Updated on 2025/06/06

写真a

 
SUDO Yuki
 
Organization
Faculty of Medicine, Dentistry and Pharmaceutical Sciences Professor
Position
Professor
Homepage
https://sites.google.com/view/laboratory-biophyschem
External link

Degree

  • PhD (Pharmaceutical Science) ( 2005.3   Hokkaido University )

Research Interests

  • Physical Chemistry

  • Protein Science

  • Biophysics

  • Photobiology

  • 蛋白質科学

  • 光生物学

  • Pharmaceutical Physical Chemistry

  • 生物物理学

  • Optogenetics

Research Areas

  • Life Science / Pharmaceutical analytical chemistry and physicochemistry

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Life Science / Biophysics

  • Nanotechnology/Materials / Chemical biology

Education

  • Hokkaido University   薬学研究科   生体分子薬学専攻

    - 2005

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    Country： Japan

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  • Hokkaido University   薬学部   総合薬学科

    - 2000

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    Country： Japan

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Research History

  • Professor, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University

    2014

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    Country：Japan

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  • Institute for Molecular Science

    2012 - 2014

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  • Nagoya University   Associate Professor, Graduate School of Science

    2009 - 2014

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    Country：Japan

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  • 科学技術振興機構（JST)・さきがけ 研究員

    2008 - 2012

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  • Nagoya University   Assistant Professor, Graduate School of Science

    2007 - 2009

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    Country：Japan

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  • The University of Texas, Houston   Postdoctoral Fellow

    2005 - 2007

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    Country：United States

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  • Researcher, Nagoya Institute of Technology   Graduate School of Engineering

    2005

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    Country：Japan

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Professional Memberships

Committee Memberships

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

    2023.7   

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  • 日本生物物理学会   理事  

    2023   

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  • 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  

    2022.10   

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    Committee type：Government

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  • 分子科学研究所   共同研究専門委員会委員  

    2022   

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    Committee type：Other

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  • The Biophysical Society of Japan   Vice Editors-In-Chief  

    2021.12   

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    Committee type：Academic society

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  • 男女共同参画学協会連絡会   第20期運営委員会・副委員長  

    2021.10 - 2022.10   

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    Committee type：Academic society

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

    2019   

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    Committee type：Government

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  • 日本生物物理学会中国四国支部   支部長  

    2019 - 2020   

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  • The Biophysical Society of Japan   Vice-President  

    2019 - 2020   

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    Committee type：Academic society

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  • 日本薬学会中国四国支部   支部役員  

    2018 - 2019   

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  • 公益財団法人 新世代研究所   バイオ単分子専門委員  

    2015.4 - 2020.3   

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    Committee type：Other

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  • 日本生物物理学会   運営委員・理事  

    2009 - 2020   

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    Committee type：Academic society

    生物物理学会

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Papers

  • Ultrafast Protein Dynamics Prior to Retinal Photoisomerization in Microbial Rhodopsins

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

    The Journal of Physical Chemistry Letters   2025.6

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    Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/acs.jpclett.5c00623

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

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

    Journal of Biological Chemistry   2025.4

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.jbc.2025.108334

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  • The use of microbial rhodopsin proteins in differential photodetection Reviewed

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

    Frontiers in Physics   12   1481341   2024.12

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    Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.3389/fphy.2024.1481341

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

    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   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

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

    DOI： 10.1093/ismejo/wrae175

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

    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   2024.8

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jpcb.4c04466

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

    Kotaro Nakanishi, Keiichi Kojima, Yoshiyuki Sowa, Yuki Sudo

    The Journal of Physical Chemistry B   128 ( 27 )   6509 - 6517   2024.7

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jpcb.4c03027

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

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

    Nature Communications   15   2926   2024.4

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/s41467-024-47009-w

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

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

    Biochemical and Biophysical Research Communications   677   1 - 5   2023.10

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.bbrc.2023.07.048

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

    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   2023.7

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jacs.3c02833

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  • Development of light-induced disruptive liposomes (LiDL) as a photoswitchable carrier for intracellular substance delivery. Reviewed International journal

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

    Chemical Communications (Cambridge, England)   59 ( 49 )   7591 - 7594   2023.6

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

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

    DOI： 10.1039/d3cc02056h

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  • A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis Reviewed International journal

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

    Scientific Reports   13 ( 1 )   6974 - 6974   2023.4

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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

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    Other Link： 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. Reviewed International journal

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

    Biochimica et Biophysica Acta. Bioenergetics   1864 ( 3 )   148980 - 148980   2023.4

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

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

    DOI： 10.1016/j.bbabio.2023.148980

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

    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 )   2023.4

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    Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

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

    DOI： 10.1038/s41467-023-36883-5

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    Other Link： 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 Reviewed

    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   2023.2

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Pharmaceutical Society of Japan  

    DOI： 10.1248/cpb.c22-00774

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

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

    ACS Omega   8   4826 - 4834   2023.1

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acsomega.2c06980

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

    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

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Microbial Ecology  

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

    DOI： 10.1264/jsme2.me23015

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  • Mutations conferring SO42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant. Reviewed International journal

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

    Scientific reports   12 ( 1 )   16422 - 16422   2022.9

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    Language：English   Publishing type：Research paper (scientific journal)  

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

    DOI： 10.1038/s41598-022-20784-6

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

    Shin Nakao, Keiichi Kojima, Yuki Sudo

    Journal of the American Chemical Society   144 ( 9 )   3771 - 3775   2022.2

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jacs.1c12608

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  • Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations. Reviewed International journal

    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   2022.2

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    Language：English   Publishing type：Research paper (scientific journal)  

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

    DOI： 10.1021/acs.jpcb.1c08684

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  • Proton-pumping rhodopsins in marine diatoms

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

    bioRxiv   2022.1

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

    Abstract

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

    DOI： 10.1101/2022.01.18.476826

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  • Proton transfer pathway in anion channelrhodopsin-1 Reviewed

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

    eLife   10   e72264   2021.12

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    Authorship：Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications, Ltd  

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

    DOI： 10.7554/elife.72264

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    Other Link： 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 Reviewed

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

    Frontiers in Molecular Biosciences   8   794948   2021.12

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

    Rhodopsins act as photoreceptors with their chromophore retinal (vitamin-A aldehyde) and they regulate light-dependent biological functions. Archaerhodopsin-3 (AR3) is an outward proton pump that has been widely utilized as a tool for optogenetics, a method for controlling cellular activity by light. To characterize the retinal binding cavity of AR3, we synthesized a dimethyl phenylated retinal derivative, (2E,4E,6E,8E)-9-(2,6-Dimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenal (DMP-retinal). QM/MM calculations suggested that DMP-retinal can be incorporated into the opsin of AR3 (archaeopsin-3, AO3). Thus, we introduced DMP-retinal into AO3 to obtain the non-natural holoprotein (AO3-DMP) and compared some molecular properties with those of AO3 with the natural A1-retinal (AO3-A1) or AR3. Light-induced pH change measurements revealed that AO3-DMP maintained slow outward proton pumping. Noteworthy, AO3-DMP had several significant changes in its molecular properties compared with AO3-A1 as follows; 1) spectroscopic measurements revealed that the absorption maximum was shifted from 556 to 508 nm and QM/MM calculations showed that the blue-shift was due to the significant increase in the HOMO-LUMO energy gap of the chromophore with the contribution of some residues around the chromophore, 2) time-resolved spectroscopic measurements revealed the photocycling rate was significantly decreased, and 3) kinetical spectroscopic measurements revealed the sensitivity of the chromophore binding Schiff base to attack by hydroxylamine was significantly increased. The QM/MM calculations show that a cavity space is present at the aromatic ring moiety in the AO3-DMP structure whereas it is absent at the corresponding <italic>β</italic>-ionone ring moiety in the AO3-A1 structure. We discuss these alterations of the difference in interaction between the natural A1-retinal and the DMP-retinal with binding cavity residues.

    DOI： 10.3389/fmolb.2021.794948

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

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

    Scientific Reports   11 ( 1 )   14756   2021.12

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

    DOI： 10.1038/s41598-021-94181-w

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    Other Link： 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 Reviewed

    Masahiro Hayashi, Keiichi Kojima, Yuki Sudo, Atsuko Yamashita

    Protein Science   30 ( 10 )   2161 - 2169   2021.7

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    DOI： 10.1002/pro.4154

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    Other Link： 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 Reviewed

    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

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    DOI： 10.2142/biophysico.bppb-v18.019

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

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

    Scientific Reports   10 ( 1 )   20857   2020.11

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    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

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    Other Link： https://www.nature.com/articles/s41598-020-77936-9

  • Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants Reviewed

    Masaki Tsujimura, Tomoyasu Noji, Keisuke Saito, Keiichi Kojima, Yuki Sudo, Hiroshi Ishikita

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   148349 - 148349   2020.11

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    DOI： 10.1016/j.bbabio.2020.148349

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

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

    Biophysical Journal   119 ( 9 )   1760 - 1770   2020.11

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    DOI： 10.1016/j.bpj.2020.09.026

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

    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   2020.10

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    Abstract

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

    DOI： 10.1002/prot.26015

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

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

    Scientific Reports   10 ( 1 )   16752   2020.10

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    Abstract

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

    DOI： 10.1038/s41598-020-73606-y

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    Other Link： https://www.nature.com/articles/s41598-020-73606-y

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

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

    Microbiology and Immunology   64 ( 9 )   593 - 601   2020.8

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    Abstract

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

    DOI： 10.1111/1348-0421.12829

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

    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   2020.7

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    DOI： 10.1021/acs.jpcb.0c06560

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

    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   2020.7

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    DOI： 10.1021/acs.jpclett.0c01406

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

    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   2020.3

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    DOI： 10.1021/acs.jcim.0c00063

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

    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   2020.1

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    DOI： 10.1021/acs.jpcb.9b10700

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  • Vectorial Proton Transport Mechanism of RxR, a Phylogenetically Distinct and Thermally Stable Microbial Rhodopsin. Reviewed International journal

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

    10 ( 1 )   282 - 282   2020.1

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    Rubrobacter xylanophilus rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton (H+) pump with the chromophore retinal. To characterize its vectorial proton transport mechanism, mutational and theoretical investigations were performed for carboxylates in the transmembrane region of RxR and the sequential proton transport steps were revealed as follows: (i) a proton of the retinylidene Schiff base (Lys209) is transferred to the counterion Asp74 upon formation of the blue-shifted M-intermediate in collaboration with Asp205, and simultaneously, a respective proton is released from the proton releasing group (Glu187/Glu197) to the extracellular side, (ii) a proton of Asp85 is transferred to the Schiff base during M-decay, (iii) a proton is taken up from the intracellular side to Asp85 during decay of the red-shifted O-intermediate. This ion transport mechanism of RxR provides valuable information to understand other ion transporters since carboxylates are generally essential for their functions.

    DOI： 10.1038/s41598-019-57122-2

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  • Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins Reviewed

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

    Microbes and Environments   35 ( 4 )   ME20085   2020

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    DOI： 10.1264/jsme2.me20085

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

    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   2019.9

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

    DOI： 10.1073/pnas.1907517116

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    Other Link： https://pnas.org/doi/pdf/10.1073/pnas.1907517116

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

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

    Molecular Crystals and Liquid Crystals   687 ( 1 )   34 - 39   2019.7

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    DOI： 10.1080/15421406.2019.1648052

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

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

    eLife   8   e44928   2019.6

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    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

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    Other Link： 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 Reviewed

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

    Biochemistry   58 ( 26 )   2934 - 2943   2019.5

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    DOI： 10.1021/acs.biochem.9b00257

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

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

    Scientific Reports   9 ( 1 )   7863   2019.3

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    DOI： 10.1038/s41598-019-44308-x

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  • Retinal–Salinixanthin Interactions in a Thermophilic Rhodopsin Reviewed

    Ramprasad Misra, Tamar Eliash, Yuki Sudo, Mordechai Sheves

    The Journal of Physical Chemistry B   123 ( 1 )   10 - 20   2018.12

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    DOI： 10.1021/acs.jpcb.8b06795

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

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

    The Journal of Physical Chemistry B   122 ( 42 )   9826 - 9826   2018.10

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    DOI： 10.1021/acs.jpcb.8b09660

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

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

    Biophysical Journal   115 ( 1 )   72 - 83   2018.7

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    DOI： 10.1016/j.bpj.2018.05.030

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

    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   2018.6

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    DOI： 10.1021/acs.jpcb.8b04894

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

    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   2018.5

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    DOI： 10.1021/acs.jpclett.8b00879

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  • Presence of a Haloarchaeal Halorhodopsin-Like Cl&lt;sup&gt;−&lt;/sup&gt; Pump in Marine Bacteria Reviewed

    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

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    DOI： 10.1264/jsme2.me17197

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

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

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

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    <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

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  • 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 Reviewed

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

    Biophysics and Physicobiology   15   179 - 188   2018

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    DOI： 10.2142/biophysico.15.0_179

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

    Shunsuke Adachi, Yuya Watanabe, Yuki Sudo, Toshinori Suzuki

    Chemical Physics Letters   683   7 - 11   2017.9

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    DOI： 10.1016/j.cplett.2017.04.001

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

    Naoya Honda, Takashi Tsukamoto, Yuki Sudo

    Chemical Physics Letters   682   6 - 14   2017.8

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    DOI： 10.1016/j.cplett.2017.05.055

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  • Hybrid Model Membrane Combining Micropatterned Lipid Bilayer and Hydrophilic Polymer Brush Reviewed

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

    Langmuir   33 ( 23 )   5752 - 5759   2017.5

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    DOI： 10.1021/acs.langmuir.7b00463

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  • Demonstration of a Light-Driven SO42– Transporter and Its Spectroscopic Characteristics Reviewed

    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   2017.3

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    DOI： 10.1021/jacs.6b12139

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

    Kanae Kanehara, Susumu Yoshizawa, Takashi Tsukamoto, Yuki Sudo

    Scientific Reports   7 ( 1 )   44427   2017.3

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    DOI： 10.1038/srep44427

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

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

    The Journal of Physical Chemistry B   121 ( 9 )   2027 - 2038   2017.3

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    DOI： 10.1021/acs.jpcb.6b11101

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

    Satoko Doi, Takashi Tsukamoto, Susumu Yoshizawa, Yuki Sudo

    Scientific Reports   7 ( 1 )   41879   2017.2

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    DOI： 10.1038/srep41879

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  • Hybrid model membrane combining micropatterned lipid bilayer and hydrophilic polymer brush Reviewed

    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

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

    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   2016.9

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    DOI： 10.1021/jacs.6b05002

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

    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   2016.6

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    DOI： 10.1093/jmcb/mjw027

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  • X-ray Crystallographic Structure of Thermophilic Rhodopsin Reviewed

    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   2016.6

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    DOI： 10.1074/jbc.m116.719815

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

    Yuki Sudo, Susumu Yoshizawa

    Photochemistry and Photobiology   92 ( 3 )   420 - 427   2016.3

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    DOI： 10.1111/php.12585

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

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

    Photochemical and Photobiological Sciences   14 ( 9 )   1628 - 1636   2015.9

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    DOI： 10.1039/c5pp00213c

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    Other Link： https://link.springer.com/article/10.1039/c5pp00213c/fulltext.html

  • Atomistic design of microbial opsin-based blue-shifted optogenetics tools Reviewed

    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   2015.5

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    DOI： 10.1038/ncomms8177

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

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

    Langmuir   31 ( 18 )   5235 - 5243   2015.4

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    DOI： 10.1021/la504972q

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  • Converting a Light-Driven Proton Pump into a Light-Gated Proton Channel Reviewed

    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   2015.2

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    DOI： 10.1021/ja511788f

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

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

    Chemical Communications   51 ( 91 )   16401 - 16404   2015

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    DOI： 10.1039/c5cc06237c

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  • Irreversible Trimer to Monomer Transition of Thermophilic Rhodopsin upon Thermal Stimulation Reviewed

    Takashi Tsukamoto, Makoto Demura, Yuki Sudo

    The Journal of Physical Chemistry B   118 ( 43 )   12383 - 12394   2014.10

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    DOI： 10.1021/jp507374q

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

    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   2014.5

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    DOI： 10.1002/anie.201309258

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

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

    The Journal of Physical Chemistry B   118 ( 6 )   1510 - 1518   2014.1

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    DOI： 10.1021/jp4112662

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  • A Blue-shifted Light-driven Proton Pump for Neural Silencing Reviewed

    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   2013.7

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    DOI： 10.1074/jbc.m113.475533

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

    Takashi Tsukamoto, Keiichi Inoue, Hideki Kandori, Yuki Sudo

    Journal of Biological Chemistry   288 ( 30 )   21581 - 21592   2013.7

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    DOI： 10.1074/jbc.m113.479394

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

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

    Chemical Physics   419   23 - 29   2013.6

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    DOI： 10.1016/j.chemphys.2012.11.020

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

    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   2013.3

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    DOI： 10.1021/jp308765t

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  • 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 Reviewed

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

    Biophysics   9   21 - 29   2013

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    DOI： 10.2142/biophysics.9.21

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

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

    Biochemistry   51 ( 44 )   8802 - 8813   2012.10

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    DOI： 10.1021/bi3009592

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

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

    Journal of Biological Chemistry   287 ( 39 )   32485 - 32493   2012.9

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    DOI： 10.1074/jbc.m112.390864

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  • Optical Silencing of C. elegans Cells with Arch Proton Pump Reviewed

    Ayako Okazaki, Yuki Sudo, Shin Takagi

    PLoS ONE   7 ( 5 )   e35370 - e35370   2012.5

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    DOI： 10.1371/journal.pone.0035370

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

    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   2012.5

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    DOI： 10.1021/jp302357m

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

    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   2011.11

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    DOI： 10.1016/j.bpj.2011.10.022

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

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

    Biochemistry   50 ( 22 )   4912 - 4922   2011.5

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    DOI： 10.1021/bi200284s

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

    Misao Mizuno, Yuki Sudo, Michio Homma, Yasuhisa Mizutani

    Biochemistry   50 ( 15 )   3170 - 3180   2011.4

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    DOI： 10.1021/bi101817y

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  • Spectral Tuning in Sensory Rhodopsin I from Salinibacter ruber Reviewed

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

    Journal of Biological Chemistry   286 ( 13 )   11328 - 11336   2011.4

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    DOI： 10.1074/jbc.m110.187948

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

    Keiichi Inoue, Yuki Sudo, Michio Homma, Hideki Kandori

    The Journal of Physical Chemistry B   115 ( 15 )   4500 - 4508   2011.3

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    DOI： 10.1021/jp2000706

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

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

    Journal of Biological Chemistry   286 ( 8 )   5967 - 5976   2011.2

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    DOI： 10.1074/jbc.m110.190058

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

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

    Biophysics   7   51 - 58   2011

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    DOI： 10.2142/biophysics.7.51

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

    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   2010.1

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    DOI： 10.1021/bi901824a

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

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

    Biochemistry   48 ( 49 )   11699 - 11705   2009.11

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    DOI： 10.1021/bi901517n

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

    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   2009.10

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    DOI： 10.1021/bi901338d

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

    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   2009.9

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    DOI： 10.1016/j.jmb.2009.06.050

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

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

    Molecular Microbiology   73 ( 4 )   710 - 718   2009.8

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    DOI： 10.1111/j.1365-2958.2009.06802.x

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

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

    Biophysics   5   45 - 52   2009

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    DOI： 10.2142/biophysics.5.45

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

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

    Biochemistry   47 ( 48 )   12750 - 12759   2008.11

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    DOI： 10.1021/bi801358b

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

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

    Journal of Biological Chemistry   283 ( 35 )   23533 - 23541   2008.8

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    DOI： 10.1074/jbc.m802990200

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

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

    Biophysical Journal   95 ( 2 )   753 - 760   2008.7

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    DOI： 10.1529/biophysj.107.125294

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

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

    Photochemistry and Photobiology   84 ( 4 )   874 - 879   2008.7

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    Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：WILEY-VCH  

    DOI： 10.1111/j.1751-1097.2008.00317.x

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

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

    Biochemistry   47 ( 23 )   6208 - 6215   2008.6

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    DOI： 10.1021/bi8003507

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

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

    Biochemistry   47 ( 9 )   2875 - 2883   2008.3

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    DOI： 10.1021/bi702050c

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

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

    Biochemistry   47 ( 9 )   2866 - 2874   2008.2

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    DOI： 10.1021/bi701885k

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

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

    Biochemistry   46 ( 50 )   14380 - 14390   2007.12

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    DOI： 10.1021/bi701837n

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

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

    Journal of Biological Chemistry   282 ( 21 )   15550 - 15558   2007.5

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Biochemistry and Molecular Biology Inc. (ASBMB)  

    DOI： 10.1074/jbc.M701271200

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

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

    Photochemistry and Photobiology   83 ( 2 )   293 - 302   2007.3

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    DOI： 10.1562/2006-06-09-RA-916

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  • 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 Reviewed

    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   2007.3

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    DOI： 10.1562/2006-06-20-RA-940

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

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

    Journal of Biological Chemistry   281 ( 45 )   34239 - 34245   2006.11

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    DOI： 10.1074/jbc.M605907200

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

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

    Biochemistry   45 ( 39 )   11836 - 11843   2006.10

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    DOI： 10.1021/bi0610597

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  • Temperature-dependent interactions between photoactivated Pharaonis phoborhodopsin and its transducer Reviewed

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

    Biochemistry   45 ( 15 )   4859 - 4866   2006.4

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    DOI： 10.1021/bi060047i

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

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

    Journal of Molecular Biology   357 ( 4 )   1274 - 1282   2006.4

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    DOI： 10.1016/j.jmb.2006.01.061

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

    Sudo, Y., Spudich, J.L.

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

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    DOI： 10.1073/pnas.0607467103

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

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

    Journal of the American Chemical Society   127 ( 46 )   16036 - 16037   2005.11

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    DOI： 10.1021/ja056203a

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

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

    Biochemistry   44 ( 16 )   6144 - 6152   2005.4

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    DOI： 10.1021/bi047573z

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

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

    Biochemistry   44 ( 8 )   2909 - 2915   2005.3

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    DOI： 10.1021/bi047893i

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  • 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) Reviewed

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

    Biophysical Journal   88 ( 2 )   1215 - 1223   2005

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    DOI： 10.1529/biophysj.104.045583

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

    Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

    Biochemistry   43 ( 43 )   13748 - 13754   2004.11

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/bi048803c

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  • 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) Reviewed

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

    Photochemical and Photobiological Sciences   3 ( 6 )   537 - 542   2004.6

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    DOI： 10.1039/b315454h

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

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

    Biochemistry   43 ( 11 )   3195 - 3203   2004.3

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    DOI： 10.1021/bi035960n

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

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

    Biophysical Journal   86 ( 5 )   3112 - 3120   2004

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

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  • 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) Reviewed

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

    Biophysical Journal   86 ( 5 )   3131 - 3140   2004

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

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

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

    Biochemistry   42 ( 48 )   14166 - 14172   2003.12

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

    DOI： 10.1021/bi035678g

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

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

    Photochemistry and Photobiology   78 ( 5 )   511 - 516   2003.11

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

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

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

    Journal of Biological Chemistry   278 ( 26 )   23882 - 23889   2003.7

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    DOI： 10.1074/jbc.M301200200

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

    Yuji Furutani, Yuki Sudo, Naoki Kamo, Hideki Kandori

    Biochemistry   42 ( 17 )   4837 - 4842   2003.5

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    DOI： 10.1021/bi034317y

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

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

    FEBS Letters   536 ( 1-3 )   237 - 240   2003.2

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

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

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

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

    Photochemistry and Photobiology   77 ( 1 )   96 - 100   2003.1

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    Language：English   Publishing type：Research paper (scientific journal)  

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

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

    Masayuki Iwamoto, Yuki Sudo, Kazumi Shimono, Naoki Kamo

    Photochemistry and Photobiology   76 ( 4 )   462 - 466   2002.10

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    Language：English   Publishing type：Research paper (scientific journal)  

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

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

    Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

    Journal of Photochemistry and Photobiology B: Biology   67 ( 3 )   171 - 176   2002.7

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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

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

    Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

    Biochimica et Biophysica Acta - Biomembranes   1558 ( 1 )   63 - 69   2002.1

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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

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

    Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

    Biophysical Journal   83 ( 1 )   427 - 432   2002

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

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

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

    Biophysical Journal   83 ( 2 )   1130 - 1135   2002

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society  

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

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

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

    Biochimica et Biophysica Acta - Biomembranes   1515 ( 2 )   92 - 100   2001.12

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

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  • Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin Reviewed

    Masayuki Iwamoto, Yuki Sudo, Kazumi Shimono, Naoki Kamo

    Biochimica et Biophysica Acta - Biomembranes   1514 ( 1 )   152 - 158   2001.9

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

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

    Yuki Sudo, Masayuki Iwamoto, Kazumi Shimono, Naoki Kamo

    Photochemistry and Photobiology   74 ( 3 )   489 - 494   2001.9

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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

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

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

    BIOCHEMISTRY   40 ( 31 )   9238 - 9246   2001.8

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    DOI： 10.1021/bo0103819

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

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

    Biophysical Journal   80 ( 2 )   916 - 922   2001

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society  

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

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▼display all

MISC

  • Light + Rhodopsin = Medicinal products!? Invited

    Yuki Sudo, Keiichi Kojima, Shiho Kawanishi

    Photonics Review   240206   2024.5

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    DOI： 10.11470/photo.240206

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  • 溶液NMR法を用いた光駆動ロドプシンRxRのプロトン放出メカニズムの解析

    廣西麗加, 長島敏夫, 鈴木里佳, 廣畑雅史, 小島慧一, 山崎俊夫, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   47th   2024

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  • 異なる膜様環境下でのプロトンポンプ型ロドプシンRxRの構造および熱安定性の比較解析

    菊間千滉, 鈴木里佳, 徳永裕二, 竹内恒, 小島慧一, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   47th   2024

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  • Convergent evolution of animal and microbial rhodopsins Invited Reviewed

    Keiichi Kojima, Yuki Sudo

    RSC Advances   13 ( 8 )   5367 - 5381   2023.2

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    Authorship：Last author,　Corresponding author   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)   Publisher：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

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

    Yuki Sudo

    Biophysics and Physicobiology   2023

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

    Yuki Sudo, Akihisa Terakita, Hideki Kandori

    Biophysics and Physicobiology   2023

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  • 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 Invited

    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   2022.3

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  • 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   2022.3

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    DOI： 10.1016/j.xpro.2021.101046

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  • 光＋ロドプシン＝くすり Invited

    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   2022.2

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  • 光がくすりになる！？―ロドプシンによる生命機能の光操作 Invited

    須藤雄気, 小島慧一

    月刊「化学」   ( 77 )   64 - 65   2022.1

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  • Local structural analysis of the late intermediates during photocycle of the proton pumping rhodopsin RxR using light-irradiated solution NMR spectroscopy

    廣西麗加, 鈴木里佳, 小島慧一, 須藤雄気, 長島敏雄, 山崎俊夫, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   45th   2022

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  • Interaction analysis of proton pump rhodopsin TR and carotenoids by solution NMR

    穂谷野知佳, 鈴木里佳, 廣畑雅史, 村田武士, 小島慧一, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   45th   2022

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  • Structural characterization of Rubrobacter xylanophilus rhodopsin R×R in the unphotolyzed state and photointermediates using photo-irradiation solution state NMR spectroscopy

    鈴木里佳, 廣西麗加, 小島慧一, 須藤雄気, 長島敏雄, 山崎俊夫, 高橋栄夫

    Abstracts. Annual Meeting of the NMR Society of Japan   61st   2022

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  • Comparative analysis of thermal stability, structure and photoreaction cycle of proton-pumped rhodopsin RxR in different membrane environments

    菊間千滉, 鈴木里佳, 藤田陽, 廣畑雅史, 小島慧一, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   45th   2022

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

    Shin Nakao, Keiichi Kojima, Yuki Sudo

    Biological and Pharmaceutical Bulletin   44 ( 10 )   1357 - 1363   2021.10

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    Publishing type：Article, review, commentary, editorial, etc. (scientific journal)   Publisher：Pharmaceutical Society of Japan  

    DOI： 10.1248/bpb.b21-00544

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  • マルチタレント光受容タンパク質「ロドプシン」 Invited

    須藤雄気, 小島慧一

    現代化学   5 ( 602 )   50 - 53   2021.5

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    J-GLOBAL

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  • 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

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    Publisher：Biophysical Society of Japan  

    DOI： 10.2142/biophys.61.049

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  • Applicability of styrene-maleic acid copolymer for G protein coupled receptors, rhodopsins

    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

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  • Analysis of functional and structural changes of proton pump rhodopsin RxR in different membrane-mimetic environments

    廣畑雅史, 鈴木里佳, 穗谷野知佳, 藤田陽, 吉田真帆子, 村田武士, 小島慧一, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   44th   2021

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  • Diversity and Potential of Microbial Rhodopsins

    須藤雄気, 小島慧一

    生物物理(Web)   60 ( 4 )   2020

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  • Student Presentation Award—Report on the Fourth Award Selection Process—

    SUDO Yuki, KODERA Noriyuki, HOSOKAWA Chie

    Seibutsu Butsuri   60 ( 1 )   47 - 48   2020

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.60.047

    CiNii Article

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  • Diversity and Potential of Microbial Rhodopsins

    Yuki SUDO, Keiichi KOJIMA

    Seibutsu Butsuri   60 ( 4 )   209 - 214   2020

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    Authorship：Lead author,　Corresponding author   Publisher：Biophysical Society of Japan  

    DOI： 10.2142/biophys.60.209

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  • 溶液NMRを用いた微生物型プロトンポンプ型ロドプシンRxRの機能・構造解析

    廣畑雅史, 鈴木里佳, 小島慧一, 吉田真帆子, 村田武士, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   43rd   2020

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  • 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

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  • 溶液NMR法を用いた界面活性剤ミセル中における膜タンパク質の比較構造解析

    鈴木里佳, 吉田真帆子, 廣畑雅史, 村田武士, 小島慧一, 須藤雄気, 高橋栄夫

    Abstracts. Annual Meeting of the NMR Society of Japan   58th (CD-ROM)   2019

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  • 異なる疑似膜環境中における耐熱性膜タンパク質RxRの構造安定性と機能の解析

    吉田真帆子, 鈴木里佳, 廣畑雅史, 村田武士, 小島慧一, 須藤雄気, 高橋栄夫

    日本分子生物学会年会プログラム・要旨集(Web)   42nd   2019

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  • 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   2017.12

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    Publisher：Springer Science and Business Media {LLC}  

    DOI： 10.1007/s12551-017-0335-x

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  • 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)   2017.1

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  • 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

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  • Structural and Functional Studies on Photoactive Retinal Proteins: Light Becomes Drugs with Proteins

    Yuki Sudo

    YAKUGAKU ZASSHI-JOURNAL OF THE PHARMACEUTICAL SOCIETY OF JAPAN   136 ( 2 )   185 - 189   2016.2

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    Authorship：Lead author   Language：Japanese   Publishing type：Book review, literature introduction, etc.  

    DOI： 10.1248/yakushi.15-00229-3

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  • Structural and Functional Studies on Photoactive Retinal Proteins: Light Becomes Drugs with Proteins

    須藤雄気, 須藤雄気

    薬学雑誌   136 ( 2 )   185 - 189   2016

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  • 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

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  • Color tuning in retinylidene proteins

    Kota Katayama, Sivakumar Sekharan, Yuki Sudo

    Optogenetics: Light-Sensing Proteins and their Applications   89 - 109   2015.1

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    Language：English   Publisher：Springer Japan  

    DOI： 10.1007/978-4-431-55516-2_7

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

    Kurihara Marie, Sudo Yuki

    Biophysics and Physicobiology   12   121 - 129   2015

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    Language：English   Publisher：The Biophysical Society of Japan  

    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

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  • 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

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  • Retinal Proteins in Thermophilic Bacteria

    塚本卓, 須藤雄気

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

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.55.092

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  • Molecular and evolutionary aspects of microbial sensory rhodopsins Invited Reviewed

    Keiichi Inoue, Takashi Tsukamoto, Yuki Sudo

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   1837 ( 5 )   562 - 577   2014.5

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    Authorship：Last author,　Corresponding author   Publishing type：Book review, literature introduction, etc.  

    DOI： 10.1016/j.bbabio.2013.05.005

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  • Sensory rhodopsins

    Tsukamoto, T, Sudo, Y

    eLS (Encyclopedia of Life Sciences)   2014

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  • 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

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  • 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

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  • 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

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  • Photosensing by Membrane-embedded Receptors and Its Application for the Life Scientists

    Sudo Yuki, Homma Michio

    YAKUGAKU ZASSHI   132 ( 4 )   407 - 416   2012

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    Language：Japanese   Publisher：The Pharmaceutical Society of Japan  

    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

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    Other Link： 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   2011.9

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    Language：Japanese   Publisher：[極限環境生物学会]学会事務局  

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  • 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

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  • What Goal should Rhodopsin Research Achieve?

    SUDO Yuki

    Seibutsu Butsuri   50 ( 4 )   160 - 161   2010.7

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.50.160

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  • 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   2010.4

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    Language：English   Publishing type：Book review, literature introduction, etc.  

    DOI： 10.3390/s100404010

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  • 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

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

    Hideki Kandori, Yuki Sudo, Yuji Furutani

    Journal of Biomedicine and Biotechnology   2010   Article ID 424760   2010

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    Language：English   Publishing type：Book review, literature introduction, etc.   Publisher：Hindawi Publishing Corporation  

    DOI： 10.1155/2010/424760

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  • Photochromicity of the Sensory Rhodopsin-I-Like Protein Regulating Two Distinct Functions

    須藤雄気

    生物物理   49 ( 1 )   2009

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  • A photochromic photoreceptor from a eubacterium. Reviewed

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

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

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

    Yuji Furutani, Yuki Sudo, Hideki Kandori

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

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    Language：English   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)   Publisher：Trivandrum : Research Trends  

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  • Towards Converting a Light-Driven Proton Pump into a Photosensory Receptor

    須藤雄気

    生物物理   46 ( 6 )   2006

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  • 【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   2005.7

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  • 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

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  • Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin Reviewed

    N Kamo, K Shimono, M Iwamoto, Y Sudo

    BIOCHEMISTRY-MOSCOW   66 ( 11 )   1277 - 1282   2001.11

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    Authorship：Last author   Language：English   Publishing type：Book review, literature introduction, etc.  

    DOI： 10.1023/A:1013187403599

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Presentations

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

    The 16th International Conference on Retinal Proteins  2014 

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  • 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 

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  • 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 

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

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

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Industrial property rights

  • 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

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    Applicant：韓国科学技術院他

    Application no：特願2021-153788  Date applied：2021.9.22

    Patent/Registration no：特許7244888  Date registered：2023.3.14  Date issued：2023.3.23

    Rights holder：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

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  • 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

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    Application no：特願2021-89800(PCT/JP2022/021364)  Date applied：2021.5.28

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  • 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

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    Application no：特願2020-196718(PCT/JP2021/043071)  Date applied：2020.11.27

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  • 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

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    Applicant：国立大学法人 東京大学

    Application no：特願2020-070136  Date applied：2020.4.9

    Announcement no：特開2021-167731  Date announced：2021.10.21

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Awards

  • Award for outstanding BPPB paper

    2024.4  

    Kojima K., Watanabe H.C., Doi S., Miyoshi N., Kato M., Ishikita H., and Sudo Y.

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  • 内山勇三科学技術賞

    2023.7   岡山工学振興会  

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  • Research Award

    2022.3   Leave a Nest Co., Ltd.  

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  • Award for outstanding BPPB paper

    2016.11  

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  • 文部科学大臣表彰 若手科学者賞

    2016.4  

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    Country：Japan

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  • 研究者表彰

    2010.3   財団法人光科学技術研究振興財団  

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Research Projects

  • 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 - 2024

    科学技術振興機構 

    須藤 雄気

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    Authorship：Principal investigator 

    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。

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  • ロドプシン基底関数の理解と利用

    Grant number：21H02446  2021.04 - 2024.03

    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

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    Grant amount：\17420000 （ Direct expense: \13400000 、 Indirect expense：\4020000 ）

    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）。

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  • 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

    Grant number：21H00404  2021.04 - 2023.03

    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

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    Grant amount：\5980000 （ Direct expense: \4600000 、 Indirect expense：\1380000 ）

    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。
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    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。

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  • Production of novel drug derivery system with light-induced disruption of liposomes (LiDL)

    Grant number：20K21482  2020.07 - 2023.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)  Grant-in-Aid for Challenging Research (Exploratory)

    須藤 雄気, 山田 勇磨

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    Grant amount：\6500000 （ Direct expense: \5000000 、 Indirect expense：\1500000 ）

    【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。
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    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。

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  • 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

    Grant number：19H04727  2019.04 - 2021.03

    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

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    Grant amount：\7540000 （ Direct expense: \5800000 、 Indirect expense：\1740000 ）

    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。
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    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。

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  • 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

    Grant number：19H05396  2019.04 - 2021.03

    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

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    Grant amount：\5850000 （ Direct expense: \4500000 、 Indirect expense：\1350000 ）

    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。
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    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。

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  • Diversity and possibility of rhodopsins

    Grant number：18H02411  2018.04 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Sudo Yuki

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    Grant amount：\17420000 （ Direct expense: \13400000 、 Indirect expense：\4020000 ）

    Rhodopsin is a photoreceptive membrane protein distributed in the three biological domains of organisms (i.e., eukaryotes, eubacteria, and archaea), and controls the various functions through photo-energy conversion. In addition, it is utilized as a tool for optogenetics, which is a method for controlling biological activity by light. However, the most of molecules are not analyzed so far. On the basis of the background, the purpose of this study is to "explore the diversity of rhodopsin and pursue its potential". We explored the diversity by expression / purification (1. search) and precise analysis (2. analysis) of uncharacterized rhodopsins. We also pursued the possibility of novel optogenetic tools (3. application).

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  • 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

    Grant number：17H05726  2017.04 - 2019.03

    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

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    Grant amount：\6500000 （ Direct expense: \5000000 、 Indirect expense：\1500000 ）

    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。

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  • 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 - 2021

    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

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    Authorship：Principal investigator 

    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。

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  • 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

    Grant number：15H00878  2015.06 - 2017.03

    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

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    Grant amount：\3900000 （ Direct expense: \3000000 、 Indirect expense：\900000 ）

    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。
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    [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。

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  • Development of solid-state NMR structural study of retinal-binding site in rhodopsin with a chromophore

    Grant number：15H04336  2015.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    Kawamura Izuru, SUDO Yuki, NAITO Akira, SHIGETA Arisu, MAKINO Yoshiteru

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    Grant amount：\16380000 （ Direct expense: \12600000 、 Indirect expense：\3780000 ）

    In order to investigate the retinal-binding pocket of microbial rhodopsin, we performed a investigation of the transformation from retinal oxime to retinal, the creation of 13C isotope-labeled retinal from Halobacteria and solid-state NMR study of retinal-binding pocket. The effective transformation from oxime to retinal was achieved. Consequently, segment 13C isotope labeled retinal was successfully created. The structure of retinal binding pocket in sensory rhodopsin II and Krokinobacter rhodopsin 2 were revealed by solid-state NMR spectroscopy. In addition, the structure of photo-intermediates in sensory rhodopsin II were revealed by in-situ photo-irradiation solid-state NMR.

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  • Photo-activated structural changes of bacterial sensory rhodopsin as revealed by photo-irradiation solid-state NMR

    Grant number：15K06963  2015.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    NAITO Akira, KAWAMURA Izuru, SUDO Yuki, KAMO Naoki, Wada Akimori

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    Grant amount：\5200000 （ Direct expense: \4000000 、 Indirect expense：\1200000 ）

    It is essential to elucidate the photoreaction cycles to understand the function of photoreceptor membrane proteins. In this study, we have developed photo-irradiation solid-state NMR spectrometer to detect the photo-reaction pathways of photoreceptor membrane proteins.
    The photoreaction pathways of Y185F-bR were examined using photo-irradiation solid-state NMR Under irradiation with 520 nm light, the CS state changed to a CS*-intermediate and AT state transformed to an N-intermediate and transformed to an O-intermediate.
    The photoreaction pathways of ppR/pHtrII complex were examined using photo-irradiation solid-state NMR. The M-, O- and N’-intermediates were observed by illuminating with green light. Under blue light irradiation, the M-intermediates transformed to the O-intermediate which is in equilibrium with the N’-intermediate.

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  • Investigation, modification and utilization of the retinal proteins

    Grant number：15H04363  2015.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    Sudo Yuki, TSUKAMOTO Takashi

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    Grant amount：\16380000 （ Direct expense: \12600000 、 Indirect expense：\3780000 ）

    Retinal protein, also called "rhodopsin", has a vitamin-A aldehyde as a chromophore. It is widely distributed in the three biological domains (animals, bacteria, archaea), and is responsible for various light-dependent functions. In addition to such biological interests, recently, the new technology called "optogenetics" which is a method for controlling biological activities by light, has been established as a collaborative work with the retinal proteins. In this research, based on the background, we investigated the retinal proteins fundamentally by using various methods. Then we modified the molecular properties to develop the novel optogenetics tools that can be widely utilized for scientific research.

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  • Study of Complex Molecular Systems by Ultrafast and Nonlinear Spectroscopy

    Grant number：25104005  2013.06 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    TAHARA Tahei, NIHONYANAGI Satoshi, KURAMOCHI Hikaru

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    Grant amount：\141050000 （ Direct expense: \108500000 、 Indirect expense：\32550000 ）

    We studied complex molecular systems by the best spectroscopic measurements. We made numerous research achievements, while strongly promoting collaboration with researchers in this project. Particularly, (1) in ultrafast spectroscopy, we have realized an “ultimate” form of time-resolved impulsive stimulated Raman spectroscopy that we developed. We also clarified the ultrafast process of various biomolecules, supramolecules and functional molecules. (2) In interface-selective nonlinear spectroscopy, we have investigated interfacial water structure by utilizing heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG)developed by us．We also studied interfacial dynamics by developing two-dimensional HD-VSFG spectroscopy and time-resolved measurement with ultraviolet excitation. (3) In the study of single molecule spectroscopy, we developed 2D fluorescence lifetime correlation spectroscopy, We studied protein folding processes, and obtained new important findings.

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  • Soft structure-function relationship revealed by functional conversion of photoreceptive proteins

    Grant number：25104009  2013.06 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Kandori Hideki, INOUE Keiichi, IWATA Tatsuya, KATAYAMA Kota, YAMADA Daichi

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    Grant amount：\131300000 （ Direct expense: \101000000 、 Indirect expense：\30300000 ）

    In this project, we studied photoreceptive proteins such as rhodopsins and flavoproteins in view of discovery, conversion, and creation of functions. Through collaborations, we liked to know functional flexibility in these proteins. Consequently, we discovered light-driven inward proton pump, new channelrhodopsin, and an enzyme rhodopsin functioning as phosphodiesterase. We achieved several functional conversions for light-driven ion pumps and photolyases, while each functional conversion was asymmetric, and related to evolution. Based on the structure of a light-driven sodium pump KR2, we engineered light-driven potassium and cesium pumps. We published about 80 articles in Nature, Nat. Commun., Chem. Rev., JACS, Angew., PNAS, JPC Letters and JBC during the project period.

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  • レチナールタンパク質の生物物理化学的解析

    Grant number：13F03076  2013.04 - 2015.03

    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

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    Grant amount：\2300000 （ Direct expense: \2300000 ）

    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。

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  • 振動分光法による過渡的膜タンパク質複合体の解析

    Grant number：24121712  2012.04 - 2014.03

    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

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    Grant amount：\11310000 （ Direct expense: \8700000 、 Indirect expense：\2610000 ）

    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]。

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  • Investigation of whole photo signal transduction cascade at high spatial and temporal resolutions

    Grant number：23687019  2011.04 - 2015.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)  Grant-in-Aid for Young Scientists (A)

    SUDO Yuki, TSUKAMOTO Takashi

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    Grant amount：\27300000 （ Direct expense: \21000000 、 Indirect expense：\6300000 ）

    Protein molecules are working in organisms with changes in spatial and temporal domains, resulting in a variety of biological functions. Thus it is essential to understand the proteins from the spatial and temporal aspects. In this study, we focused on photo signal transduction mechanism regulated by the photoactive retinal proteins and we investigated it at various spatial and temporal resolutions.

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  • Investigation of color tuning mechanism in rhodopsins and production of multi-colored pigments

    Grant number：23657100  2011 - 2013

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    SUDO Yuki, HAYASHI Shigehiko

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    Grant amount：\3900000 （ Direct expense: \3000000 、 Indirect expense：\900000 ）

    Rhodopsins are known to show a large variation in their colors depending on the interaction between the apoprotein (opsin) and the retinal chromophore. In this project, we have investigated the color tuning mechanism in the rhodopsins and have also produced molecules showing a variety of colors such as blue, orange, red and purple, without loss of biological function. Thus the combination of experimental and theoretical studies could provide a useful research tool in a number of scientific fields.

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  • 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

    Grant number：22018010  2010 - 2011

    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

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    Grant amount：\4200000 （ Direct expense: \4200000 ）

    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。

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  • 全反射型赤外分光法による過渡的複合体の解析

    Grant number：22121508  2010 - 2011

    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

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    Grant amount：\11440000 （ Direct expense: \8800000 、 Indirect expense：\2640000 ）

    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]。

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  • Development of 2-step excitation transient grating method, and elucidation of photo-reaction mechanism and control of signal transferring protein.

    Grant number：21770165  2009 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    INOUE Keiichi, SUDO Yuki

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    Grant amount：\4420000 （ Direct expense: \3400000 、 Indirect expense：\1020000 ）

    Sensory rhodopsin I from eubacterium Salinibacter ruber is the photo-censor for the bacterial photo-taxis. In this study the photo-reaction dynamics of this protein was studied by transient grating (TG) method. As the result, the presences of new photo-intermediates were identified in the photo-cycle of sensory rhodopsin I. In addition, the enthalpy differences of the intermediates were determined by TG method and we found that they are significantly affected by the binding and dissociation of chloride ion.

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  • Analysis of interaction, ion transport and structural change in a stator complex of bacterial flagellar motor

    Grant number：21770166  2009 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    SUDO Yuki

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    Grant amount：\4550000 （ Direct expense: \3500000 、 Indirect expense：\1050000 ）

    Motile microorganisms, such as bacteria and archaea, sense and respond to extracellular stimuli by changing their swimming mode to migrate towards more favorite habitats. In this research, we analyzed interaction, ion transport and structural changes in a stator complex of the bacterial flagellar motor using biophysical techniques. By means of attenuated total reflection Fourier-transform infrared spectroscopy, we directly observed binding of Na^+ to carboxylates in the Pom/B complex, including the functionally essential residue Asp24 (Sudo et al.2009b, Biochemistry). We also demonstrated that Ala39-MotB and Cys31-PomB form part of the ion flux pathway (Sudo et al. 2009, Biophysics), and reported the crystal structure of C-terminal region of MotB (Kojima et al. 2009, Mol.Microbiol.). Moreover we found and characterized new receptor proteins (Suzuki et al. 2009, J.Mol.Biol., Sudo et al.2009a, Biochemistry, Yagasaki et al.2010, Biochemistry, Sudo et al. 2011, J.Biol.Chem.).

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  • 光機能性・制御性蛋白質による細胞・個体操作

    2008 - 2011

    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

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    Authorship：Principal investigator 

    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。

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  • 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

    Grant number：20050012  2008 - 2010

    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

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    Grant amount：\3400000 （ Direct expense: \3400000 ）

    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。

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  • 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

    Grant number：19870010  2007 - 2008

    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

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    Grant amount：\3125000 （ Direct expense: \2720000 、 Indirect expense：\405000 ）

    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。

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  • Basic Mathematical and Data Sciences （2022academic year） Third semester  - 月5～6

  • Physical Chemistry 1 （2022academic year） Second semester  - 金1～2

  • Physical Chemistry 1 （2022academic year） Second semester  - 金1～2

  • Physical Chemistry 3 （2022academic year） Third semester  - 火7～8

  • Physical Chemistry 3 （2022academic year） Third semester  - 火7～8

  • Physical Chemistry 4 （2022academic year） Fourth semester  - 火1～2

  • Physical Chemistry 4 （2022academic year） Fourth semester  - 火1～2

  • Physical Chemistry 5 （2022academic year） Second semester  - 木3～4

  • Physical Chemistry 5 （2022academic year） Second semester  - 木3～4

  • Physical Chemistry A （2022academic year） 2nd and 3rd semester  - [第２学期]金1～2, [第３学期]火1～2

  • Physical Chemistry A （2022academic year） 2nd and 3rd semester  - [第２学期]金1～2, [第３学期]火1～2

  • Physical Chemistry B （2022academic year） 3rd and 4th semester  - [第３学期]火7～8, [第４学期]火1～2

  • Physical Chemistry B （2022academic year） 3rd and 4th semester  - [第３学期]火7～8, [第４学期]火1～2

  • Physical Chemistry C （2022academic year） 2nd and 3rd semester  - [第２学期]木3～4, [第３学期]金1～2

  • Physical Chemistry C （2022academic year） 2nd and 3rd semester  - [第２学期]木3～4, [第３学期]金1～2

  • Physical Analysis of Biomolecules A （2022academic year） special  - その他

  • Seminar in Physical Analysis of Biomolecules A （2022academic year） special  - その他

  • Physical Analysis of Biomolecules I （2022academic year） special  - その他

  • Physical Analysis of Biomolecules II （2022academic year） special  - その他

  • Practice in Fundamental Pharmaceutical Sciences I （2022academic year） 1st semester  - その他5～9

  • Practice in Fundamental Pharmaceutical Sciences I （2022academic year） 1st semester  - その他5～9

  • Practice in Fundamental Pharmaceutical Sciences I （2022academic year） 1st semester  - その他5～9

  • Practice in Fundamental Pharmaceutical Sciences I （2022academic year） 1st semester  - その他5～9

  • Advanced Pharmaceutical Research （2021academic year） Summer concentration  - その他

  • Analytical Sciences and Physical Chemistry （2021academic year） Prophase  - その他

  • Basic Physics （2021academic year） 1st semester  - 火5,火6,金3,金4

  • Basic Physics （2021academic year） 1st semester  - 火5,火6,金3,金4

  • Basic Physics （2021academic year） 1st semester  - 火5,火6,金3,金4

  • Basic Physics （2021academic year） 1st semester  - 火5,火6,金3,金4

  • Senses for Organisms （2021academic year） Third semester  - 月3～4

  • Senses for Organisms （2021academic year） Fourth semester  - 金3～4

  • Basic Mathematical and Data Sciences （2021academic year） Third semester  - 月5～6

  • Physical Chemistry 1 （2021academic year） Second semester  - 金5,金6

  • Physical Chemistry 1 （2021academic year） Second semester  - 金5,金6

  • Physical Chemistry 3 （2021academic year） Third semester  - 火7,火8

  • Physical Chemistry 3 （2021academic year） Third semester  - 火7～8

  • Physical Chemistry 4 （2021academic year） 1st semester  - 木3,木4

  • Physical Chemistry 4 （2021academic year） 1st semester  - 木3,木4

  • Physical Chemistry 5 （2021academic year） Second semester  - 木3,木4

  • Physical Chemistry 5 （2021academic year） Second semester  - 木3,木4

  • Physical Chemistry A （2021academic year） 2nd and 3rd semester  - [第２学期]金5,金6, [第３学期]火1,火2

  • Physical Chemistry A （2021academic year） 2nd and 3rd semester  - [第２学期]金5,金6, [第３学期]火1,火2

  • Physical Chemistry B （2021academic year） 3rd and 4th semester  - [第３学期]火7,火8, [第４学期]火1,火2

  • Physical Chemistry B （2021academic year） 3rd and 4th semester  - [第３学期]火7,火8, [第４学期]火1,火2

  • Physical Analysis of Biomolecules A （2021academic year） special  - その他

  • Seminar in Physical Analysis of Biomolecules A （2021academic year） special  - その他

  • Physical Analysis of Biomolecules I （2021academic year） special  - その他

  • Physical Analysis of Biomolecules II （2021academic year） special  - その他

  • Guidance for Pharmaceutical Sciences （2021academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Guidance for Pharmaceutical Sciences （2021academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Guidance for Pharmaceutical Sciences （2021academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Guidance for Pharmaceutical Sciences （2021academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Practice in Fundamental Pharmaceutical Sciences I （2021academic year） 1st semester  - その他6～9

  • Practice in Fundamental Pharmaceutical Sciences I （2021academic year） 1st semester  - その他6～9

  • Practice in Fundamental Pharmaceutical Sciences I （2021academic year） 1st semester  - その他6～9

  • Practice in Fundamental Pharmaceutical Sciences I （2021academic year） 1st semester  - その他6～9

  • Frontier in Pharmaceutical Sciences （2020academic year） special  - その他

  • Advanced Pharmaceutical Research （2020academic year） Summer concentration  - その他

  • Analytical Sciences and Physical Chemistry （2020academic year） Prophase  - その他

  • Basic Physics （2020academic year） 1st semester  - その他

  • Basic Physics （2020academic year） 1st semester  - 火4,火5,火6

  • Basic Physics （2020academic year） 1st semester  - 火4,火5,火6

  • Senses for Organisms （2020academic year） Third semester  - 月3,月4

  • Senses for Organisms （2020academic year） Fourth semester  - 金3,金4

  • Basic Mathematical and Data Sciences （2020academic year） Third semester  - 月5,月6

  • Physical Chemistry III （2020academic year） Second semester  - 木3,木4

  • Physical Chemistry 1 （2020academic year） Second semester  - 火5,火6

  • Physical Chemistry 1 （2020academic year） Second semester  - 火5,火6

  • Physical Chemistry 4 （2020academic year） 1st semester  - 木3,木4

  • Physical Chemistry 4 （2020academic year） 1st semester  - 木3,木4

  • Physical Chemistry 5 （2020academic year） Second semester  - 木3,木4

  • Physical Chemistry 5 （2020academic year） Second semester  - 木3,木4

  • Physical Analysis of Biomolecules A （2020academic year） special  - その他

  • Seminar in Physical Analysis of Biomolecules A （2020academic year） special  - その他

  • Physical Analysis of Biomolecules I （2020academic year） special  - その他

  • Physical Analysis of Biomolecules II （2020academic year） special  - その他

  • Guidance for Pharmaceutical Sciences （2020academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Guidance for Pharmaceutical Sciences （2020academic year） 1st and 2nd semester  - 月1,水4

  • Guidance for Pharmaceutical Sciences （2020academic year） 1st and 2nd semester  - 月1,水4

  • Guidance for Pharmaceutical Sciences （2020academic year） 1st and 2nd semester  - [第１学期]水4, [第２学期]月1

  • Practice in Fundamental Pharmaceutical Sciences I （2020academic year） special  - その他

  • Practice in Fundamental Pharmaceutical Sciences I （2020academic year） special  - その他

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