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

• Project/Area Number: 23687019
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: Okayama University (2014); Nagoya University (2011-2013)
• Principal Investigator: SUDO Yuki 岡山大学, 医歯(薬)学総合研究科, 教授 (10452202)
• Research Collaborator: TSUKAMOTO Takashi
• Project Period (FY): 2011-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥27,300,000 (Direct Cost: ¥21,000,000、Indirect Cost: ¥6,300,000); Fiscal Year 2014: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2013: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2012: ¥9,230,000 (Direct Cost: ¥7,100,000、Indirect Cost: ¥2,130,000); Fiscal Year 2011: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
• Keywords: 情報伝達 / 光 / 構造変化 / レチナールタンパク質 / 膜タンパク質 / 光情報伝達 / 生物物理学 / 発色団 / 生物物理 / 分子認識 / 光生物 / 分光法

Outline of Final Research Achievements

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.

Research Products

• [Journal Article] Converting a light-driven proton pump into a light-gated proton channel (2015)
  • Author(s): K. Inoue, T. Tsukamoto, K. Shimono, Y. Suzuki, S. Miyauchi, S. Hayashi, H. Kandori, Y. Sudo*
  • Journal Title: J. Am. Chem. Soc. Volume: 137 Issue: 9 Pages: 3291-3299
  • DOI: 10.1021/ja511788f
  • Peer Reviewed
• [Journal Article] Atomistic design of microbial opsin-based blue-Shifted optogenetics tools (2015)
  • Author(s): Kato, H. E., Kamiya, M., Sugo, S., Ito, J., Taniguchi, R., Orito, A., Hirata, K., Inutsuka, A., Yamanaka, A., Maturana, A., Ishitani, R., Sudo, Y., *Hayashi, S., & *Nureki, O.
  • Journal Title: Nat. Commun. Volume: 印刷中
  • NAID: 120005745621
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Factors affecting the stability and performance of ionic liquid-based planar transient photodetectors (2015)
  • Author(s): *Dalgleish, S., Reissig, L., Hu, L., Matsushita, M.M., Sudo, Y., & *Awaga, K.
  • Journal Title: Langmuir Volume: 印刷中 Issue: 18 Pages: 5235-5243
  • DOI: 10.1021/la504972q
  • Peer Reviewed
• [Journal Article] Irreversible trimer to monomer transition of thermophilic rhodopsin upon thermal stimulation (2014)
  • Author(s): Tsukamoto, T., Demura, M., & *Sudo, Y.
  • Journal Title: J. Phys. Chem. B Volume: 118 Issue: 43 Pages: 12383-12394
  • DOI: 10.1021/jp507374q
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Color discriminating retinal configurations of sensory rhodopsin I by photo-irradiation solid state NMR spectroscopy. (2014)
  • Author(s): Yornoda, H., Makino, Y., Tomonaga, Y., Hidaka, T., Kawamura, I., Okitsu, T., Wada, A., Sudo, Y., Naito, A.
  • Journal Title: Angew. Chem. Int. Ed. Volume: (印刷中) Issue: 27 Pages: 7080-7084
  • DOI: 10.1002/ange.201309258
  • Peer Reviewed
• [Journal Article] The early steps in the photocycle of a photosensor protein sensory rhodopsin I from Salinibacter ruber (2014)
  • Author(s): Sudo, Y., Mizuno, M., Wei, Z., Takeuchi S., Tahara. T., Mizutani. Y.
  • Journal Title: J. Phys. Chem. B Volume: 118 Issue: 6 Pages: 1510-1518
  • DOI: 10.1021/jp4112662
  • Peer Reviewed
• [Journal Article] Thermal and spectroscopic characterization of a proton pumping rhodopsin from an extreme thermophile (2013)
  • Author(s): Tsukamoto, T., Inoue, K., Kandori, H., Sudo, Y.
  • Journal Title: J. Biol. Chem. Volume: 288 Issue: 30 Pages: 21581-21592
  • DOI: 10.1074/jbc.m113.479394
  • Peer Reviewed
• [Journal Article] A blue-shifted light-driven proton pump for neural silencing (2013)
  • Author(s): Sudo, Y., Okazaki, A., Ono, H., Yagasaki, J., Sugo, S., Kamiya, M., Reissig, L., Inoue, K., Ihara, K., Kandori, H., Takagi, S., Hayashi, S.
  • Journal Title: J. Biol. Chem. Volume: 288 Issue: 28 Pages: 20624-20632
  • DOI: 10.1074/jbc.m113.475533
  • Peer Reviewed
• [Journal Article] Investigation of the chromophore binding cavity in the 11-cis acceptable microbial rhodopsin MR (2013)
  • Author(s): Mori, A., Yagasaki, J., Homma, M., Reissig, L., & *Sudo, Y.
  • Journal Title: Chem. Phys. Volume: 419 Pages: 23-29
  • DOI: 10.1016/j.chemphys.2012.11.020
  • Peer Reviewed
• [Journal Article] Large spectral change due to amide modes of a β-sheet upon the formation of an early photointermediate of middle rhodopsin (2013)
  • Author(s): Furutani, Y., Okitsu, T., Reissig, L., Mizuno, M., Homma, M., Wada, A., Mizutani, Y., Sudo, Y.
  • Journal Title: J. Phys. Chem. B Volume: 117 Issue: 13 Pages: 3449-3458
  • DOI: 10.1021/jp308765t
  • Peer Reviewed
• [Journal Article] Expression, purification and biochemical characterization of the cytoplasmic loop of PomA, a stator component of the Na⁺ driven flagellar motor (2013)
  • Author(s): Abe R
  • Journal Title: BIOPHYSICS Volume: 9 Issue: 0 Pages: 21-29
  • DOI: 10.2142/biophysics.9.21
  • NAID: 130003366026
  • ISSN: 1349-2942
  • Peer Reviewed
• [Journal Article] "The influence of halide binding on the hydrogen bonding network in the active site of Salinibacter sensory rhodopsin I" (2012)
  • Author(s): L. Reissig, T. Iwata, T. Kikukawa, M. Demura, N. Kamo, H. Kandori and Y. Sudo
  • Journal Title: Biochemistry Volume: 51 Issue: 44 Pages: 8802-8813
  • DOI: 10.1021/bi3009592
  • Peer Reviewed
• [Journal Article] Photo-induced regulation of the chromatic adaptive gene expression by Anabaena sensory rhodopsin (2012)
  • Author(s): Irieda, H., Morita, T., Maki, K., Homma, M., Aiba, H., & *Sudo, Y.
  • Journal Title: J. Biol. Chem. Volume: 287 Issue: 39 Pages: 32485-32493
  • DOI: 10.1074/jbc.m112.390864
  • Peer Reviewed
• [Journal Article] Optical Silencing of C. elegans Cells with Arch Proton Pump (2012)
  • Author(s): Okazaki A, Sudo Y, Takagi S
  • Journal Title: PLoS ONE Volume: 7(5) Issue: 5 Pages: e35370-e35370
  • DOI: 10.1371/journal.pone.0035370
  • Peer Reviewed
• [Journal Article] "Absorption spectra and photochemical reactions in a unique photoactive protein, middle rhodopsin MR" (2012)
  • Author(s): K. Inoue, L. Reissig, M. Sakai, S. Kobayashi, M. Homma, M. Fujii, H. Kandori, and Y. Sudo
  • Journal Title: J. Phys. Chem. B Volume: 116 Issue: 20 Pages: 5888-5899
  • DOI: 10.1021/jp302357m
  • Peer Reviewed
• [Journal Article] Spectral tuning in sensory rhodopsin I from Salinibacter ruber (2011)
  • Author(s): Sudo, Y., Yuasa, Y., Shibata, J., Suzuki, D., Homma, M.
  • Journal Title: J.Biol.Chem. Volume: 286 Issue: 13 Pages: 11328-11336
  • DOI: 10.1074/jbc.m110.187948
  • Peer Reviewed
• [Journal Article] Direct observation of the structural change of Tyr174 in the primary reaction of sensory rhodopsin II (2011)
  • Author(s): Misao Mizuno, Yuki Sudo, Michio Homma and Yasuhisa Mizutani
  • Journal Title: Biochemistry Volume: 50 Issue: 15 Pages: 3170-3180
  • DOI: 10.1021/bi101817y
  • Peer Reviewed
• [Journal Article] Spectrally silent intermediates during the photochemical reactions of Salinibacter sensory rhodopsin I (2011)
  • Author(s): K.Inoue, Y.Sudo, M.Homma, H.Kandori
  • Journal Title: J.Phys.Chem.B Volume: 115 Issue: 15 Pages: 4500-4508
  • DOI: 10.1021/jp2000706
  • Peer Reviewed
• [Journal Article] Structural characteristics around β-ionone ring of the retinal chromophore in Salinibacter sensory rhodopsin I (2011)
  • Author(s): H.Irieda, L.Reissig, A.Kawanabe, M.Homma, H.Kandori, Y.Sudo
  • Journal Title: Biochemistry Volume: 50 Issue: 22 Pages: 4912-4922
  • DOI: 10.1021/bi200284s
  • Peer Reviewed
• [Journal Article] Functional expression of a two-transmembrane HtrII protein using cell-free synthesis (2011)
  • Author(s): Sudo, Y., Tanaka, R., Kobayashi, T., Kamo, N., Kohno, T., Kojima, C.
  • Journal Title: BIOPHYSICS Volume: 7 Pages: 51-58
  • DOI: 10.2142/biophysics.7.51
  • NAID: 130000741389
  • ISSN: 1349-2942
  • Peer Reviewed
• [Journal Article] An active photoreceptor intermediate revealed by in situ photoirradiated solid-state NMR spectroscopy (2011)
  • Author(s): Tomonaga, Y., Hidaka, T, Kawamura, I, Nishio, T, Ohsawa, K, Okitsu, T, Wada, A, Sudo, Y, Kamo, N, Ramamoorthy, A, Naito, A.
  • Journal Title: Biophys.J. Volume: 101 Issue: 10 Pages: L50-L52
  • DOI: 10.1016/j.bpj.2011.10.022
  • Peer Reviewed
• [Presentation] 光受容レチナールタンパク質の構造・機能解析：光 + タンパク質 = 薬！？ (2015)
  • Author(s): 須藤雄気
  • Organizer: 日本薬学会第135年会・シンポジウム 「受容体とトランスポーターの構造薬理学」
  • Place of Presentation: 神戸市, 兵庫県
  • Year and Date: 2015-03-27
  • Invited
• [Presentation] ビタミンAアルデヒドを発色団とする光受容タンパク質の多様性と可能性が拓く光創薬科学 (2015)
  • Author(s): 須藤雄気
  • Organizer: 神戸薬科大学特別研究セミナー
  • Place of Presentation: 神戸市, 兵庫県
  • Year and Date: 2015-02-20
  • Invited
• [Presentation] レチナールタンパク質が拓くフォトクロミックバイオマテリアル (2015)
  • Author(s): 須藤雄気
  • Organizer: 第３回 日本バイオマテリアル学会中四国シンポジウム
  • Place of Presentation: 岡山市, 岡山県
  • Year and Date: 2015-01-28
  • Invited
• [Presentation] 高い安定性を示す新規レチナールタンパク質TRの機能・構造と光操作への展開 (2015)
  • Author(s): 須藤雄気
  • Organizer: 新学術領域研究 『柔らかな分子系』 第8回ワークショップ
  • Place of Presentation: 瀬戸内市, 岡山県
  • Year and Date: 2015-01-25
  • Invited
• [Presentation] 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！？ (2014)
  • Author(s): 須藤雄気
  • Organizer: 自然科学研究機構 分間連携ワークショップ
  • Place of Presentation: 蒲郡市, 愛知県
  • Year and Date: 2014-10-25
  • Invited
• [Presentation] Molecular-based rational design and engineering of microbial retinal proteins for optogenetics (2014)
  • Author(s): Sudo, Y.
  • Organizer: The 16th International Conference on Retinal Proteins
  • Place of Presentation: Nagahama, Shiga, Japan
  • Year and Date: 2014-10-09
  • Invited
• [Presentation] 光駆動イオンポンプから光開閉性イオンチャネルへの機能変換 (2014)
  • Author(s): 須藤雄気
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌市, 北海道
  • Year and Date: 2014-09-26
  • Invited
• [Presentation] Rational Design and Engineering of Photoactive Retinal Proteins (2014)
  • Author(s): Sudo, Y.
  • Organizer: The 2nd Awaji International Workshop on “Electron Spin Science & Technology: Biological and Materials Science Oriented Applications (2nd AWEST 2014)
  • Place of Presentation: 淡路島, 兵庫県
  • Year and Date: 2014-06-17
  • Invited
• [Presentation] Photobiophysical chemistry: What should we learn from retinal proteins? (2014)
  • Author(s): Sudo, Y.
  • Organizer: iCeMS symposium on Mesoscopic Chemical Biology: Integrated Chemical-Physical Systems Towards Cell Control
  • Place of Presentation: Kyoto
  • Invited
• [Presentation] 微生物型レチナールタンパク質の非常識で未来を拓く (2013)
  • Author(s): 須藤雄気
  • Organizer: 分子科学研究所研究会「ロドプシン研究の故きを温ねて新しきを知る」
  • Place of Presentation: 岡崎
  • Invited
• [Presentation] 光受容レチナールタンパク質の常識と非常識 (2013)
  • Author(s): 須藤雄気
  • Organizer: 東京工業大学第1回生体分子専攻・若手コロキウム
  • Place of Presentation: 横浜
  • Invited
• [Presentation] 微生物型レチナールタンパク質の理解と利用 (2013)
  • Author(s): 須藤雄気
  • Organizer: 大阪市立大学セミナー
  • Place of Presentation: 大阪
  • Invited
• [Presentation] ロドプシンの、ロドプシンによる、ロドプシンのための蛋白質科学 (2013)
  • Author(s): 須藤雄気
  • Organizer: 大阪大学蛋白研セミナー
  • Place of Presentation: 大阪
  • Invited
• [Presentation] Functional diversity of sensory rhodopsins from microbes
  • Author(s): Sudo, Y.
  • Organizer: 15th International Conference on Retinal Proteins
  • Place of Presentation: Monte Verita (Ascona, Switzerland)
  • Invited
• [Presentation] 光操作技術の基盤となるロドプシン分子の多様性と可能性
  • Author(s): 須藤雄気
  • Organizer: 第7回・NIBBバイオイメージングフォーラム
  • Place of Presentation: 自然科学研究機構 基礎生物学研究所（愛知県）
  • Invited
• [Presentation] 分子からのボトムアップ研究で拓く光細胞・個体操作
  • Author(s): 須藤雄気
  • Organizer: 細胞を創る」研究会5.0
  • Place of Presentation: 東京工業大学（神奈川県）
  • Invited
• [Presentation] 微生物の光利用と光制御ツール開発
  • Author(s): 須藤雄気
  • Organizer: 「次世代の光の利用と物質材料・生命機能」研究会
  • Place of Presentation: 早稲田大学（東京都）
  • Invited
• [Presentation] 「Simple is the first? 」: 微生物由来レチナール蛋白質の分子進化と多様性
  • Author(s): 須藤雄気
  • Organizer: 第14回日本進化学会年会
  • Place of Presentation: 首都大学東京（東京都）
  • Invited
• [Presentation] 微生物型光受容タンパク質の解析と光制御ツール開発
  • Author(s): 須藤雄気
  • Organizer: 第17回日本光生物学協会年会
  • Place of Presentation: 大阪大学（大阪府）
  • Invited
• [Presentation] 光生物物理学-基礎研究のススメ。渇望される薬学部生
  • Author(s): 須藤雄気
  • Organizer: 北海道大学薬学部 第19回「先輩と語る」講演会
  • Place of Presentation: 北海道大学（北海道）
  • Invited
• [Presentation] Cell and micro-organism manipulations with photo-functional and photo-controllable proteins
  • Author(s): Sudo, Y.
  • Organizer: AS-JST Joint Workshop on Innovative Use of Light and Nano/Bio
  • Place of Presentation: アカデミアシニカ（台北市,台湾）
  • Invited
• [Presentation] 7回膜貫通型色素結合タンパク質（ロドプシン）の調製法
  • Author(s): 須藤雄気
  • Organizer: 第11回・日本蛋白質科学会年会 蛋白質科学会アーカイブワークショップ
  • Place of Presentation: ホテル阪急エキスポパーク（大阪府）
  • Invited
• [Presentation] Molecular and evolutionary aspects of microbial sensory rhodopsin
  • Author(s): Sudo, Y., Homma, M.
  • Organizer: 5th Asia and Oceania Conference for Photobiology (AOCP)
  • Place of Presentation: 奈良県新公会堂（奈良県）
  • Invited
• [Presentation] 微生物型ロドプシンタンパク質における特異な光反応
  • Author(s): 須藤雄気, 本間道夫
  • Organizer: 生理学研究所研究会「作動中の膜機能分子の姿を捉える-静止画から動画へ-」
  • Place of Presentation: 自然科学研究機構 生理学研究所（愛知県）
  • Invited
• [Presentation] What should we learn from sensory rhodopsins? : Signal transfer mechanism and its application for protein expression
  • Author(s): 須藤雄気, 本間道夫
  • Organizer: 日本生物物理学会 第49回年会
  • Place of Presentation: 兵庫県立大学（兵庫県）
  • Invited
• [Presentation] 色付きタンパク質の生物学的・化学的・物理学的研究の面白さと奥深さ
  • Author(s): 須藤雄気
  • Organizer: 第1回超異分野学会
  • Place of Presentation: お茶の水女子大学（東京都）
  • Invited
• [Book] Optogenetics, Chapter 7, Color tuning in retinylidene proteins (2015)
  • Author(s): Katayama, K., Sekharan, S., & *Sudo, Y.
  • Publisher: Springer Verlag Tokyo
• [Book] 好熱性細菌のレチナールタンパク質 (2015)
  • Author(s): 塚本卓、須藤雄気
  • Total Pages: 3
  • Publisher: 生物物理
• [Book] 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 (2015)
  • Author(s): 土井聡子、須藤雄気
  • Total Pages: 4
  • Publisher: ビタミン学会誌
• [Book] オプトジェネティクス（光遺伝学）の原理と基礎 (2015)
  • Author(s): 須藤雄気、神取秀樹
  • Total Pages: 5
  • Publisher: ファルマシア
• [Book] 膜タンパク質の可溶化（抽出）(2) (2014)
  • Author(s): 須藤雄気、塚本卓
  • Total Pages: 10
  • Publisher: 蛋白質科学会・アーカイブ
• [Book] Molecular and evolutionary aspects of microbial sensory rhodopsins (2014)
  • Author(s): Inoue, K., Tsukamoto, T., & *Sudo, Y.
  • Total Pages: 16
  • Publisher: Biochim. Biophys. Acta
• [Book] Sensory rhodopsins (2014)
  • Author(s): Tsukamoto, T., & *Sudo, Y.
  • Total Pages: 7
  • Publisher: In: eLS. John Wiley & Sons, Ltd: Chichester.
• [Book] オプトジェネティクス-光工学と遺伝学による行動制御技術の最前線（分担執筆） (2013)
  • Author(s): 須藤雄気
  • Total Pages: 324
  • Publisher: エヌ・ティー・エス
• [Book] 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 (2011)
  • Author(s): 須藤雄気、井原邦夫、本間道夫、加茂直樹
  • Total Pages: 7
  • Publisher: 極限環境微生物学会誌
• [Remarks] 須藤研究室ホームページ
  • URL: http://www.pharm.okayama-u.ac.jp/lab/bukka/page3.html