1
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Jacobson DR, Perkins TT. Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2313818121. [PMID: 38324569 PMCID: PMC10873598 DOI: 10.1073/pnas.2313818121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Ligand-induced conformational changes are critical to the function of many membrane proteins and arise from numerous intramolecular interactions. In the photocycle of the model membrane protein bacteriorhodopsin (bR), absorption of a photon by retinal triggers a conformational cascade that results in pumping a proton across the cell membrane. While decades of spectroscopy and structural studies have probed this photocycle in intricate detail, changes in intramolecular energetics that underlie protein motions have remained elusive to experimental quantification. Here, we measured these energetics on the millisecond time scale using atomic-force-microscopy-based single-molecule force spectroscopy. Precisely, timed light pulses triggered the bR photocycle while we measured the equilibrium unfolding and refolding of the terminal 8-amino-acid region of bR's G-helix. These dynamics changed when the EF-helix pair moved ~9 Å away from this end of the G helix during the "open" portion of bR's photocycle. In ~60% of the data, we observed abrupt light-induced destabilization of 3.4 ± 0.3 kcal/mol, lasting 38 ± 3 ms. The kinetics and pH-dependence of this destabilization were consistent with prior measurements of bR's open phase. The frequency of light-induced destabilization increased with the duration of illumination and was dramatically reduced in the triple mutant (D96G/F171C/F219L) thought to trap bR in its open phase. In the other ~40% of the data, photoexcitation unexpectedly stabilized a longer-lived putative misfolded state. Through this work, we establish a general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.
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Affiliation(s)
- David R. Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO80309
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2
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Suzuki R, Nagashima T, Kojima K, Hironishi R, Hirohata M, Ueta T, Murata T, Yamazaki T, Sudo Y, Takahashi H. Nuclear Magnetic Resonance Detection of Hydrogen Bond Network in a Proton Pump Rhodopsin RxR and Its Alteration during the Cyclic Photoreaction. J Am Chem Soc 2023. [PMID: 37410967 DOI: 10.1021/jacs.3c02833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Hydrogen bond formation and deformation are crucial for the structural construction and functional expression of biomolecules. However, direct observation of exchangeable hydrogens, especially for oxygen-bound hydrogens, relevant to hydrogen bonds is challenging for current structural analysis approaches. Using solution-state NMR spectroscopy, this study detected the functionally important exchangeable hydrogens (i.e., Y49-ηOH and Y178-ηOH) involved in the pentagonal hydrogen bond network in the active site of R. xylanophilus rhodopsin (RxR), which functions as a light-driven proton pump. Moreover, utilization of the original light-irradiation NMR approach allowed us to detect and characterize the late photointermediate state (i.e., O-state) of RxR and revealed that hydrogen bonds relevant to Y49 and Y178 are still maintained during the photointermediate state. In contrast, the hydrogen bond between W75-εNH and D205-γCOO- is strengthened and stabilizes the O-state.
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Affiliation(s)
- Rika Suzuki
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Toshio Nagashima
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Kojima
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Reika Hironishi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Masafumi Hirohata
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Ueta
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, Inage, Chiba 263-8522, Japan
| | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
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3
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Noji T, Ishikita H. Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle. J Phys Chem B 2022; 126:9945-9955. [PMID: 36413506 DOI: 10.1021/acs.jpcb.2c04359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR13-cis, J, K0, KE, KL, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
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4
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Kouyama T, Ihara K. Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183998. [PMID: 35753392 DOI: 10.1016/j.bbamem.2022.183998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/12/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X1) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.
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Affiliation(s)
- Tsutomu Kouyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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5
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Kouyama T, Ihara K. Two substates in the O intermediate of the light-driven proton pump archaerhodopsin-2. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183919. [PMID: 35304864 DOI: 10.1016/j.bbamem.2022.183919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/16/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The proton pumping cycle of archaerhodopsin-2 (aR2) was investigated over a wide pH range and at different salt concentrations. We have found that two substates, which are spectroscopically and kinetically distinguishable, occur in the O intermediate. The first O-intermediate (O1) absorbs maximumly at ~580 nm, whereas the late O-intermediate (O2) absorbs maximumly at 605 nm. At neutral pH, O1 is in rapid equilibrium with the N intermediate. When the medium pH is increased, O1 becomes less stable than N and, in proportion to the amount of O1 in the dynamic equilibrium between N and O1, the formation rate of O2 decreases. By contrast, the decay rate of O2 increases ~100 folds when the pH of a low-salt membrane suspension is increased from 5.5 to 7.5 or when the salt concentration is increased to 2 M KCl. Together with our recent study on two substates in the O intermediate of bacteriorhodopsin (bR), the present study suggests that the thermally activated re-isomerization of the retinylidene chromophore into the initial all-trans configuration takes place in the O1-to-O2 transition; that is, O1 contains a distorted 13-cis chromophore. It is also found that the pKa value of the key ionizable residue (Asp101aR2, Asp96bR) in the proton uptake channel is elevated in the O1 state of aR2 as compared to the O1 state of bR. This implies that the structural property of O1 in the aR2 photocycle can be investigated over a wide pH range.
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Affiliation(s)
- Tsutomu Kouyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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6
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Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc Natl Acad Sci U S A 2022; 119:2117433119. [PMID: 35197289 PMCID: PMC8892520 DOI: 10.1073/pnas.2117433119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 01/06/2023] Open
Abstract
Light-driven chloride pumps have been identified in various species, including archaea and marine flavobacteria. The function of ion transportation controllable by light is utilized for optogenetics tools in neuroscience. Chloride pumps differ among species, in terms of amino acid homology and structural similarity. Our time-resolved crystallographic studies using X-ray free electron lasers reveal the molecular mechanism of halide ion transfer in a light-driven chloride pump from a marine flavobacterium. Our data indicate a common mechanism in chloride pumping rhodopsins, as compared to previous low-temperature trapping studies of chloride pumps. These findings are significant not only for further improvements of optogenetic tools but also for a general understanding of the ion pumping mechanisms of microbial rhodopsins. Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-µs and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.
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7
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Tsuneishi T, Takahashi M, Tsujimura M, Kojima K, Ishikita H, Takeuchi Y, Sudo Y. Exploring the Retinal Binding Cavity of Archaerhodopsin-3 by Replacing the Retinal Chromophore With a Dimethyl Phenylated Derivative. Front Mol Biosci 2022; 8:794948. [PMID: 34988122 PMCID: PMC8721008 DOI: 10.3389/fmolb.2021.794948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Rhodopsins act as photoreceptors with their chromophore retinal (vitamin-A aldehyde) and they regulate light-dependent biological functions. Archaerhodopsin-3 (AR3) is an outward proton pump that has been widely utilized as a tool for optogenetics, a method for controlling cellular activity by light. To characterize the retinal binding cavity of AR3, we synthesized a dimethyl phenylated retinal derivative, (2E,4E,6E,8E)-9-(2,6-Dimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenal (DMP-retinal). QM/MM calculations suggested that DMP-retinal can be incorporated into the opsin of AR3 (archaeopsin-3, AO3). Thus, we introduced DMP-retinal into AO3 to obtain the non-natural holoprotein (AO3-DMP) and compared some molecular properties with those of AO3 with the natural A1-retinal (AO3-A1) or AR3. Light-induced pH change measurements revealed that AO3-DMP maintained slow outward proton pumping. Noteworthy, AO3-DMP had several significant changes in its molecular properties compared with AO3-A1 as follows; 1) spectroscopic measurements revealed that the absorption maximum was shifted from 556 to 508 nm and QM/MM calculations showed that the blue-shift was due to the significant increase in the HOMO-LUMO energy gap of the chromophore with the contribution of some residues around the chromophore, 2) time-resolved spectroscopic measurements revealed the photocycling rate was significantly decreased, and 3) kinetical spectroscopic measurements revealed the sensitivity of the chromophore binding Schiff base to attack by hydroxylamine was significantly increased. The QM/MM calculations show that a cavity space is present at the aromatic ring moiety in the AO3-DMP structure whereas it is absent at the corresponding β-ionone ring moiety in the AO3-A1 structure. We discuss these alterations of the difference in interaction between the natural A1-retinal and the DMP-retinal with binding cavity residues.
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Affiliation(s)
- Taichi Tsuneishi
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masataka Takahashi
- Laboratory of Synthetic and Medicinal Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan
| | - Keiichi Kojima
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yasuo Takeuchi
- Laboratory of Synthetic and Medicinal Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuki Sudo
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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8
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Abstract
Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms of these proteins is not possible without the knowledge of their high-resolution structures, which can be primarily obtained by X-ray crystallography. This technique, however, requires high-quality crystals, growing of which is a great challenge especially in case of membrane proteins. In this chapter, we summarize methods applied for crystallization of microbial rhodopsins with the emphasis on crystallization in lipidic mesophases, also known as in meso approach. In particular, we describe in detail the methods of crystallization using lipidic cubic phase to grow both large crystals optimized for traditional crystallographic data collection and microcrystals for serial crystallography.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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9
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Weinert T, Skopintsev P, James D, Dworkowski F, Panepucci E, Kekilli D, Furrer A, Brünle S, Mous S, Ozerov D, Nogly P, Wang M, Standfuss J. Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography. Science 2020; 365:61-65. [PMID: 31273117 DOI: 10.1126/science.aaw8634] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/11/2019] [Indexed: 11/02/2022]
Abstract
Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize protein motions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.
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Affiliation(s)
- Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| | - Petr Skopintsev
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Demet Kekilli
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sandra Mous
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Meitian Wang
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
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10
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Mei G, Mamaeva N, Ganapathy S, Wang P, DeGrip WJ, Rothschild KJ. Analog Retinal Redshifts Visible Absorption of QuasAr Transmembrane Voltage Sensors into Near-infrared. Photochem Photobiol 2019; 96:55-66. [PMID: 31556123 PMCID: PMC7004139 DOI: 10.1111/php.13169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/01/2022]
Abstract
Opsin‐based transmembrane voltage sensors (OTVSs) are increasingly important tools for neuroscience enabling neural function in complex brain circuits to be explored in live, behaving animals. However, the visible wavelengths required for fluorescence excitation of the current generation of OTVSs limit optogenetic imaging in the brain to depths of only a few mm due to the strong absorption and scattering of visible light by biological tissues. We report that substitution of the native A1 retinal chromophore of the widely used QuasAr1/2 OTVSs with the retinal analog MMAR containing a methylamino‐modified dimethylphenyl ring results in over a 100‐nm redshift of the maxima of the absorption and fluorescence emission bands to near 700 and 840 nm, respectively. FT‐Raman spectroscopy reveals that at pH 7 QuasAr1 with both the A1 and MMAR chromophores possess predominantly an all‐trans protonated Schiff base configuration with the MMAR chromophore exhibiting increased torsion of the polyene single‐/double‐bond system similar to the O‐intermediate of the BR photocycle. In contrast, the A1 and the MMAR chromophores of QuasAr2 exist partially in a 13‐cis PSB configuration. These results demonstrate that QuasArs containing the MMAR chromophore are attractive candidates for use as NIR‐OTVSs, especially for applications such as deep brain imaging.
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Affiliation(s)
- Gaoxiang Mei
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
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11
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Wickstrand C, Nogly P, Nango E, Iwata S, Standfuss J, Neutze R. Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation. Annu Rev Biochem 2019; 88:59-83. [DOI: 10.1146/annurev-biochem-013118-111327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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12
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Miyahara T, Nakatsuji H. Light-Driven Proton, Sodium Ion, and Chloride Ion Transfer Mechanisms in Rhodopsins: SAC-CI Study. J Phys Chem A 2019; 123:1766-1784. [DOI: 10.1021/acs.jpca.8b10203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
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13
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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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14
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Dai G, Geng X, Chaoluomeng, Tamogami J, Kikukawa T, Demura M, Kamo N, Iwasa T. Photocycle of Sensory Rhodopsin II from Halobacterium salinarum (HsSRII): Mutation of D103 Accelerates M Decay and Changes the Decay Pathway of a 13-cis O-like Species. Photochem Photobiol 2018. [PMID: 29512821 DOI: 10.1111/php.12917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aspartic acid 103 (D103) of sensory rhodopsin II from Halobacterium salinarum (HsSRII, or also called phoborhodopsin) corresponds to D115 of bacteriorhodopsin (BR). This amino acid residue is functionally important in BR. This work reveals that a substitution of D103 with asparagine (D103N) or glutamic acid (D103E) can cause large changes in HsSRII photocycle. These changes include (1) shortened lifetime of the M intermediate in the following order: the wild-type > D103N > D103E; (2) altered decay pathway of a 13-cis O-like species. The 13-cis O-like species, tentatively named Px, was detected in HsSRII photocycle. Px appeared to undergo branched reactions at 0°C, leading to a recovery of the unphotolyzed state and formation of a metastable intermediate, named P370, that slowly decayed to the unphotolyzed state at room temperature. In wild-type HsSRII at 0°C, Px mainly decayed to the unphotolyzed state, and the decay reaction toward P370 was negligible. In mutant D103E at 0°C, Px decayed to P370, while the recovery of the unphotolyzed state became unobservable. In mutant D103N, the two reactions proceeded at comparable rates. Thus, D103 of HsSRII may play an important role in regulation of the photocycle of HsSRII.
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Affiliation(s)
- Gang Dai
- College of Chemistry and Environmental Science, Inner Mongolia Normal University, Hohhot, 010018, China
| | - Xiong Geng
- Division of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Chaoluomeng
- Division of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Jun Tamogami
- College of Pharmaceutical Science, Matsuyama University, Matsuyama, 790-8578, 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, 001-0021, Japan
| | - Makoto Demura
- 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, 001-0021, Japan
| | - Naoki Kamo
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tatsuo Iwasa
- Division of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
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15
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Tamogami J, Kikukawa T, Nara T, Demura M, Kimura-Someya T, Shirouzu M, Yokoyama S, Miyauchi S, Shimono K, Kamo N. Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga. Biophys Physicobiol 2017; 14:49-55. [PMID: 28560129 PMCID: PMC5437830 DOI: 10.2142/biophysico.14.0_49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/02/2017] [Indexed: 12/01/2022] Open
Abstract
A spectrally silent change is often observed in the photocycle of microbial rhodopsins. Here, we suggest the presence of two O intermediates in the photocycle of Acetabularia rhodopsin II (ARII or also called Ace2), a light-driven algal proton pump from Acetabularia acetabulum. ARII exhibits a photocycle including a quasi-equilibrium state of M, N, and O (M⇄N⇄O→) at near neutral and above pH values. However, acidification of the medium below pH ~5.5 causes no accumulation of N, resulting in that the photocycle of ARII can be described as an irreversible scheme (M→O→). This may facilitate the investigation of the latter part of the photocycle, especially the rise and decay of O, during which molecular events have not been sufficiently understood. Thus we analyzed the photocycle under acidic conditions (pH ≤ 5.5). Analysis of the absorbance change at 610 nm, which mainly monitors the fractional concentration changes of K and O, was performed and revealed a photocycle scheme containing two sequential O-states with the different molar extinction coefficients. These photoproducts, termed O1 and O2, may be even produced at physiological pH, although they are not clearly observed under this condition due to the existence of a long M-N-O equilibrium.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, 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 001-0021, Japan
| | - Toshifumi Nara
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Makoto Demura
- 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 001-0021, Japan
| | - Tomomi Kimura-Someya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
| | - Seiji Miyauchi
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Kazumi Shimono
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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16
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Ge X, Gunner MR. Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Proteins 2016; 84:639-54. [DOI: 10.1002/prot.25013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/24/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaoxia Ge
- Physics Department; City College of New York; New York NY 10031
| | - M. R. Gunner
- Physics Department; City College of New York; New York NY 10031
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17
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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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18
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Tavanti F, Tozzini V. A multi-scale-multi-stable model for the rhodopsin photocycle. Molecules 2014; 19:14961-78. [PMID: 25237751 PMCID: PMC6271392 DOI: 10.3390/molecules190914961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/28/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022] Open
Abstract
We report a multi-scale simulation study of the photocycle of the rhodopsins. The quasi-atomistic representation ("united atoms" UA) of retinal is combined with a minimalist coarse grained (CG, one-bead-per amino acid) representation of the protein, in a hybrid UA/CG approach, which is the homolog of QM/MM, but at lower resolution. An accurate multi-stable parameterization of the model allows simulating each state and transition among them, and the combination of different scale representation allows addressing the entire photocycle. We test the model on bacterial rhodopsin, for which more experimental data are available, and then also report results for mammalian rhodopsins. In particular, the analysis of simulations reveals the spontaneous appearance of meta-stable states in quantitative agreement with experimental data.
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Affiliation(s)
- Francesco Tavanti
- NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Valentina Tozzini
- NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy.
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19
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Wickstrand C, Dods R, Royant A, Neutze R. Bacteriorhodopsin: Would the real structural intermediates please stand up? Biochim Biophys Acta Gen Subj 2014; 1850:536-53. [PMID: 24918316 DOI: 10.1016/j.bbagen.2014.05.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined. SCOPE OF REVIEW We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data. MAJOR CONCLUSIONS An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212. GENERAL SIGNIFICANCE A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Antoine Royant
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France; European Synchrotron Radiation Facility, F-38043 Grenoble, France.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.
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20
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Good DB, Wang S, Ward ME, Struppe J, Brown LS, Lewandowski JR, Ladizhansky V. Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR. J Am Chem Soc 2014; 136:2833-42. [DOI: 10.1021/ja411633w] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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21
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Geibel S, Lörinczi È, Bamberg E, Friedrich T. Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate. PLoS One 2013; 8:e73338. [PMID: 24019918 PMCID: PMC3760879 DOI: 10.1371/journal.pone.0073338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum is tightly regulated by the [H(+)] gradient and transmembrane potential. BR exhibits optoelectric properties, since spectral changes during the photocycle are kinetically controlled by voltage, which predestines BR for optical storage or processing devices. BR mutants with prolonged lifetime of the blue-shifted M intermediate would be advantageous, but the optoelectric properties of such mutants are still elusive. Using expression in Xenopus oocytes and two-electrode voltage-clamping, we analyzed photocurrents of BR mutants with kinetically destabilized (F171C, F219L) or stabilized (D96N, D96G) M intermediate in response to green light (to probe H(+) pumping) and blue laser flashes (to probe accumulation/decay of M). These mutants have divergent M lifetimes. As for BR-WT, this strictly correlates with the voltage dependence of H(+) pumping. BR-F171C and BR-F219L showed photocurrents similar to BR-WT. Yet, BR-F171C showed a weaker voltage dependence of proton pumping. For both mutants, blue laser flashes applied during and after green-light illumination showed reduced M accumulation and shorter M lifetime. In contrast, BR-D96G and BR-D96N exhibited small photocurrents, with nonlinear current-voltage curves, which increased strongly in the presence of azide. Blue laser flashes showed heavy M accumulation and prolonged M lifetime, which accounts for the strongly reduced H(+) pumping rate. Hyperpolarizing potentials augmented these effects. The combination of M-stabilizing and -destabilizing mutations in BR-D96G/F171C/F219L (BR-tri) shows that disruption of the primary proton donor Asp-96 is fatal for BR as a proton pump. Mechanistically, M destabilizing mutations cannot compensate for the disruption of Asp-96. Accordingly, BR-tri and BR-D96G photocurrents were similar. However, BR-tri showed negative blue laser flash-induced currents even without actinic green light, indicating that Schiff base deprotonation in BR-tri exists in the dark, in line with previous spectroscopic investigations. Thus, M-stabilizing mutations, including the triple mutation, drastically interfere with electrochemical H(+) gradient generation.
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Affiliation(s)
- Sven Geibel
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Èva Lörinczi
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Thomas Friedrich
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
- Technical University of Berlin, Institute of Chemistry, Berlin, Germany
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22
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Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T. Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. Biophys J 2013; 104:377-85. [PMID: 23442859 DOI: 10.1016/j.bpj.2012.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 02/01/2023] Open
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.
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