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Discovery of Light-Powered Organic Ion Transport by a Natural Protein

Simiao Shen, Shoichiro Akita, Joji Wada, Mako Eguchi, Takashi Tsukamoto, Kwang-Hwan Jung, Yuki Sudo, Takashi Kikukawa

2025年7月

Ultrafast Protein Dynamics Prior to Retinal Photoisomerization in Microbial Rhodopsins 査読

Shinya Tahara, Rika Kurihara, Keiichi Kojima, Hikaru Kuramochi, Satoshi Takeuchi, Yuki Sudo, Tahei Tahara

The Journal of Physical Chemistry Letters 16 ( 23 ) 5732 - 5738 2025年6月

A repertoire of visible light-sensitive opsins in the deep-sea hydrothermal vent shrimp Rimicaris hybisae 査読

Yuya Nagata, Norio Miyamoto, Keita Sato, Yosuke Nishimura, Yuki Tanioka, Yuji Yamanaka, Susumu Yoshizawa, Kuto Takahashi, Kohei Obayashi, Hisao Tsukamoto, Ken Takai, Hideyo Ohuchi, Takahiro Yamashita, Yuki Sudo, Keiichi Kojima

Journal of Biological Chemistry 110291 - 110291 2025年5月

Roles of basic amino acid residues in substrate binding and transport of the light-driven anion pump Synechocystis halorhodopsin (SyHR) 査読

Masaki Nakama, Tomoyasu Noji, Keiichi Kojima, Susumu Yoshizawa, Hiroshi Ishikita, Yuki Sudo

Journal of Biological Chemistry 2025年4月

The use of microbial rhodopsin proteins in differential photodetection 査読

Louisa Reissig, Kirstin Buchanan, Thea Lindner, Marie Kurihara, Po-Chuan Chan, Falk Kibowski, Keiichi Kojima, Simon Dalgleish, Kunio Awaga, Yuki Sudo

Frontiers in Physics 12 1481341 2024年12月

Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria 査読

Masumi Hasegawa-Takano, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Marie Kurihara, Yu Nakajima, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa

The ISME Journal 18 ( 1 ) wrae175 2024年11月

掲載種別：研究論文（学術雑誌）出版者・発行元：Oxford University Press (OUP)

Abstract

Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.

DOI： 10.1093/ismejo/wrae175

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Unusual Vibrational Coupling of the Schiff Base in the Retinal Chromophore of Sodium Ion-Pumping Rhodopsins 査読

Taiki Nakamura, Yuka Shinozaki, Akihiro Otomo, Taito Urui, Misao Mizuno, Rei Abe-Yoshizumi, Manami Hashimoto, Keiichi Kojima, Yuki Sudo, Hideki Kandori, Yasuhisa Mizutani

The Journal of Physical Chemistry B 128 ( 32 ) 7813 - 7821 2024年8月

Bidirectional Optical Control of Proton Motive Force in Escherichia coli Using Microbial Rhodopsins 査読

Kotaro Nakanishi, Keiichi Kojima, Yoshiyuki Sowa, Yuki Sudo

The Journal of Physical Chemistry B 128 ( 27 ) 6509 - 6517 2024年7月

Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography 査読

Atsushi Shibukawa, Ryota Higuchi, Gookho Song, Hideharu Mikami, Yuki Sudo, Mooseok Jang

Nature Communications 15 2926 2024年4月

Demonstration of iodide-dependent UVA-triggered growth inhibition in Saccharomyces cerevisiae cells and identification of its suppressive molecules 査読

Ryota Ono, Nozomu Saeki, Keiichi Kojima, Hisao Moriya, Yuki Sudo

Biochemical and Biophysical Research Communications 677 1 - 5 2023年10月

Nuclear Magnetic Resonance Detection of Hydrogen Bond Network in a Proton Pump Rhodopsin RxR and Its Alteration during the Cyclic Photoreaction 査読

Rika Suzuki, Toshio Nagashima, Keiichi Kojima, Reika Hironishi, Masafumi Hirohata, Tetsuya Ueta, Takeshi Murata, Toshio Yamazaki, Yuki Sudo, Hideo Takahashi

Journal of the American Chemical Society 145 ( 28 ) 15295 - 15302 2023年7月

Development of light-induced disruptive liposomes (LiDL) as a photoswitchable carrier for intracellular substance delivery. 査読国際誌

Taichi Tsuneishi, Keiichi Kojima, Fumika Kubota, Hideyoshi Harashima, Yuma Yamada, Yuki Sudo

Chemical Communications (Cambridge, England) 59 ( 49 ) 7591 - 7594 2023年6月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

Light-driven inward proton pump rhodopsin RmXeR was embedded in pH-sensitive liposomes. Substance release from the proteoliposomes was observed following light illumination both in vitro and in cells, indicating the successful production of light-induced disruptive liposomes (LiDL). Thus, LiDL is a photoswitchable carrier utilized for intracellular substance delivery.

DOI： 10.1039/d3cc02056h

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A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis 査読国際誌

Keiichi Kojima, Shiho Kawanishi, Yosuke Nishimura, Masumi Hasegawa, Shin Nakao, Yuya Nagata, Susumu Yoshizawa, Yuki Sudo

Scientific Reports 13 ( 1 ) 6974 - 6974 2023年4月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

Microbial rhodopsins, a family of photoreceptive membrane proteins containing the chromophore retinal, show a variety of light-dependent molecular functions. Channelrhodopsins work as light-gated ion channels and are widely utilized for optogenetics, which is a method for controlling neural activities by light. Since two cation channelrhodopsins were identified from the chlorophyte alga Chlamydomonas reinhardtii, recent advances in genomic research have revealed a wide variety of channelrhodopsins including anion channelrhodopsins (ACRs), describing their highly diversified molecular properties (e.g., spectral sensitivity, kinetics and ion selectivity). Here, we report two channelrhodopsin-like rhodopsins from the Colpodellida alga Vitrella brassicaformis, which are phylogenetically distinct from the known channelrhodopsins. Spectroscopic and electrophysiological analyses indicated that these rhodopsins are green- and blue-sensitive pigments (λ_max = ~ 550 and ~ 440 nm) that exhibit light-dependent ion channeling activities. Detailed electrophysiological analysis revealed that one of them works as a monovalent anion (Cl⁻, Br⁻ and NO₃⁻) channel and we named it V. brassicaformis anion channelrhodopsin-2, VbACR2. Importantly, the absorption maximum of VbACR2 (~ 440 nm) is blue-shifted among the known ACRs. Thus, we identified the new blue-shifted ACR, which leads to the expansion of the molecular diversity of ACRs.

DOI： 10.1038/s41598-023-34125-8

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その他リンク： https://www.nature.com/articles/s41598-023-34125-8

Concerted primary proton transfer reactions in a thermophilic rhodopsin studied by time-resolved infrared spectroscopy at high temperature. 査読国際誌

Kunisato Kuroi, Takashi Tsukamoto, Naoya Honda, Yuki Sudo, Yuji Furutani

Biochimica et Biophysica Acta. Bioenergetics 1864 ( 3 ) 148980 - 148980 2023年4月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

The primary proton transfer reactions of thermophilic rhodopsin, which was first discovered in an extreme thermophile, Thermus thermophilus JL-18, were investigated using time-resolved Fourier transform infrared spectroscopy at various temperatures ranging from 298 to 343 K (25 to 70 °C) and proton transport activity analysis. The analyses were performed using counterion (D95E, D95N, D229E, and D229N) and proton donor mutants (E106D and E106Q) as well. First, the initial proton transfer from the protonated retinal Schiff base (PRSB) to D95 was identified. The temperature dependency showed that the proton transfer reaction in the intermediate states dramatically changed above 318 K (45 °C). In addition, the proton transfer reaction correlated well with the structural change from turn to β-strand in the protein moiety, suggesting that this step may be regulated by the rigidity of the loop region. We also elucidated that the proton transfer reaction from proton donor E106 to the retinal Schiff base occurred synchronously with the primary proton transfer from the PRSB to D95. Surprisingly, we discovered that the direction of proton transfer was regulated by the secondary counterion, D229. Comparative analysis of Gloeobacter rhodopsin from the mesophile, Gloeobacter violaceus, highlighted that the primary proton transfer reactions in thermophilic rhodopsin were optimized at high temperatures partly due to the specific turn to β-strand structural change. This was not observed in Gloeobacter rhodopsin and other related proteins such as bacteriorhodopsin.

DOI： 10.1016/j.bbabio.2023.148980

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Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota 査読

Titouan Jaunet-Lahary, Tatsuro Shimamura, Masahiro Hayashi, Norimichi Nomura, Kouta Hirasawa, Tetsuya Shimizu, Masao Yamashita, Naotaka Tsutsumi, Yuta Suehiro, Keiichi Kojima, Yuki Sudo, Takashi Tamura, Hiroko Iwanari, Takao Hamakubo, So Iwata, Kei-ichi Okazaki, Teruhisa Hirai, Atsuko Yamashita

Nature Communications 14 ( 1 ) 2023年4月

掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.

DOI： 10.1038/s41467-023-36883-5

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その他リンク： https://www.nature.com/articles/s41467-023-36883-5

Identification of a Functionally Efficient and Thermally Stable Outward Sodium-Pumping Rhodopsin BeNaR from a Thermophilic Bacterium 査読

Marie Kurihara, Vera Thiel, Hirona Takahashi, Keiichi Kojima, David M. Ward, Donald A. Bryant, Makoto Sakai, Susumu Yoshizawa, Yuki Sudo

Chemical and Pharmaceutical Bulletin 71 ( 2 ) 154 - 164 2023年2月

Detection of Membrane Potential-Dependent Rhodopsin Fluorescence Using Low-Intensity Light Emitting Diode for Long-Term Imaging 査読

Shiho Kawanishi, Keiichi Kojima, Atsushi Shibukawa, Masayuki Sakamoto, Yuki Sudo

ACS Omega 8 4826 - 4834 2023年1月

Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms 査読

Susumu Yoshizawa, Tomonori Azuma, Keiichi Kojima, Keisuke Inomura, Masumi Hasegawa, Yosuke Nishimura, Masuzu Kikuchi, Gabrielle Armin, Yuya Tsukamoto, Hideaki Miyashita, Kentaro Ifuku, Takashi Yamano, Adrian Marchetti, Hideya Fukuzawa, Yuki Sudo, Ryoma Kamikawa

Microbes and Environments 38 ( 2 ) ME23015 2023年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Japanese Society of Microbial Ecology

Diatoms are a major phytoplankton group responsible for approximately 20% of carbon fixation on Earth. They perform photosynthesis using light-harvesting chlo-rophylls located in plastids, an organelle obtained through eukaryote-eukaryote endosymbiosis. Microbial rhodopsin, a photoreceptor distinct from chlo-rophyll-based photosystems, was recently identified in some diatoms. However, the physiological function of diatom rhodopsin remains unclear. Heterologous expression techniques were herein used to investigate the protein function and subcellular localization of diatom rhodopsin. We demonstrated that diatom rhodopsin acts as a light-driven proton pump and localizes primarily to the outermost membrane of four membrane-bound complex plastids. Using model simulations, we also examined the effects of pH changes inside the plastid due to rhodopsin-mediated proton transport on photosynthesis. The results obtained suggested the involvement of rhodopsin-mediated local pH changes in a photosynthetic CO2-concentrating mechanism in rhodopsin-possessing diatoms.

DOI： 10.1264/jsme2.me23015

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Mutations conferring SO42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant. 査読国際誌

Yuhei Doi, Jo Watanabe, Ryota Nii, Takashi Tsukamoto, Makoto Demura, Yuki Sudo, Takashi Kikukawa

Scientific reports 12 ( 1 ) 16422 - 16422 2022年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl- and Br-, but SyHR also transports SO42-, despite the close sequence similarity to MrHR. We sought a determinant that could confer SO42- pumping ability on MrHR and found that the removal of a negative charge at the anion entrance is a prerequisite for SO42- transport by MrHR. Consistently, the reverse mutation in SyHR significantly weakened SO42- pump activity. Notably, the MrHR and SyHR mutants did not show SO42- induced absorption spectral shifts or changes in the photoreactions, suggesting no bindings of SO42- in their initial states or the bindings to the sites far from the protein centers. In other words, unlike wild-type SyHR, these mutants take up SO42- into their centers after illumination and release it before the ends of the photoreactions.

DOI： 10.1038/s41598-022-20784-6

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Phototriggered Apoptotic Cell Death (PTA) Using the Light-Driven Outward Proton Pump Rhodopsin Archaerhodopsin-3 査読

Shin Nakao, Keiichi Kojima, Yuki Sudo

Journal of the American Chemical Society 144 ( 9 ) 3771 - 3775 2022年2月

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations. 査読国際誌

Satoshi Yasuda, Tomoki Akiyama, Keiichi Kojima, Tetsuya Ueta, Tomohiko Hayashi, Satoshi Ogasawara, Satoru Nagatoishi, Kouhei Tsumoto, Naoki Kunishima, Yuki Sudo, Masahiro Kinoshita, Takeshi Murata

The Journal of Physical Chemistry B 126 ( 5 ) 1004 - 1015 2022年2月

記述言語：英語掲載種別：研究論文（学術雑誌）

We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation Tm is ∼91.8 °C. The TSSMs previously identified in step (1) were F90K, F90R, and Y91I with ΔTm ∼5.6, ∼5.5, and ∼2.9 °C, respectively, and those in step (2) were V79K, T114D, A115P, and A116E with ΔTm ∼2.7, ∼4.2, ∼2.6, and ∼2.3 °C, respectively (ΔTm denotes the increase in Tm). In this study, we construct triple and quadruple mutants, F90K+Y91I+T114D and F90K+Y91I+V79K+T114D. The values of ΔTm for these multiple mutants are ∼11.4 and ∼13.5 °C, respectively. Tm of the quadruple mutant (∼105.3 °C) establishes a new record in a class of outward proton pumping rhodopsins. It is higher than Tm of Rubrobacter xylanophilus rhodopsin (∼100.8 °C) that was the most thermostable in the class before this study.

DOI： 10.1021/acs.jpcb.1c08684

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Proton-pumping rhodopsins in marine diatoms

Susumu Yoshizawa, Tomonori Azuma, Keiichi Kojima, Keisuke Inomura, Masumi Hasegawa, Yosuke Nishimura, Masuzu Kikuchi, Gabrielle Armin, Hideaki Miyashita, Kentaro Ifuku, Takashi Yamano, Adrian Marchetti, Hideya Fukuzawa, Yuki Sudo, Ryoma Kamikawa

bioRxiv 2022年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Cold Spring Harbor Laboratory

Abstract

Diatoms are a major phytoplankton group responsible for about 20% of Earth’s primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. However, the physiological function of diatom rhodopsin is not well understood. Here we show that the diatom rhodopsin acts as a light-driven proton pump and localizes to the outermost membrane of the four membrane-bound complex plastids. Heterologous expression techniques were used to investigate the protein function and subcellular localization of diatom rhodopsin. Using model simulations, we further evaluated the physiological role of the acidic pool in the plastid produced by proton-transporting rhodopsin. Our results propose that the rhodopsin-derived acidic pool may be involved in a photosynthetic CO₂-concentrating mechanism and assist CO₂ fixation in diatom cells.

DOI： 10.1101/2022.01.18.476826

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Proton transfer pathway in anion channelrhodopsin-1 査読

Masaki Tsujimura, Keiichi Kojima, Shiho Kawanishi, Yuki Sudo, Hiroshi Ishikita

eLife 10 e72264 2021年12月

担当区分：責任著者掲載種別：研究論文（学術雑誌）出版者・発行元：eLife Sciences Publications, Ltd

Anion channelrhodopsin from <italic>Guillardia theta</italic> (<italic>Gt</italic>ACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here, we investigate mutant <italic>Gt</italic>ACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths was also analyzed using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shorten and lengthen the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild-type <italic>Gt</italic>ACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients toward the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism.

DOI： 10.7554/elife.72264

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その他リンク： https://cdn.elifesciences.org/articles/72264/elife-72264-v1.xml

Exploring the Retinal Binding Cavity of Archaerhodopsin-3 by Replacing the Retinal Chromophore With a Dimethyl Phenylated Derivative 査読

Taichi Tsuneishi, Masataka Takahashi, Masaki Tsujimura, Keiichi Kojima, Hiroshi Ishikita, Yasuo Takeuchi, Yuki Sudo

Frontiers in Molecular Biosciences 8 794948 2021年12月

担当区分：最終著者,　責任著者掲載種別：研究論文（学術雑誌）出版者・発行元：Frontiers Media SA

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 <italic>β</italic>-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.

DOI： 10.3389/fmolb.2021.794948

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Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization 査読

Masuzu Kikuchi, Keiichi Kojima, Shin Nakao, Susumu Yoshizawa, Shiho Kawanishi, Atsushi Shibukawa, Takashi Kikukawa, Yuki Sudo

Scientific Reports 11 ( 1 ) 14756 2021年12月

担当区分：最終著者,　責任著者掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

<title>Abstract</title>Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an <italic>Escherichia coli</italic> expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate <italic>Oxyrrhis marina</italic> (<italic>O. marina</italic> rhodopsin-2, <italic>Om</italic>R2) that can be expressed in <italic>E. coli</italic> cells. <italic>E. coli</italic> cells harboring the <italic>Om</italic>R2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified <italic>Om</italic>R2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-<italic>trans</italic> retinal chromophore, (2) the possession of the deprotonated counterion (p<italic>K</italic>_a = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of <italic>Om</italic>R2 expressed in <italic>E. coli</italic> cells could build a basis for understanding and utilizing eukaryotic rhodopsins.

DOI： 10.1038/s41598-021-94181-w

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その他リンク： http://www.nature.com/articles/s41598-021-94181-w

An optogenetic assay method for electrogenic transporters using Escherichia coli co‐expressing light‐driven proton pump 査読

Masahiro Hayashi, Keiichi Kojima, Yuki Sudo, Atsuko Yamashita

Protein Science 30 ( 10 ) 2161 - 2169 2021年7月

Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy 査読

Izuru Kawamura, Hayato Seki, Seiya Tajima, Yoshiteru Makino, Arisu Shigeta, Takashi Okitsu, Akimori Wada, Akira Naito, Yuki Sudo

Biophysics and Physicobiology 18 177 - 185 2021年

Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift 査読

Keiichi Kojima, Susumu Yoshizawa, Masumi Hasegawa, Masaki Nakama, Marie Kurihara, Takashi Kikukawa, Yuki Sudo

Scientific Reports 10 ( 1 ) 20857 2020年11月

担当区分：最終著者,　責任著者掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pK_a = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pK_a = 3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral ‘blue-shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift.

DOI： 10.1038/s41598-020-77936-9

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その他リンク： https://www.nature.com/articles/s41598-020-77936-9

Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants 査読

Tsujimura M, Noji T, Saito K, Kojima K, Sudo Y, Ishikita H.

Biochim Biophys Acta (Bioenerg) 148349 - 148349 2020年11月

Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI 査読

Tetsuya Ueta, Keiichi Kojima, Tomoya Hino, Mikihiro Shibata, Shingo Nagano, Yuki Sudo

Biophysical Journal 119 ( 9 ) 1760 - 1770 2020年11月

Further thermo‐stabilization of thermophilic rhodopsin from Thermus thermophilus JL‐18 through engineering in extramembrane regions 査読

Tomoki Akiyama, Naoki Kunishima, Sayaka Nemoto, Kazuki Kazama, Masako Hirose, Yuki Sudo, Yoshinori Matsuura, Hisashi Naitow, Takeshi Murata

Proteins: Structure, Function, and Bioinformatics 89 ( 3 ) 301 - 310 2020年10月

掲載種別：研究論文（学術雑誌）出版者・発行元：Wiley

Abstract

It is known that a hyperthermostable protein tolerable at temperatures over 100°C can be designed from a soluble globular protein by introducing mutations. To expand the applicability of this technology to membrane proteins, here we report a further thermo‐stabilization of the thermophilic rhodopsin from Thermus thermophilus JL‐18 as a model membrane protein. Ten single mutations in the extramembrane regions were designed based on a computational prediction of folding free‐energy differences upon mutation. Experimental characterizations using the UV‐visible spectroscopy and the differential scanning calorimetry revealed that four of ten mutations were thermo‐stabilizing: V79K, T114D, A115P, and A116E. The mutation‐structure relationship of the TR constructs was analyzed using molecular dynamics simulations at 300 K and at 1800 K that aimed simulating structures in the native and in the random‐coil states, respectively. The native‐state simulation exhibited an ion‐pair formation of the stabilizing V79K mutant as it was designed, and suggested a mutation‐induced structural change of the most stabilizing T114D mutant. On the other hand, the random‐coil‐state simulation revealed a higher structural fluctuation of the destabilizing mutant S8D when compared to the wild type, suggesting that the higher entropy in the random‐coil state deteriorated the thermal stability. The present thermo‐stabilization design in the extramembrane regions based on the free‐energy calculation and the subsequent evaluation by the molecular dynamics may be useful to improve the production of membrane proteins for structural studies.

DOI： 10.1002/prot.26015

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/prot.26015

A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage 査読

Masumi Hasegawa, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Yu Nakajima, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa

Scientific Reports 10 ( 1 ) 16752 2020年10月

掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H⁺ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.

DOI： 10.1038/s41598-020-73606-y

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その他リンク： https://www.nature.com/articles/s41598-020-73606-y

Interaction of Escherichia coli and its culture supernatant with Vibrio vulnificus during biofilm formation 査読

Han‐Min Ohn, Tamaki Mizuno, Yuki Sudo, Shin‐Ichi Miyoshi

Microbiology and Immunology 64 ( 9 ) 593 - 601 2020年8月

掲載種別：研究論文（学術雑誌）出版者・発行元：Wiley

Abstract

Vibrio vulnificus is a foodborne pathogen causing septicemia with high mortality rate. In this study, we explored how Escherichia coli, one of the commensal bacteria in the human gastrointestinal tract, can interact with V. vulnificus. Our study results show that the amount of biofilm produced by V. vulnificus was reduced in the presence of E. coli ATCC 35218, although the growth of V. vulnificus L‐180 remained unaffected. We also detected an antibiofilm effect of E. coli culture supernatant against V. vulnificus, which could not be reduced even after heat treatment. These findings indicate that E. coli and its culture supernatant may be suitable to prevent biofilm formation by V. vulnificus. By contrast, live cells of V. vulnificus could reduce the amount of preformed E. coli biofilm, but its culture supernatant could not. This suggests that the cell‐associated factors contribute toward reduction in E. coli biofilm. Therefore, we speculate that ingestion of an infectious dose of V. vulnificus might induce dislodging of the commensal bacteria from the intestinal epithelia and thus can colonize to initiate the infection.

DOI： 10.1111/1348-0421.12829

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1348-0421.12829

Comparative Studies of the Fluorescence Properties of Microbial Rhodopsins: Spontaneous Emission Versus Photointermediate Fluorescence 査読

Keiichi Kojima, Rika Kurihara, Masayuki Sakamoto, Tsukasa Takanashi, Hikaru Kuramochi, Xiao Min Zhang, Haruhiko Bito, Tahei Tahara, Yuki Sudo

The Journal of Physical Chemistry B 124 ( 34 ) 7361 - 7367 2020年7月

Green-Sensitive, Long-Lived, Step-Functional Anion Channelrhodopsin-2 Variant as a High-Potential Neural Silencing Tool 査読

Keiichi Kojima, Natsuki Miyoshi, Atsushi Shibukawa, Srikanta Chowdhury, Masaki Tsujimura, Tomoyasu Noji, Hiroshi Ishikita, Akihiro Yamanaka, Yuki Sudo

The Journal of Physical Chemistry Letters 11 ( 15 ) 6214 - 6218 2020年7月

Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained 査読

Satoshi Yasuda, Tomoki Akiyama, Sayaka Nemoto, Tomohiko Hayashi, Tetsuya Ueta, Keiichi Kojima, Takashi Tsukamoto, Satoru Nagatoishi, Kouhei Tsumoto, Yuki Sudo, Masahiro Kinoshita, Takeshi Murata

Journal of Chemical Information and Modeling 60 ( 3 ) 1709 - 1716 2020年3月

How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained? 査読

Tomohiko Hayashi, Satoshi Yasuda, Kano Suzuki, Tomoki Akiyama, Kanae Kanehara, Keiichi Kojima, Mikio Tanabe, Ryuichi Kato, Toshiya Senda, Yuki Sudo, Takeshi Murata, Masahiro Kinoshita

The Journal of Physical Chemistry B 124 ( 6 ) 990 - 1000 2020年1月

Vectorial proton transport mechanism of RxR, a phylogenetically distinct and thermally stable microbial rhodopsin 査読国際誌

Keiichi Kojima, Tetsuya Ueta, Tomoyasu Noji, Keisuke Saito, Kanae Kanehara, Susumu Yoshizawa, Hiroshi Ishikita, Yuki Sudo

Scientific Reports 10 ( 1 ) 282 - 282 2020年1月

Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins 査読

Yu Nakajima, Keiichi Kojima, Yuichiro Kashiyama, Satoko Doi, Ryosuke Nakai, Yuki Sudo, Kazuhiro Kogure, Susumu Yoshizawa

Microbes and Environments 35 ( 4 ) ME20085 2020年

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators 査読

David M. Needham, Susumu Yoshizawa, Toshiaki Hosaka, Camille Poirier, Chang Jae Choi, Elisabeth Hehenberger, Nicholas A. T. Irwin, Susanne Wilken, Cheuk-Man Yung, Charles Bachy, Rika Kurihara, Yu Nakajima, Keiichi Kojima, Tomomi Kimura-Someya, Guy Leonard, Rex R. Malmstrom, Daniel R. Mende, Daniel K. Olson, Yuki Sudo, Sebastian Sudek, Thomas A. Richards, Edward F. DeLong, Patrick J. Keeling, Alyson E. Santoro, Mikako Shirouzu, Wataru Iwasaki, Alexandra Z. Worden

Proceedings of the National Academy of Sciences 116 ( 41 ) 20574 - 20583 2019年9月

掲載種別：研究論文（学術雑誌）出版者・発行元：Proceedings of the National Academy of Sciences

Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirR _DTS ) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirR _DTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae . Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

DOI： 10.1073/pnas.1907517116

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その他リンク： https://pnas.org/doi/pdf/10.1073/pnas.1907517116

Application of High-Sensitivity UV photoemission Spectroscopy to Examine the Electronic Structure of Thermophilic Rhodopsin 査読

Daisuke Sano, Ichiro Ide, Tomoki Akiyama, Yuya Tanaka, Yuki Sudo, Takeshi Murata, Hisao Ishii

Molecular Crystals and Liquid Crystals 687 ( 1 ) 34 - 39 2019年7月

GABA neurons in the ventral tegmental area regulate non-rapid eye movement sleep in mice 査読

Srikanta Chowdhury, Takanori Matsubara, Toh Miyazaki, Daisuke Ono, Noriaki Fukatsu, Manabu Abe, Kenji Sakimura, Yuki Sudo, Akihiro Yamanaka

eLife 8 e44928 2019年6月

掲載種別：研究論文（学術雑誌）出版者・発行元：eLife Sciences Publications, Ltd

Sleep/wakefulness cycle is regulated by coordinated interactions between sleep- and wakefulness-regulating neural circuitry. However, the detailed mechanism is far from understood. Here, we found that glutamic acid decarboxylase 67-positive GABAergic neurons in the ventral tegmental area (VTA_Gad67+) are a key regulator of non-rapid eye movement (NREM) sleep in mice. VTA_Gad67+ project to multiple brain areas implicated in sleep/wakefulness regulation such as the lateral hypothalamus (LH). Chemogenetic activation of VTA_Gad67+ promoted NREM sleep with higher delta power whereas optogenetic inhibition of these induced prompt arousal from NREM sleep, even under highly somnolescent conditions, but not from REM sleep. VTA_Gad67+ showed the highest activity in NREM sleep and the lowest activity in REM sleep. Moreover, VTA_Gad67+ directly innervated and inhibited wake-promoting orexin/hypocretin neurons by releasing GABA. As such, optogenetic activation of VTA_Gad67+ terminals in the LH promoted NREM sleep. Taken together, we revealed that VTA_Gad67+ play an important role in the regulation of NREM sleep.

DOI： 10.7554/elife.44928

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その他リンク： https://cdn.elifesciences.org/articles/44928/elife-44928-v2.xml

Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12 査読

Atsushi Shibukawa, Keiichi Kojima, Yu Nakajima, Yosuke Nishimura, Susumu Yoshizawa, Yuki Sudo

Biochemistry 58 ( 26 ) 2934 - 2943 2019年5月

Quantitation of the neural silencing activity of anion channelrhodopsins in Caenorhabditis elegans and their applicability for long-term illumination 査読

Taro Yamanashi, Misayo Maki, Keiichi Kojima, Atsushi Shibukawa, Takashi Tsukamoto, Srikanta Chowdhury, Akihiro Yamanaka, Shin Takagi, Yuki Sudo

Scientific Reports 9 ( 1 ) 7863 2019年3月

Retinal–Salinixanthin Interactions in a Thermophilic Rhodopsin 査読

Ramprasad Misra, Tamar Eliash, Yuki Sudo, Mordechai Sheves

The Journal of Physical Chemistry B 123 ( 1 ) 10 - 20 2018年12月

Correction to “High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment” 査読

Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, Yasuhisa Mizutani

The Journal of Physical Chemistry B 122 ( 42 ) 9826 - 9826 2018年10月

Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT 査読

Yoshiteru Makino, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Naoki Kamo, Yuki Sudo, Kazuyoshi Ueda, Akira Naito

Biophysical Journal 115 ( 1 ) 72 - 83 2018年7月

High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment 査読

Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, Yasuhisa Mizutani

The Journal of Physical Chemistry B 122 ( 27 ) 6945 - 6953 2018年6月

Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative 査読

Riho Takayama, Akimasa Kaneko, Takashi Okitsu, Satoshi P. Tsunoda, Kazumi Shimono, Misao Mizuno, Keiichi Kojima, Takashi Tsukamoto, Hideki Kandori, Yasuhisa Mizutani, Akimori Wada, Yuki Sudo

The Journal of Physical Chemistry Letters 9 ( 11 ) 2857 - 2862 2018年5月

Presence of a Haloarchaeal Halorhodopsin-Like Cl− Pump in Marine Bacteria 査読

Yu Nakajima, Takashi Tsukamoto, Yohei Kumagai, Yoshitoshi Ogura, Tetsuya Hayashi, Jaeho Song, Takashi Kikukawa, Makoto Demura, Kazuhiro Kogure, Yuki Sudo, Susumu Yoshizawa

Microbes and Environments 33 ( 1 ) 89 - 97 2018年

Spectroscopic characteristics ofRubricoccus marinusxenorhodopsin (RmXeR) and a putative model for its inward H⁺transport mechanism 査読

Saki Inoue, Susumu Yoshizawa, Yu Nakajima, Keiichi Kojima, Takashi Tsukamoto, Takashi Kikukawa, Yuki Sudo

Physical Chemistry Chemical Physics 20 ( 5 ) 3172 - 3183 2018年

担当区分：最終著者,　責任著者掲載種別：研究論文（学術雑誌）出版者・発行元：Royal Society of Chemistry (RSC)

On the basis of functional and spectroscopic characterization, we propose a model for the inward proton transport inRmXeR, a newly discovered microbial rhodopsin.

DOI： 10.1039/c7cp05033j

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Mutational analysis of the conserved carboxylates of anion channelrhodopsin-2 (ACR2) expressed in Escherichia coli and their roles in anion transport 査読

Keiichi Kojima, Hiroshi C. Watanabe, Satoko Doi, Natsuki Miyoshi, Misaki Kato, Hiroshi Ishikita, Yuki Sudo

Biophysics and Physicobiology 15 179 - 188 2018年

Few-cycle pulse generation from noncollinear optical parametric amplifier with static dispersion compensation 査読

Shunsuke Adachi, Yuya Watanabe, Yuki Sudo, Toshinori Suzuki

Chemical Physics Letters 683 7 - 11 2017年9月

Comparative evaluation of the stability of seven-transmembrane microbial rhodopsins to various physicochemical stimuli 査読

Naoya Honda, Takashi Tsukamoto, Yuki Sudo

Chemical Physics Letters 682 6 - 14 2017年8月

Hybrid Model Membrane Combining Micropatterned Lipid Bilayer and Hydrophilic Polymer Brush 査読

Toshiki Nishimura, Fuyuko Tamura, Sawako Kobayashi, Yasushi Tanimoto, Fumio Hayashi, Yuki Sudo, Yasuhiko Iwasaki, Kenichi Morigaki

Langmuir 33 ( 23 ) 5752 - 5759 2017年5月

Demonstration of a Light-Driven SO₄^2– Transporter and Its Spectroscopic Characteristics 査読

Akiko Niho, Susumu Yoshizawa, Takashi Tsukamoto, Marie Kurihara, Shinya Tahara, Yu Nakajima, Misao Mizuno, Hikaru Kuramochi, Tahei Tahara, Yasuhisa Mizutani, Yuki Sudo

Journal of the American Chemical Society 139 ( 12 ) 4376 - 4389 2017年3月

A phylogenetically distinctive and extremely heat stable light-driven proton pump from the eubacterium Rubrobacter xylanophilus DSM 9941T 査読

Kanae Kanehara, Susumu Yoshizawa, Takashi Tsukamoto, Yuki Sudo

Scientific Reports 7 ( 1 ) 44427 2017年3月

Implications for the Light-Driven Chloride Ion Transport Mechanism of Nonlabens marinus Rhodopsin 3 by Its Photochemical Characteristics 査読

Takashi Tsukamoto, Susumu Yoshizawa, Takashi Kikukawa, Makoto Demura, Yuki Sudo

The Journal of Physical Chemistry B 121 ( 9 ) 2027 - 2038 2017年3月

An inhibitory role of Arg-84 in anion channelrhodopsin-2 expressed in Escherichia coli 査読

Satoko Doi, Takashi Tsukamoto, Susumu Yoshizawa, Yuki Sudo

Scientific Reports 7 ( 1 ) 41879 2017年2月

Hybrid model membrane combining micropatterned lipid bilayer and hydrophilic polymer brush 査読

Morigaki, Kenichi, Nishimura, Toshiki, Tamura, Fuyuko, Tanimoto, Yasushi, Ando, Koji, Sudo, Yuki, Hayashi, Fumio, Iwasaki, Yasuhiko

Abstracts of Papers of the American Chemical Society 253 2017年

Temperature Independence of Ultrafast Photoisomerization in Thermophilic Rhodopsin: Assessment versus Other Microbial Proton Pumps 査読

E. Siva Subramaniam Iyer, Ramprasad Misra, Arnab Maity, Oleg Liubashevski, Yuki Sudo, Mordechai Sheves, Sanford Ruhman

Journal of the American Chemical Society 138 ( 38 ) 12401 - 12407 2016年9月

Live-cell single-molecule imaging of the cytokine receptor MPL for analysis of dynamic dimerization 査読

Akihiko Sakamoto, Takashi Tsukamoto, Yuji Furutani, Yuki Sudo, Kazuyuki Shimada, Akihiro Tomita, Hitoshi Kiyoi, Takashi Kato, Takashi Funatsu

Journal of Molecular Cell Biology 8 ( 6 ) 553 - 555 2016年6月

X-ray Crystallographic Structure of Thermophilic Rhodopsin 査読

Takashi Tsukamoto, Kenji Mizutani, Taisuke Hasegawa, Megumi Takahashi, Naoya Honda, Naoki Hashimoto, Kazumi Shimono, Keitaro Yamashita, Masaki Yamamoto, Seiji Miyauchi, Shin Takagi, Shigehiko Hayashi, Takeshi Murata, Yuki Sudo

Journal of Biological Chemistry 291 ( 23 ) 12223 - 12232 2016年6月

Functional and Photochemical Characterization of a Light‐Driven Proton Pump from the Gammaproteobacterium Pantoea vagans 査読

Yuki Sudo, Susumu Yoshizawa

Photochemistry and Photobiology 92 ( 3 ) 420 - 427 2016年3月

Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1 査読

Satoko Doi, Arisa Mori, Takashi Tsukamoto, Louisa Reissig, Kunio Ihara, Yuki Sudo

Photochemical and Photobiological Sciences 14 ( 9 ) 1628 - 1636 2015年9月

Atomistic design of microbial opsin-based blue-shifted optogenetics tools 査読

Hideaki E. Kato, Motoshi Kamiya, Seiya Sugo, Jumpei Ito, Reiya Taniguchi, Ayaka Orito, Kunio Hirata, Ayumu Inutsuka, Akihiro Yamanaka, Andrés D. Maturana, Ryuichiro Ishitani, Yuki Sudo, Shigehiko Hayashi, Osamu Nureki

Nature Communications 6 ( 1 ) 7177 2015年5月

Factors Affecting the Stability and Performance of Ionic Liquid-Based Planar Transient Photodetectors 査読

Simon Dalgleish, Louisa Reissig, Laigui Hu, Michio M. Matsushita, Yuki Sudo, Kunio Awaga

Langmuir 31 ( 18 ) 5235 - 5243 2015年4月

Converting a Light-Driven Proton Pump into a Light-Gated Proton Channel 査読

Keiichi Inoue, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Shigehiko Hayashi, Hideki Kandori, Yuki Sudo

Journal of the American Chemical Society 137 ( 9 ) 3291 - 3299 2015年2月

On-tip photodetection: a simple and universal platform for optoelectronic screening 査読

S. Dalgleish, L. Reissig, Y. Sudo, K. Awaga

Chemical Communications 51 ( 91 ) 16401 - 16404 2015年

Irreversible Trimer to Monomer Transition of Thermophilic Rhodopsin upon Thermal Stimulation 査読

Takashi Tsukamoto, Makoto Demura, Yuki Sudo

The Journal of Physical Chemistry B 118 ( 43 ) 12383 - 12394 2014年10月

Color‐Discriminating Retinal Configurations of Sensory Rhodopsin I by Photo‐Irradiation Solid‐State NMR Spectroscopy 査読

Hiroki Yomoda, Yoshiteru Makino, Yuya Tomonaga, Tetsurou Hidaka, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Yuki Sudo, Akira Naito

Angewandte Chemie International Edition 53 ( 27 ) 6960 - 6964 2014年5月

The Early Steps in the Photocycle of a Photosensor Protein Sensory Rhodopsin I from Salinibacter ruber 査読

Yuki Sudo, Misao Mizuno, Zhengrong Wei, Satoshi Takeuchi, Tahei Tahara, Yasuhisa Mizutani

The Journal of Physical Chemistry B 118 ( 6 ) 1510 - 1518 2014年1月

A Blue-shifted Light-driven Proton Pump for Neural Silencing 査読

Yuki Sudo, Ayako Okazaki, Hikaru Ono, Jin Yagasaki, Seiya Sugo, Motoshi Kamiya, Louisa Reissig, Keiichi Inoue, Kunio Ihara, Hideki Kandori, Shin Takagi, Shigehiko Hayashi

Journal of Biological Chemistry 288 ( 28 ) 20624 - 20632 2013年7月

Thermal and Spectroscopic Characterization of a Proton Pumping Rhodopsin from an Extreme Thermophile 査読

Takashi Tsukamoto, Keiichi Inoue, Hideki Kandori, Yuki Sudo

Journal of Biological Chemistry 288 ( 30 ) 21581 - 21592 2013年7月

Investigation of the chromophore binding cavity in the 11-cis acceptable microbial rhodopsin MR 査読

Arisa Mori, Jin Yagasaki, Michio Homma, Louisa Reissig, Yuki Sudo

Chemical Physics 419 23 - 29 2013年6月

Large Spectral Change due to Amide Modes of a β-Sheet upon the Formation of an Early Photointermediate of Middle Rhodopsin 査読

Yuji Furutani, Takashi Okitsu, Louisa Reissig, Misao Mizuno, Michio Homma, Akimori Wada, Yasuhisa Mizutani, Yuki Sudo

The Journal of Physical Chemistry B 117 ( 13 ) 3449 - 3458 2013年3月

Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na+ driven flagellar motor 査読

Rei Abe Yoshizumi, Shiori Kobayashi, Mizuki Gohara, Kokoro Hayashi, Chojiro Kojima, Seiji Kojima, Yuki Sudo, Yasuo Asami, Michio Homma

Biophysics 9 21 - 29 2013年

Influence of Halide Binding on the Hydrogen Bonding Network in the Active Site of Salinibacter Sensory Rhodopsin I 査読

Louisa Reissig, Tatsuya Iwata, Takashi Kikukawa, Makoto Demura, Naoki Kamo, Hideki Kandori, Yuki Sudo

Biochemistry 51 ( 44 ) 8802 - 8813 2012年10月

Photo-induced Regulation of the Chromatic Adaptive Gene Expression by Anabaena Sensory Rhodopsin 査読

Hiroki Irieda, Teppei Morita, Kimika Maki, Michio Homma, Hiroji Aiba, Yuki Sudo

Journal of Biological Chemistry 287 ( 39 ) 32485 - 32493 2012年9月

Optical Silencing of C. elegans Cells with Arch Proton Pump 査読

Ayako Okazaki, Yuki Sudo, Shin Takagi

PLoS ONE 7 ( 5 ) e35370 - e35370 2012年5月

Absorption Spectra and Photochemical Reactions in a Unique Photoactive Protein, Middle Rhodopsin MR 査読

Keiichi Inoue, Louisa Reissig, Makoto Sakai, Shiori Kobayashi, Michio Homma, Masaaki Fujii, Hideki Kandori, Yuki Sudo

The Journal of Physical Chemistry B 116 ( 20 ) 5888 - 5899 2012年5月

An Active Photoreceptor Intermediate Revealed by In Situ Photoirradiated Solid-State NMR Spectroscopy 査読

Yuya Tomonaga, Tetsurou Hidaka, Izuru Kawamura, Takudo Nishio, Kazuhiro Ohsawa, Takashi Okitsu, Akimori Wada, Yuki Sudo, Naoki Kamo, Ayyalusamy Ramamoorthy, Akira Naito

Biophysical Journal 101 ( 10 ) L50 - L52 2011年11月

Structural Characteristics around the β-Ionone Ring of the Retinal Chromophore in Salinibacter Sensory Rhodopsin I 査読

Hiroki Irieda, Louisa Reissig, Akira Kawanabe, Michio Homma, Hideki Kandori, Yuki Sudo

Biochemistry 50 ( 22 ) 4912 - 4922 2011年5月

Direct observation of the structural change of Tyr174 in the primary reaction of sensory Rhodopsin II 査読

Misao Mizuno, Yuki Sudo, Michio Homma, Yasuhisa Mizutani

Biochemistry 50 ( 15 ) 3170 - 3180 2011年4月

Spectral Tuning in Sensory Rhodopsin I from Salinibacter ruber 査読

Yuki Sudo, Yasufumi Yuasa, Jun Shibata, Daisuke Suzuki, Michio Homma

Journal of Biological Chemistry 286 ( 13 ) 11328 - 11336 2011年4月

Spectrally Silent Intermediates during the Photochemical Reactions of Salinibacter Sensory Rhodopsin I 査読

Keiichi Inoue, Yuki Sudo, Michio Homma, Hideki Kandori

The Journal of Physical Chemistry B 115 ( 15 ) 4500 - 4508 2011年3月

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties 査読

Yuki Sudo, Kunio Ihara, Shiori Kobayashi, Daisuke Suzuki, Hiroki Irieda, Takashi Kikukawa, Hideki Kandori, Michio Homma

Journal of Biological Chemistry 286 ( 8 ) 5967 - 5976 2011年2月

Functional expression of a two-transmembrane HtrII protein using cell-free synthesis 査読

Yuki Sudo, Rikou Tanaka, Toshitatsu Kobayashi, Naoki Kamo, Toshiyuki Kohno, Chojiro Kojima

Biophysics 7 51 - 58 2011年

Spectroscopic Studies of a Sensory Rhodopsin I Homologue from the Archaeon Haloarcula vallismortis 査読

Jin Yagasaki, Daisuke Suzuki, Kunio Ihara, Keiichi Inoue, Takashi Kikukawa, Makoto Sakai, Masaaki Fujii, Michio Homma, Hideki Kandori, Yuki Sudo

Biochemistry 49 ( 6 ) 1183 - 1190 2010年1月

Interaction between Na⁺ Ion and Carboxylates of the PomA−PomB Stator Unit Studied by ATR-FTIR Spectroscopy 査読

Yuki Sudo, Yuya Kitade, Yuji Furutani, Masaru Kojima, Seiji Kojima, Michio Homma, Hideki Kandori

Biochemistry 48 ( 49 ) 11699 - 11705 2009年11月

Characterization of a Signaling Complex Composed of Sensory Rhodopsin I and Its Cognate Transducer Protein from the EubacteriumSalinibacter ruber 査読

Yuki Sudo, Akiko Okada, Daisuke Suzuki, Keiichi Inoue, Hiroki Irieda, Makoto Sakai, Masaaki Fujii, Yuji Furutani, Hideki Kandori, Michio Homma

Biochemistry 48 ( 42 ) 10136 - 10145 2009年10月

Effects of Chloride Ion Binding on the Photochemical Properties of Salinibacter Sensory Rhodopsin I 査読

Daisuke Suzuki, Yuji Furutani, Keiichi Inoue, Takashi Kikukawa, Makoto Sakai, Masaaki Fujii, Hideki Kandori, Michio Homma, Yuki Sudo

Journal of Molecular Biology 392 ( 1 ) 48 - 62 2009年9月

Stator assembly and activation mechanism of the flagellar motor by the periplasms region of MotB 査読

Seiji Kojima, Katsumi Imada, Mayuko Sakuma, Yuki Sudo, Chojiro Kojima, Tohru Minamino, Michio Homma, Keiichi Namba

Molecular Microbiology 73 ( 4 ) 710 - 718 2009年8月

Comparative study of the ion flux pathway in stator units of proton- and sodium-driven flagellar motors 査読

Yuki Sudo, Hiroyuki Terashima, Rei Abe-Yoshizumi, Seiji Kojima, Michio Homma

Biophysics 5 45 - 52 2009年

Structural Changes of Salinibacter Sensory Rhodopsin I upon Formation of the K and M Photointermediates 査読

Daisuke Suzuki, Yuki Sudo, Yuji Furutani, Hazuki Takahashi, Michio Homma, Hideki Kandori

Biochemistry 47 ( 48 ) 12750 - 12759 2008年11月

Salinibacter Sensory Rhodopsin: Sensory rhodopsin I-like protein from a eubacterium 査読

Tomomi Kitajima-Ihara, Yuji Furutani, Daisuke Suzuki, Kunio Ihara, Hideki Kandori, Michio Homma, Yuki Sudo

Journal of Biological Chemistry 283 ( 35 ) 23533 - 23541 2008年8月

A Long-Lived M-Like State of Phoborhodopsin that Mimics the Active State 査読

Yuki Sudo, Tatsuya Nishihori, Masayuki Iwamoto, Kazumi Shimono, Chojiro Kojima, Naoki Kamo

Biophysical Journal 95 ( 2 ) 753 - 760 2008年7月

Protein-protein interaction of a pharaonis halorhodopsin mutant forming a complex with pharaonis halobacterial transducer protein ii detected by fourier-transform infrared spectroscopy 査読

Yuji Furutani, Motohiro Ito, Yuki Sudo, Naoki Kamo, Hideki Kandori

Photochemistry and Photobiology 84 ( 4 ) 874 - 879 2008年7月

Steric constraint in the primary photoproduct of sensory rhodopsin II is a prerequisite for light-signal transfer to HtrII 査読

Motohiro Ito, Yuki Sudo, Yuji Furutani, Takashi Okitsu, Akimori Wada, Michio Homma, John L. Spudich, Hideki Kandori

Biochemistry 47 ( 23 ) 6208 - 6215 2008年6月

Structural changes of sensory rhodopsin I and its transducer protein are dependent on the protonated state of Asp76 査読

Yuji Furutani, Hazuki Takahashi, Jun Sasaki, Yuki Sudo, John L. Spudich, Hideki Kandori

Biochemistry 47 ( 9 ) 2875 - 2883 2008年3月

Structural Changes in the O-Decay Accelerated Mutants of pharaonis Phoborhodopsin 査読

Yuki Sudo, Yuji Furutani, Masayuki Iwamoto, Naoki Kamo, Hideki Kandori

Biochemistry 47 ( 9 ) 2866 - 2874 2008年2月

Structural analysis of the phototactic transducer protein HtrII linker region from Natronomonas pharaonis 査読

Kokoro Hayashi, Yuki Sudo, JunGoo Jee, Masaki Mishima, Hideyuki Hara, Naoki Kamo, Chojiro Kojima

Biochemistry 46 ( 50 ) 14380 - 14390 2007年12月

Early photocycle structural changes in a bacteriorhodopsin mutant engineered to transmit photosensory signals 査読

Yuki Sudo, Yuji Furutani, John L. Spudich, Hideki Kandori

Journal of Biological Chemistry 282 ( 21 ) 15550 - 15558 2007年5月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：American Society for Biochemistry and Molecular Biology Inc. (ASBMB)

DOI： 10.1074/jbc.M701271200

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その他リンク： http://orcid.org/0000-0001-5284-8773

Interaction of the halobacterial transducer to a halorhodopsin mutant engineered so as to bind the transducer: Cl- circulation within the extracellular channel 査読

Chisa Hasegawa, Takashi Kikukawa, Seiji Miyauchi, Akiteru Seki, Yuki Sudo, Megumi Kubo, Makoto Demura, Naoki Kamo

Photochemistry and Photobiology 83 ( 2 ) 293 - 302 2007年3月

Participation of the surface structure of Pharaonis phoborhodopsin, ppR and its A149S and A149V mutants, consisting of the C-terminal α-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed 13C solid-state NMR 査読

Izuru Kawamura, Yoichi Ikeda, Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Satoru Yamaguchi, Satoru Tuzi, Hazime Saitô, Naoki Kamo, Akira Naito

Photochemistry and Photobiology 83 ( 2 ) 339 - 345 2007年3月

Functional importance of the interhelical hydrogen bond between Thr 204 and Tyr174 of sensory rhodopsin II and its alteration during the signaling process 査読

Yuki Sudo, Yuji Furutani, Hideki Kandori, John L. Spudich

Journal of Biological Chemistry 281 ( 45 ) 34239 - 34245 2006年11月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：American Society for Biochemistry and Molecular Biology Inc. (ASBMB)

DOI： 10.1074/jbc.M605907200

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その他リンク： http://orcid.org/0000-0001-5284-8773

Assignment of the hydrogen-out-of-plane and -in-plane vibrations of the retinal chromophore in the K intermediate of pharaonis phoborhodopsin 査読

Yuji Furutani, Yuki Sudo, Akimori Wada, Masayoshi Ito, Kazumi Shimono, Naoki Kamo, Hideki Kandori

Biochemistry 45 ( 39 ) 11836 - 11843 2006年10月

Temperature-dependent interactions between photoactivated Pharaonis phoborhodopsin and its transducer 査読

Kentaro Kamada, Yuji Furutani, Yuki Sudo, Naoki Kamo, Hideki Kandori

Biochemistry 45 ( 15 ) 4859 - 4866 2006年4月

Importance of specific hydrogen bonds of archaeal rhodopsins for the binding to the transducer protein 査読

Yuki Sudo, Masaki Yamabi, Shinnosuke Kato, Chisa Hasegawa, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Journal of Molecular Biology 357 ( 4 ) 1274 - 1282 2006年4月

Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor 査読

Sudo, Y., Spudich, J.L.

Proceedings of the National Academy of Sciences of the United States of America 103 ( 44 ) 16129 - 16134 2006年

Steric constraint in the primary photoproduct of an archaeal rhodopsin from regiospecific perturbation of C-D stretching vibration of the retinyl chromophore 査読

Yuki Sudo, Yuji Furutani, Akimori Wada, Masayoshi Ito, Naoki Kamo, Hideki Kandori

Journal of the American Chemical Society 127 ( 46 ) 16036 - 16037 2005年11月

Linker region of a halobacterial transducer protein interacts directly with its sensor retinal protein 査読

Yuki Sudo, Hideyasu Okuda, Masaki Yamabi, Yuta Fukuzaki, Masaki Mishima, Naoki Kamo, Chojiro Kojima

Biochemistry 44 ( 16 ) 6144 - 6152 2005年4月

Structural changes of the complex between pharaonis phoborhodopsin and its cognate transducer upon formation of the M photointermediate 査読

Yuji Furutani, Kentaro Kamada, Yuki Sudo, Kazumi Shimono, Naoki Kamo, Hideki Kandori

Biochemistry 44 ( 8 ) 2909 - 2915 2005年3月

Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II) 査読

Masayuki Iwamoto, Yuki Sudo, Kazumi Shimono, Tsunehisa Araiso, Naoki Kamo

Biophysical Journal 88 ( 2 ) 1215 - 1223 2005年

Role of charged residues of pharaonis phoborhodopsin (sensory rhodopsin II) in its interaction with the transducer protein 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Biochemistry 43 ( 43 ) 13748 - 13754 2004年11月

Transient movement of helix F revealed by photo-induced inactivation by reaction of a bulky SH-reagent to cysteine-introduced pharaonis phoborhodopsin (sensory rhodopsin II) 査読

Hideaki Yoshida, Yuki Sudo, Kazumi Shimono, Masayuki Iwamoto, Naoki Kamo

Photochemical and Photobiological Sciences 3 ( 6 ) 537 - 542 2004年6月

Proton Release and Uptake of pharaonis Phoborhodopsin (Sensory Rhodopsin II) Reconstituted into Phospholipids 査読

Masayuki Iwamoto, Chisa Hasegawa, Yuki Sudo, Kazumi Shimono, Tsunehisa Araiso, Naoki Kamo

Biochemistry 43 ( 11 ) 3195 - 3203 2004年3月

Role of Arg-72 of pharaonis Phoborhodopsin (Sensory Rhodopsin II) on its Photochemistry 査読

Yukako Ikeura, Kazumi Shimono, Masayuki Iwamoto, Yuki Sudo, Naoki Kamo

Biophysical Journal 86 ( 5 ) 3112 - 3120 2004年

Conformation and Dynamics of the [3-13C]Ala,[1- 13C]Val-Labeled Truncated pharaonis Transducer, pHtrll(1-159), as Revealed by Site-Directed 13C Solid-State NMR: Changes Due to Association with Phoborhodopsin (Sensory Rhodopsin II) 査読

Satoru Yamaguchi, Kazumi Shimono, Yuki Sudo, Satoru Tuzi, Akira Naito, Naoki Kamo, Hazime Saitô

Biophysical Journal 86 ( 5 ) 3131 - 3140 2004年

Hydrogen Bonding Alteration of Thr-204 in the Complex between pharaonis Phoborhodopsin and Its Transducer Protein 査読

Yuki Sudo, Yuji Furutani, Kazumi Shimono, Naoki Kamo, Hideki Kandori

Biochemistry 42 ( 48 ) 14166 - 14172 2003年12月

Interaction of Natronobacterium pharaonis Phoborhodopsin (Sensory Rhodopsin II) with its Cognate Transducer Probed by Increase in the Thermal Stability 査読

Yuki Sudo, Masaki Yamabi, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Photochemistry and Photobiology 78 ( 5 ) 511 - 516 2003年11月

Importance of the broad regional interaction for spectral Tuning in natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) 査読

Kazumi Shimono, Takanori Hayashi, Yukako Ikeura, Yuki Sudo, Masayuki Iwamoto, Naoki Kamo

Journal of Biological Chemistry 278 ( 26 ) 23882 - 23889 2003年7月

FTIR spectroscopy of the complex between pharaonis phoborhodopsin and its transducer protein 査読

Yuji Furutani, Yuki Sudo, Naoki Kamo, Hideki Kandori

Biochemistry 42 ( 17 ) 4837 - 4842 2003年5月

Dynamic structure of pharaonis phoborhodopsin (sensory rhodopsin II) and complex with a cognate truncated transducer as revealed by site-directed 13C solid-state NMR 査読

Tadashi Arakawa, Kazumi Shimono, Satoru Yamaguchi, Satoru Tuzi, Yuki Sudo, Naoki Kamo, Hazime Saitô

FEBS Letters 536 ( 1-3 ) 237 - 240 2003年2月

Arg-72 of pharaonis Phoborhodopsin (Sensory Rhodopsin II) is Important for the Maintenance of the Protein Structure in the Solubilized State 査読

Yukako Ikeura, Kazumi Shimono, Masayuki Iwamoto, Yuki Sudo, Naoki Kamo

Photochemistry and Photobiology 77 ( 1 ) 96 - 100 2003年1月

Illumination accelerates the decay of the O-intermediate of pharaonis phoborhodopsin (sensory rhodopsin II) 査読

Masayuki Iwamoto, Yuki Sudo, Kazumi Shimono, Naoki Kamo

Photochemistry and Photobiology 76 ( 4 ) 462 - 466 2002年10月

Association between a photo-intermediate of a M-lacking mutant D75N of pharaonis phoborhodopsin and its cognate transducer 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Journal of Photochemistry and Photobiology B: Biology 67 ( 3 ) 171 - 176 2002年7月

Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Biochimica et Biophysica Acta - Biomembranes 1558 ( 1 ) 63 - 69 2002年1月

Tyr-199 and charged residues of pharaonis phoborhodopsin are important for the interaction with its transducer 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Biophysical Journal 83 ( 1 ) 427 - 432 2002年

Role of Asp193 in chromophore-protein interaction of pharaonis phoborhodopsin (sensory rhodopsin II) 査読

Masayuki Iwamoto, Yuji Furutani, Yuki Sudo, Kazumi Shimono, Hideki Kandori, Naoki Kamo

Biophysical Journal 83 ( 2 ) 1130 - 1135 2002年

Environment around the chromophore in pharaonis phoborhodopsin: Mutation analysis of the retinal binding site 査読

Kazumi Shimono, Yukako Ikeura, Yuki Sudo, Masayuki Iwamoto, Naoki Kamo

Biochimica et Biophysica Acta - Biomembranes 1515 ( 2 ) 92 - 100 2001年12月

Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin 査読

Masayuki Iwamoto, Yuki Sudo, Kazumi Shimono, Naoki Kamo

Biochimica et Biophysica Acta - Biomembranes 1514 ( 1 ) 152 - 158 2001年9月

Pharaonis phoborhodopsin binds to its cognate truncated transducer even in the presence of a detergent with a 1:1 stoichiometry 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

Photochemistry and Photobiology 74 ( 3 ) 489 - 494 2001年9月

Structural changes of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: Infrared spectral comparison with bacteriorhodopsin 査読

H Kandori, K Shimono, Y Sudo, M Iwamoto, Y Shichida, N Kamo

BIOCHEMISTRY 40 ( 31 ) 9238 - 9246 2001年8月

Photo-induced proton transport of pharaonis phoborhodopsin (sensory rhodopsin II) is ceased by association with the transducer 査読

Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Masato Sumi, Naoki Kamo

Biophysical Journal 80 ( 2 ) 916 - 922 2001年

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