1
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Zhang X, Tamaki H, Kikukawa T, Fujiwara T, Matsuki Y. Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy. Biophys Chem 2024; 315:107329. [PMID: 39369577 DOI: 10.1016/j.bpc.2024.107329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/21/2024] [Accepted: 09/22/2024] [Indexed: 10/08/2024]
Abstract
Natronomonas pharaonis halorhodopsin (NpHR) is a light-driven Cl- inward pump that is widely used as an optogenetic tool. Although NpHR is previously extensively studied, its Cl- uptake process is not well understood from the protein structure perspective, mainly because in crystalline lattice, it has been difficult to analyze the structural changes associated with the Cl- uptake process. In this study, we used solid-state NMR to analyze NpHR both in the Cl--bound and -free states under near-physiological transmembrane condition. Chemical shift perturbation analysis suggested that while the structural change caused by the Cl- depletion is widespread over the NpHR molecule, residues in the extracellular (EC) part of helix D exhibited significant conformational changes that may be related to the Cl- uptake process. By combining photochemical analysis and dynamic nuclear polarization (DNP)-enhanced solid-state NMR measurement on NpHR point mutants for the suggested residues, we confirmed their importance in the Cl- uptake process. In particular, we found the mutation at Ala165 position, located at the trimer interface, to an amino acid with bulky sidechain (A165V) significantly perturbs the late photocycle and disrupts its trimeric assembly in the Cl--free state as well as during the ion-pumping cycle under the photo-irradiated condition. This strongly suggested an outward movement of helix D at EC part, disrupting the trimer integrity. Together with the spectroscopic data and known NpHR crystal structures, we proposed a model that this helix movement is required for creating the Cl- entrance path on the extracellular surface of the protein and is crucial to the Cl- uptake process.
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Affiliation(s)
- Xin Zhang
- Institute for Protein Research, Osaka University, Japan
| | - Hajime Tamaki
- Institute for Protein Research, Osaka University, Japan
| | | | | | - Yoh Matsuki
- Institute for Protein Research, Osaka University, Japan; Center for Quantum Information and Quantum Biology, Osaka University, Japan.
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2
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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 PMCID: PMC11258790 DOI: 10.1021/jacs.4c03891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [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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3
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Singh M, Ito S, Hososhima S, Abe-Yoshizumi R, Tsunoda SP, Inoue K, Kandori H. Light-Driven Chloride and Sulfate Pump with Two Different Transport Modes. J Phys Chem B 2023; 127:7123-7134. [PMID: 37552856 DOI: 10.1021/acs.jpcb.3c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ion pumps are membrane proteins that actively translocate ions by using energy. All known pumps bind ions in the resting state, and external energy allows ion transport through protein structural changes. The light-driven sodium-ion pump Krokinobacter eikastus rhodopsin 2 (KR2) is an exceptional case in which ion binding follows the energy input. In this study, we report another case of this unusual transport mode. The NTQ rhodopsin from Alteribacter aurantiacus (AaClR) is a natural light-driven chloride pump, in which the chloride ion binds to the resting state. AaClR is also able to pump sulfate ions, though the pump efficiency is much lower for sulfate ions than for chloride ions. Detailed spectroscopic analysis revealed no binding of the sulfate ion to the resting state of AaClR, indicating that binding of the substrate (sulfate ion) to the resting state is not necessary for active transport. This property of the AaClR sulfate pump is similar to that of the KR2 sodium pump. Photocycle dynamics of the AaClR sulfate pump resemble a non-functional cycle in the absence of anions. Despite this, flash photolysis and difference Fourier transform infrared spectroscopy suggest transient binding of the sulfate ion to AaClR. The molecular mechanism of this unusual active transport by AaClR is discussed.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shota Ito
- 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
| | - 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 466-855, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-855, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-855, Japan
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4
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Mous S, Gotthard G, Ehrenberg D, Sen S, Weinert T, Johnson PJM, James D, Nass K, Furrer A, Kekilli D, Ma P, Brünle S, Casadei CM, Martiel I, Dworkowski F, Gashi D, Skopintsev P, Wranik M, Knopp G, Panepucci E, Panneels V, Cirelli C, Ozerov D, Schertler GFX, Wang M, Milne C, Standfuss J, Schapiro I, Heberle J, Nogly P. Dynamics and mechanism of a light-driven chloride pump. Science 2022; 375:845-851. [PMID: 35113649 DOI: 10.1126/science.abj6663] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.
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Affiliation(s)
- Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Philip J M Johnson
- Laboratory of Nonlinear Optics, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Karol Nass
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Cecilia Maria Casadei
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Florian Dworkowski
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland.,Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petr Skopintsev
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Maximilian Wranik
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gregor Knopp
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Valerie Panneels
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard F X Schertler
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Chris Milne
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
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5
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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6
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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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7
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Fujisawa T, Kiyota H, Kikukawa T, Unno M. Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts. Biochemistry 2019; 58:4159-4167. [PMID: 31538771 DOI: 10.1021/acs.biochem.9b00643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
From the low-temperature absorption and Raman measurements of halorhodopsin from Natronomonas pharaonis (pHR), we observed that the two photoproducts were generated after exciting pHR at 80 K by green light. One photoproduct was the red-shifted K intermediate (pHRK) as the primary photointermediate for Cl- pumping, and the other was the blue-shifted one (pHRhypso), which was not involved in the Cl- pumping and thermally relaxed to the original unphotolyzed state by increasing temperature. The formation of these two kinds of photoproducts was previously reported for halorhodopsin from Halobacterium sarinarum [ Zimanyi et al. Biochemistry 1989 , 28 , 1656 ]. We found that the same took place in pHR, and we revealed the chromophore structures of the two photointermediates from their Raman spectra for the first time. pHRhypso had the distorted all-trans chromophore, while pHRK contained the distorted 13-cis form. The present results revealed that the structural analyses of pHRK carried out so far at ∼80 K potentially included a significant contribution from pHRhypso. pHRhypso was efficiently formed via the photoexcitation of pHRK, indicating that pHRhypso was likely a side product after photoexcitation of pHRK. The formation of pHRhypso suggested that the active site became tight in pHRK due to the slight movement of Cl-, and the back photoisomerization then produced the distorted all-trans chromophore in pHRhypso.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Hayato Kiyota
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science , Hokkaido University , Sapporo 060-0810 , Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education , Hokkaido University , Sapporo 060-0810 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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8
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Kouyama T, Ihara K, Maki K, Chan SK. Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin. Biochemistry 2018; 57:6013-6026. [PMID: 30211543 DOI: 10.1021/acs.biochem.8b00631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The anion pumping cycle of halorhodopsin from Natronomonas pharaonis ( pHR) is initiated when the all- trans/15- anti isomer of retinal is photoisomerized into the 13- cis/15- anti configuration. A recent crystallographic study suggested that a reaction state with 13- cis/15- syn retinal occurred during the anion release process, i.e., after the N state with the 13- cis/15- anti retinal and before the O state with all- trans/15- anti retinal. In this study, we investigated the retinal isomeric composition in a long-living reaction state at various bromide ion concentrations. It was found that the 13- cis isomer (csHR'), in which the absorption spectrum was blue-shifted by ∼8 nm compared with that of the trans isomer (taHR), accumulated significantly when a cold suspension of pHR-rich claret membranes in 4 M NaBr was illuminated with continuous light. Analysis of flash-induced absorption changes suggested that the branching of the trans photocycle into the 13- cis isomer (csHR') occurs during the decay of an O-like state (O') with 13- cis/15- syn retinal; i.e., O' can decay to either csHR' or O with all- trans/15- anti retinal. The efficiency of the branching reaction was found to be dependent on the bromide ion concentration. At a very high bromide ion concentration, the anion pumping cycle is described by the scheme taHR -( hν) → K → L1a ↔ L1b ↔ N ↔ N' ↔ O' ↔ csHR' ↔ taHR. At a low bromide ion concentration, on the other hand, O' decays into taHR via O.
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Affiliation(s)
- Tsutomu Kouyama
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Kunio Ihara
- Center for Gene Research , Nagoya University , Nagoya 464-8602 , Japan
| | - Kosuke Maki
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Siu Kit Chan
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
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9
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Engelhard C, Chizhov I, Siebert F, Engelhard M. Microbial Halorhodopsins: Light-Driven Chloride Pumps. Chem Rev 2018; 118:10629-10645. [DOI: 10.1021/acs.chemrev.7b00715] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, OE8830 Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Albert-Ludwigs-Universität Freiburg, Hermann-Herderstr. 9, 79104 Freiburg, Germany
| | - Martin Engelhard
- Max Planck Institute for Molecular Physiology, Otto Hahn Str. 11, 44227 Dortmund, Germany
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10
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Harris A, Saita M, Resler T, Hughes-Visentin A, Maia R, Pranga-Sellnau F, Bondar AN, Heberle J, Brown LS. Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Phys Chem Chem Phys 2018; 20:3184-3199. [PMID: 29057415 DOI: 10.1039/c7cp06068h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microbial rhodopsins are well known as versatile and ubiquitous light-driven ion transporters and photosensors. While the proton transport mechanism has been studied in great detail, much less is known about various modes of anion transport. Until recently, only two main groups of light-driven anion pumps were known, archaeal halorhodopsins (HRs) and bacterial chloride pumps (known as ClRs or NTQs). Last year, another group of cyanobacterial anion pumps with a very distinct primary structure was reported. Here, we studied the chloride-transporting photocycle of a representative of this new group, Mastigocladopsis repens rhodopsin (MastR), using time-resolved spectroscopy in the infrared and visible ranges and site-directed mutagenesis. We found that, in accordance with its unique amino acid sequence containing many polar residues in the transmembrane region of the protein, its photocycle features a number of unusual molecular events not known for other anion-pumping rhodopsins. It appears that light-driven chloride ion transfers by MastR are coupled with translocation of protons and water molecules as well as perturbation of several polar sidechains. Of particular interest is transient deprotonation of Asp-85, homologous to the cytoplasmic proton donor of light-driven proton pumps (such as Asp-96 of bacteriorhodopsin), which may serve as a regulatory mechanism.
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Affiliation(s)
- Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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11
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Mizuno M, Nakajima A, Kandori H, Mizutani Y. Structural Evolution of a Retinal Chromophore in the Photocycle of Halorhodopsin from Natronobacterium pharaonis. J Phys Chem A 2018; 122:2411-2423. [DOI: 10.1021/acs.jpca.7b12332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
| | - Ayumi Nakajima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
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12
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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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13
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Tsukamoto T, Yoshizawa S, Kikukawa T, Demura M, Sudo Y. Implications for the Light-Driven Chloride Ion Transport Mechanism of Nonlabens marinus Rhodopsin 3 by Its Photochemical Characteristics. J Phys Chem B 2017; 121:2027-2038. [PMID: 28194973 DOI: 10.1021/acs.jpcb.6b11101] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several new retinal-based photoreceptor proteins that act as light-driven electrogenic halide ion pumps have recently been discovered. Some of them, called "NTQ" rhodopsins, contain a conserved Asn-Thr-Gln motif in the third or C-helix. In this study, we investigated the photochemical characteristics of an NTQ rhodopsin, Nonlabens marinus rhodopsin 3 (NM-R3), which was discovered in the N. marinus S1-08T strain, using static and time-resolved spectroscopic techniques. We demonstrate that NM-R3 binds a Cl- in the vicinity of the retinal chromophore accompanied by a spectral blueshift from 568 nm in the absence of Cl- to 534 nm in the presence of Cl-. From the Cl- concentration dependence, we estimated the affinity (dissociation constant, Kd) for Cl- in the original state as 24 mM, which is ca. 10 times weaker than that of archaeal halorhodopsins but ca. 3 times stronger than that of a marine bacterial Cl- pumping rhodopsin (C1R). NM-R3 showed no dark-light adaptation of the retinal chromophore and predominantly possessed an all-trans-retinal, which is responsible for the light-driven Cl- pump function. Flash-photolysis experiments suggest that NM-R3 passes through five or six photochemically distinct intermediates (K, L(N), O1, O2, and NM-R3'). From these results, we assume that the Cl- is released and taken up during the L(N)-O1 transition from a transiently formed cytoplasmic (CP) binding site and the O2-NM-R3' or the NM-R3'-original NM-R3 transitions from the extracellular (EC) side, respectively. We propose a mechanism for the Cl- transport by NM-R3 based on our results and its recently reported crystal structure.
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Affiliation(s)
- Takashi Tsukamoto
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University , 700-8530 Okayama, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo , Chiba 277-8564, Japan
| | | | | | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University , 700-8530 Okayama, Japan
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14
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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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15
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Chan SK, Kawaguchi H, Kubo H, Murakami M, Ihara K, Maki K, Kouyama T. Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States. Biochemistry 2016; 55:4092-104. [DOI: 10.1021/acs.biochem.6b00277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Siu Kit Chan
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Haruki Kawaguchi
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroki Kubo
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Midori Murakami
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Kunio Ihara
- Center
for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Kosuke Maki
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tsutomu Kouyama
- Department
of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- RIKEN Harima Branch, 1-1-1, Kouto, Sayo, Hyogo, Japan
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16
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Kouyama T, Kawaguchi H, Nakanishi T, Kubo H, Murakami M. Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin. Biophys J 2016; 108:2680-90. [PMID: 26039169 PMCID: PMC4457492 DOI: 10.1016/j.bpj.2015.04.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/15/2023] Open
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR) functions as a light-driven halide ion pump. In the presence of halide ions, the photochemical reaction of pHR is described by the scheme: K→ L1 → L2 → N → O → pHR′ → pHR. Here, we report light-induced structural changes of the pHR-bromide complex observed in the C2 crystal. In the L1-to-L2 transition, the bromide ion that initially exists in the extracellular vicinity of retinal moves across the retinal Schiff base. Upon the formation of the N state with a bromide ion bound to the cytoplasmic vicinity of the retinal Schiff base, the cytoplasmic half of helix F moves outward to create a water channel in the cytoplasmic interhelical space, whereas the extracellular half of helix C moves inward. During the transition from N to an N-like reaction state with retinal assuming the 13-cis/15-syn configuration, the translocated bromide ion is released into the cytoplasmic medium. Subsequently, helix F relaxes into its original conformation, generating the O state. Anion uptake from the extracellular side occurs when helix C relaxes into its original conformation. These structural data provide insight into the structural basis of unidirectional anion transport.
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Affiliation(s)
- Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan; RIKEN Harima Branch, 1-1-1, Kouto, Sayo, Hyogo, Japan.
| | - Haruki Kawaguchi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Taichi Nakanishi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiroki Kubo
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
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17
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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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18
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The role of retinal light induced dipole in halorhodopsin structural alteration. FEBS Lett 2015; 589:3576-80. [PMID: 26467279 DOI: 10.1016/j.febslet.2015.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/05/2015] [Accepted: 10/02/2015] [Indexed: 11/20/2022]
Abstract
The present work studies the mechanism of light induced protein conformational changes in the over-expressed mutant of halorhodopsin (phR) from Natronomonas pharaonis. The catalytic effect of light is reflected in accelerating hydroxyl amine reaction rate of light adapted phR. Light catalysis was detected in native phR but also in artificial pigments derived from tailored retinal analogs locked at the crucial C13=C14 double bond. It is proposed that the photoexcited retinal chromophore induces protein concerted motion that decreases the energy gap between reactants ground and transition states. This energy gap is overcome by coupling to specific protein vibrations. Surprisingly, the rate constants show unusual decreasing trend following temperature increase both for native and artificial pigments.
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19
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Kikukawa T, Kusakabe C, Kokubo A, Tsukamoto T, Kamiya M, Aizawa T, Ihara K, Kamo N, Demura M. Probing the Cl − -pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:748-58. [DOI: 10.1016/j.bbabio.2015.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
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20
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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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21
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Inoue K, Koua FHM, Kato Y, Abe-Yoshizumi R, Kandori H. Spectroscopic study of a light-driven chloride ion pump from marine bacteria. J Phys Chem B 2014; 118:11190-9. [PMID: 25166488 DOI: 10.1021/jp507219q] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thousands of light-driven proton-pumping rhodopsins have been found in marine microbes, and a light-driven sodium-ion pumping rhodopsin was recently discovered, which utilizes sunlight for the energy source of the cell. Similarly, a light-driven chloride-ion pump has been found from marine bacteria, and three eubacterial light-driven pumps possess the DTE (proton pump), NDQ (sodium-ion pump), and NTQ (chloride-ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR). The corresponding motif of the known haloarchaeal chloride-ion pump, halorhodopsin (HR), is TSA, which is entirely different from the NTQ motif of a eubacterial chloride-ion pump. It is thus intriguing to compare the molecular mechanism of these two chloride-ion pumps. Here we report the spectroscopic study of Fulvimarina rhodopsin (FR), a eubacterial light-driven chloride-ion pump from marine bacterium. FR binds a chloride-ion near the retinal chromophore and chloride-ion binding causes a spectral blue-shift. FR predominantly possesses an all-trans retinal, which is responsible for the light-driven chloride-ion pump. Upon light absorption, the red-shifted K intermediate is formed, followed by the appearance of the L and O intermediates. When the M intermediate does not form, this indicates that the Schiff base remains in the protonated state during the photocycle. These molecular mechanisms are common in HR, and a common mechanism for chloride-ion pumping by evolutionarily distant proteins suggests the importance of the electric quadrupole in the Schiff base region and their changes through hydrogen-bonding alterations. One noticeable difference between FR and HR is the uptake of chloride-ion from the extracellular surface. While the uptake occurs upon decay of the O intermediate in HR, chloride-ion uptake accompanies the rise of the O intermediate in FR. This suggests the presence of a second chloride-ion binding site near the extracellular surface of FR, which is unique to the NTQ rhodopsin.
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Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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22
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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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23
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Shibasaki K, Shigemura H, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M. Role of Thr218 in the light-driven anion pump halorhodopsin from Natronomonas pharaonis. Biochemistry 2013; 52:9257-68. [PMID: 24298916 DOI: 10.1021/bi401295e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halorhodopsin (HR) is an inward-directed light-driven halogen ion pump, and NpHR is a HR from Natronomonas pharaonis. Unphotolyzed NpHR binds halogen ion in the vicinity of the Schiff base, which links retinal to Lys256. This halogen ion is transported during the photocycle. We made various mutants of Thr218, which is located one half-turn up from the Schiff base to the cytoplasm (CP) channel, and analyzed the photocycle using a sequential irreversible model. Four photochemically defined intermediates (P(i), i = 1-4) were adequate to describe the photocycle. The third component, P₃, was a quasi-equilibrium complex between the N and O intermediates, where a N ↔ O + Cl⁻ equilibrium was attained. The K(d,N↔O) values of this equilibrium for various mutants were determined, and the value of Thr (wild type) was the highest. The partial molar volume differences between N and O, ΔV(N→O), were estimated from the pressure dependence of K(d,N↔O). A comparison between K(d,N↔O) and ΔV(N→O) led to the conclusion that water entry by the F-helix opening at O may occur, which may increase K(d,N↔O). For some mutants, however, large ΔV(N→O) values were found, whereas the K(d,N↔O) values were small. This suggests that the special coordination of a water molecule with the OH group of Thr is necessary for the increase in K(d,N↔O). Mutants with a small K(d,N↔O) showed low pumping activities in the presence of inside negative membrane potential, while the mutant activities were not different in the absence of membrane potential. The effect of the mutation on the pumping activities is discussed.
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Affiliation(s)
- Kousuke Shibasaki
- Faculty of Advanced Life Science, Hokkaido University , Sapporo 060-0810, Japan
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24
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Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating. Proc Natl Acad Sci U S A 2013; 110:E1273-81. [PMID: 23509282 DOI: 10.1073/pnas.1219502110] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The discovery of the light-gated ion channel channelrhodopsin (ChR) set the stage for the novel field of optogenetics, where cellular processes are controlled by light. However, the underlying molecular mechanism of light-induced cation permeation in ChR2 remains unknown. Here, we have traced the structural changes of ChR2 by time-resolved FTIR spectroscopy, complemented by functional electrophysiological measurements. We have resolved the vibrational changes associated with the open states of the channel (P(2)(390) and P(3)(520)) and characterized several proton transfer events. Analysis of the amide I vibrations suggests a transient increase in hydration of transmembrane α-helices with a t(1/2) = 60 μs, which tallies with the onset of cation permeation. Aspartate 253 accepts the proton released by the Schiff base (t(1/2) = 10 μs), with the latter being reprotonated by aspartic acid 156 (t(1/2) = 2 ms). The internal proton acceptor and donor groups, corresponding to D212 and D115 in bacteriorhodopsin, are clearly different from other microbial rhodopsins, indicating that their spatial position in the protein was relocated during evolution. Previous conclusions on the involvement of glutamic acid 90 in channel opening are ruled out by demonstrating that E90 deprotonates exclusively in the nonconductive P(4)(480) state. Our results merge into a mechanistic proposal that relates the observed proton transfer reactions and the protein conformational changes to the gating of the cation channel.
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25
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Furutani Y, Fujiwara K, Kimura T, Kikukawa T, Demura M, Kandori H. Dynamics of Dangling Bonds of Water Molecules in pharaonis Halorhodopsin during Chloride Ion Transportation. J Phys Chem Lett 2012; 3:2964-2969. [PMID: 26292234 DOI: 10.1021/jz301287n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ion transportation via the chloride ion pump protein pharaonis halorhodopsin (pHR) occurs through the sequential formation of several intermediates during a photocyclic reaction. Although the structural details of each intermediate state have been studied, the role of water molecules in the translocation of chloride ions inside of the protein at physiological temperatures remains unclear. To analyze the structural dynamics of water inside of the protein, we performed time-resolved Fourier transform infrared (FTIR) spectroscopy under H2O or H2(18)O hydration and successfully assigned water O-H stretching bands. We found that a dangling water band at 3626 cm(-1) in pHR disappears in the L1 and L2 states. On the other hand, relatively intense positive bands at 3605 and 3608 cm(-1) emerged upon the formation of the X(N) and O states, respectively, suggesting that the chloride transportation is accompanied by dynamic rearrangement of the hydrogen-bonding network of the internal water molecules in pHR.
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Affiliation(s)
- Yuji Furutani
- †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, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Kuniyo Fujiwara
- †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, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Tetsunari Kimura
- †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, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Takashi Kikukawa
- ¶Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Makoto Demura
- ¶Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideki Kandori
- #Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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26
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Homotrimer formation and dissociation of pharaonis halorhodopsin in detergent system. Biophys J 2012; 102:2906-15. [PMID: 22735541 DOI: 10.1016/j.bpj.2012.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 05/06/2012] [Accepted: 05/08/2012] [Indexed: 12/13/2022] Open
Abstract
Halorhodopsin from NpHR is a light-driven Cl(-) pump that forms a trimeric NpHR-bacterioruberin complex in the native membrane. In the case of NpHR expressed in Escherichia coli cell, NpHR forms a robust homotrimer in a detergent DDM solution. To identify the important residue for the homotrimer formation, we carried out mutation experiments on the aromatic amino acids expected to be located at the molecular interface. The results revealed that Phe(150) was essential to form and stabilize the NpHR trimer in the DDM solution. Further analyses for examining the structural significance of Phe(150) showed the dissociation of the trimer in F150A (dimer) and F150W (monomer) mutants. Only the F150Y mutant exhibited dissociation into monomers in an ionic strength-dependent manner. These results indicated that spatial positions and interactions between F150-aromatic side chains were crucial to homotrimer stabilization. This finding was supported by QM calculations. In a functional respect, differences in the reaction property in the ground and photoexcited states were revealed. The analysis of photointermediates revealed a decrease in the accumulation of O, which is important for Cl(-) release, and the acceleration of the decay rate in L1 and L2, which are involved in Cl(-) transfer inside the molecule, in the trimer-dissociated mutants. Interestingly, the affinity of them to Cl(-) in the photoexcited state increased rather than the trimer, whereas that in the ground state was almost the same without relation to the oligomeric state. It was also observed that the efficient recovery of the photocycle to the ground state was inhibited in the mutants. In addition, a branched pathway that was not included in Cl(-) transportation was predicted. These results suggest that the trimer assembly may contribute to the regulation of the dynamics in the excited state of NpHR.
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27
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Muroda K, Nakashima K, Shibata M, Demura M, Kandori H. Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps. Biochemistry 2012; 51:4677-84. [PMID: 22583333 DOI: 10.1021/bi300485r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.
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Affiliation(s)
- Kosuke Muroda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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28
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Kleinlogel S, Terpitz U, Legrum B, Gökbuget D, Boyden ES, Bamann C, Wood PG, Bamberg E. A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins. Nat Methods 2011; 8:1083-8. [DOI: 10.1038/nmeth.1766] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 09/19/2011] [Indexed: 01/24/2023]
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29
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Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T. Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin. J Mol Biol 2011; 413:162-76. [PMID: 21871461 DOI: 10.1016/j.jmb.2011.08.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/06/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR) was previously crystallized into a monoclinic space group C2, and the structure of the chloride-bound purple form was determined. Here, we report the crystal structures of two chloride-free forms of pHR, that is, an O-like blue form and an M-like yellow form. When the C2 crystal was soaked in a chloride-free alkaline solution, the protein packing was largely altered and the yellow form containing all-trans retinal was generated. Upon neutralization, this yellow form was converted into the blue form. From structural comparison of the different forms of pHR, it was shown that the removal of a chloride ion from the primary binding site (site I), which is located between the retinal Schiff base and Thr126, is accompanied by such a deformation of helix C that the side chain of Thr126 moves toward helix G, leading to a significant shrinkage of site I. A large structural change is also induced in the chloride uptake pathway, where a flip motion of the side chain of Glu234 is accompanied by large movements of the surrounding aromatic residues. Irrespective of different charge distributions at the active site, there was no large difference in the structures of the yellow form and the blue form. It is shown that the yellow-to-purple transition is initiated by the entrance of one water and one HCl to the active site, where the proton and the chloride ion in HCl are transferred to the Schiff base and site I, respectively.
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Affiliation(s)
- Soun Kanada
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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Radu I, Schleeger M, Nack M, Heberle J. Time-resolved FT-IR Spectroscopy of Membrane Proteins. Aust J Chem 2011. [DOI: 10.1071/ch10286] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Time-resolved Fourier transform infrared spectroscopy (FT-IR) offers distinct advantages concerning restrictions pertinent to biomolecules. In particular, it is possible to monitor the temporal evolution of the reaction mechanism of complex machineries as membrane proteins, where other techniques encounter significant experimental difficulties. Here, we present the classical principles and experimental realizations of time-resolved FT-IR spectroscopy together with recent developments employed in our laboratory. Examples from applications to retinal proteins are reviewed that underline the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds.
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Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K. Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis. J Mol Biol 2010; 396:564-79. [DOI: 10.1016/j.jmb.2009.11.061] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/21/2009] [Accepted: 11/24/2009] [Indexed: 10/20/2022]
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32
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Gross R, Wolf MMN, Schumann C, Friedman N, Sheves M, Li L, Engelhard M, Trentmann O, Neuhaus HE, Diller R. Primary photoinduced protein response in bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 2010; 131:14868-78. [PMID: 19778046 DOI: 10.1021/ja904218n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential for the biological function of the light-driven proton pump, bacteriorhodopsin (BR), and the light sensor, sensory rhodopsin II (SRII), is the coupling of the activated retinal chromophore to the hosting protein moiety. In order to explore the dynamics of this process we have performed ultrafast transient mid-infrared spectroscopy on isotopically labeled BR and SRII samples. These include SRII in D(2)O buffer, BR in H(2)(18)O medium, SRII with (15)N-labeled protein, and BR with (13)C(14)(13)C(15)-labeled retinal chromophore. Via observed shifts of infrared difference bands after photoexcitation and their kinetics we provide evidence for nonchromophore bands in the amide I and the amide II region of BR and SRII. A band around 1550 cm(-1) is very likely due to an amide II vibration. In the amide I region, contributions of modes involving exchangeable protons and modes not involving exchangeable protons can be discerned. Observed bands in the amide I region of BR are not due to bending vibrations of protein-bound water molecules. The observed protein bands appear in the amide I region within the system response of ca. 0.3 ps and in the amide II region within 3 ps, and decay partially in both regions on a slower time scale of 9-18 ps. Similar observations have been presented earlier for BR5.12, containing a nonisomerizable chromophore (R. Gross et al. J. Phys. Chem. B 2009, 113, 7851-7860). Thus, the results suggest a common mechanism for ultrafast protein response in the artificial and the native system besides isomerization, which could be induced by initial chromophore polarization.
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Affiliation(s)
- Ruth Gross
- University of Kaiserslautern, Department of Physics, Erwin-Schrodinger-Strasse, 67663 Kaiserslautern, Germany
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Gross R, Schumann C, Wolf MMN, Herbst J, Diller R, Friedman N, Sheves M. Ultrafast Protein Conformational Alterations in Bacteriorhodopsin and Its Locked Analogue BR5.12. J Phys Chem B 2009; 113:7851-60. [PMID: 19422251 DOI: 10.1021/jp810042f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruth Gross
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Schumann
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias M. N. Wolf
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Herbst
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rolf Diller
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Noga Friedman
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
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34
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Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Furutani Y, Ito M, Sudo Y, Kamo N, Kandori H. ProteinProtein Interaction of aPharaonisHalorhodopsin Mutant Forming a Complex withPharaonisHalobacterial Transducer Protein II Detected by Fourier-Transform Infrared Spectroscopy. Photochem Photobiol 2008; 84:874-9. [DOI: 10.1111/j.1751-1097.2008.00317.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Characterization of the primary photochemistry of proteorhodopsin with femtosecond spectroscopy. Biophys J 2008; 94:4020-30. [PMID: 18234812 DOI: 10.1529/biophysj.107.121376] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteorhodopsin is an ion-translocating member of the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization, leading to transmembrane translocation of a proton toward the extracellular side of the cytoplasmic membrane. Here we report a study on the photoisomerization dynamics of the retinal chromophore of proteorhodopsin, using femtosecond time-resolved spectroscopy, by probing in the visible- and in the midinfrared spectral regions. Experiments were performed both at pH 9.5 (a physiologically relevant pH value in which the primary proton acceptor of the protonated Schiff base, Asp(97), is deprotonated) and at pH 6.5 (with Asp(97) protonated). Simultaneous analysis of the data sets recorded in the two spectral regions and at both pH values reveals a multiexponential excited state decay, with time constants of approximately 0.2 ps, approximately 2 ps, and approximately 20 ps. From the difference spectra associated with these dynamics, we conclude that there are two chromophore-isomerization pathways that lead to the K-state: one with an effective rate of approximately (2 ps)(-1) and the other with a rate of approximately (20 ps)(-1). At high pH, both pathways are equally effective, with an estimated quantum yield for K-formation of approximately 0.7. At pH 6.5, the slower pathway is less productive, which results in an isomerization quantum yield of 0.5. We further observe an ultrafast response of residue Asp(227), which forms part of the counterion complex, corresponding to a strengthening of its hydrogen bond with the Schiff base on K-state formation; and a feature that develops on the 0.2 ps and 2 ps timescale and probably reflects a response of an amide II band in reaction to the isomerization process.
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Klare JP, Chizhov I, Engelhard M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 2007; 45:73-122. [PMID: 17898961 DOI: 10.1007/400_2007_041] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Microbial rhodopsins have been intensively researched for the last three decades. Since the discovery of bacteriorhodopsin, the scope of microbial rhodopsins has been considerably extended, not only in view of the large number of family members, but also their functional properties as pumps, sensors, and channels. In this review, we give a short overview of old and newly discovered microbial rhodopsins, the mechanism of signal transfer and ion transfer, and we discuss structural and mechanistic aspects of phototaxis.
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Affiliation(s)
- Johann P Klare
- Fachbereich Physik, University Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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38
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Shibata M, Saito Y, Demura M, Kandori H. Deprotonation of Glu234 during the photocycle of Natronomonas pharaonis halorhodopsin. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.10.111] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Makarov VI, Khmelinskii IV. Dynamics of secondary and tertiary structure relaxation of a cyclic penta-peptide: Time-resolved FTIR studies. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Mevorat-Kaplan K, Weiner L, Sheves M. Spin Labeling ofNatronomonaspharaonisHalorhodopsin: Probing the Cysteine Residues Environment. J Phys Chem B 2006; 110:8825-31. [PMID: 16640441 DOI: 10.1021/jp054750c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR) is a light-driven chloride pump that transports a chloride anion across the plasma membrane following light absorption by a retinal chromophore which initiates a photocycle. Analysis of the amino acid sequence of pHR reveals three cysteine residues (Cys160, Cys184, and Cys186) in helices D and E. Here we have labeled the cysteine residues with nitroxide spin labels and studied using electron paramagnetic resonance (EPR) spectroscopy their mobility, accessibility to various reagents, and the distance between the labels. It was revealed by following the d(1)/d parameter that the distance between the spin labels is ca. 13-15 Angstrom. The EPR spectrum suggests that one label has a restricted mobility while the other two are more mobile. Only one label is accessible to hydrophilic paramagnetic broadening reagents leading to the conclusion that this label is exposed to the water phase. All three labels are reduced by ascorbic acid and reoxidized by molecular oxygen. The rate of the oxidation is accelerated following retinal irradiation indicating that the protein experiences conformation alterations in the vicinity of the labels during the pigment photocycle. It is suggested that Cys186 is exposed to the bulk medium while Cys184, located close to the retinal ionone ring, exhibits an immobilized EPR signal and is characterized by a hydrophobic environment.
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Affiliation(s)
- Keren Mevorat-Kaplan
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Peters F, Herbst J, Tittor J, Oesterhelt D, Diller R. Primary reaction dynamics of halorhodopsin, observed by sub-picosecond IR – vibrational spectroscopy. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Bálint Z, Lakatos M, Ganea C, Lanyi JK, Váró G. The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin. Biophys J 2004; 86:1655-63. [PMID: 14990493 PMCID: PMC1304001 DOI: 10.1016/s0006-3495(04)74234-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Time-resolved spectroscopy, absorption kinetic and electric signal measurement techniques were used to study the nitrate transporting photocycle of the pharaonis halorhodopsin. The spectral titration reveals two nitrate-binding constants, assigned to two independent binding sites. The high-affinity binding site (K(a) = 11 mM) contributes to the appearance of the nitrate transporting photocycle, whereas the low-affinity constant (having a K(a) of approximately 7 M) slows the last decay process in the photocycle. Although the spectra of the intermediates are not the same as those found in the chloride transporting photocycle, the sequence of the intermediates and the energy diagrams are similar. The differences in spectra and energy levels can be attributed to the difference in the size of the transported chloride or nitrate. Electric signal measurements show that a charge is transferred across the membrane during the photocycle, as expected. A new observation is an apparent release and rebinding of a small fraction of the retinal, inside the retinal pocket, during the photocycle. The release occurs during the N-to-O transition, whereas the rebinding happens in several seconds, well after the other steps of the photocycle are over.
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Affiliation(s)
- Zoltán Bálint
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, H-6701, Hungary
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43
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44
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Hein M, Radu I, Klare JP, Engelhard M, Siebert F. Consequences of Counterion Mutation in Sensory Rhodopsin II ofNatronobacterium pharaonisfor Photoreaction and Receptor Activation: An FTIR Study. Biochemistry 2003; 43:995-1002. [PMID: 14744144 DOI: 10.1021/bi0354381] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many retinal proteins the proton transfer from the Schiff base to the counterion represents a functionally important step of the photoreaction. In the signaling state of sensory rhodopsin II from Natronobacterium pharaonis this transfer has already occurred, but in the counterion mutant Asp75Asn it is blocked during all steps of the photocycle. Therefore, the study of the molecular changes during the photoreaction of this mutant should provide a deeper understanding of the activation mechanism, and for this, we have applied time-resolved step-scan FTIR spectroscopy. The photoreaction is drastically altered; only red-shifted intermediates are formed with a chromophore strongly twisted around the 14-15 single bond. In addition, the photocycle is shortened by 2 orders of magnitude. Nevertheless, a transition involving only protein changes similar to that of the wild type is observed, which has been correlated with the formation of the signaling state. However, whereas in the wild type this transition occurs in the millisecond range, it is shortened to 200 micros in the mutant. The results are discussed with respect to the altered electrostatic interactions, role of proton transfer, the published 3D structure, and physiological activity.
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Affiliation(s)
- Michael Hein
- Sektion Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität, Hermann-Herderstrasse 9, 79104 Freiburg, Germany
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45
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Tatulian SA. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy: A Method of Choice for Studying Membrane Proteins and Lipids†. Biochemistry 2003; 42:11898-907. [PMID: 14556620 DOI: 10.1021/bi034235+] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suren A Tatulian
- Biomolecular Science Center and Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida 32826, USA.
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Sato M, Kikukawa T, Araiso T, Okita H, Shimono K, Kamo N, Demura M, Nitta K. Ser-130 of Natronobacterium pharaonis halorhodopsin is important for the chloride binding. Biophys Chem 2003; 104:209-16. [PMID: 12834839 DOI: 10.1016/s0301-4622(02)00368-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pharaonis halorhodopsin (phR) is an inward light-driven chloride ion pump from Natronobacterium pharaonis. In order to clarify the role of Ser-130(phR) residue which corresponds to Ser-115(shR) for salinarum hR on the anion-binding affinity, the wild-type and Ser-130 mutants substituted with Thr, Cys and Ala were expressed in E. coli cells and solubilized with 0.1% n-dodecyl beta-D-maltopyranoside The absorption maximum (lambda(max)) of the S130T mutant indicated a blue shift from that of the wild type in the absence and presence of chloride. For S130A, a large red shift (12 nm) in the absence of chloride was observed. The wild-type and all mutants showed the blue-shift of lambda(max) upon Cl(-) addition, from which the dissociation constants of Cl(-) were determined. The dissociation constants were 5, 89, 153 and 159 mM for the wild-type, S130A, S130T and S130C, respectively, at pH 7.0 and 25 degrees C. Circular dichroic spectra of the wild-type and the Ser-130 mutants exhibited an oligomerization. The present study revealed that the Ser-130 of N. pharaonis halorhodopsin is important for the chloride binding.
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Affiliation(s)
- Maki Sato
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Hein M, Wegener AA, Engelhard M, Siebert F. Time-resolved FTIR studies of sensory rhodopsin II (NpSRII) from Natronobacterium pharaonis: implications for proton transport and receptor activation. Biophys J 2003; 84:1208-17. [PMID: 12547800 PMCID: PMC1302696 DOI: 10.1016/s0006-3495(03)74935-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The photocycle of the photophobic receptor from Natronobacterium pharaonis, NpSRII, is studied by static and time-resolved step-scan Fourier transform infrared spectroscopy. Both low-temperature static and time-resolved spectra resolve a K-like intermediate, and the corresponding spectra show little difference within the noise of the time-resolved data. As compared to intermediate K of bacteriorhodopsin, relatively large amide I bands indicate correspondingly larger distortions of the protein backbone. The time-resolved spectra identify an intermediate L-like state with surprisingly small additional molecular alterations. With the formation of intermediate M, the Schiff-base proton is transferred to the counterion Asp-75. This state is characterized by larger amide bands indicating larger distortions of the protein. We can identify a second M state that differs only in small-protein bands. Reisomerization of the chromophore to all-trans occurs with the formation of intermediate O. The accelerated decay of intermediate M caused by azide results in another red-shifted intermediate with a protonated Schiff base. The chromophore in this state, however, still has 13-cis geometry. Nevertheless, the reisomerization is still as slow as under the conditions without azide. The results are discussed with respect to mechanisms of the observed proton pumping and the possible roles of the intermediates in receptor activation.
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Affiliation(s)
- Michael Hein
- Sektion Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert Ludwigs Universität, 79104 Freiburg, Germany
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Abstract
Halorhodopsin, a light-driven halide pump, is the second archaeal rhodopsin involved in ion pumping to be studied at high resolution by X-ray crystallography. Like its cousin bacteriorhodopsin, halorhodopsin couples vectorial ion transport to the isomerisation state of a covalently linked retinal. Given the similarity and interconvertability of these two ion pumps, a unified mechanism for ion translocation by archaeal rhodopsins is now emerging.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Chemistry, Philipps University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.
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49
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Chizhov I, Engelhard M. Temperature and halide dependence of the photocycle of halorhodopsin from Natronobacterium pharaonis. Biophys J 2001; 81:1600-12. [PMID: 11509373 PMCID: PMC1301638 DOI: 10.1016/s0006-3495(01)75814-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The photocycle kinetics of halorhodopsin from Natronobacterium pharaonis (pHR(575)) was analyzed at different temperatures and chloride concentrations as well as various halides. Over the whole range of modified parameters the kinetics can be adequately modeled with six apparent rate constants. Assuming a model in which the observed rates are assigned to irreversible transitions of a single relaxation chain, six kinetically distinguishable states (P(1-6)) are discernible that are formed from four chromophore states (spectral archetypes S(j): K(570), L(N)(520), O(600), pHR'(575)). Whereas P(1) coincides with K(570) (S(1)), both P(2) and P(3) have identical spectra resembling L(520) (S(2)), thus representing a true spectral silent transition between them. P(4) constitutes a fast temperature-dependent equilibrium between the chromophore states S(2) and S(3) (L(520) and O(600), respectively). The subsequent equilibrium (P(5)) of the same spectral archetypes is only moderately temperature dependent but shows sensitivity toward the type of anion and the chloride concentration. Therefore, S(2) and S(3) occurring in P(4) as well as in P(5) have to be distinguished and are assigned to L(520)<--> O(1)(600) and O(2)(600)<--> N(520) equilibrium, respectively. It is proposed that P(4) and P(5) represent the anion release and uptake steps. Based on the experimental data affinities of the halide binding sites are estimated.
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Affiliation(s)
- I Chizhov
- Max-Planck-Institut für Molekulare Physiologie, 44227 Dortmund, Germany.
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