis experiments showed that channel closing occurs upon reprotonation of the Schiff base, suggesting that the dynamics of retinal and channels are tightly coupled in GtCCR4. From Fourier transform infrared (FTIR) spectroscopy at 77 K, we found that the primary reaction is an all-trans to a 13-cis photoisomerization, like other microbial rhodopsins, although perturbations in the secondary structure were much smaller in GtCCR4 than in CrCCR2.
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Affiliation(s)
- Yumeka Yamauchi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Masae Konno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.,Frontier Research Institute for Material Science, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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20
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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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21
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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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22
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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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23
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Stensitzki T, Yang Y, Muders V, Schlesinger R, Heberle J, Heyne K. Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:043208. [PMID: 27191011 PMCID: PMC4851625 DOI: 10.1063/1.4948338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
Vibrational dynamics of the retinal all-trans to 13-cis photoisomerization in channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by femtosecond visible pump mid-IR probe spectroscopy. After photoexcitation, the transient infrared absorption of C-C stretching modes was detected. The formation of the 13-cis photoproduct marker band at 1193 cm(-1) was observed within the time resolution of 0.3 ps. We estimated the photoisomerization yield to (60 ± 6) %. We found additional time constants of (0.55 ± 0.05) ps and (6 ± 1) ps, assigned to cooling, and cooling processes with a back-reaction pathway. An additional bleaching band demonstrates the ground-state heterogeneity of retinal.
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Affiliation(s)
- T Stensitzki
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Y Yang
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - V Muders
- Genetic Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - R Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - J Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - K Heyne
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
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24
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Mohrmann H, Kube I, Lórenz-Fonfría VA, Engelhard M, Heberle J. Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes. J Phys Chem B 2016; 120:4383-7. [DOI: 10.1021/acs.jpcb.6b01900] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hendrik Mohrmann
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ines Kube
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Víctor A. Lórenz-Fonfría
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Martin Engelhard
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Joachim Heberle
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
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25
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Schnedermann C, Muders V, Ehrenberg D, Schlesinger R, Kukura P, Heberle J. Vibronic Dynamics of the Ultrafast all-trans to 13-cis Photoisomerization of Retinal in Channelrhodopsin-1. J Am Chem Soc 2016; 138:4757-62. [DOI: 10.1021/jacs.5b12251] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Schnedermann
- Physical
and Theoretical Chemistry Laboratory, University of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | | | | | | | - Philipp Kukura
- Physical
and Theoretical Chemistry Laboratory, University of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
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26
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Stensitzki T, Muders V, Schlesinger R, Heberle J, Heyne K. The primary photoreaction of channelrhodopsin-1: wavelength dependent photoreactions induced by ground-state heterogeneity. Front Mol Biosci 2015; 2:41. [PMID: 26258130 PMCID: PMC4510425 DOI: 10.3389/fmolb.2015.00041] [Citation(s) in RCA: 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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27
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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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28
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Doi S, Mori A, Tsukamoto T, Reissig L, Ihara K, Sudo Y. Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1. Photochem Photobiol Sci 2015; 14:1628-36. [PMID: 26098533 DOI: 10.1039/c5pp00213c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Channelrhodopsins have become a focus of interest because of their ability to control neural activity by light, used in a technology called optogenetics. The channelrhodopsin in the eukaryote Chlamydomonas reinhardtii (CrChR-1) is a light-gated cation channel responsible for motility changes upon photo-illumination and a member of the membrane-embedded retinal protein family. Recent crystal structure analysis revealed that CrChR-1 has unique extended modules both at its N- and C-termini compared to other microbial retinal proteins. This study reports the first successful expression of a ChR-1 variant in Escherichia coli as a holoprotein: the ChR-1 variant lacking both the N- and C-termini (CrChR-1_82-308). However, compared to ChR-1 having the extended modules (CrChR-1_1-357), truncation of the termini greatly altered the absorption maximum and photochemical properties, including the pKa values of its charged residues around the chromophore, the reaction rates in the photocycle and the photo-induced ion channeling activity. The results of some experiments regarding ion transport activity suggest that CrChR-1_82-308 has a proton channeling activity even in the dark. On the basis of these results, we discuss the structural and functional roles of the N- and C-terminal extended modules in CrChR-1.
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Affiliation(s)
- Satoko Doi
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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29
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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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30
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Inaguma A, Tsukamoto H, Kato HE, Kimura T, Ishizuka T, Oishi S, Yawo H, Nureki O, Furutani Y. Chimeras of channelrhodopsin-1 and -2 from Chlamydomonas reinhardtii exhibit distinctive light-induced structural changes from channelrhodopsin-2. J Biol Chem 2015; 290:11623-34. [PMID: 25796616 DOI: 10.1074/jbc.m115.642256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 01/18/2023] Open
Abstract
Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins.
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Affiliation(s)
- Asumi Inaguma
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hisao Tsukamoto
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hideaki E Kato
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tetsunari Kimura
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Toru Ishizuka
- CREST, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, and Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan
| | - Satomi Oishi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiromu Yawo
- CREST, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, and Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuji Furutani
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan,
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31
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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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32
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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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