1
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Kato T, Tsukamoto T, Demura M, Kikukawa T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J Biol Chem 2021; 296:100792. [PMID: 34019877 PMCID: PMC8219890 DOI: 10.1016/j.jbc.2021.100792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na+-pump rhodopsin. We triggered the transport cycle of Na+-pump rhodopsin using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions and elucidated the sequential formation of the Na+-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na+ concentration, indicating that Na+ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na+ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na+ release on the extracellular side. Thus, there is an irreversible switch in “accessibility” during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na+ transport.
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Affiliation(s)
- Tomoya Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
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2
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Functional Mechanism of Cl --Pump Rhodopsin and Its Conversion into H + Pump. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:55-71. [PMID: 33398807 DOI: 10.1007/978-981-15-8763-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cl--pump rhodopsin is the second discovered microbial rhodopsin. Although its physiological role has not been fully clarified, its functional mechanism has been studied as a model for anion transporters. After the success of neural activation by channel rhodopsin, the first Cl--pump halorhodopsin (HR) had become widely used as a neural silencer. The emergence of artificial and natural anion channel rhodopsins lowered the importance of HRs. However, the longer absorption maxima of approximately 585-600 nm for HRs are still advantageous for applications in mammalian brains and collaborations with neural activators possessing shorter absorption maxima. In this chapter, the variation and functional mechanisms of Cl- pumps are summarized. After the discovery of HR, Cl--pump rhodopsins were confined to only extremely halophilic haloarchaea. However, after 2014, two Cl--pump groups were newly discovered in marine and terrestrial bacteria. These Cl- pumps are phylogenetically distinct from HRs and have unique characteristics. In particular, the most recently identified Cl- pump has close similarity with the H+ pump bacteriorhodopsin and was converted into the H+ pump by a single amino acid replacement.
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3
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Murabe K, Tsukamoto T, Aizawa T, Demura M, Kikukawa T. Direct Detection of the Substrate Uptake and Release Reactions of the Light-Driven Sodium-Pump Rhodopsin. J Am Chem Soc 2020; 142:16023-16030. [PMID: 32844642 DOI: 10.1021/jacs.0c07264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the requirements of the experimental methods, which are to detect the timing of the formation and decay of intermediates and to detect the timing of substrate uptake and release. We report successfully achieving this for the light-driven Na+ pump rhodopsin (NaR). Here, a Na+-selective membrane, which consists of polyvinyl chloride and a Na+ ionophore, was employed to detect Na+ uptake and release. When one side of the membrane was covered by the lipid-reconstituted NaR, continuous illumination induced an increase in membrane potential, which reflected Na+ uptake by the photolyzed NaR. Via use of nanosecond laser pulses, two kinds of data were obtained during a single transport cycle: one was the flash-induced absorbance change in NaR to detect the formation and decay of structural intermediates, and the other was the flash-induced change in membrane potential, which reflects the transient Na+ uptake and release reactions. Their comparison clearly indicated that Na+ is captured and released during the formation and decay of the O intermediate, the red-shifted intermediate that appears in the latter half of the transport cycle.
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Affiliation(s)
- Keisuke Murabe
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Tsukamoto
- 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
| | - Tomoyasu Aizawa
- 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
| | - 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
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4
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Yamamoto A, Tsukamoto T, Suzuki K, Hashimoto E, Kobashigawa Y, Shibasaki K, Uchida T, Inagaki F, Demura M, Ishimori K. Spectroscopic Characterization of Halorhodopsin Reconstituted into Nanodisks Using Native Lipids. Biophys J 2020; 118:2853-2865. [PMID: 32396848 DOI: 10.1016/j.bpj.2020.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022] Open
Abstract
We successfully reconstituted single Natronomonas pharaonis halorhodopsin (NpHR) trimers into a nanodisk (ND) using the native archaeal lipid (NL) and an artificial lipid having a zwitterionic headgroup, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Incorporation of single trimeric NpHR into NDs was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, size-exclusion chromatography, and visible circular dichroism spectroscopy. The Cl- binding affinity of NpHR in NDs using NL (NL-ND NpHR) or POPC (POPC-ND NpHR) was examined by absorption spectroscopy, showing that the Cl--releasing affinities (Kd,N↔O) of these ND-reconstituted NpHRs are more than 10 times higher than that obtained from native NpHR membrane fragments (MFs) harvested from a NpHR-overexpressing archaeal strain (MF NpHR). The photoreaction kinetics of these ND-reconstituted NpHRs revealed that the Cl- uptake was faster than that of MF NpHR. These differences in the Cl--releasing and uptake properties of ND-reconstituted NpHRs and MF NpHR may arise from suppression of protein conformational changes associated with Cl- release from the trimeric NpHR caused by ND reconstitution, conformational perturbation in the trimeric state, and loss of the trimer-trimer interactions. On the other hand, POPC-ND NpHR demonstrated accelerated Cl- uptake compared to NL-ND NpHR, suggesting that the negative charge on the archaeal membrane surface regulates the photocycle of NpHR. Although NL-ND NpHR and MF NpHR are embedded in the same lipid, the lower Cl--binding affinity at the initial state (Kd,initial) and faster recovering from the NpHR' state to the original state of the photoreaction cycle were observed for NL-ND NpHR, probably because of insufficient interactions with a chromophore in the native membrane, bacterioruberin in reconstituted NDs. Our results indicate that specific interactions of NpHR with surrounding lipids and bacterioruberin, structural flexibility of the membrane, and interactions between trimeric NpHRs may be necessary for efficient Cl- pumping.
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Affiliation(s)
- Ayumi Yamamoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Kenshiro Suzuki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Eri Hashimoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | | | - Kousuke Shibasaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Fuyuhiko Inagaki
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
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5
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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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6
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Nakajima Y, Tsukamoto T, Kumagai Y, Ogura Y, Hayashi T, Song J, Kikukawa T, Demura M, Kogure K, Sudo Y, Yoshizawa S. Presence of a Haloarchaeal Halorhodopsin-Like Cl - Pump in Marine Bacteria. Microbes Environ 2018; 33:89-97. [PMID: 29553064 PMCID: PMC5877348 DOI: 10.1264/jsme2.me17197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl--pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl- pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl--transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl--pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.
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Affiliation(s)
- Yu Nakajima
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Yohei Kumagai
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Jaeho Song
- Department of Biological Sciences, Inha University
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Kazuhiro Kogure
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Susumu Yoshizawa
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
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7
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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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8
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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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9
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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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10
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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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11
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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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12
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Schreiner M, Schlesinger R, Heberle J, Niemann HH. Structure of Halorhodopsin from Halobacterium salinarum in a new crystal form that imposes little restraint on the E-F loop. J Struct Biol 2015; 190:373-8. [PMID: 25916754 DOI: 10.1016/j.jsb.2015.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
Abstract
Halorhodopsin from the halophilic archaeon Halobacterium salinarum is a membrane located light-driven chloride pump. Upon illumination Halorhodopsin undergoes a reversible photocycle initiated by the all-trans to 13-cis isomerization of the covalently bound retinal chromophore. The photocycle consists of several spectroscopically distinct intermediates. The structural basis of the chloride transport mechanism remains elusive, presumably because packing contacts have so far precluded protein conformational changes in the available crystals. With the intention to structurally characterize late photocycle intermediates by X-ray crystallography we crystallized Halorhodopsin in a new crystal form using the vesicle fusion method. In the new crystal form lateral contacts are mediated by helices A and G. Helices E and F that were suggested to perform large movements during the photocycle are almost unrestrained by packing contacts. This feature might permit the displacement of these helices without disrupting the crystal lattice. Therefore, this new crystal form might be an excellent system for the structural characterization of late Halorhodopsin photocycle intermediates by trapping or by time resolved experiments, especially at XFELs.
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Affiliation(s)
- Madeleine Schreiner
- Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Ramona Schlesinger
- Genetic Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hartmut H Niemann
- Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
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