2024/11/13 更新

写真a

スドウ ユウキ
須藤 雄気
SUDO Yuki
所属
医歯薬学域 教授
職名
教授
外部リンク

学位

  • 博士(薬学) ( 2005年3月   北海道大学 )

研究キーワード

  • Physical Chemistry

  • Protein Science

  • Biophysics

  • Photobiology

  • 蛋白質科学

  • 光生物学

  • 物理系薬学

  • 生物物理学

  • 光遺伝学

研究分野

  • ライフサイエンス / 薬系分析、物理化学

  • ナノテク・材料 / 基礎物理化学

  • ライフサイエンス / 生物物理学

  • ナノテク・材料 / ケミカルバイオロジー

学歴

  • 北海道大学    

    - 2005年

      詳細を見る

    国名: 日本国

    researchmap

  • 北海道大学   Faculty of Pharmaceutical Sciences  

    - 2000年

      詳細を見る

    国名: 日本国

    researchmap

経歴

  • 岡山大学学術研究院医歯薬学域 教授

    2014年 - 現在

      詳細を見る

    国名:日本国

    researchmap

  • 分子科学研究所 客員准教授

    2012年 - 2014年

      詳細を見る

  • 名古屋大学   Associate Professor, Graduate School of Science

    2009年 - 2014年

      詳細を見る

    国名:日本国

    researchmap

  • 科学技術振興機構(JST)・さきがけ 研究員

    2008年 - 2012年

      詳細を見る

  • 名古屋大学   Assistant Professor, Graduate School of Science

    2007年 - 2009年

      詳細を見る

    国名:日本国

    researchmap

  • テキサス大学ヒューストン校   ポスドク   Postdoctoral Fellow

    2005年 - 2007年

      詳細を見る

    国名:アメリカ合衆国

    researchmap

  • 名古屋工業大学大学院工学研究科 研究員   Graduate School of Engineering

    2005年

      詳細を見る

    国名:日本国

    researchmap

▼全件表示

所属学協会

  • 薬学会

    2014年 - 現在

      詳細を見る

  • 分子科学会

    2013年 - 現在

      詳細を見る

  • 蛋白質科学会

    2012年 - 現在

      詳細を見る

  • 細胞を創る研究会

    2012年 - 現在

      詳細を見る

  • 生物物理学会

    2000年 - 現在

      詳細を見る

委員歴

  • The Journal of Biological Chemistry (The American Society for Biochemistry and Molecular Biology)   Editorial Board Member  

    2023年7月 - 現在   

      詳細を見る

    団体区分:学協会

    researchmap

  • 日本生物物理学会   理事  

    2023年 - 現在   

      詳細を見る

  • 日本学術会議 生命科学ジェンダー・ダイバーシティ分科会   「学協会における男女共同参画のあり方に関する検討小委員会」・幹事  

    2022年10月 - 現在   

      詳細を見る

    団体区分:政府

    researchmap

  • 分子科学研究所   共同研究専門委員会委員  

    2022年 - 現在   

      詳細を見る

    団体区分:その他

    researchmap

  • Biophysics and Physicobiology (日本生物物理学会欧文誌)   副編集長  

    2021年12月 - 現在   

      詳細を見る

    団体区分:学協会

    researchmap

  • 男女共同参画学協会連絡会   第20期運営委員会・副委員長  

    2021年10月 - 2022年10月   

      詳細を見る

    団体区分:学協会

    researchmap

  • 文部科学省・科学技術学術政策研究所(NISTEP)   専門調査員  

    2019年 - 現在   

      詳細を見る

    団体区分:政府

    researchmap

  • 日本生物物理学会中国四国支部   支部長  

    2019年 - 2020年   

      詳細を見る

  • 日本生物物理学会   副会長  

    2019年 - 2020年   

      詳細を見る

    団体区分:学協会

    researchmap

  • 日本薬学会中国四国支部   支部役員  

    2018年 - 2019年   

      詳細を見る

  • 公益財団法人 新世代研究所   バイオ単分子専門委員  

    2015年4月 - 2020年3月   

      詳細を見る

    団体区分:その他

    researchmap

  • 日本生物物理学会   運営委員・理事  

    2009年 - 2020年   

      詳細を見る

    団体区分:学協会

    生物物理学会

    researchmap

▼全件表示

 

論文

  • 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

     詳細を見る

    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

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.4c04466

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.4c03027

    researchmap

  • 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

     詳細を見る

    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)  

    DOI: 10.1038/s41467-024-47009-w

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1016/j.bbrc.2023.07.048

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.3c02833

    researchmap

  • 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

     詳細を見る

    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

    PubMed

    researchmap

  • 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

     詳細を見る

    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 (λmax =  ~ 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

    PubMed

    researchmap

    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

     詳細を見る

    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

    PubMed

    researchmap

  • 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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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:Pharmaceutical Society of Japan  

    DOI: 10.1248/cpb.c22-00774

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acsomega.2c06980

    researchmap

  • 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

     詳細を見る

    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

    PubMed

    researchmap

  • 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

     詳細を見る

    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

    PubMed

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.1c12608

    researchmap

  • 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

     詳細を見る

    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

    PubMed

    researchmap

  • 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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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

    researchmap

  • 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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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:Wiley  

    DOI: 10.1002/pro.4154

    researchmap

    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pro.4154

  • 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

     詳細を見る

    担当区分:最終著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophysico.bppb-v18.019

    researchmap

  • 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

     詳細を見る

    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, pKa = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pKa = 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

    researchmap

    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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.bbabio.2020.148349

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1016/j.bpj.2020.09.026

    PubMed

    researchmap

  • 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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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

    researchmap

    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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.0c06560

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpclett.0c01406

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jcim.0c00063

    PubMed

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.9b10700

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    DOI: 10.1038/s41598-019-57122-2

    PubMed

    researchmap

  • 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

     詳細を見る

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

    DOI: 10.1264/jsme2.me20085

    researchmap

  • 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

     詳細を見る

    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

    PubMed

    researchmap

    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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Informa UK Limited  

    DOI: 10.1080/15421406.2019.1648052

    researchmap

  • 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

     詳細を見る

    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 (VTAGad67+) are a key regulator of non-rapid eye movement (NREM) sleep in mice. VTAGad67+ project to multiple brain areas implicated in sleep/wakefulness regulation such as the lateral hypothalamus (LH). Chemogenetic activation of VTAGad67+ 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. VTAGad67+ showed the highest activity in NREM sleep and the lowest activity in REM sleep. Moreover, VTAGad67+ directly innervated and inhibited wake-promoting orexin/hypocretin neurons by releasing GABA. As such, optogenetic activation of VTAGad67+ terminals in the LH promoted NREM sleep. Taken together, we revealed that VTAGad67+ play an important role in the regulation of NREM sleep.

    DOI: 10.7554/elife.44928

    PubMed

    researchmap

    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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.biochem.9b00257

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    DOI: 10.1038/s41598-019-44308-x

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.8b06795

    Scopus

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.bpj.2018.05.030

    Scopus

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.8b04894

    PubMed

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpclett.8b00879

    Scopus

    researchmap

  • Presence of a Haloarchaeal Halorhodopsin-Like Cl&lt;sup&gt;−&lt;/sup&gt; 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

     詳細を見る

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

    DOI: 10.1264/jsme2.me17197

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

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

    DOI: 10.1039/c7cp05033j

    PubMed

    researchmap

  • Mutational analysis of the conserved carboxylates of anion channelrhodopsin-2 (ACR2) expressed in &lt;i&gt;Escherichia coli&lt;/i&gt; 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

     詳細を見る

    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:Biophysical Society of Japan  

    DOI: 10.2142/biophysico.15.0_179

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.cplett.2017.04.001

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1016/j.cplett.2017.05.055

    Web of Science

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.langmuir.7b00463

    Web of Science

    researchmap

  • Demonstration of a Light-Driven SO42– 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.6b12139

    Web of Science

    researchmap

  • 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

     詳細を見る

    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

    Rhodopsins are proteins that contain seven transmembrane domains with a chromophore retinal and that function as photoreceptors for light-energy conversion and light-signal transduction in a wide variety of organisms. Here we characterized a phylogenetically distinctive new rhodopsin from the thermophilic eubacterium Rubrobacter xylanophilus DSM 9941T that was isolated from thermally polluted water. Although R. xylanophilus rhodopsin (RxR) is from Actinobacteria, it is located between eukaryotic and archaeal rhodopsins in the phylogenetic tree. Escherichia coli cells expressing RxR showed a light-induced decrease in environmental pH and inhibition by a protonophore, indicating that it works as a light-driven outward proton pump. We characterized purified RxR spectroscopically, and showed that it has an absorption maximum at 541 nm and binds nearly 100% all-trans retinal. The pKa values for the protonated retinal Schiff base and its counterion were estimated to be 10.7 and 1.3, respectively. Time-resolved flash-photolysis experiments revealed the formation of a red-shifted intermediate. Of note, RxR showed an extremely high thermal stability in comparison with other proton pumping rhodopsins such as thermophilic rhodopsin TR (by 16-times) and bacteriorhodopsin from Halobacterium salinarum (HsBR, by 4-times).

    DOI: 10.1038/srep44427

    Web of Science

    researchmap

    その他リンク: https://www.nature.com/articles/srep44427

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.6b11101

    Web of Science

    researchmap

  • 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

     詳細を見る

    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

    Anion channelrhodopsin-2 (ACR2) was recently identified from the cryptophyte algae Guillardia theta and has become a focus of interest in part because of its novel light-gated anion channel activity and its extremely high neural silencing activity. In this study, we tried to express ACR2 in Escherichia coli cells as a recombinant protein. The E. coli cells expressing ACR2 showed an increase in pH upon blue-light illumination in the presence of monovalent anions and the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP), indicating an inward anion channel activity. Then, taking advantage of the E. coli expression system, we performed alanine-scanning mutagenesis on conserved basic amino acid residues. One of them, R84A, showed strong signals compared with the wild-type, indicating an inhibitory role of R84 on Cl transportation. The signal was strongly enhanced in R84E, whereas R84K was less effective than the wild-type (i.e., R84). These results suggest that the positive charge at position 84 is critical for the inhibition. Thus we succeeded in functional expression of ACR2 in E. coli and found the inhibitory role of R84 during the anion transportation.

    DOI: 10.1038/srep41879

    Web of Science

    researchmap

    その他リンク: https://www.nature.com/articles/srep41879

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)  

    Web of Science

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.6b05002

    Web of Science

    researchmap

  • 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

     詳細を見る

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

    DOI: 10.1093/jmcb/mjw027

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1074/jbc.m116.719815

    Web of Science

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    Abstract

    Photoactive retinal proteins are widely distributed throughout the domains of the microbial world (i.e., bacteria, archaea, and eukarya). Here we describe three retinal proteins belonging to a phylogenetic clade with a unique DTG motif. Light‐induced decrease in the environmental pH and its inhibition by carbonyl cyanide m‐chlorophenylhydrazone revealed that these retinal proteins function as light‐driven outward electrogenic proton pumps. We further characterized one of these proteins, Pantoea vagans rhodopsin (PvR), spectroscopically. Visible spectroscopy and high‐performance liquid chromatography revealed that PvR has an absorption maximum at 538 nm with the retinal chromophore predominantly in the all‐trans form (&gt;90%) under both dark and light conditions. We estimated the pKa values of the protonated Schiff base of the retinal chromophore and its counterion as approximately 13.5 and 2.1, respectively, by using pH titration experiments, and the photochemical reaction cycle of PvR was measured by time‐resolved flash‐photolysis in the millisecond timeframe. We observed a blue‐shifted and a red‐shifted intermediate, which we assigned as M‐like and O‐like intermediates, respectively. Decay of the M‐like intermediate was highly sensitive to environmental pH, suggesting that proton uptake is coupled to decay of the M‐like intermediate. From these results, we propose a putative model for the photoreaction of PvR.

    DOI: 10.1111/php.12585

    Web of Science

    researchmap

  • 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

     詳細を見る

    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  

    DOI: 10.1039/c5pp00213c

    Web of Science

    researchmap

    その他リンク: https://link.springer.com/article/10.1039/c5pp00213c/fulltext.html

  • 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

     詳細を見る

    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 opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein–chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its π-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.

    DOI: 10.1038/ncomms8177

    Web of Science

    researchmap

    その他リンク: https://www.nature.com/articles/ncomms8177

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/la504972q

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/ja511788f

    Web of Science

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>Using an optical fiber tip as a sampling probe allows for efficient photoresponse screening of any photoactive film.</p>

    DOI: 10.1039/c5cc06237c

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/jp507374q

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:Wiley  

    Abstract

    SRI (sensory rhodopsin I) can discriminate multiple colors for the attractant and repellent phototaxis. Studies aimed at revealing the color‐dependent mechanism show that SRI is a challenging system not only in photobiology but also in photochemistry. During the photoreaction of SRI, an M‐intermediate (attractant) transforms into a P‐intermediate (repellent) by absorbing blue light. Consequently, SRI then cycles back to the G‐state. The photoreactions were monitored with the 13C NMR signals of [20‐13C]retnal‐SrSRI using in situ photo‐irradiation solid‐state NMR spectroscopy. The M‐intermediate was trapped at −40 °C by illumination at 520 nm. It was transformed into the P‐intermediate by subsequent illumination at 365 nm. These results reveal that the G‐state could be directly transformed to the P‐intermediate by illumination at 365 nm. Thus, the stationary trapped M‐ and P‐intermediates are responsible for positive and negative phototaxis, respectively.

    DOI: 10.1002/anie.201309258

    Web of Science

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jp4112662

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1074/jbc.m113.479394

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1074/jbc.m113.475533

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1016/j.chemphys.2012.11.020

    Scopus

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/jp308765t

    Scopus

    PubMed

    researchmap

  • Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na&lt;sup&gt;+&lt;/sup&gt; 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophysics.9.21

    Scopus

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/bi3009592

    Web of Science

    Scopus

    PubMed

    J-GLOBAL

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1074/jbc.m112.390864

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Public Library of Science (PLoS)  

    DOI: 10.1371/journal.pone.0035370

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/jp302357m

    Scopus

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.bpj.2011.10.022

    Scopus

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/bi200284s

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sensory rhodopsin II (SRII) is a negative phototaxis receptor containing retinal as its chromophore, which mediates the avoidance of blue light. The signal transduction is initiated by the photoisomerization of the retinal chromophore, resulting in conformational changes of the protein which are transmitted to a transducer protein. To gain insight into the SRII sensing mechanism, we employed time-resolved ultraviolet resonance Raman spectroscopy monitoring changes in the protein structure in the picosecond time range following photoisomerization. We used a 450 nm pump pulse to initiate the SRII photocycle and two kinds of probe pulses with wavelengths of 225 and 238 nm to detect spectral changes in the tryptophan and tyrosine bands, respectively. The observed spectral changes of the Raman bands are most likely due to tryptophan and tyrosine residues located in the vicinity of the retinal chromophore, i.e., Trp76, Trp171, Tyr51, or Tyr174. The 225 nm UVRR spectra exhibited bleaching of the intensity for all the tryptophan bands within the instrumental response time, followed by a partial recovery with a time constant of 30 ps and no further changes up to 1 ns. In the 238 nm UVRR spectra, a fast recovering component was observed in addition to the 30 ps time constant component. A comparison between the spectra of the WT and Y174F mutant of SRII indicates that Tyr174 changes its structure and/or environment upon chromophore photoisomerization. These data represent the first real-time observation of the structural change of Tyr174, of which functional importance was pointed out previously. © 2011 American Chemical Society.

    DOI: 10.1021/bi101817y

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1074/jbc.m110.187948

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jp2000706

    Web of Science

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1074/jbc.m110.190058

    Web of Science

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophysics.7.51

    CiNii Article

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/bi901824a

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/bi901517n

    Web of Science

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/bi901338d

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1016/j.jmb.2009.06.050

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Torque generation in the Salmonella flagellar motor is coupled to translocation of H+ ions through the protonconducting channel of the Mot protein stator complex. The Mot complex is believed to be anchored to the peptidoglycan (PG) layer by the putative peptidoglycan-binding (PGB) domain of MotB. Proton translocation is activated only when the stator is installed into the motor. We report the crystal structure of a C-terminal periplasmic fragment of MotB (MotBc) that contains the PGB domain and includes the entire periplasmic region essential for motility. Structural and functional analyses indicate that the PGB domains must dimerize in order to form the proton-conducting channel. Drastic conformational changes in the N-terminal portion of MotBc are required both for PG binding and the proton channel activation. © 2009 Blackwell Publishing Ltd.

    DOI: 10.1111/j.1365-2958.2009.06802.x

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophysics.5.45

    Scopus

    researchmap

  • 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

     詳細を見る

    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:American Chemical Society (ACS)  

    DOI: 10.1021/bi801358b

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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:Elsevier BV  

    DOI: 10.1074/jbc.m802990200

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1529/biophysj.107.125294

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:WILEY-VCH  

    Pharaonis halorhodopsin (pHR) functions as a light-driven inward chloride ion pump in Natoronomonas pharaonis, while pharaonis phoborhodopsin (ppR
    also called pharaonis sensory rhodopsin II, pSRII), is a light sensor for negative phototaxis. ppR forms a 2:2 complex with its cognate transducer protein (pHtrII) through intramembranous hydrogen bonds: Tyr199ppR-Asn74 pHtrII and Thr189ppR-Glu43pHtrII, Ser62 pHtrII. It was reported that a pHR mutant (P240T / F250Y), which possesses the hydrogen-bonding sites, impairs its pumping activity upon complexation with pHtrII. In this study, effect of the complexation with pHtrII on the structural changes upon formation of the K, L1 and L 2 intermediates of pHR was investigated by use of Fourier-transform infrared spectroscopy. The vibrational changes of Tyr250pHR and Asn74pHtrII were detected for the L1 and L2 intermediates, supporting that Tyr250pHR forms a hydrogen bond with Asn74pHtrII as similarly to Tyr199ppR. The conformational changes of the retinal chromophore were never affected by complexation with pHtrII, but amide-I vibrations were clearly different in the absence and presence of pHtrII. The molecular environment around Asp156pHR in helix D is also slightly affected. These additional structural changes are probably related to blocking of translocation of a chloride ion from the extracellular to the cytoplasmic side during the photocycle.

    DOI: 10.1111/j.1751-1097.2008.00317.x

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sensory rhodopsin II (SRII, also called pharaonis phoborhodopsin, ppR) is responsible for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all-trans to 13-cis initiates conformational changes in the protein, leading to activation of the cognate transducer protein (HtrII). We previously observed enhancement of the C 14-D stretching vibration of the retinal chromophore at 2244 cm -1 upon formation of the K state and interpreted that a steric constraint occurs at the C14D group in SRIIK. Here, we identify the counterpart of the C14D group as Thr204, because the C14-D stretching signal disappeared in T204A, T204S, and T204C mutants as well as a C14-HOOP (hydrogen out-of-plane) vibration at 864 cm-1. Although the K state of the wild-type bacteriorhodopsin (BR), a light-driven proton pump, possesses neither 2244 nor 864 cm-1 bands, both signals appeared for the K state of a triple mutant of BR that functions as a light sensor (P200T/V210Y/A215T). We found a positive correlation between these vibrational amplitudes of the C14 atom at 77 K and the physiological phototaxis response. These observations strongly suggest that the steric constraint between the C14 group of retinal and Thr204 of the protein is a prerequisite for light-signal transduction by SRII. © 2008 American Chemical Society.

    DOI: 10.1021/bi8003507

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sensory rhodopsin I (SRI) functions in both positive and negative phototaxis in complex with halobacterial transducer protein I (HtrI). Orange light activation of SRI results in deprotonation of the retinylidene chromophore of SRI to produce the S373 photocycle intermediate, the signaling state for positive phototaxis. In this study, we observed pH dependence on structural coupling between the two molecules upon the formation of the S 373 intermediate by means of Fourier transform infrared spectroscopy. At alkaline pH, where Asp76 (one of the counterions of the protonated retinylidene Schiff base) is deprotonated, HtrI-dependent alteration of the light-induced difference spectra is limited to reduction of amide I bands at 1661 (+)/ 1647 (-) cm-1, and perturbation of one of the protonated carboxylic acid bands occurs at 1734 (-) cm-1 (which appears to become ionized only when complexed with HtrI). However, at acidic pH, HtrI-complexed SRI exhibits not only light-induced reduction of the amide I changes but a wider range of spectral alterations including the appearance of several new amide I bands, perturbation of the chromophore-related vibrational modes, and other additional changes characteristic of tyrosine, glutamate, and aspartate residues. Since such pH dependence of structural changes was not observed in the complex of the D76N mutant of SRI, which behaves much like HtrI-complexed SRI in acidic conditions, we conclude that extensive orange light-induced conformational coupling between SRI and HtrI occurs only when Asp76 is neutralized. © 2008 American Chemical Society.

    DOI: 10.1021/bi702050c

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/bi701885k

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Halobacterial pharaonis phoborhodopsin [ppR, also called Natronomonas pharaonis sensory rhodopsin II (NpSRII)] is a phototaxis protein which transmits a light signal to the cytoplasm through its transducer protein (pHtrII). pHtrII, a two-transmembrane protein that interacts with ppR, belongs to the group of methyl-accepting chemotaxis proteins (MCPs). Several mutation studies have indicated that the linker region connecting the transmembrane and methylation regions is necessary for signal transduction. However, the three-dimensional (3D) structure of an MCP linker region has yet to be reported, and hence, details concerning the signal transduction mechanism remain unknown. Here the structure of the pHtrII linker region was investigated biochemically and biophysically. Following limited proteolysis, only one trypsin resistant fragment in the pHtrII linker region was identified. This fragment forms a homodimer with a Kd value of 115 μM. The 3D structure of this fragment was determined by solution NMR, and only one α-helix was found between two HAMP domains of the linker region. This α-helix was significantly stabilized within transmembrane protein pHtrII as revealed by CW-EPR. The presence of Af1503 HAMP domain-like structures in the linker region was supported by CD, NMR, and ELDOR data. The α-helix determined here presumably works as a mechanical joint between two HAMP domains in the linker region to transfer the photoactivated conformational change downstream. © 2007 American Chemical Society.

    DOI: 10.1021/bi701837n

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    Bacteriorhodopsin (BR) and sensory rhodopsin II (SRII) function as a light-driven proton pump and a receptor for negative phototaxis in haloarchaeal membranes, respectively. SRII transmits light signals through changes in protein-protein interaction with its transducer HtrII. Recently, we converted BR by three mutations into a form capable of transmitting photosignals to HtrII to mediate phototaxis responses. The BR triple mutant (BR-T) provides an opportunity to identify structural changes necessary to activate HtrII by comparing light-induced infrared spectral changes of BR, BR-T, and SRII. The hydrogen out-of-plane (HOOP) vibrations of the BR-T were very similar to those of SRII, indicating that they are distributed more extensively along the retinal chromophore than in BR, as in SRII. On the other hand, the bands of the protein moiety in BR-T are similar to those of BR, indicating that they are not specific to photosensing. The alteration of the O-H stretching vibration of Thr-204 in SRII, which we had previously shown to be essential for signal relay to HtrII, occurs also in BR-T. In addition, 1670(+)/1664(-) cm-1 bands attributable to a distorted α-helix were observed in BR-T in a HtrII-dependent manner, as is seen in SRII. Thus, we identified similarities and dissimilarities of BR-T to BR and SRII. The results suggest signaling function of the structural changes of the HOOP vibrations, the O-H stretching vibration of the Thr-215 residue, and a distorted α-helix for the signal generation. We also succeeded in measurements of L minus initial state spectra of BR-T, which are the first FTIR spectra of L intermediates among sensory rhodopsins. © 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

    DOI: 10.1074/jbc.M701271200

    Scopus

    PubMed

    researchmap

    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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:2  

    An alkali-halophilic archaeum, Natronomonas pharaonis, contains two rhodopsins that are halorhodopsin (phR), a light-driven inward Cl- pump and phoborhodopsin (ppR), the receptor of negative phototaxis functioning by forming a signaling complex with a transducer, pHtrII (Sudo Y. et al., J. Mol. Biol. 357 [2006] 1274). Previously, we reported that the phR double mutant, P240T/F250YphR, can bind with pHtrII. This mutant itself can transport Cl-, while the net transport was stopped upon formation of the complex. The flash-photolysis data were analyzed by a scheme in which phR→P1→P2→P3→P 4→phR. The P3 of the wild-type and the double mutant contained two components, X- and O-intermediates. After the complex formation, however, the P3 of the double mutant lacked the X-intermediate. These observations imply that the X-intermediate (probably the N-intermediate) is the state having Cl- in the cytoplasmic binding site and that the complex undergoes an extracellular Cl- circulation because of the inhibition of formation of the X-intermediate. © 2007 American Society for Photobiology.

    DOI: 10.1562/2006-06-09-RA-916

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)  

    We have recorded 13C solid state NMR spectra of [3- 13C]Ala-labeled pharaonis phoborhodopsin (ppR) and its mutants, A149S and A149V, complexed with the cognate transducer pharaonis halobacterial transducer II protein (pHtrII) (1-159), to gain insight into a possible role of their cytoplasmic surface structure including the C-terminal α-helix and E-F loop for stabilization of the 2:2 complex, by both cross-polarization magic angle spinning (CP-MAS) and dipolar decoupled (DD)-MAS NMR techniques. We found that 13C CP-MAS NMR spectra of [3-13C]Ala-ppR, A149S and A149V complexed with the transducer pHtrII are very similar, reflecting their conformation and dynamics changes caused by mutual interactions through the transmembrane α-helical surfaces. In contrast, their DD-MAS NMR spectral features are quite different between [3-13C]Ala- A149S and A149V in the complexes with pHtrII: 13C DD-MAS NMR spectrum of [3- 13C]Ala-A149S complex is rather similar to that of the uncomplexed form, while the corresponding spectral feature of A149V complex is similar to that of ppR complex in the C-terminal tip region. This is because more flexible surface structure detected by the DD-MAS NMR spectra are more directly influenced by the dynamics changes than the CP-MAS NMR. It turned out, therefore, that an altered surface structure of A149S resulted in destabilized complex as viewed from the 13C NMR spectrum of the surface areas, probably because of modified conformation at the corner of the helix E in addition to the change of hydropathy. It is, therefore, concluded that the surface structure of ppR including the C-terminal α-helix and the E-F loops is directly involved in the stabilization of the complex through conformational stability of the helix E. © 2007 American Society for Photobiology.

    DOI: 10.1562/2006-06-20-RA-940

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    Sensory rhodopsin II (SRII), a receptor for negative phototaxis in haloarchaea, transmits light signals through changes in protein-protein interaction with its transducer HtrII. Light-induced structural changes throughout the SRII-HtrII interface, which spans the periplasmic region, membrane-embedded domains, and cytoplasmic domains near the membrane, have been identified by several studies. Here we demonstrate by site-specific mutagenesis and analysis of phototaxis behavior that two residues in SRII near the membrane-embedded interface (Tyr174 on helix F and Thr204 on helix G) are essential for signaling by the SRII-HtrII complex. These residues, which are the first in SRII shown to be required for phototaxis function, provide biological significance to the previous observation that the hydrogen bond between them is strengthened upon the formation of the earliest SRII photointermediate (SRIIK) only when SRII is complexed with HtrII. Here we report frequency changes of the S-H stretch of a cysteine substituted for SRII Thr204 in the signaling state intermediates of the SRII photocycle, as well as an influence of HtrII on the hydrogen bond strength, supporting a direct role of the hydrogen bond in SRII-HtrII signal relay chemistry. Our results suggest that the light signal is transmitted to HtrII from the energized interhelical hydrogen bond between Thr204 and Tyr174, which is located at both the retinal chromophore pocket and in helices F and G that form the membrane-embedded interaction surface to the signal-bearing second transmembrane helix of HtrII. The results argue for a critical process in signal relay occurring at this membrane interfacial region of the complex. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

    DOI: 10.1074/jbc.M605907200

    Scopus

    PubMed

    researchmap

    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

     詳細を見る

    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 Chemical Society ({ACS})  

    pharaonis phoborhodopsin (ppR
    also called pharaonis sensory rhodopsin II, psR-II) is a photoreceptor protein for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all-trans to 13-cis initiates conformational changes of the protein leading to activation of the cognate transducer protein (pHtrII). Elucidation of the initial photoreaction, formation of the K intermediate of ppR, is important for understanding the mechanism of storage of photon energy. We have reported the K minus ppR Fourier transform infrared (FTIR) spectra, including several vibrational bands of the retinal, the protein, and internal water molecules. It is interesting that more vibrational bands were observed in the hydrogen-out-of-plane (HOOP) region than for the light-driven proton pump, bacteriorhodopsin. This result implied that the steric constraints on the retinal chromophore in the binding pocket of ppR are distributed more widely upon formation of the initial intermediate. In this study, we assigned the HOOP and hydrogen-in-plane vibrations by means of low-temperature FTIR spectroscopy applied to ppR reconstituted with retinal deuterated at C7, C8, C10-C12, C14, and C15. As a result, the 966 (+)/ 971 (-) and 958 (+)/961 (-) cm-1 bands were assigned to the C7=C8 and C11=C12 Au HOOP modes, respectively, suggesting that the structural changes spread to the middle part of the retinal. The positive bands at 1001, 994, 987, and 979 cm-1 were assigned to the C15-HOOP vibrations of the K intermediate, whose frequencies are similar to those of the KL intermediate of bacteriorhodopsin trapped at 135 K. Another positive band at 864 cm-1 was assigned to the C14-HOOP vibration. Relatively many positive bands of hydrogen-in-plane vibrations supported the wide distribution of structural changes of the retinal as well. These results imply that the light energy was stored mainly in the distortions around the Schiff base region while some part of the energy was transferred to the distal part of the retinal. © 2006 American Chemical Society.

    DOI: 10.1021/bi0610597

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    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 Chemical Society ({ACS})  

    Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronomonas pharaonis. In membranes, it forms a 2:2 complex with its transducer protein pHtrII, and the association is weakened by 2 orders of magnitude in the M intermediate (ppR M). Such a change is believed to correspond to the transfer of the light signal to pHtrII. A previous Fourier transform infrared (FTIR) study observed hydrogen-bonding alteration of Asn74 in pHtrII in the M state, suggesting a light-signaling pathway from the receptor to the transducer [Furutani, Y., Kamada, K., Sudo, Y., Shimono, K., Kamo, N., and Kandori, H. (2005) Biochemistry 44, 2909-2915]. In this paper, we measure temperature dependence of the ppRM minus ppR spectra in the absence and presence of pHtrII at 250-293 K. Significant temperature dependence was observed for the amide-I vibrations of helices only for the ppR/pHtrII complex, where the amplitude of amide-I vibrations was reduced at room temperature. 13C-Labeling of ppR or pHtrII revealed that such spectral changes of helices originate from ppR and not pHtrII. The hydrogen-bonding alteration of Asn74 in pHtrII was temperature-independent, implying that the observed helical structural perturbation in ppR takes place in different region. On the other hand, temperature-dependent structural changes of helices were diminished for the complex of ppR with the G83C and G83F mutants of pHtrII. Gly83 is believed to connect the transmembrane helix and cytosolic linker region in a flexible kink near the membrane surface of pHtrII, and its replacement by Cys or Phe abolishes the photosensory function. The present study provides direct experimental evidence that Gly83 plays an important structural role in the activation processes of the ppR/pHtrII complex. A molecular mechanism of protein structural changes in the ppR/pHtrII complex is discussed on the basis of the present FTIR results. © 2006 American Chemical Society.

    DOI: 10.1021/bi060047i

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Four rhodopsins, bacteriorhodopsin (bR), halorhodopsin (hR), sensory rhodopsin (sR) and phoborhodopsin (pR) exist in archaeal membranes. bR and hR work as a light-driven ion pump. sR and pR work as a photo-sensor of phototaxis, and form signaling complexes in membranes with their respective cognate transducer proteins HtrI (with sR) and HtrII (with pR), through which light signals are transmitted to the cytoplasm. What is the determining factor(s) of the specific binding to form the complex? Binding of the wild-type or mutated rhodopsins with HtrII was measured by isothermal titration calorimetric analysis (ITC). bR and hR could not bind with HtrII. On the other hand, sR could bind to HtrII, although the dissociation constant (KD) was about 100 times larger than that of pR. An X-ray crystallographic structure of the pR/HtrII complex revealed formation of two specific hydrogen bonds whose pairs are Tyr199pR/Asn74HtrII and Thr189pR/Glu43 HtrII/Ser62HtrII. To investigate the importance of these hydrogen bonds, the KD value for the binding of various mutants of bR, hR, sR and pR with HtrII was estimated by ITC. The KD value of T189VpR/Y199FpR, double mutant/HtrII complex, was about 100-fold larger than that of the wild-type pR, whose KD value was 0.16 μM. On the other hand, bR and hR double mutants, P200T bR/V210YbR and P240ThR/F250YhR, were able to bind with HtrII. The KD value of these complexes was estimated to be 60.1(±10.7) μM for bR and to be 29.1(±6.1) μM for hR, while the wild-type bR and hR did not bind with HtrII. We concluded that these two specific hydrogen bonds play important roles in the binding between the rhodopsins and transducer protein. © 2006 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.jmb.2006.01.061

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1073/pnas.0607467103

    Scopus

    researchmap

  • 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

     詳細を見る

    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 Chemical Society ({ACS})  

    In visual and archaeal rhodopsins, light energy is stored in the chromophore-protein interaction after retinal photoisomerization. This paper reports a novel method to monitor the steric constraint after retinal isomerization by use of enhanced C-D stretching vibrations. In the difference FTIR spectra between an archaeal light-sensor pharaonis phoborhodopsin (ppR) and the primary K intermediate at 77 K, no peaks were observed in the 2160-2330 cm-1 region for deuterated retinals at position 7, 8, 10, 11, 12, and 15, whereas a strong peak appeared at 2244 cm-1 for the K intermediate of ppR possessing a C14-D-labeled retinal. The 2244-cm-1 band is assigned as the C14-D stretching vibration, and enhanced absorption in the K state probably originates from the local steric constraint at the C14-D position (also possible electrostatic field effects) after the C13=C14 double bond rotation. Copyright © 2005 American Chemical Society.

    DOI: 10.1021/ja056203a

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    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)  

    pHtrII, a pharaonis halobacterial transducer protein, possesses two transmembrane helices and forms a signaling complex with pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, NpSRII) within the halobacterial membrane. This complex transmits a light signal to the sensory system located in the cytoplasm. It has been suggested that the linker region connecting the transmembrane region and the methylation region of pHtrII is important for binding to ppR and subsequent photosignal transduction. In this study, we present evidence to suggest that the linker region itself interacts directly with ppR in addition to the interaction in the membrane region. An in vitro pull-down assay revealed that the linker region bound to ppR, and its dissociation constant (KD) was estimated to be approximately 10 μM using isothermal titration calorimetry (ITC). Solution NMR analyses showed that ppR interacted with the linker region of pHtrII (pHtrIIG83-Q149) and resulted in the broadening of many peaks, indicating structural changes within this region. These results suggest that the pHtrII linker region interacts directly with ppR. There was no demonstrable interaction between the C-terminal region of ppR (ppRGly224-His247) and either the linker region (pHtrIIG83-Q149) or the transmembrane region (pHtrII M1-E114) of pHtrII. On the basis of the NMR, CD, and photochemical data, we discuss the structural changes and role of the linker region of pHtrII in relation to photosignal transduction. © 2005 American Chemical Society.

    DOI: 10.1021/bi047573z

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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 Chemical Society ({ACS})  

    pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronobacterium pharaonis. It forms a 2:2 complex with its transducer protein, pHtrII, in membranes, and the association is weakened by 2 orders of magnitude in the M intermediate. Such change is believed to correspond to the transfer of the light signal to pHtrII. In this paper, we applied Fourier transform infrared (FTIR) spectroscopy to the active M intermediate in the absence and presence of pHtrII. The obtained difference FTIR spectra were surprisingly similar, notwithstanding the presence of pHtrII. This result strongly suggests that the transducer activation in the ppR-pHtrII system does not induce secondary structure alterations of the pHtrII itself. On the other hand, we found that the hydrogen bond of the OH group of Thr204 is altered in the primary K intermediate, but restored in the M intermediate. The hydrogen bond of Asn74 in pHtrII is strengthened in M, presumably because of the change in interaction with Tyr199 of ppR. These facts provided a light signaling pathway from Lys205 (retinal) of the receptor to Asn74 of the transducer through Thr204 and Tyr199. Transducer activation is likely to involve a relaxation of Thr204 in the receptor and hydrogen bonding alteration of Asn74 in the transducer, during which the helices of the transducer perform rigid-body motion without changing their secondary structures. © 2005 American Chemical Society.

    DOI: 10.1021/bi047893i

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society  

    Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor of negative phototaxis in Natronomonas (Natronobacterium) pharaonis. The photocycle rate of ppR is slow compared to that of bacteriorhodopsin, despite the similarity in their x-ray structures. The decreased rate of the photocycle of ppR is a result of the longer lifetime of later photo-intermediates such as M- (ppRM) and O-intermediates (ppRO). In this study, mutants were prepared in which mutated residues were located on the extracellular surface (P182, P183, and V194) and near the Schiff base (T204) including single, triple (P182S/P183E/V194T), and quadruple mutants. The decay of ppRO of the triple mutant was accelerated ∼20-times from 690 ms for the wild-type to 36 ms. Additional mutation resulting in a triple mutant at the 204th position such as T204C or T204S further decreased the decay half-time to 6.6 or 8 ms, almost equal to that of bacteriorhodopsin. The decay half-times of the ppRO of mutants (11 species) and those of the wild-type were well-correlated with the pK a value of Asp-75 in the dark for the respective mutants as spectroscopically estimated, although there are some exceptions. The implications of these observations are discussed in detail. © 2005 by the Biophysical Society.

    DOI: 10.1529/biophysj.104.045583

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    pharaonis phoborhodopsin (ppR
    also called pharaonis sensory rhodopsin II, NpSRII) is a receptor for negative phototaxis in Natronomonas (Natronobacterium) pharaonis. In membranes, it forms a 2:2 complex with its transducer protein, pHtrII, which transmits light signals into the cytoplasmic space through protein-protein interactions. We previously found that a specific deprotonated carboxyl of ppR or pHtrII strengthens their binding [Sudo, Y., et al. (2002) Biophys. J. 83, 427-432]. In this study we aim to identify this carboxyl group. Since the D75N mutant has only one photointermediate (ppRo-like) whose existence spans the millisecond time range, the analysis of its decay rate is simple. We prepared various D75N mutants such as D75N/D214N, D75N/K157Q/R162Q/R164Q (D75N/3Gln), D75N/D193N, and D75N/D193E, among which only D75N/D193N did not show pH dependence with regard to the ppRo-like decay rate and KD value for binding, implying that the carboxyl group in question is from Asp-193. The pKa of this group decreased to below 2 when a complex was formed. Therefore, we conclude that Asp-193ppR is connected to the distant transducer-ppR binding surface via hydrogen bonds, thereby modulating its pKa. In addition, we discuss the importance of Arg-162 ppR with respect to the binding activity.

    DOI: 10.1021/bi048803c

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Pharaonis phoborhodopsin (ppR) is a photosensor of negative phototaxis in Natronomonas (Natronobacterium) pharaonis, an alkalophilic halophile. This protein has seven transmembrane helices into which a chromophore, all-trans retinal, binds to a specific lysine residue (located in helix G) via a protonated Schiff base. Various mutants were engineered to have a single cysteine in the F-helix. In the presence of a bulky fluorescent SH-reagent, MIANS, (2-(4′-maleimidylanilino)naphthalene-6-sulfonic acid, illumination decreased the photoreactivity or flash-yield (absorbance deflection immediately after the flash) of the L163C ppR mutant (in which Leu-163 was replaced with Cys) without changing the photocycling rate. The fluorescence of the isolated protein increased with increasing illumination. These observations suggest that during photocycling, the space around Cys-163 in the F-helix might open, permitting reaction with the relatively large molecule. This reaction occurred only at the M-state and not at the O-state. The implications are discussed. © The Royal Society of Chemistry and Owner Societies 2004.

    DOI: 10.1039/b315454h

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, psRII) is a photo-receptor for negative phototaxis in Natronobacterium pharaonis. During the photoreaction cycle (photocycle), ppR exhibits intraprotein proton movements, resulting in proton pumping from the cytoplasmic to the extracellular side, although it is weak. In this study, light-induced proton uptake and release of ppR reconstituted with phospholipid were analyzed using a SnO2 electrode. The reconstituted ppR exhibited properties in proton uptake and release that are different from those of dodecyl maltoside solubilized samples. It showed fast proton release before the decay of ppR M (M-photointermediate) followed by proton uptake, which was similar to that of bacteriorhodopsin (BR), a light-driven proton pump. Mutant analysis assigned Asp193 to one (major) of the members of the proton-releasing group (PRG). Fast proton release was observed only when the pH was approximately 5-8 in the presence of Cl-. When Cl- was replaced with SO 42-, the reconstituted ppR did not exhibit fast proton release at any pH, suggesting Cl- binding around PRG. PRG in BR consists of Glu204 (Asp193 in ppR) and Glu194 (Pro183 in ppR). Replacement of Pro183 by Glu/Asp, a negatively charged residue, led to Cl --independent fast proton release. The transducer binding affected the properties of PRG in ppR in the ground state and in the ppRM state, suggesting that interaction with the transducer extends to the extracellular surface of ppR. Differences and similarities in the molecular mechanism of the proton movement between ppR and BR are discussed.

    DOI: 10.1021/bi035960n

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society  

    Pharaonis phoborhodopsin (ppR, or pharaonis sensory rhodopsin II, NpsRII) is a sensor for the negative phototaxis of Natronomonas (Natronobacterium) pharaonis. Arginine 72 of ppR corresponds to Arg-82 of bacteriorhodopsin, which is a highly conserved residue among microbial rhodopsins. Using various Arg-72 ppR mutants, we obtained the following results: 1), Arg-72ppR together possibly with Asp-193 influenced the pKa of the counterion of the protonated Schiff base. 2), The M-rise became approximately four times faster than the wild-type. 3), Illumination causes proton uptake and release, and the pH profiles of the sequence of these two proton movements were different between R72A mutant and the wild-type
    it is inferred that Arg-72 connects the proton transfer events occurring at both the Schiff base and an extracellular proton-releasing residue (Asp-193). 4), The M-decays of Arg-72 mutants were faster (∼8-27 folds at pH 8 depending on mutants) than the wild-type, implying that the guanidinium prevents the proton transfer from the extracellular space to the deprotonated Schiff base. 5), The proton-pumping activities were decreased for mutants having increased M-decay rates, but the extent of the decrease was smaller than expected. The role of Arg-72 of ppR on the photochemistry was discussed.

    DOI: 10.1016/S0006-3495(04)74359-3

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society  

    We have recorded 13C NMR spectra of the [3-13C]Ala, [1-13C]Val-labeled pharaonis transducer pHtrll(1-159) in the presence and absence of phoborhodopsin (ppR or sensory rhodopsin II) in egg phosphatidylcholine or dimyristoylphosphatidylcholine bilayers by means of site-directed (amino acid specific) solid-state NMR. Two kinds of 13C NMR signals of [3-13C]Ala-pHtrll complexed with ppR were clearly seen with dipolar decoupled magic angle spinning (DD-MAS) NMR. One of these resonances was at the peak position of the low-field α-helical peaks (αII-helix) and is identified with cytoplasmic α-helices protruding from the bilayers
    the other was the high-field α-helical peak (αI-helix) and is identified with the transmembrane α-helices. The first peaks, however, were almost completely suppressed by cross-polarization magic angle spinning (CP-MAS) regardless of the presence or absence of ppR or by DD-MAS NMR in the absence of ppR. This is caused by an increased fluctuation frequency of the cytoplasmic α-helix from 105 Hz in the uncomplexed states to &gt
    106 Hz in the complexed states, leading to the appearance of peaks that were suppressed because of the interference of the fluctuation frequency with the frequency of proton decoupling (105 Hz), as viewed from the 13C NMR spectra of [3-13C]Ala-labeled pHtrll. Consistent with this view, the 13C DD-MAS NMR signals of the cytoplasmic α-helices of the complexed [3-13C]Ala-pHtrll in the dimyristoylphosphatidylcholine (DMPC) bilayer were partially suppressed at 0°C due to a decreased fluctuation frequency at the low temperature. In contrast, examination of the 13C CP-MAS spectra of [1-13C]Val-labeled complexed pHtrll showed that the 13C NMR signals of the transmembrane α-helix were substantially suppressed. These spectral changes are again interpreted in terms of the increased fluctuation frequency of the transmembrane α-helices from 103 Hz of the uncomplexed states to 10 4 Hz of the complexed states. These findings substantiate the view that the transducers alone are in an aggregated or clustered state but the ppR-pHtrll complex is not aggregated. We show that 13C NMR is a very useful tool for achieving a better understanding of membrane proteins which will serve to clarify the molecular mechanism of signal transduction in this system.

    DOI: 10.1016/S0006-3495(04)74361-1

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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 Chemical Society ({ACS})  

    pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronobacterium pharaonis. It forms a 2:2 complex with its transducer protein, pHtrII, in membranes and transmits light signals through the change in the protein-protein interaction. We previously found that the ppRK minus ppR spectrum in D20 possesses vibrational bands of ppR at 3479 (-)/3369 (+) cm-1 only in the presence of pHtrII [Furutani, Y., Sudo, Y., Kamo, N., and Kandori, H. (2003) Biochemistry 42, 4837-4842]. A D/H-unexchangeable X-H group appears to form a stronger hydrogen bond upon retinal photoisomerization in the ppR-pHtrII complex. This article aims to identify the group by use of various mutant proteins. According to the crystal structure, Tyr-199 of ppR forms a hydrogen bond with Asn-74 of pHtrII in the complex. Nevertheless, the 3479 (-)/3369 (+) cm-1 bands were preserved in the Y199F mutant, excluding the possibility that the bands are O-H stretches of Tyr-199. On the other hand, Thr-204 and Tyr-174 form a hydrogen bond between the retinal chromophore pocket and the binding surface of the ppR-pHtrII complex. These FTIR measurements revealed that the bands at 3479 (-)/3369 (+) cm-1 disappeared in the T204A mutant, while being shifted to 3498 (-) and 3474 (+) cm-1 in the T204S mutant. They appear at 3430 (-)/3402 (+) cm-1 in the Y174F mutant. From these results, we concluded that the bands at 3479 (-)/3369 (+) cm-1 originate from the O-H stretch of Thr-204. A stronger hydrogen bond as shown by a large spectral downshift (110 cm-1) suggests that the specific hydrogen bonding alteration of Thr-204 takes place upon retinal photoisomerization, which does not occur in the absence of the transducer protein. Thr-204 has been known as an important residue for color tuning and photocycle kinetics in ppR. The results presented here point to an additional important role of Thr-204 in ppR for the interaction with pHtrII. Specific interaction in the complex that involves Thr-204 presumably affects the decay kinetics and binding affinity in the M intermediate.

    DOI: 10.1021/bi035678g

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    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)  

    Pharaonis phoborhodopsin (ppR, also called Natronobacterium pharaonis sensory rhodopsin II) and its transducer protein, pharaonis halobacterial transducer of ppR (pHtrII), form a signaling complex, and light signals are transmitted from the sensor to the transducer by the protein-protein interaction. A truncated pHtrII(1-159) consisting of intramembrane helices (expressing amino acid residues from the first to the 159th position) and ppR form the complex in a solution containing 0.1% n-dodecyl-β-D-maltoside. At 75-85°C, the time-dependent color loss of ppR was caused by denaturation. We found that pHtrII(1-159) retarded the denaturation rate of ppR. This increase in the thermal stability was used as a probe for the binding ability in the dark. Tyr199 of ppR and Asn74 of pHtrII(1-114) were proposed as amino acid residues interacting with each other through hydrogen bonding. Then, ppR and pHtrII(1-159) mutants at these positions were prepared to examine the effect on the binding in the dark. The wild-type and Y199F mutant can bind pHtrII(1-159), suggesting that the hydrogen bonding between these specific amino acid residues may not be the only cause of the binding, but the hydrophobic interaction via phenyl ring of ppR may contribute dominantly.

    DOI: 10.1562/0031-8655(2003)078<0511:IONPPS>2.0.CO;2

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Natronobacterium pharaonis phoborhodopsin (ppR
    also called N. pharaonis sensory rhodopsin II, NpsRII) is a photophobic sensor in N. pharaonis, and has a shorter absorption maximum (λmax 500 nm) than those of other archaeal retinal proteins (λmax, 560-590 nm) such as bacteriorhodopsin (bR). We constructed chimeric proteins between bR and ppR to investigate the long range interactions effecting the color regulation among archaeal retinal proteins. The λmax of B-DEFG/P-ABC was 545 nm, similar to that of bR expressed in Escherichia coli (λmax, 550 nm). B-DEFG/P-ABC means a chimera composed of helices D, E, F, and G of bR and helices A, B, and C of ppR. This indicates that the major factor(s) determining the difference in λmax between bR and ppR exist in helices DEFG. To specify the more minute regions for the color determination between bR and ppR, we constructed 15 chimeric proteins containing helices D, E, F, and G of bR. According to the absorption spectra of the various chimeric proteins, the interaction between helices D and E as well as the effect of the hydroxyl group around protonated Schiff base on helix G (Thr-204 for ppR and Ala-215 for bR) are the main factors for spectral tuning between bR and ppR.

    DOI: 10.1074/jbc.M301200200

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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 Chemical Society ({ACS})  

    pharaonis phoborhodopsin (ppR
    also called pharaonis sensory rhodopsin II, psRII) is a photoreceptor for negative phototaxis in Natronobacterium pharaonis. ppR activates the cognate transducer protein, pHtrII, upon absorption of light. ppR and pHtrII form a tight 2:2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR. In this paper, we studied the influence of pHtrII on the structural changes occurring upon retinal photoisomerization in ppR by means of low-temperature FTIR spectroscopy. We trapped the K intermediate at 77 K and compared the ppRK minus ppR spectra in the absence and presence of pHtrII. There are no differences in the X-D stretching vibrations (2700-1900 cm-1) caused by presence of pHtrII. This result indicates that the hydrogen-bonding network in the Schiff base region is not altered by interaction with pHtrII, which is consistent with the same absorption spectrum of ppR with or without pHtrII. In contrast, the ppRK minus ppR infrared difference spectra are clearly influenced by the presence of pHtrII in amide-I (1680-1640 cm-1) and amide-A (3350-3250 cm-1) vibrations. The identical spectra for the complex of the unlabeled ppR and 13C- or 15N-labeled pHtrII indicate that the observed structural changes for the peptide backbone originate from ppR only and are altered by retinal photoisomerization. The changes do not come from pHtrII, implying that the light signal is not transmitted to pHtrII in ppRK. In addition, we observed D2O-insensitive bands at 3479 (-)/3369 (+) cm-1 only in the presence of pHtrII, which presumably originate from an X-H stretch of an amino acid side chain inside the protein.

    DOI: 10.1021/bi034317y

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

    We have recorded 13C nuclear magnetic resonance (NMR) spectra of [3-13C]Ala, [1-13C]Val-labeled pharaonis phoborhodopsin (ppR or sensory rhodopsin II) incorporated into egg PC (phosphatidylcholine) bilayer, by means of site-directed high-resolution solid-state NMR techniques. Seven 13C NMR signals from transmembrane α-helices were resolved for [3-13C]Ala-ppR at almost the same positions as those of bacteriorhodopsin (bR), except for the suppressed peaks in the loop regions in spite of the presence of at least three Ala residues. In contrast, 13C NMR signals from the loops were visible from [1-13C]Val-ppR but their peak positions of the transmembrane α-helices are not always the same between ppR and bR. The motional frequency of the loop regions in ppR was estimated as 105 Hz in view of the suppressed peaks from [3-13C]Ala-ppR due to interference with proton decoupling frequency. We found that conformation and dynamics of ppR were appreciably altered by complex formation with a cognate truncated transducer pHtr II (1-159). In particular, the C-terminal α-helix protruding from the membrane surface is involved in the complex formation and subsequent fluctuation frequency is reduced by one order of magnitude. © 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

    DOI: 10.1016/S0014-5793(03)00065-6

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    In bacteriorhodopsin (bR), Arg-82bR has been proven to be a very important residue for functional role of this light-driven proton pump. The arginine residue at this position is a super-conserved residue among archaeal rhodopsins. pharaonis phoborhodopsin (ppR
    or called as "pharaonis sensory rhodopsin II") has its absorption maximum at 498 nm and acts as a sensor in the membrane of Natronobacterium pharaonis, mediating the negative phototaxis from the light of wavelength shorter than 520 nm. To investigate the role of the arginine residue (Arg-72ppR) of ppR corresponding to Arg-82bR, mutants whose Arg-72ppR was replaced by alanine (R72A), lysine (R72K), glutamine (R72Q) and serine (R72S) were prepared. These mutants were unstable in low concentrations of NACl and lost their color gradually when the proteins were solubilized with 0.1% n-dodecyl-β-D-maltoside. The order of instability was R72S &gt
    R72A &gt
    R72K &gt
    R72Q &gt
    the wild type. The rates of denaturation were reduced in a solution of high concentrations of monovalent anions.

    DOI: 10.1562/0031-8655(2003)077<0096:AOPPSR>2.0.CO;2

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II [psRII]) is a member of the archaeal rhodopsin family and acts as a repellent phototaxis receptor of Natronobacterium pharaonis. Upon illumination, ppR is excited and undergoes a linear cyclic photoreaction, namely, a photocycle that constitutes photointermediates such as M- and O-intermediates (ppRM and ppRO, respectively). Under a constant background illumination (&gt
    600 nm) that irradiates ppRO, the decay rate of the flash-induced ppRO increased with an increase in the background light intensity, indicating the photoreactivity of ppRO. Azide did not influence the light-accelerated ppRO decay, but the time required for the cycle to be completed became shortened in an azide concentration-dependent manner because of acceleration of ppRM decay. Hence, the turnover rate of photocycling increased appreciably in the presence of both the background illumination and the azide. The observation reported previously (Schmies, G. et al. 2000, Biophys. J. 78:967-976) is discussed in connection with the present observations.

    DOI: 10.1562/0031-8655(2002)076<0462:IATDOT>2.0.CO;2

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    Pharaonis phoborhodopsin (ppR or pharaonis sensory rhodopsin II) is a receptor of the negative phototaxis of Natronobacterium pharaonis and forms a complex with its transducer pHtrII in membranes. Flash-photolyis of a D75N mutant did not yield the M-intermediate, but an O-like intermediate is observed in a ms time range. We examined the interaction between the D75N of ppR and t-Htr (truncated pHtrII). These formed a complex in the presence of 0.1% n-dodecyl-β-maltoside, and the association accelerated the decay of the O of D75N from 15 to 56 s-1. From the decay time constants under varying ratios of D75N and t-Htr, n, the molar ratio of D75N/t-Htr in the complex, and KD, the dissociation constant, were estimated. The value of n was unity and KD was estimated to 146 nM. This KD value can be considered to be the association between the photo-intermediate and t-Htr, which is deduced by the method of estimation. Previously we (Photochem. Photobiol. 74 (2001) 489) reported a KD of 15 μM for the interaction between the wild-type and t-Htr by means of the change in M-decay rates. Therefore, this value should be the KD value for the interaction between M of the wild-type and t-Htr. © 2002 Elsevier Science B. V. All rights reserved.

    DOI: 10.1016/S1011-1344(02)00322-6

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    pharaonis phoborhodopsin (ppR
    also pharaonis sensory rhodopsin II, psRII) is a receptor of the negative phototaxis of Natronobacterium pharaonis. In halobacterial membrane, ppR forms a complex with its transducer pHtrII, and this complex transmits the light signal to the sensory system in the cytoplasm. In the present work, the truncated transducer, t-Htr, was used which interacts with ppR [Sudo et al. (2001) Photochem. Photobiol. 74, 489-494]. Two water-soluble reagents, hydroxylamine and azide, reacted both with the transducer-free ppR and with the complex ppR/t-Htr (the complex between ppR and its truncated transducer). In the dark, the bleaching rates caused by hydroxylamine were not significantly changed between transducer-free ppR and ppR/t-Htr, or that of the free ppR was a little slower. Illumination accelerated the bleach rates, which is consistent with our previous conclusion that the reaction occurs selectively at the M-intermediate, but the rate of the complex was about 7.4-fold slower than that of the transducer-free ppR. Azide accelerated the M-decay, and its reaction rate of ppR/t-Htr was about 4.6-fold slower than free ppR. These findings suggest that the transducer binding decreases the water accessibility around the chromophore at the M-intermediate. Its implication is discussed. © 2002 Elsevier Science B.V. All rights reserved.

    DOI: 10.1016/S0005-2736(01)00423-0

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society  

    Pharaonis phoborhodopsin (ppR
    also pharaonis sensory rhodopsin II, psRII) is a receptor of the negative phototaxis of Natronobacterium pharaonis. By spectroscopic titration of D193N and D193E mutants, the PKa of the Schiff base was evaluated. Asp193 corresponds to Glu204 of bacteriorhodopsin (bR). The pKa of the Schiff base (SBH+) of D193N was ∼10.1-10.0 (at XH+) and ∼11.4-11.6 (at X) depending on the protonation state of a certain residue (designated by X) and independent of Cl-, whereas those of the wild type and D193E were &gt
    12. The pKa values of XH+ were ∼11.8-11.2 at the state of SB, 10.5 at SBH+ state in the presence of Cl-, and 9.6 at SBH+ without Cl-. These imply the presence of a long-range interaction in the extracellular channel. Asp193 was suggested to be deprotonated in the present dodecylmaltoside (DDM) solubilized wild-type ppR, which is contrary to Glu204 of bR. In the absence of salts, the irreversible denaturation of D193N (but not the wild type and D193E) occurred via a metastable state, into which the addition of Cl- reversed the intact pigment. This suggests that the negative charge at residue 193, which can be substituted by Cl-, is necessary to maintain the proper conformation in the DDM-solubilized ppR.

    DOI: 10.1016/S0006-3495(02)75236-3

    Scopus

    PubMed

    researchmap

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

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society  

    pharaonis Phoborhodopsin (ppR
    also pharaonis sensory rhodopsin II, psRII) is a retinal protein in Natronobacterium pharaonis and is a receptor of negative phototaxis. It forms a complex with its transducer, pHtrII, in membranes and transmits light signals by protein-protein interaction. Tyr-199 is conserved completely in phoborhodopsins among a variety of archaea, but it is replaced by Val (for bacteriorhodopsin) and Phe (for sensory rhodopsin I). Previously, we (Sudo, Y., M. Iwamoto, K. Shimono, and N. Kamo, submitted for publication) showed that analysis of flash-photolysis data of a complex between D75N and the truncated pHtrII (t-Htr) give a good estimate of the dissociation constant KD in the dark. To investigate the importance of Tyr-199, KD of double mutants of D75N/Y199F or D75N/Y199V with t-Htr was estimated by flash-photolysis and was ∼10-fold larger than that of D75N, showing the significant contribution of Tyr-199 to binding. The KD of the D75N/t-Htr complex increased with decreasing pH, and the data fitted well with the Henderson-Hasselbach equation with a single pKa of 3.86 ± 0.02. This suggests that certain deprotonated carboxyls at the surface of the transducer (possibly Asp-102, Asp-104, and Asp-106) are needed for the binding.

    DOI: 10.1016/S0006-3495(02)75180-1

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Phoborhodopsin (pR or sensory rhodopsin II, sRII) and pharaonis phoborhodopsin (ppR or pharaonis sRII, psRII) have a unique absorption maximum (λmax) compared with three other archaeal rhodopsins: λmax of pR and ppR is approx. 500 nm and of others (e.g. bacteriorhodopsin, bR) is 560-590 nm. To determine the residue contributing to the opsin shift from ppR to bR, we constructed various ppR mutants, in which a single residue was substituted for a residue corresponding to that of bR. The residues mutated were those which differ from that of bR and locate within 5 Å from the conjugated polyene chain of the chromophore or any methyl group of the polyene chain. The shifts of λmax of all mutants were small, however. We constructed a mutant in which all residues which differ from those of bR in the retinal binding site were simultaneously substituted for those of bR, but the shift was only from 499 to 509 nm. Next, we constructed a mutant in which 10 residues located within 5 Å from the polyene as described above were simultaneously substituted. Only 44% of the opsin shift (λmax of 524 nm) from ppR to bR was obtained even when all amino acids around the chromophore were replaced by the same residues as bR. We therefore conclude that the structural factor is more important in accounting for the difference of λmax between ppR and bR rather than amino acid substitutions. The possible structural factors are discussed. © 2001 Elsevier Science B.V. All rights reserved.

    DOI: 10.1016/S0005-2736(01)00394-7

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Phoborhodopsin (pR
    also called sensory rhodopsin II, sRII) is a receptor of negative phototaxis of Halobacterium salinarum, and pharaonis phoborhodopsin (ppR
    also pharaonis sensory rhodopsin II, psRII) is a corresponding protein of Natronobacterium pharaonis. These receptors contain retinal as a chromophore which binds to a lysine residue via Schiff base. This Schiff base can be cleaved with hydroxylamine to loose their color (bleaching). In dark, the bleaching rate of ppR was very slow whereas illumination accelerated considerably the bleaching rate. Addition of azide accelerated the decay of the M-intermediate while its formation (decay of the L-intermediate) is not affected. The bleaching rate of ppR under illumination was decreased by addition of azide. Essentially no reactivity with hydroxylamine under illumination was observed in the case of D75N mutant which lacks the M-intermediate in its photocycle. Moreover, we provided illumination by flashes to ppR in the presence of varying concentrations of azide to measure the bleaching rate per one flash. A good correlation was obtained between the rate and the mean residence time, MRT, which was calculated from flash photolysis data of the M-decay. These findings reveal that water-soluble hydroxylamine reacts selectively with the M-intermediate and its implication was discussed. © 2001 Published by Elsevier Science B.V.

    DOI: 10.1016/S0005-2736(01)00380-7

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    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)  

    Pharaonis phoborhodopsin (ppR) (also pharaonis sensory rhodopsin II) is a receptor of the negative phototaxis of Natronobacterium pharaonis. ppR forms a complex with its pharaonis halobacterial transducer (pHtrII), and this complex transmits the light signal to the sensory system in the cytoplasm. The expressed C-terminal-His tagged ppR and C-terminal-His tagged truncated pHtrII (t-Htr) in Escherichia coli (His means the 6x histidine tag) form a complex even in the presence of 0.1% of n-dodecyl-β-D-maltoside, and the M-decay of the complex became about twice slower than that of ppR alone. The photocycling rates under varying concentration ratios of ppR to t-Htr in the presence of detergent were measured. The data were analyzed on the following assumptions: (1) the M-decay of both ppR alone and the complex followed a single exponential decay with different time constants
    and (2) the M-decay under varying concentration ratios of ppR to t-Htr, therefore, followed a biexponential decay function which combined the decay of the free ppR and that of the complex as photoreactive species. From these analyses we estimated the dissociation constant (15.2 ± 1.8 μM) and the number of binding sites (1.2 ± 0.08).

    DOI: 10.1562/0031-8655(2001)074<0489:PPBTIC>2.0.CO;2

    Scopus

    PubMed

    researchmap

  • 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

     詳細を見る

    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Archaeal rhodopsins possess a retinal molecule as their chromophores, and their light energy and light signal conversions are triggered by all-traps to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of the protein then leads to functional processes, proton pump in bacteriorhodopsin and transducer activation in sensory rhodopsins. In the present paper, low-temperature Fourier transform infrared spectroscopy is applied to phoborhodopsin from Natronobacterium pharaonis (ppR), a photoreceptor for the negative phototaxis of the bacteria, and infrared spectral changes before and after photoisomerization are compared with those of bacteriorhodopsin (BR) at 77 K. Spectral comparison of the C-C stretching vibrations of the retinal chromophore shows that chromophore conformation of the polyene chain is similar between ppR and BR. This fact implies that the unique chromophore-protein interaction in ppR, such as the blue-shifted absorption spectrum with vibrational fine structure, originates from both ends, the beta -ionone ring and the Schiff base regions. In fact, less planer ring structure and stronger hydrogen bond of the Schiff base were suggested for ppR. Similar frequency changes upon photoisomerization are observed for the C=N stretch of the retinal Schiff base and the stretch of the neighboring threonine side chain (Thr79 in ppR and Thr89 in BR), suggesting that photoisomerization in ppR is driven by the motion of the Schiff base like BR. Nevertheless, the structure of the K state after photoisomerization is different between ppR and BR. In BR, chromophore distortion is localized in the Schiff base region, as shown in its hydrogen out-of-plane vibrations. In contrast, more extended structural changes take place in ppR in view of chromophore distortion and protein structural changes. Such structure of the K intermediate of ppR is probably correlated with its high thermal stability. In fact, almost identical infrared spectra are obtained between 77 and 170 K in ppR. Unique chromophore-protein interaction and photoisomerization processes in ppR are discussed on the basis of the present infrared spectral comparison with BR.

    DOI: 10.1021/bo0103819

    Web of Science

    researchmap

  • 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

     詳細を見る

    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:Biophysical Society  

    Phoborhodopsin (pR
    also sensory rhodopsin II, sRII) is a retinoid protein in Halobacterium salinarum and works as a receptor of negative phototaxis. Pharaonis phoborhodopsin (ppR
    also pharaonis sensory rhodopsin II, psRII) is a corresponding protein of Natronobacterium pharaonis. In bacterial membrane, ppR forms a complex with its transducer pHtrII, and this complex transmits the light signal to the sensory system in the cytoplasm. We expressed pHtrII-free ppR or ppR-pHtrII complex in H. salinarum Pho81/wr- cells. Flash-photolysis experiments showed no essential changes between pHtrII-free ppR and the complex. Using SnO2 electrode, which works as a sensitive pH electrode, and envelope membrane vesicles, we showed the photo-induced outward proton transport. This membranous proton transport was also shown using membrane vesicles from Escherichia coli in which ppR was functionally expressed. On the other hand, the proton transport was ceased when ppR formed a complex with pHtrII. Using membrane sheet, it was shown that the complex undergoes first proton uptake and then release during the photocycle, the same as pHtrII-free ppR, although the net proton transport ceases. Taking into consideration that the complex of sRII (pR) and its transducer undergoes extracellular proton circulation (J. Sasaki and J. L. Spudich, 1999, Biophys. J. 77:2145-2152), we inferred that association with pHtrII closes a cytoplasmic channel of ppR, which lead to the extracellular proton circulation.

    DOI: 10.1016/S0006-3495(01)76070-5

    Scopus

    PubMed

    researchmap

▼全件表示

MISC

  • Light + Rhodopsin = Medicinal products!? 招待

    Yuki Sudo, Keiichi Kojima, Shiho Kawanishi

    Photonics Review   240206   2024年5月

     詳細を見る

    担当区分:筆頭著者, 責任著者  

    DOI: 10.11470/photo.240206

    researchmap

  • Convergent evolution of animal and microbial rhodopsins 招待 査読

    Keiichi Kojima, Yuki Sudo

    RSC Advances   13 ( 8 )   5367 - 5381   2023年2月

     詳細を見る

    担当区分:最終著者, 責任著者   掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    Animal and microbial rhodopsins have common molecular properties (e.g. protein structure, retinal structure, color sensitivity, and photoreaction) while their functions are distinctively different (e.g. GPCRs versus and ion transporters).

    DOI: 10.1039/D2RA07073A

    researchmap

  • Introduction of Session 1, “Photochemistry of retinal proteins”

    Yuki Sudo

    Biophysics and Physicobiology   2023年

  • Editorial: Forewords to the special issue “Recent advances in retinal protein research”

    Yuki Sudo, Akihisa Terakita, Hideki Kandori

    Biophysics and Physicobiology   2023年

  • バイオマスを2倍にする新技術:ロドプシンを用いた緑藻クラミドモナスの生育制御 招待

    小島慧一, 長瀬友里恵, 田村丞, 須藤雄気

    クリーンエネルギー   ( 31 )   49 - 57   2022年3月

     詳細を見る

    担当区分:最終著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

    researchmap

  • Expression of microbial rhodopsins in Escherichia coli and their extraction and purification using styrene-maleic acid copolymers

    Kojima, K., Sudo, Y.

    STAR Protocols   3 ( 1 )   101046 - 101046   2022年3月

     詳細を見る

    担当区分:最終著者, 責任著者   掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.xpro.2021.101046

    Scopus

    researchmap

  • 光+ロドプシン=くすり 招待

    須藤雄気, 小島慧一, 川西志歩

    フォトニクスニュース   ( 7 )   153 - 158   2022年2月

     詳細を見る

    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)  

    researchmap

  • 光がくすりになる!?―ロドプシンによる生命機能の光操作 招待

    須藤雄気, 小島慧一

    月刊「化学」   ( 77 )   64 - 65   2022年1月

     詳細を見る

    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

    researchmap

  • Microbial Rhodopsins as Multi-functional Photoreactive Membrane Proteins for Optogenetics 査読

    Shin Nakao, Keiichi Kojima, Yuki Sudo

    Biological and Pharmaceutical Bulletin   44 ( 10 )   1357 - 1363   2021年10月

     詳細を見る

    掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:Pharmaceutical Society of Japan  

    DOI: 10.1248/bpb.b21-00544

    researchmap

  • マルチタレント光受容タンパク質「ロドプシン」 招待

    須藤雄気, 小島慧一

    現代化学   5 ( 602 )   50 - 53   2021年5月

     詳細を見る

    担当区分:筆頭著者, 責任著者   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

    J-GLOBAL

    researchmap

  • Early Career Award in Biophysics and Early Career Presentation Award—Report on the Sixteenth Award Selection Process—

    Yuki SUDO, Takeshi MURATA

    Seibutsu Butsuri   61 ( 1 )   049 - 050   2021年

     詳細を見る

    出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophys.61.049

    researchmap

  • Gタンパク質共役型受容体・ロドプシンを対象としたスチレンマレイン酸(SMA)コポリマーの適用と有用性の検討

    小島慧一, 上田哲也, 日野智也, 永野真吾, 須藤雄気

    日本薬学会年会要旨集(Web)   141st   2021年

     詳細を見る

  • 微生物ロドプシンの多様性と可能性

    須藤雄気, 小島慧一

    生物物理(Web)   60 ( 4 )   2020年

     詳細を見る

  • 日本生物物理学会第57回年会報告 学生発表賞:―選考過程・結果報告―

    須藤 雄気, 古寺 哲幸, 細川 千絵

    生物物理   60 ( 1 )   47 - 48   2020年

     詳細を見る

    記述言語:日本語   出版者・発行元:一般社団法人 日本生物物理学会  

    DOI: 10.2142/biophys.60.047

    CiNii Article

    researchmap

  • 微生物ロドプシンの多様性と可能性

    須藤雄気, 小島慧一

    生物物理   60 ( 4 )   209 - 214   2020年

     詳細を見る

    担当区分:筆頭著者, 責任著者  

    DOI: 10.2142/biophys.60.209

    researchmap

  • スチレンコポリマー中における微生物型ロドプシンの機能・物性解析

    上田哲也, 小島慧一, 日野智也, 柴田幹大, 永野真吾, 須藤雄気

    生体膜と薬物の相互作用シンポジウム講演要旨集   41st   2019年

     詳細を見る

  • Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering

    Kaneko, A., Inoue, K., Kojima, K., K, ori, H., Sudo, Y.

    Biophysical Reviews   9 ( 6 )   861 - 876   2017年12月

     詳細を見る

    出版者・発行元:Springer Science and Business Media {LLC}  

    DOI: 10.1007/s12551-017-0335-x

    Scopus

    researchmap

  • 微生物型ロドプシンTRのX線結晶構造解析

    水谷健二, 橋本直記, 塚本卓, 須藤雄気, 村田武士

    KEK Progress Report (Web)   ( 2016-8 )   ROMBUNNO.242 (WEB ONLY)   2017年1月

     詳細を見る

    記述言語:日本語  

    J-GLOBAL

    researchmap

  • 光エネルギー変換の新常識! – 光駆動2価多原子アニオン輸送体の発見とその分光特性

    仁保亜希子, 須藤雄気

    academist Journal   2017年

     詳細を見る

    担当区分:最終著者, 責任著者  

    researchmap

  • Structural and functional studies on photoactive retinal proteins

    Yuki Sudo*

    Yakugaku Zasshi, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan   136 ( 2 )   185 - 189   2016年2月

     詳細を見る

    担当区分:筆頭著者   記述言語:日本語   掲載種別:書評論文,書評,文献紹介等  

    DOI: 10.1248/yakushi.15-00229-3

    Web of Science

    J-GLOBAL

    researchmap

  • オプトジェネティクス

    須藤雄気

    光と生命の事典 日本光生物学協会「光と生命の事典」編集委員会 編 [朝倉書店]   372 - 373   2016年

     詳細を見る

  • 光受容レチナールタンパク質の構造・機能解析:光+タンパク質=薬!?

    須藤雄気

    薬学雑誌   136 ( 2 )   185 - 189   2016年

  • Color tuning in retinylidene proteins

    Kota Katayama, Sivakumar Sekharan, Yuki Sudo

    Optogenetics: Light-Sensing Proteins and their Applications   89 - 109   2015年1月

     詳細を見る

    記述言語:英語   出版者・発行元:Springer Japan  

    Retinylidene proteins (also called rhodopsins) are membrane-embedded photoreceptors that contain a vitamin A aldehyde linked to a lysine residue by a Schiff base as their light-sensing chromophore. The chromophore is surrounded by seven-transmembrane α-helices and absorbs light at different wavelengths due to differences in the electronic energy gap between its ground and excited states. The variation in the wavelength of maximal absorption (λmax: 360–620 nm) of rhodopsins arises due to interaction between the apoprotein (opsin) and the retinyl chromophore, the ‘opsin shift’. This chapter reviews the color tuning mechanisms in type-1 microbial and type-2 animal rhodopsins as revealed mainly by our experimental and theoretical studies.

    DOI: 10.1007/978-4-431-55516-2_7

    Scopus

    researchmap

  • Microbial rhodopsins: wide distribution, rich diversity and great potential

    Kurihara M, Sudo Y

    BIophysics and Physicobiology   12   121 - 129   2015年

     詳細を見る

    記述言語:英語   出版者・発行元:一般社団法人 日本生物物理学会  

    One of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. Taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. Rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. In this review, we summarize progress of microbial rhodopsin research from the viewpoint of distribution, diversity and potential.

    DOI: 10.2142/biophysico.12.0_121

    CiNii Article

    researchmap

  • ビタミンAアルデヒドを発色団とするレチナールタンパク質の多様性と可能性

    土井聡子, 須藤雄気

    ビタミン学会誌   89 ( 2 )   83 - 86   2015年

  • 好熱性細菌のレチナールタンパク質

    塚本卓, 須藤雄気

    生物物理   55 ( 2 )   092-094 (J-STAGE) - 94   2015年

     詳細を見る

    記述言語:日本語   出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

    DOI: 10.2142/biophys.55.092

    CiNii Article

    J-GLOBAL

    researchmap

  • Molecular and evolutionary aspects of microbial sensory rhodopsins 招待 査読

    Keiichi Inoue, Takashi Tsukamoto, Yuki Sudo

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   1837 ( 5 )   562 - 577   2014年5月

     詳細を見る

    担当区分:最終著者, 責任著者   掲載種別:書評論文,書評,文献紹介等   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.bbabio.2013.05.005

    Web of Science

    researchmap

  • Sensory rhodopsins

    Tsukamoto, T, Sudo, Y

    eLS (Encyclopedia of Life Sciences)   2014年

  • 膜タンパク質の可溶化(抽出)(2)

    須藤雄気、塚本卓

    蛋白質科学会・アーカイブ   7   e079   2014年

     詳細を見る

    担当区分:筆頭著者, 責任著者  

    researchmap

  • オプトジェネティクス(光遺伝学)の原理と基礎

    須藤雄気, 神取秀樹

    ファルマシア   50 ( 10 )   958 - 962   2014年

     詳細を見る

    担当区分:筆頭著者  

    J-GLOBAL

    researchmap

  • 正方形の古細菌が持つ光受容タンパク質の特徴的な構造変化

    須藤雄気

    分子研レターズ   68   2013年

     詳細を見る

  • 光受容タンパク質による微生物の光センシングの理解とその利用

    須藤 雄気, 本間 道夫

    YAKUGAKU ZASSHI   132 ( 4 )   407 - 416   2012年

     詳細を見る

    記述言語:日本語   出版者・発行元:公益社団法人 日本薬学会  

    Light is one of the most important energy sources and signals providing critical information to biological systems. The photoreceptor rhodopsin, which possesses retinal chromophore (vitamin A aldehyde) surrounded by seven transmembrane alpha-helices, is widely dispersed in prokaryotes and in eukaryotes. Although rhodopsin molecules work as distinctly different photoreceptors, they can be divided according to their two basic functions such as light-energy conversion and light-signal transduction. Thus rhodopsin molecules have great potential for controlling cellular activity by light. Indeed, a light-energy converter channel rhodopsin is used to control neural activity. From 2001, we have been working on various microbial sensory rhodopsins functioning as light-signal converters. In this review, we will introduce rhodopsin molecules from microbes, and will describe artificial and light-dependent protein expression system in Escherichia coli using Anabeana sensory rhodopsin (ASR). The newly developed tools would be widely useful for life scientists.<br>

    DOI: 10.1248/yakushi.132.407

    CiNii Article

    CiNii Books

    J-GLOBAL

    researchmap

    その他リンク: https://jlc.jst.go.jp/DN/JALC/10000140750?from=CiNii

  • 高度好塩性微生物の"目" : センサリーロドプシンへのCl⁻イオン結合の役割

    須藤 雄気, 井原 邦夫, 本間 道夫

    極限環境生物学会誌 = Journal of Japanese Society for Extremophiles   10 ( 1 )   23 - 29   2011年9月

     詳細を見る

    記述言語:日本語   出版者・発行元:[極限環境生物学会]学会事務局  

    CiNii Article

    researchmap

  • 高度好塩性微生物の“目”:センサリーロドプシンへのCl-イオン結合の役割

    須藤雄気, 須藤雄気, 井原邦夫, 本間道夫, 加茂直樹

    極限環境生物学会誌   10 ( 1 )   2011年

     詳細を見る

  • ロドプシン研究はどこへ行くのか? : 吉澤透先生に応えて

    須藤 雄気

    生物物理   50 ( 4 )   160 - 161   2010年7月

     詳細を見る

    記述言語:日本語   出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

    DOI: 10.2142/biophys.50.160

    CiNii Article

    CiNii Books

    researchmap

  • Phototactic and chemotactic signal transduction by transmembrane receptors and transducers in microorganisms

    Daisuke Suzuki, Hiroki Irieda, Michio Homma, Ikuro Kawagishi, Yuki Sudo

    Sensors   10 ( 4 )   4010 - 4039   2010年4月

     詳細を見る

    記述言語:英語   掲載種別:書評論文,書評,文献紹介等  

    Microorganisms show attractant and repellent responses to survive in the various environments in which they live. Those phototaxic (to light) and chemotaxic (to chemicals) responses are regulated by membrane-embedded receptors and transducers. This article reviews the following: (1) the signal relay mechanisms by two photoreceptors, Sensory Rhodopsin I (SRI) and Sensory Rhodopsin II (SRII) and their transducers (HtrI and HtrII) responsible for phototaxis in microorganisms
    and (2) the signal relay mechanism of a chemoreceptor/transducer protein, Tar, responsible for chemotaxis in E. coli. Based on results mainly obtained by our group together with other findings, the possible molecular mechanisms for phototaxis and chemotaxis are discussed. © 2010 by the authors.

    DOI: 10.3390/s100404010

    Scopus

    PubMed

    researchmap

  • 光で/を動かす技術 光で動きを変える微生物-ロドプシン分子による光受容と情報伝達機構-

    割石学, 本間道夫, 須藤雄気

    O plus E   ( 366 )   2010年

     詳細を見る

  • Protein-protein interaction changes in an archaeal light-signal transduction 査読

    Hideki Kandori, Yuki Sudo, Yuji Furutani

    Journal of Biomedicine and Biotechnology   2010   Article ID 424760   2010年

     詳細を見る

    記述言語:英語   掲載種別:書評論文,書評,文献紹介等   出版者・発行元:Hindawi Publishing Corporation  

    Negative phototaxis in Natronomonas pharaonis is initiated by transient interaction changes between photoreceptor and transducer. pharaonis phoborhodopsin (ppR
    also called pharaonis sensory rhodopsin II, psR-II) and the cognate transducer protein, pHtrII, form a tight 2:2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR. We have studied the signal transduction mechanism in the ppR/pHtrII system by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy. In the paper, spectral comparison in the absence and presence of pHtrII provided fruitful information in atomic details, where vibrational bands were identified by the use of isotope-labeling and site-directed mutagenesis. From these studies, we established the two pathways of light-signal conversion from the receptor to the transducer
    (i) from Lys205 (retinal) of ppR to Asn74 of pHtrII through Thr204 and Tyr199, and (ii) from Lys205 of ppR to the cytoplasmic loop region of pHtrII that links Gly83. Copyright © 2010 Hideki Kandori et al.

    DOI: 10.1155/2010/424760

    Scopus

    PubMed

    researchmap

  • 真正細菌から得られた2つの機能をもつフォトクロミック光受容体ホモログ

    須藤雄気

    生物物理   49 ( 1 )   2009年

     詳細を見る

  • FTIR Studies of Protein-Protein Interaction Changes between pharaonis Phoborhodopsin and its Cognate Transducer Protein 査読

    Yuji Furutani, Yuki Sudo, Hideki Kandori

    Current topics in biochemical research   10 ( 2 )   63 - 77   2008年

     詳細を見る

    記述言語:英語   掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:Trivandrum : Research Trends  

    researchmap

  • A photochromic photoreceptor from a eubacterium. 査読

    Suzuki D, Kitajima-Ihara T, Furutani Y, Ihara K, Kandori H, Homma M, Sudo Y

    Communicative & integrative biology   1 ( 2 )   150 - 152   2008年

     詳細を見る

  • 光駆動イオンポンプから光情報伝達への機能変換の試み

    須藤雄気

    生物物理   46 ( 6 )   2006年

     詳細を見る

  • 【図・写真で観るタンパク構造・機能解析実験実践ガイド】タンパク質の立体構造解析を行うために 膜タンパク質の機能的大量発現

    須藤 雄気, 河野 俊之, 田中 利好, 加茂 直樹, 児嶋 長次郎

    遺伝子医学MOOK   別冊 ( 図・写真で観るタンパク構造・機能解析実験実践カ )   41 - 46   2005年7月

     詳細を見る

    記述言語:日本語   出版者・発行元:(株)メディカルドゥ  

    researchmap

  • Close Up実験法 Series144 無細胞タンパク質合成系を用いた膜タンパク質発現の新規手法

    須藤雄気, 須藤雄気, 河野俊之, 児嶋長次郎

    実験医学   23 ( 12 )   2005年

     詳細を見る

  • Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin 査読

    N Kamo, K Shimono, M Iwamoto, Y Sudo

    BIOCHEMISTRY-MOSCOW   66 ( 11 )   1277 - 1282   2001年11月

     詳細を見る

    担当区分:最終著者   記述言語:英語   掲載種別:書評論文,書評,文献紹介等   出版者・発行元:MAIK NAUKA/INTERPERIODICA  

    Phoborhodopsin (pR or sensory rhodopsin II, sRII) is a photoreceptor of the negative phototaxis of Halobacterium salinarum, and pharaonis phoborhodopsin (ppR or pharaonis sensory rhodopsin II, psRII) is a corresponding protein of Natronobacterium pharaonis. The photocycle of ppR is essentially as follows: ppR(498) --&gt; ppR(K)(similar to540) --&gt; ppR(KL)(512) --&gt; ppR(L)(488) --&gt; ppR(M)(390) --&gt; ppR(O)(560) --&gt; ppR (numbers in parenthesis denote the maximum absorbance). The photocycle is very similar to that of bacteriorhodopsin, but the rate of initial pigment recovery is about two-orders of magnitude slower. By low-temperature spectroscopy, two K-intermediates were found but the L intermediate was not detected. The lack of L indicates extraordinary stability of K at low temperature. ppR(M) is photoactive similar to M of bR. The ground state ppR contains only all-trans retinal whereas ppR(M) and ppR(O) contain 13-cis and all-trans, respectively. ppR has the ability of light-induced proton transport from the inside to the outside. Proton uptake occurs at the formation of ppRO and the release at its decay. ppR associates with its transducer and this complex transmits a signal to the cytoplasm, The proton transport ability is lost when the complex forms, but the proton uptake and release still occur, suggesting that the proton movement is non-electrogenic (release and uptake occur from the same side). The stoichiometry of the complex between ppR and the transducer is 1 : 1. ppR or pR has absorption maximum at similar to500 nm, which is blue-shifted from those of other archaeal rhodopsins. The molecular mechanism of this color regulation is not yet solved.

    DOI: 10.1023/A:1013187403599

    Web of Science

    researchmap

▼全件表示

講演・口頭発表等

  • Molecular-based rational design and engineering of microbial retinal proteins for optogenetics

    The 16th International Conference on Retinal Proteins  2014年 

     詳細を見る

  • レチナールタンパク質による光合成モドキが 世界を救う!?

    自然科学研究機構 分間連携ワークショップ  2014年 

     詳細を見る

  • Rational Design and Engineering of Photoactive Retinal Proteins

    The 2nd Awaji International Workshop on “Electron Spin Science & Technology: Biological and Materials Science Oriented Applications (2nd AWEST 2014)  2014年 

     詳細を見る

  • Converting a Light-driven Proton Pump into a Light-gated Ion Channel

    The 52th Annual Meeting of the Biophysical Society of Japa  2014年 

     詳細を見る

産業財産権

  • 光変調装置及び集光装置

    渋川敦史, 須藤雄気, ムサクジャング

     詳細を見る

    出願人:韓国科学技術院他

    出願番号:特願2021-153788  出願日:2021年9月22日

    特許番号/登録番号:特許7244888  登録日:2023年3月14日  発行日:2023年3月23日

    権利者:国立大学法人北海道大学, 国立大学法人岡山大学, 韓国科学技術院

    researchmap

  • 光合成生物の形質転換体およびその用途

    須藤雄気、小島慧一

     詳細を見る

    出願番号:特願2021-89800(PCT/JP2022/021364)  出願日:2021年5月28日

    researchmap

  • 光により細胞死を制御する方法

    須藤雄気, 小島慧一, 中尾新

     詳細を見る

    出願番号:特願2020-196718(PCT/JP2021/043071)  出願日:2020年11月27日

    researchmap

  • 膜電位センサー

    坂本 雅行, チョウ シャオミン, 尾藤 晴彦, 須藤 雄気, 小島 慧一

     詳細を見る

    出願人:国立大学法人 東京大学

    出願番号:特願2020-070136  出願日:2020年4月9日

    公開番号:特開2021-167731  公開日:2021年10月21日

    J-GLOBAL

    researchmap

受賞

  • 第13回BPPB論文賞

    2024年4月   Biophysical Society of Japan  

     詳細を見る

  • 内山勇三科学技術賞

    2023年7月   岡山工学振興会  

     詳細を見る

  • 研究アワード2022(先端研究推進部門)

    2022年3月   株式会社リバネス  

     詳細を見る

  • 第5回BPPB論文賞

    2016年11月   Biophysical Socienty of Japan  

     詳細を見る

  • 文部科学大臣表彰 若手科学者賞

    2016年4月  

     詳細を見る

    受賞国:日本国

    researchmap

  • 研究者表彰

    2010年3月   財団法人光科学技術研究振興財団  

     詳細を見る

▼全件表示

共同研究・競争的資金等の研究

  • バイオマス増産を実現するロドプシンによる藻類成長促進技術の社会実装

    2023年 - 2024年

    科学技術振興機構 

    須藤 雄気

      詳細を見る

    担当区分:研究代表者 

    ロドプシンは、動物・微生物に広く分布し、主に緑色光を吸収する光受容タンパク質である。本課題は、藻類クラミドモナスの細胞密度がロドプシン導入により2倍程度に上昇(成長促進)する効果を基礎に、バイオマス(燃料・化粧品等)増産の実証と、成長因子同定から他の藻類への展開と起業の可能性を検証することを目的とする。

    researchmap

  • ロドプシン基底関数の理解と利用

    研究課題/領域番号:21H02446  2021年04月 - 2024年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    須藤 雄気

      詳細を見る

    配分額:17420000円 ( 直接経費:13400000円 、 間接経費:4020000円 )

    ロドプシンは、多様な生物に存在する光受容膜タンパク質の総称で、生命における光依存的機能を司るとともに、人為的な光操作(オプトジェネティクス)分子として利用されている。
    本研究は、ロドプシンとは何か?という根源的な問いに答えるため、「ロドプシン基底関数(x1a1 + x2a2 + … xiai)の理解と利用」を目的とした。
    本年度は、これまでに培ってきた技術(生物物理学,遺伝子工学,タンパク質科学,分光学,光遺伝学,生化学,神経科学,細胞生物学)と人的資源(研究協力者)を総動員し、「①探索、②解析、③操作」の3項目の研究に取り組んだ。
    具体的には、数百種類の未解析ロドプシンの発現・精製(①探索)と精密解析(②解析)を行い、既知情報とあわせて、ロドプシン間の機能や物性を定量的かつ様々な観点から比較した。これにより、基底ベクトル:x1, x2, … xi を算出し、ロドプシンを定義する素因子を明らかにした【例:x1 = 波長、x2 = 機能、x3 = 発色団、.... 】(理解)。ここでは、係数を表す a1, a2, …ai もあわせて算出した。以上より、ロドプシンとは何かの理解と分類に成功した。これにより、ロドプシンの拡張要素を炙り出すことに成功し、その情報からロドプシン分子の合理的分子設計と新奇光操作ツール開発および開発したツールによる生命機能の光操作を実現した(③操作)【例:a1 = 青・緑・赤(色パレット)、a2 = イオン輸送・走光性能、a3 = レチナール+第二発色団カロテノイド、.... 】(利用)。

    researchmap

  • ロドプシンを起動分子とした「化学・力学・光」エネルギー発動機構の理解と利用

    研究課題/領域番号:21H00404  2021年04月 - 2023年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:5980000円 ( 直接経費:4600000円 、 間接経費:1380000円 )

    ロドプシンは光エネルギーを吸収し、レチナールの異性化を介して化学エネルギーへと変換する。化学エネルギーは、タンパク質の構造変化として力学エネルギーに変換され、分子機能が発現する。また、ロドプシンは、蛍光を発する特性を有し、光エネルギーにも変換可能である。このように、本領域における『発動分子』の定義(外部エネルギーを別エネルギーへ変えるもの)から、ロドプシンはまさに“発動分子”そのものと言える。このような背景のもと、本研究では、ロドプシンによる『光-->化学・力学・光』エネルギーへの変換機構の理解と光遺伝学的利用を行うことで、ロドプシン型『発動分子』の基礎学理構築を行うことを目的とした。
    <BR>
    本年度は以下の成果を得た。
    (1)『光→化学変換』:ここでは、特に色(吸収波長)と反応速度に着目し、その改変体を作成した。色の変化は励起可能な波長域を拡げ、光操作に新たなツールを提供することとなった。また、反応が早い分子は、分子機能の高速制御が可能となり、遅いものは、活性型中間体の滞留時間の延長により、1光子あたりの分子機能活性が大きくなることが期待される。
    (2)『光→力学変換』:ここでは、タンパク質の力学的構造変化が生理応答に直結していることに着目し、これまでの成果を基盤に、ロドプシンで多様な力学変換分子の創成と生命機能操作(細胞死、神経制御など)を行った。
    (3)『光→光変換』:一部のロドプシンが、高発光性を示すことを明らかにし、さらに網羅的変異導入による高発光化にも成功した。さらに、動物個体において閾値以下かつ高速(ms)の膜電位センサーとして利用可能であることを実証した。これらのロドプシンは、従来のCa2+インディケーター型膜電位センサーに代わるツールとなることが期待される。

    researchmap

  • 光誘起崩壊リポソーム(LiDL)の開発による新奇薬物送達手法の確立

    研究課題/領域番号:20K21482  2020年07月 - 2023年03月

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)  挑戦的研究(萌芽)

    須藤 雄気, 山田 勇磨

      詳細を見る

    配分額:6500000円 ( 直接経費:5000000円 、 間接経費:1500000円 )

    【目的】物理化学(代表者)と薬剤学(分担者・協力者)の融合による光誘起崩壊リポソーム:Light-induced Disruption of Liposomes(LiDL)の開発と、それに基づく新奇薬物送達手法の確立すること。【背景】狙った時間と場所に薬物を届け・働かせることは、薬学における大きな『夢』である。【計画】光受容タンパク質・ロドプシンとpH感受性ポリマーおよび任意の化合物(薬物)を内封させたリポソームを開発することで、時空間制御性に優れた『光』により、狙った時間・場所で薬物を放出させる新奇手法を確立する。【意義】薬学における『夢』の一つを叶える手法となり、大きな波及効果をもたらす。
    <BR>
    具体的には、光受容タンパク質「(1) ロドプシン(H+ポンプ・チャネル)」と「(2) pH 感受性ポリマー」を含む「(3) リポソーム」を作成する。その際、「(4)化合物 (薬物)」を内封させる。このリポソームに「(5) 光」を照射すると、ロドプシンが活性化され、リポソーム内外のpH が大きく(> 5 ユニット)変化する。これにより、pH 感受性ポリマーの物理的形状が変化し、リポソームが崩壊し、化合物が「(6) 放出」される。LiDL と命名するこの手法は、時空間分解能に優れた「光」により薬物を放出させるという、新奇かつ独創性・汎用性の高い薬物送達(DDS)手法になる。昨年度までは、ロドプシンを組み込んだリポソームの作成と、光によるpH変化を定量的に測定し、ロドプシン組み込みリポソームが狙い通りに機能することを明らかにした。さらに、このリポソームにpH感受性分子を組み込むとともに、光により崩壊することを内部に導入する蛍光分子の蛍光変化により確認した。これにより、LiDLの開発は概ね終了した。今年度は、これを生体系(in cell、ex-vivo)で実証する。

    researchmap

  • ロドプシンによる葉緑体プロトン勾配制御システムの確立と植物応答解析への展開

    研究課題/領域番号:19H04727  2019年04月 - 2021年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:7540000円 ( 直接経費:5800000円 、 間接経費:1740000円 )

    植物による光合成は、水と二酸化炭素から炭素固定・酸素発生・ATP産生を行う反応であある。ここで、生物のエネルギー通貨とも呼ばれるATPは、光合成タンパク質における細胞内から細胞外にプロトン(H+)の輸送により実現している。また、植物には光強度にあわせて余剰なエネルギーを熱として放出する機構(Non Photochemical Quenching:NPQ)が備わっており、効率的な光合成を実現している。これらは光合成に伴う葉緑体ルーメン側の酸性化(プロトン濃度上昇)が引き金になることがわかっているが、その制御機構の詳細は不明である。
    本研究では、光合成色素クロロフィルがほとんど吸収しない緑色光で働くロドプシンを緑藻(クラミドモナス)および陸上植物(シロイヌナズナ)の葉緑体に異種発現させる組み換え体を創出する。次に、ロドプシンを光により励起し、人為的に膜を介したプロトン移動を誘起する。これにより、擬似的に強・弱光条件を作り出し、その際に起こる植物応答(ATP合成、NPQ制御、成長、形態、その他)を光で制御し、それらのメカニズムの解明を目指す。
    <BR>
    本年度は、以下の生化学的・細胞生物学的解析を行った。
    ①生化学的解析:クラミドモナスおよびシロイヌナズナにおけるロドプシンの発現を検討する。加えて、葉緑体への局在を中心に確認する。具体的には、確認用の抗体の検討および細かな実験条件の設定を行った。クラミドモナスおよびシロイヌナズナともに、ロドプシンの葉緑体への局在を示唆する結果が得られ、計画は順調に進んでいる。
    ②細胞生物学的解析:NPQをはじめとした応答解析を進めた。(1)クラミドモナスについては、NPQ誘導の確認に加え、細胞形態や生育などへのロドプシンおよび光の影響を検討した。(2)シロイヌナズナについては、上記に加えレチナールの添加法の検討と、レチナールが及ぼす細胞毒性について検討した。

    researchmap

  • ロドプシンを起動分子とした「化学・力学・光」エネルギー発動機構の理解と利用

    研究課題/領域番号:19H05396  2019年04月 - 2021年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:5850000円 ( 直接経費:4500000円 、 間接経費:1350000円 )

    ロドプシンは光エネルギーを吸収し、レチナールの異性化を介して化学エネルギーへと変換する。化学エネルギーは、タンパク質の構造変化として力学エネルギーに変換され、分子機能が発現する。また、ロドプシンは、蛍光を発する特性を有し、光エネルギーにも変換可能である。このように、本領域における『発動分子』の定義(外部エネルギーを別エネルギーに変えるもの)から、ロドプシンはまさに“発動分子”そのものと言える。このような背景のもと、本研究では、ロドプシンによる『光-->化学・力学・光』エネルギーへの変換機構の理解と光遺伝学的利用を行うことで、ロドプシン型『発動分子』の基礎学理構築を行うことを目的とした。
    <BR>
    本年度は、以下に示す多様なロドプシンのマルチ『光-->化学・力学・光』発動機構(エネルギー変換)の理解を進めた。 さらに、これらを基盤に、分子機能(速度,収率,構造変化,生理応答,発光)の合理的改変の試みと光遺伝学への展開を行った。
    1)『光-->化学』:多様なロドプシンに対し、“時間”分解測定(過渡吸収,ラマン・赤外)及び“空間”分解測定(ラマン・赤外,X線結晶構造,NMR)を行い異性化速度,量子収率,異性化に伴うレチナール及びタンパク質の構造変化を調べた。得られた定量的な数値とその比較から、『光-->化学』エネルギー変換の分子機構の理解を進めた。
    (2)『光-->(化学)-->力学』:レチナールの異性化を引き金するロドプシンの構造変化,他分子との相互作用とその変化を、“時間”分解及び“空間”分解測定により明らかにした。加えて、生化学的・細胞生物学的解析を行い、構造と機能に関わる『化学-->力学』エネルギー変換機構を明らかにした。
    (3)『光-->光』:定常蛍光分光法と各種時間分解分光法を組み合わせ、多様なロドプシンの蛍光特性の定量的比較解析と発光機構の解明を行った。

    researchmap

  • ロドプシンの多様性の探求と可能性の追求

    研究課題/領域番号:18H02411  2018年04月 - 2021年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    須藤 雄気

      詳細を見る

    配分額:17420000円 ( 直接経費:13400000円 、 間接経費:4020000円 )

    ロドプシンは、生物の三大ドメイン(真核生物・真正細菌・古細菌)に分布する光受容膜タンパク質の総称で、光エネルギー・情報変換を介し生命機能の根幹を司る:基礎的重要性。また、光遺伝学:オプトジェネティクスを生み出した分子として知られ、脳神経科学に利用されている:応用的重要性。このような重要性にもかかわらず、研究が行われているロドプシンはわずかであり、大部分は手つかずのまま残されている。そこで本研究は「ロドプシンの多様性の探究と可能性の追求」を目的とした。すなわち未解析ロドプシンの発現・精製(1. 探索)と精密解析(2. 解析)で多様性を探求し、基礎を強化する。さらに、それらの機能・特性を利用した新奇オプトジェネティクス(3. 操作)を実現し応用の可能性を追求することを目的とした。
    <BR>
    本年度は、昨年度に引き続き以下の3項目に取り組んだ。
    1.探索:(1)公開および未公開遺伝子情報から、様々な推定新規ロドプシン遺伝子を絞り込んだ。(2)これらの情報から分子系統樹を作成し、グループに分類した。(3)各グループ中央に位置する数種類と末端に位置する数種類を選抜した。(4)絞り込んだ遺伝子について、組み換え生物(大腸菌,古細菌,酵母,動物細胞)のコドンに最適化した遺伝子を合成し、発現プラスミドを作成した。タンパク質発現は宿主細胞の色により確認し、新奇ロドプシンの発現・精製系を構築した。
    2.解析:探索により発現・精製系を構築した新規ロドプシンの分子機能を様々な時空間領域「フェムト秒-ペタ秒・Å-ミリメートル」で、解析した。
    3.操作:解析が終了したロドプシンについて、その新奇機能や特性を生かした新しい光操作を実現した。特に4つのロドプシン(RmXeR,ACR2,SyHR, AR3)について、その特性を生かした新奇オプトジェネティクスを実現した。

    researchmap

  • ロドプシンによる葉緑体プロトン勾配制御システムの確立と植物応答解析への展開

    研究課題/領域番号:17H05726  2017年04月 - 2019年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:6500000円 ( 直接経費:5000000円 、 間接経費:1500000円 )

    植物による光合成は、水と二酸化炭素から、炭素固定・酸素発生・ATP産生を行う反応で、生命活動の源でもある。植物には、光強度にあわせて余剰なエネルギーを熱として放出する機構(Non photochemical quenching:NPQ)が備わっており、効率的な光合成を実現している。これらは、光合成に伴うルーメン側の酸性化(プロトン濃度上昇)が引き金になることがわかっているが、その制御機構はわかっていない。本研究では、光合成色素クロロフィルがほとんど吸収しない緑色光で働くロドプシンを植物の葉緑体に異種発現させ、人為的に膜を介したプロトン移動を誘起する。これにより、擬似的に強・弱光条件を再現し、その際に起こる植物応答を解析することで、NPQ制御メカニズムを解明することを目的としている。
    本年(H30年度)は、(1)内向きプロトンポンプロドプシンと外向きプロトンポンプロドプシンを植物モデルとしてのクラミドモナスおよびシロイヌナズナへの遺伝子導入を行い、その組み換え体においてそれぞれのロドプシン発現を確認した。植物細胞における異種ロドプシンの発現は世界初となる成果である。(2)クラミドモナスについては、NPQ測定を行い内向きプロトンポンプを発現した際に狙い通り光照射によりNPQが有意に増大することを確認した。外向きプロトンポンプでは若干の低下がみられた。このようにロドプシンを用いてNPQを制御することに世界で初めて成功した。シロイヌナズナについては、内向きプロトンポンプの発現は確認できたが、外向きプロトンポンプの発現は確認できなかった。
    以上のように、植物にロドプシンを発現させその生理応答(NPQ)を調節するという当初の目的は達成された。

    researchmap

  • ファイバーレス光遺伝学による高次脳機能を支える本能機能の解明

    2016年 - 2021年

    科学技術振興機構  戦略的な研究開発の推進 戦略的創造研究推進事業 CREST 

    須藤 雄気

      詳細を見る

    担当区分:研究代表者 

    睡眠覚醒などの本能機能は、記憶や意志決定などの高次脳機能にも影響を及ぼしています。従来の光遺伝学では、侵襲や行動制限のために、この機能連関の研究には不十分でした。新開発するファイバーレス光遺伝学では、光ファイバーを刺入せずに脳深部の神経活動を体外から照射した近赤外光で操作可能になります。これを応用することで睡眠覚醒と記憶との関係の解明に迫れるだけでなく、様々な生体機能の解明に大幅な進展が期待されます。

    researchmap

  • カロテノイドを光捕集系とするレチナールタンパク質の創出と展開

    研究課題/領域番号:15H00878  2015年06月 - 2017年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:3900000円 ( 直接経費:3000000円 、 間接経費:900000円 )

    ロドプシン(レチナールタンパク質)は、動物から微生物まで幅広い生物が共通にもっている光受容体タンパク質であり、アポタンパク質を構成する7本の膜貫通αヘリックスの中央部に、アルデヒド型ビタミンAである発色団レチナールが結合した構造を持つ。ロドプシンは、クロロフィルの吸収がほとんどない領域の光(450-600 nm)を吸収することで機能する。具体的には、光吸収によりレチナールの異性化が起こり、続いて様々な特徴を持った光中間体(活性型)となることで、多彩な機能(視覚、ATP合成、膜電位の調節など)が発現する。本研究では、ロドプシンの反応を生物の光応答のモデルと捉え、新規分子の探索・解析とその高機能化を実現することで、人工光合成の可能性を拡げることを目的とした研究を行い、以下の3つの成果をあげた。
    <BR>
    [1] ロドプシンは一般に熱に不安定で、その不安定性は高機能化を行う上で支障になる。そこで、安定な分子の探索と解析を行い、安定化分子の取得に成功した。またそれらの高分解能構造を明らかにし、安定化機構の解明に成功した。
    [2] 新しい機能を持ったロドプシンの発見や創成は、新しい光生物応答制御を可能とする。そこで、新規ロドプシンの単離・取得・創成を行った。その結果、二価アニオン・SO42-を輸送する新規分子の発見・解析と輸送方向・基質の変換に成功した。
    [3] ロドプシンの光反応素子および光遺伝学ツールとしての有用性を高めるため、その高機能化を試みた。アミノ酸変異によるイオン輸送力の10倍の向上、カロテノイドアンテナ結合型分子の創成に成功した。
    これらの成果は、JACS誌2報、Sci. Rep.誌2報を含む原著論文として報告するなど、H27-28年の公募期間2年間の間に、当初想定した予想を超える成果をあげることが出来たと自負している。

    researchmap

  • 固体NMRによる光受容蛋白質ロドプシンのレチナール結合部位の精密構造解析法の開発

    研究課題/領域番号:15H04336  2015年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    川村 出, 五東 弘昭, 須藤 雄気, 内藤 晶, 重田 安里寿, 槇野 義輝

      詳細を見る

    配分額:16380000円 ( 直接経費:12600000円 、 間接経費:3780000円 )

    本研究では、微生物型タンパク質であるロドプシンの発色団レチナールの結合部位の精密構造解析のために、レチナールオキシム体からアルデヒドへの変換反応の探索と高度好塩菌由来のバクテリオロドプシンから13C標識レチナールの抽出および固体NMRを用いたレチナール結合部位の構造解析を行った。その結果、オキシム体からレチナールへの効率的な変換反応の構築を達成し、13Cセグメント標識レチナールの生成に成功した。また、固体NMRを用いてセンサリーロドプシンIIやクロキノバクターロドプシン2などのレチナール結合部位の構造を明らかにした。さらに、光照射固体NMRによるセンサリーロドプシンIIの光中間体を観測した。

    researchmap

  • 光照射固体NMRによる細菌型センサリーロドプシンの光活性構造変化の解明

    研究課題/領域番号:15K06963  2015年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    内藤 晶, 川村 出, 須藤 雄気, 加茂 直樹, 和田 昭盛

      詳細を見る

    配分額:5200000円 ( 直接経費:4000000円 、 間接経費:1200000円 )

    細菌型光受容膜タンパク質は物質輸送や信号伝達に重要な役割を果たしている。発色団レチナールが光サイクルを回る間に光受容体としての機能が発現する。本研究では光サイクル中に生成する光中間体を固体NMRによって観測するため、光照射固体NMR装置の開発を行った。この装置を用いて、プロトン輸送活性をもつバクテリオロドプシンの変異体Y185F-bRを用いて、光サイクル中に生成するO-中間体やCS*-中間体のNMR信号の観測に成功した。次に負の光走性を示すppR/pHtrII複合体について光照射を行った結果、M-中間体からO-中間体が生成し、N’-中間体がO-中間体から平衡反応で生成することが判明した。

    researchmap

  • レチナールタンパク質を「知る・変える・役立てる」

    研究課題/領域番号:15H04363  2015年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    須藤 雄気, 塚本 卓

      詳細を見る

    配分額:16380000円 ( 直接経費:12600000円 、 間接経費:3780000円 )

    ビタミンAのアルデヒド型であるレチナールを発色団とするタンパク質は、総称してレチナールタンパク質と呼ばれる。生物の三大ドメイン(動物・細菌・古細菌)に万を越える分子が広く分布し、様々な光依存性機能を担っている。このような生物学的興味に加え、近年レチナールタンパク質を利用し、細胞や個体の機能を光で操作する技術(光遺伝学)が確立してきた。本研究では、これまでの研究を礎に、レチナールタンパク質を様々な手法により根源的に理解し(知る)、その知見に基づいた分子機能の改変・創成を行い(変える)、さらには様々な生命科学研究に利用できる光操作ツールを開発する(役立てる)ことを目的とした研究を行い成果を挙げた。

    researchmap

  • 先端的な超高速分光と非線形分光による多自由度複雑分子系の研究

    研究課題/領域番号:25104005  2013年06月 - 2018年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    田原 太平, 竹内 佐年, 石井 邦彦, 山口 祥一, 須藤 雄気, 二本柳 聡史, 倉持 光

      詳細を見る

    配分額:141050000円 ( 直接経費:108500000円 、 間接経費:32550000円 )

    最高の分光計測を開発・駆使して多自由度複雑分子系の研究を行った。領域の研究者との共同研究を強力に進めながら多くの研究成果をあげた。特に(1)超高速分光では独自の時間分解インパルシブ誘導ラマン分光法の極限化を推し進めるとともに、種々の生体分子、超分子、機能性分子の超高速過程を解明した。(2)界面選択的非線形分光では、我々が開発したヘテロダイン検出振動和周波発生分光法を駆使して界面水構造を解明し、また二次元分光法や紫外励起時間分解測定に発展させて界面のダイナミクス研究を実現した。(3)単分子分光では、独自の二次元蛍光寿命相関分光法を開発してタンパク質の折り畳み過程を研究し、新しい重要な知見を得た。

    researchmap

  • 光応答性タンパク質の機能転換が明らかにする柔らかな構造機能相関

    研究課題/領域番号:25104009  2013年06月 - 2018年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    神取 秀樹, 須藤 雄気, 井上 圭一, 岩田 達也, 片山 耕大, 山田 大智

      詳細を見る

    配分額:131300000円 ( 直接経費:101000000円 、 間接経費:30300000円 )

    多くの生体分子は共通の構造をもとに多彩な機能を演出している。本課題で我々は、ロドプシンやフラビンタンパク質などを対象として機能の発見・転換・創成をテーマに柔らかさと機能との関わりを研究した。その結果、内向きプロトンポンプや新規チャネルロドプシン、環状ヌクレオチドを光で分解する酵素ロドプシンなどの発見を報告した。一方、機能転換については、ロドプシンやDNA光回復酵素に対して限られた変異導入により機能転換に成功したが逆方向は成功せず、非対称な機能転換が明らかになった。機能の創成に関しては、光駆動ナトリウムポンプの構造基盤に基づき、カリウムやセシウムをポンプするタンパク質を創成することができた。

    researchmap

  • レチナールタンパク質の生物物理化学的解析

    研究課題/領域番号:13F03076  2013年04月 - 2015年03月

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    阿波賀 邦夫, 須藤 雄気, REISSIG Louisa, REISISIG Louisa

      詳細を見る

    配分額:2300000円 ( 直接経費:2300000円 )

    これまでの研究により超好熱菌から新しいレチナールタンパク質を発見し、サーモフィリックロドプシン・TRと命名している。この分子は、これまで見つかっているレチナールタンパク質の中で最も熱に対して安定な分子であった。この分子について、構造および構造変化を過渡吸収スペクトル(可視、赤外、ラマン、蛍光)によって追跡し、さらにNMR分光法を用いた発色団構造の決定に成功した。さらに今年度は、過渡光電流の発生が期待される [電極1(M)|電荷分離層(S)|絶縁分極層(I)|電極2(M’)] なる構造をもつ光学セルにおいて、その安定作動の最適化を行った後に、電荷分離層を光活性生体物質とすることによってより、環境応答型の光応答を求めた。
    [金属(M)|電荷分離層(S)|絶縁分極層(I)|金属(M’)]光電セルにおいて、絶縁分極層としてイオン液体(IL)を用いた系において、実用化に向けた検討を行った。この光電セルでは、界面電気二重層の形成による巨大電場によって電荷分離が促進されることが期待されている。近赤外外部に吸収をもつVOナフタロシアニンとC60の固溶体膜を電荷分離層とし、二つの電極を平行に同一基板上に配置したIL-MSIM光電セルの特性を調べところ、電気二重層の生成が電極間距離に依存しないことを利用し、電極間距離を7 mmに広げても過渡光電流を取り出せることが分かった。このように、透明電極を必要とせず、また電極の位置を厭わない柔軟性は、IL-MISM光電セル光検出器としての実用性を保証する。さらに、[M|S|I|M’]光電セルのM’電極を光ファイバーのジャケットとすることによって、On-tip型の光センサー構造を実現し、S層に生体物質を用い過渡光電流の検出に成功した。

    researchmap

  • 振動分光法による過渡的膜タンパク質複合体の解析

    研究課題/領域番号:24121712  2012年04月 - 2014年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:11310000円 ( 直接経費:8700000円 、 間接経費:2610000円 )

    細胞内外の情報や物質のやり取りを行う”膜タンパク質”は、全タンパク質分子の約20%を占め、生命活動に必須である。一方で、細胞膜中で機能するため取り扱いが難しい、発現量が少ないなどの理由からそのメカニズムの理解は遅れている。我々は、光受容体・ロドプシンと伝達膜タンパク質の“膜分子複合体の過渡的変化”を様々な手法により解析している。このうち、赤外分光(FTIR) 法やラマン分光法に代表される振動分光法は、分子振動を鋭敏に捉える手法で、側鎖, 主鎖, 低分子(イオンや水など)の微細構造変化を捉えることができ、X線結晶構造解析やNMR解析では得ることが難しい情報を取得することができる。本研究では以下の4点について研究を行い、成果を得た。本研究を通じて、膜蛋白質解析のボトルネックである、試料調製法や解析手法を確立できたと考えている。
    (1) 試料調製法の確立 [Sudo et al. 2013, J. Biol. Chem., Tsukamoto et al., 2013, J. Biol. Chem.], (2) 時間分解FTIR法による分子構造変化 [Furutani et al. 2013, J. Phys. Chem. B], (3) 時間分解ラマン分光法による分子構造変化 [Sudo et al. 2014, J. Phys. Chem. B], (4) 光照射固体NMR分光法による発色団構造変化 [Yomoda et al., 2014, Angew. Chem. Int. Ed.], (5) 全反射型FTIR法による2次構造測定 [東京大学船津研究室との共同研究]。

    researchmap

  • 光情報伝達のサブÅ・ピコ秒分解能での全経路詳細解析

    研究課題/領域番号:23687019  2011年04月 - 2015年03月

    日本学術振興会  科学研究費助成事業 若手研究(A)  若手研究(A)

    須藤 雄気, 塚本 卓

      詳細を見る

    配分額:27300000円 ( 直接経費:21000000円 、 間接経費:6300000円 )

    生体中に存在するタンパク質分子は、時々刻々とその形を変化させることで、様々な生理機能を担っている。そのため、タンパク質分子の本質的な理解には、「時々刻々=時間」・「形=空間」の2つの側面からの理解が重要となる。本研究では、光受容体の1種であるレチナールタンパク質による光情報伝達を、様々な「時間」および「空間」分解能で理解することを目的とした。

    researchmap

  • 色を知り、色を作る:ロドプシンタンパク質群の挑戦

    研究課題/領域番号:23657100  2011年 - 2013年

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    須藤 雄気, 林 重彦

      詳細を見る

    配分額:3900000円 ( 直接経費:3000000円 、 間接経費:900000円 )

    本研究は、実験及び理論の両面から、光受容レチナールタンパク質の発色機構を探り、得られた知見を基盤に、様々な色を呈する分子を創成することを目的とした。主な成果は以下の通りである。(1) 発色機構の実験的解明(4報)、(2) 発色機構の理論的解明(2報)、(3)様々な色を呈する分子の創成(2報)。このように実験と理論の融合により、色素タンパク質の新しい発色機構の解明とそれをもとにした分子創成は、様々な分野の研究者に取って有用な情報を提供するだろう。

    researchmap

  • センサー型ロドプシンの分子科学:機能と構造変化の連関性

    研究課題/領域番号:22018010  2010年 - 2011年

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    須藤 雄気

      詳細を見る

    配分額:4200000円 ( 直接経費:4200000円 )

    ロドプシン類は、光で反応のオン・オフを容易に調節できる点から、現在の生命科学研究の主題である構造-機能相関を分子論的に理解できる有用なツールである。本研究では微生物の光センサー型ロドプシンに着目し、機能と構造変化の連関性を明らかにすることを目的とした。当該年度の主な研究成果は以下の通りである。
    [1]新しいロドプシン類の単離・同定・発現・精製
    不安定で解析が困難だった誘因光受容体・センサリーロドプシンI(SRI)について、安定な分子を見いだした。また、新規ロドプシン分子を見いだしミドルロドプシン(MR)と名付けた。さらに、これら光センサータンパク質の下流分子(情報伝達に関わる分子群)についても単離・同定に成功し、発現・精製系を構築した。これにより、これまで困難であった測定が可能となった。
    [2]構造・構造変化・機能解析
    SRIや忌避光受容体・センサリーロドプシンII(SRH)を中心に、種々の分光法や生化学的・生物物理学的・分子生理学的手法を駆使して、タンパク質分子の形(構造)、やその変化(構造変化)を明らかにし、機能との連関性をアミノ酸レベルで明らかにした。SRHのTyr174の構造変化、SRIの体積変化など、物理化学的性質から、細菌運動解析など細胞生物学的解析までをうまく融合することができた。MRについては、光反応が極めて特徴的であることを見いだし、さらに光反応中における構造変化を時間分解分光法により明らかにした。

    researchmap

  • 全反射型赤外分光法による過渡的複合体の解析

    研究課題/領域番号:22121508  2010年 - 2011年

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    須藤 雄気

      詳細を見る

    配分額:11440000円 ( 直接経費:8800000円 、 間接経費:2640000円 )

    細胞内外の情報や物質のやり取りを行う"膜タンパク質"は、生命活動に重要である。我々は、光受容体・ロドプシンと伝達膜タンパク質の"膜分子複合体の過渡的変化"を様々な手法により解析している。このうち、赤外分光(FTIR)法やラマン分光法に代表される振動分光法は、分子振動を鋭敏に捉える手法で、側鎖,主鎖,低分子(イオンや水など)の微細構造変化を捉えることができ、X線結晶構造解析やNMR解析では得ることが難しい情報を取得することができる。本研究では以下の4点について研究を行い、成果を得た。本研究を通じて、膜蛋白質解析のボトルネックである、試料調製法や解析手法を確立できたと考えている。
    1)FTIR解析に適した試料調製[Sudo et al.2011a,J.Biol.Chem.,Sudo et al.2011,Biophysics]
    2)低温/時間分解赤外分光法によるロドプシンタンパク質の構造変化解析[Sudo et al.2011b,J.Biol.Chem.,Irieda et al.2011,Biochemistry]
    3)ラマン分光法など他の分光測定[Mizuno et al.,2011,Biochemistry,Inoue et al.,2011,J.Phys.Chem.B]
    4)全反射型FTIR(ATR-FTIR)におけるイオンと膜タンパク質の相互作用解析を行い、解析の難しい膜タンパク質の微細構造変化を明らかにした[投稿準備中]。

    researchmap

  • 2段階励起過渡回折格子法の開発と情報伝達タンパク質の光反応機構の解明と制御

    研究課題/領域番号:21770165  2009年 - 2010年

    日本学術振興会  科学研究費助成事業 若手研究(B)  若手研究(B)

    井上 圭一, 須藤 雄気

      詳細を見る

    配分額:4420000円 ( 直接経費:3400000円 、 間接経費:1020000円 )

    過渡回折格子法を用い、真正細菌Salinibacter ruber由来の細胞の走光性を引き起こすための光受容タンパク質、Sensory Rhodopsin Iの光反応ダイナミクスを調べた。その結果これまで知られていなかった中間体の存在を明らかにした。そしてさらにそれぞれの中間体のエンタルピーを決定することにも成功し、それらが塩化物イオンの結合によって大きく影響を受けることを突き止めた。

    researchmap

  • べん毛モーター固定子複合体の相互作用・イオン透過・構造変化の解析

    研究課題/領域番号:21770166  2009年 - 2010年

    日本学術振興会  科学研究費助成事業 若手研究(B)  若手研究(B)

    須藤 雄気

      詳細を見る

    配分額:4550000円 ( 直接経費:3500000円 、 間接経費:1050000円 )

    細菌は環境を認識するレセプターと運動器官(べん毛モーター)により過酷な環境を生き抜く。本研究では、全反射型赤外分光法により、これまで謎とされてきた固定子複合体(PomAB)とNa^+の結合にAsp24が直接関与すること(Sudo et al.2009b,Biochemistry)、その親和性と他に2つのカルボン酸が結合に関与することを明らかにした。変異体解析からCys31-PomBがイオン透過を制御すること(Sudo et al.2009,Biophysics)、サルモネラ菌の固定子・MotBのC末端の構造を明らかにした(Kojima et al.2009,Mol.Microbiol.)。さらに本研究の一部として、新規受容体を単離し物理化学的性質を明らかにした(Suzuki et al.2009,J.Mol.Biol.,Sudo et al.2009a,Biochemistry,Yagasaki et al.2010,Biochemistry,Sudo et al.2011,J.Biol.Chem.)。

    researchmap

  • 光機能性・制御性蛋白質による細胞・個体操作

    2008年 - 2011年

    科学技術振興機構  戦略的な研究開発の推進 戦略的創造研究推進事業 さきがけ 

    須藤 雄気

      詳細を見る

    担当区分:研究代表者 

    光による物質操作は、高い空間分解能と時間分解能を実現できます。本研究は、光受容蛋白質で細胞機能を操作することを目的とし、生命反応が「いつ・どこで・どのように・どれぐらい」起こっているかを明らかにします。特にキナーゼ活性化・不活性化、及び転写調節は生命科学分野で極めて重要な研究課題であり、本研究では、これを人為的に制御し、他の手法ではわからない新しい情報を得ます。

    researchmap

  • 膜蛋白質の機能変換から観る機能-構造変化の連関性と分子論的理解

    研究課題/領域番号:20050012  2008年 - 2010年

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    須藤 雄気

      詳細を見る

    配分額:3400000円 ( 直接経費:3400000円 )

    2-1. 忌避応答光センサー蛋白質、SRIIの機能発現分子メカニズム
    現在阪大/水谷グループと共同で、機能・構造変化に必須のアミノ酸残基(Tyr174)の変化を検出するため、時間分解紫外共鳴ラマン測定を行っている。
    2-2. デュアル光センサー蛋白質、SRIの機能発現メカニズム
    (1)新しいSRI分子、SrSRIのCl^-依存的光反応変化を見出した[J.Mol.Biol. 2009](A01:藤井グループとの共同研究)。(2)新しいSRI分子、HvSRIの発現・精製と分光解析[Biochemistry 2010](A01:藤井グループとの共同研究)。(3)SrSRIと伝達タンパク質、SrHtrIの複合体の機能発現系構築に成功し、その分光学的解析を行った[Biochemistry 2009a](A01:藤井グループとの共同研究)。
    2-3. SRI-HtrIが制御するべん毛蛋白質の解析
    SRI-HtrIが受けた光情報は、最終的にべん毛モーターの回転方向の制御として出力される。ここでは、べん毛固定子タンパク質MotBの部分結晶構造と[Mol.Microbiol. 2009]、赤外分光法によるNa^+透過経路の検討を行った[Biochemistry 2009b]
    このように光センサータンパク質の機能発現機構について、分子科学的に迫ることが出来た。

    researchmap

  • 分子生理学的解析から探る膜蛋白質複合体の機能発現機構

    研究課題/領域番号:19870010  2007年 - 2008年

    日本学術振興会  科学研究費助成事業 若手研究(スタートアップ)  若手研究(スタートアップ)

    須藤 雄気

      詳細を見る

    配分額:3125000円 ( 直接経費:2720000円 、 間接経費:405000円 )

    1)SRII-HtrII膜蛋白質複合体を介した光情報伝達(忌避応答)
    代表者らは、これまでSRII-HtrIIを介した細菌の光忌避行動について、生化学的・生理学的検討を行ってきた。今年度は、固体NMRを用いたSRII-HtrIIの相互作用解析(雑誌論文7)、溶液NMRを用いたHtrIIの部分構造の決定(雑誌論文6)、安定な活性型中間体の発見(雑誌論文2)、赤外分光法(FTIR)を用いた構造変化の解析(雑誌論文5)を行った。さらに得られた結果を基に、様々な変異体での比較解析から構造変化と忌避応答性に相関があることを見出した(雑誌論文1)。この結果は、Biochemistry誌の注目論文(Hot Article)として掲載される予定である。
    2)SRI-HtrI膜蛋白質複合体を介した光情報伝達(誘因応答)
    上記SRII-HtrIIを介した忌避応答機構に比べ、SRI-HtrIを介した光誘因応答に関する解析は著しく遅れている。今年度は、構造変化解析に優れたFTIR分光法を用いて、SRI-HtrI複合体の構造変化解析を行った(雑誌論文4)。また、これまで用いてきたSRIが極めて不安定であることから、古細菌、真正細菌で新たなSRI遺伝子を探索し、発現を試みたところ、真正細菌であるSalinibacter ruberから極めて安定なSRIを単離することに成功した(論文投稿中)。このように、誘因応答メカニズムについてもその分子機構を理解できる目処がたってきた。
    3その他光受容体解析
    イオンポンプであるバクテリオロドプシン(BR)をSRII型へ機能転換した論文(2006年Sudo and Spudich, PNAS)が注目され、機能変換を通じた機能「創出」から蛋白質由来の人工光素子構築を目指している。今年度は、クロライドポンプであるハロロドプシン(HR)からSRIIへの機能変換を試みた(雑誌論文3)。上述の通り誘因レセプターも研究対象と出来る目処がつき、これまで知られているレセプター間での機能改変を行っている。

    researchmap

▼全件表示

 

担当授業科目

  • 分析科学・物理化学 (2024年度) 特別  - その他

  • 分析科学・物理化学 (2024年度) 特別  - その他

  • 創薬・育薬特別演習(生体分子解析学A) (2024年度) 特別  - その他

  • 基礎物理学 (2024年度) 第1学期  - 火1~2,金3~4

  • 基礎物理学 (2024年度) 第1学期  - 火1~2,金3~4

  • 基礎物理学 (2024年度) 第1学期  - 火1~2,金3~4

  • 基礎物理学 (2024年度) 第1学期  - 火1~2,金3~4

  • 感じる科学 (2024年度) 第3学期  - 月3~4

  • 感じる科学 (2024年度) 第4学期  - 金3~4

  • 物理化学1 (2024年度) 第2学期  - 金1~2

  • 物理化学1 (2024年度) 第2学期  - 金1~2

  • 物理化学3 (2024年度) 第3学期  - 火7~8

  • 物理化学3 (2024年度) 第3学期  - 火7~8

  • 物理化学4 (2024年度) 第4学期  - 火1~2

  • 物理化学4 (2024年度) 第4学期  - 火1~2

  • 物理化学5 (2024年度) 第1学期  - 木7~8

  • 物理化学5 (2024年度) 第1学期  - 木7~8

  • 物理化学A (2024年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学A (2024年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学B (2024年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学B (2024年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学C (2024年度) 1・2学期  - [第1学期]木7~8, [第2学期]木3~4

  • 物理化学C (2024年度) 1・2学期  - [第1学期]木7~8, [第2学期]木3~4

  • 物理系基礎実習 (2024年度) 第1学期  - その他5~9

  • 物理系基礎実習 (2024年度) 第1学期  - その他5~9

  • 生体分子解析学A (2024年度) 特別  - その他

  • 生体分子解析学A (2024年度) 特別  - その他

  • 生体分子解析学A演習 (2024年度) 特別  - その他

  • 生体分子解析学I (2024年度) 特別  - その他

  • 生体分子解析学II (2024年度) 特別  - その他

  • 生体物理化学特論 (2024年度) 特別  - その他

  • 薬学基礎実習Ⅰ (2024年度) 第1学期  - その他5~9

  • 薬学基礎実習Ⅰ (2024年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2024年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2024年度) 第1学期  - その他5~9

  • 分析科学・物理化学 (2023年度) 特別  - その他

  • 分析科学・物理化学 (2023年度) 特別  - その他

  • 創薬・育薬特別演習(生体分子解析学A) (2023年度) 特別  - その他

  • 基礎物理学 (2023年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2023年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2023年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2023年度) 第1学期  - 火5~6,金3~4

  • 感じる科学 (2023年度) 第3学期  - 月3~4

  • 感じる科学 (2023年度) 第4学期  - 金3~4

  • 物理化学1 (2023年度) 第2学期  - 金1~2

  • 物理化学1 (2023年度) 第2学期  - 金1~2

  • 物理化学3 (2023年度) 第3学期  - 火7~8

  • 物理化学3 (2023年度) 第3学期  - 火7~8

  • 物理化学4 (2023年度) 第4学期  - 火1~2

  • 物理化学4 (2023年度) 第4学期  - 火1~2

  • 物理化学5 (2023年度) 第1学期  - 木7~8

  • 物理化学5 (2023年度) 第1学期  - 木7~8

  • 物理化学A (2023年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学A (2023年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学B (2023年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学B (2023年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学C (2023年度) 1・2学期  - [第1学期]木7~8, [第2学期]木3~4

  • 物理化学C (2023年度) 1・2学期  - [第1学期]木7~8, [第2学期]木3~4

  • 物理系基礎実習 (2023年度) 第1学期  - その他5~9

  • 物理系基礎実習 (2023年度) 第1学期  - その他5~9

  • 生体分子解析学A (2023年度) 特別  - その他

  • 生体分子解析学A (2023年度) 特別  - その他

  • 生体分子解析学A演習 (2023年度) 特別  - その他

  • 生体分子解析学I (2023年度) 特別  - その他

  • 生体分子解析学II (2023年度) 特別  - その他

  • 生体物理化学特論 (2023年度) 特別  - その他

  • 薬学基礎実習Ⅰ (2023年度) 第1学期  - その他5~9

  • 薬学基礎実習Ⅰ (2023年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2023年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2023年度) 第1学期  - その他5~9

  • 分析科学・物理化学 (2022年度) 特別  - その他

  • 基礎物理学 (2022年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2022年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2022年度) 第1学期  - 火5~6,金3~4

  • 基礎物理学 (2022年度) 第1学期  - 火5~6,金3~4

  • 感じる科学 (2022年度) 第3学期  - 月3~4

  • 感じる科学 (2022年度) 第4学期  - 金3~4

  • 数理・データサイエンスの基礎 (2022年度) 第3学期  - 月5~6

  • 物理化学1 (2022年度) 第2学期  - 金1~2

  • 物理化学1 (2022年度) 第2学期  - 金1~2

  • 物理化学3 (2022年度) 第3学期  - 火7~8

  • 物理化学3 (2022年度) 第3学期  - 火7~8

  • 物理化学4 (2022年度) 第4学期  - 火1~2

  • 物理化学4 (2022年度) 第4学期  - 火1~2

  • 物理化学5 (2022年度) 第2学期  - 木3~4

  • 物理化学5 (2022年度) 第2学期  - 木3~4

  • 物理化学A (2022年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学A (2022年度) 2・3学期  - [第2学期]金1~2, [第3学期]火1~2

  • 物理化学B (2022年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学B (2022年度) 3・4学期  - [第3学期]火7~8, [第4学期]火1~2

  • 物理化学C (2022年度) 2・3学期  - [第2学期]木3~4, [第3学期]金1~2

  • 物理化学C (2022年度) 2・3学期  - [第2学期]木3~4, [第3学期]金1~2

  • 生体分子解析学A (2022年度) 特別  - その他

  • 生体分子解析学A演習 (2022年度) 特別  - その他

  • 生体分子解析学I (2022年度) 特別  - その他

  • 生体分子解析学II (2022年度) 特別  - その他

  • 薬学基礎実習Ⅰ (2022年度) 第1学期  - その他5~9

  • 薬学基礎実習Ⅰ (2022年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2022年度) 第1学期  - その他5~9

  • 薬学基礎実習I (2022年度) 第1学期  - その他5~9

  • 先端薬学研究 (2021年度) 夏季集中  - その他

  • 分析科学・物理化学 (2021年度) 前期  - その他

  • 基礎物理学 (2021年度) 第1学期  - 火5,火6,金3,金4

  • 基礎物理学 (2021年度) 第1学期  - 火5,火6,金3,金4

  • 基礎物理学 (2021年度) 第1学期  - 火5,火6,金3,金4

  • 基礎物理学 (2021年度) 第1学期  - 火5,火6,金3,金4

  • 感じる科学 (2021年度) 第3学期  - 月3~4

  • 感じる科学 (2021年度) 第4学期  - 金3~4

  • 数理・データサイエンスの基礎 (2021年度) 第3学期  - 月5~6

  • 物理化学1 (2021年度) 第2学期  - 金5,金6

  • 物理化学1 (2021年度) 第2学期  - 金5,金6

  • 物理化学3 (2021年度) 第3学期  - 火7,火8

  • 物理化学3 (2021年度) 第3学期  - 火7~8

  • 物理化学4 (2021年度) 第1学期  - 木3,木4

  • 物理化学4 (2021年度) 第1学期  - 木3,木4

  • 物理化学5 (2021年度) 第2学期  - 木3,木4

  • 物理化学5 (2021年度) 第2学期  - 木3,木4

  • 物理化学A (2021年度) 2・3学期  - [第2学期]金5,金6, [第3学期]火1,火2

  • 物理化学A (2021年度) 2・3学期  - [第2学期]金5,金6, [第3学期]火1,火2

  • 物理化学B (2021年度) 3・4学期  - [第3学期]火7,火8, [第4学期]火1,火2

  • 物理化学B (2021年度) 3・4学期  - [第3学期]火7,火8, [第4学期]火1,火2

  • 生体分子解析学A (2021年度) 特別  - その他

  • 生体分子解析学A演習 (2021年度) 特別  - その他

  • 生体分子解析学I (2021年度) 特別  - その他

  • 生体分子解析学II (2021年度) 特別  - その他

  • 薬学ガイダンス (2021年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学ガイダンス (2021年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学ガイダンス (2021年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学ガイダンス (2021年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学基礎実習Ⅰ (2021年度) 第1学期  - その他6~9

  • 薬学基礎実習Ⅰ (2021年度) 第1学期  - その他6~9

  • 薬学基礎実習I (2021年度) 第1学期  - その他6~9

  • 薬学基礎実習I (2021年度) 第1学期  - その他6~9

  • 先端薬学特論 (2020年度) 特別  - その他

  • 先端薬学研究 (2020年度) 夏季集中  - その他

  • 分析科学・物理化学 (2020年度) 前期  - その他

  • 基礎物理学 (2020年度) 第1学期  - その他

  • 基礎物理学 (2020年度) 第1学期  - 火4,火5,火6

  • 基礎物理学 (2020年度) 第1学期  - 火4,火5,火6

  • 感じる科学 (2020年度) 第3学期  - 月3,月4

  • 感じる科学 (2020年度) 第4学期  - 金3,金4

  • 数理・データサイエンスの基礎 (2020年度) 第3学期  - 月5,月6

  • 物理化学Ⅲ (2020年度) 第2学期  - 木3,木4

  • 物理化学1 (2020年度) 第2学期  - 火5,火6

  • 物理化学1 (2020年度) 第2学期  - 火5,火6

  • 物理化学4 (2020年度) 第1学期  - 木3,木4

  • 物理化学4 (2020年度) 第1学期  - 木3,木4

  • 物理化学5 (2020年度) 第2学期  - 木3,木4

  • 物理化学5 (2020年度) 第2学期  - 木3,木4

  • 生体分子解析学A (2020年度) 特別  - その他

  • 生体分子解析学A演習 (2020年度) 特別  - その他

  • 生体分子解析学I (2020年度) 特別  - その他

  • 生体分子解析学II (2020年度) 特別  - その他

  • 薬学ガイダンス (2020年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学ガイダンス (2020年度) 1・2学期  - 月1,水4

  • 薬学ガイダンス (2020年度) 1・2学期  - 月1,水4

  • 薬学ガイダンス (2020年度) 1・2学期  - [第1学期]水4, [第2学期]月1

  • 薬学基礎実習I (2020年度) 特別  - その他

  • 薬学基礎実習I (2020年度) 特別  - その他

▼全件表示