Crystal structural analysis of photosystem II in pH dependence for trapping S2 intermediate state

• Project/Area Number: 15H05588
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Okayama University
• Principal Investigator: Umena Yasufumi 岡山大学, 異分野基礎科学研究所, 特別契約職員(准教授) (10468267)
• Co-Investigator(Renkei-kenkyūsha): Furutani Yuji 分子科学研究所, 生体分子情報研究部門, 准教授 (80432285)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥23,530,000 (Direct Cost: ¥18,100,000、Indirect Cost: ¥5,430,000); Fiscal Year 2017: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2016: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2015: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
• Keywords: 結晶構造解析 / 光合成 / 光化学系II蛋白質 / pH / 反応中間状態 / 光合成蛋白質 / 反応中間構造 / 生物物理 / 蛋白質 / X線結晶構造解析 / 構造生物 / 膜蛋白質結晶化 / 混合緩衝液 / Ｘ線結晶構造解析 / 構造生物化学 / らん藻培養 / 膜蛋白質精製 / 緩衝液

Outline of Final Research Achievements

Crystal structures of cyanobacterium Photosystem II (PSII) in pH4 or pH9 condition were solved at 2.0-angstrom resolution. These acidic or basic PSII crystals changed from the neutral state were obtained by using the mixture solution of three kinds of buffers for the linear pH gradient without changing the composition of crystal mother liquid. Whole structures were no differences among neutral, acidic and basic structure. However, the pH-dependant structure changes were observed on the proton pathways from the active site of water-oxidation. The each of structural change was in the different locations between acidic and basic structure, respectively. We concluded that these parts were essential for proton transfer from the water-splitting reaction in PSII.

Research Products

• [Journal Article] Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II (2018)
  • Author(s): Kato Yuki、Akita Fusamichi、Nakajima Yoshiki、Suga Michihiro、Umena Yasufumi、Shen Jian-Ren、Noguchi Takumi
  • Journal Title: The Journal of Physical Chemistry Letters Volume: 9 Issue: 9 Pages: 2121-2126
  • DOI: 10.1021/acs.jpclett.8b00638
  • Peer Reviewed / Open Access
• [Journal Article] Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem?II: Applicability of the Jahn-Teller Deformation Formula (2017)
  • Author(s): Shoji Mitsuo、Isobe Hiroshi、Tanaka Ayako、Fukushima Yoshimasa、Kawakami Keisuke、Umena Yasufumi、Kamiya Nobuo、Nakajima Takahito、Yamaguchi Kizashi
  • Journal Title: ChemPhotoChem Volume: 2 Issue: 3 Pages: 257-270
  • DOI: 10.1002/cptc.201700162
  • Peer Reviewed / Open Access
• [Journal Article] Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II (2017)
  • Author(s): S. Uto, K. Kawakami, Y. Umena, M. Iwai, M. Ikeuchi, J.-R. Shenf and N. Kamiya
  • Journal Title: Faraday Discussions Volume: 印刷中 Pages: 107-120
  • DOI: 10.1039/c6fd00213g
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. (2017)
  • Author(s): Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
  • Journal Title: Nature Volume: 543 Issue: 7643 Pages: 131-135
  • DOI: 10.1038/nature21400
  • NAID: 120006344935
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Dynamics of Excitation Energy Transfer Between the Subunits of Photosystem II Dimer. (2016)
  • Author(s): Yusuke Yoneda, Tetsuro Katayama, Yutaka Nagasawa, Hiroshi Miyasaka and Yasufumi Umena
  • Journal Title: J. Am. Chem. Soc. Volume: 138 Issue: 36 Pages: 11599-11605
  • DOI: 10.1021/jacs.6b04316
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Novel features of eukaryotic photosystem II revealed by its crystal structure analysis from a red alga (2016)
  • Author(s): Hideo Ago, Hideyuki Adachi, Yasufumi Umena, Takayoshi Tashiro, Keisuke Kawakami, Nobuo Kamiya, Lirong Tian, Guangye Han, Tingyun Kuang, Zheyi Liu, Fangjun Wang, Hanfa Zou, Isao Enami, Masashi Miyano, Jian-Ren Shen
  • Journal Title: J. Biol. Chem. Volume: 291 Issue: 11 Pages: 5676-5687
  • DOI: 10.1074/jbc.m115.711689
  • Peer Reviewed / Open Access
• [Journal Article] Large-scale QM/MM calc8lations of hydrogen onding networks for proton transfer and water inlet channels for water oxidation-Theoretical system models of the oxygen-evolving comlex of photosystem II- (2015)
  • Author(s): M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, T. Nakajima, K. Yamaguchi
  • Journal Title: Adv. Quantum Chem. Volume: 70 Pages: 325-413
  • DOI: 10.1016/bs.aiq.2014.10.001
  • Peer Reviewed
• [Journal Article] Theoretical modeling of biomolecular system I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II (2015)
  • Author(s): M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, T. Nakajima, K. Yamaguchi
  • Journal Title: Molecular Physics Volume: 113 Issue: 3-4 Pages: 359-384
  • DOI: 10.1080/00268976.2014.960021
  • Peer Reviewed
• [Presentation] Proton transfer inhibition by molecular anion substitutions in Photosystem II (2017)
  • Author(s): Yasufumi Umena, Shouya Tamaru, Jian-Ren Shen
  • Organizer: 24th Congress and General Assembly of the International Union of Crystallography (IUCr2017)
  • Int'l Joint Research / Invited
• [Presentation] 塩素イオンを分子陰イオンへ置換した PSIIの結晶構造解析による阻害機構の解明 (2017)
  • Author(s): 梅名泰史，田丸翔也，沈建仁
  • Organizer: 第8回日本光合成学会年会
• [Presentation] 光化学系IIと阻害剤アジ化物イオンとの共結晶化とX線結晶構造解析 (2016)
  • Author(s): 田丸 翔也, 梅名 泰史, 沈 建仁
  • Organizer: 第54回日本生物物理学会年会
  • Place of Presentation: つくば、茨城（ポスター）
  • Year and Date: 2016-11-25
• [Presentation] 活性阻害剤アジ化物イオンが結合した光化学系 II 蛋白質の X 線結晶構造解析 (2016)
  • Author(s): 梅名泰史・田丸翔也・沈建仁
  • Organizer: 日本結晶学会平成28年度年会
  • Place of Presentation: 水戸、茨城（ポスター）
  • Year and Date: 2016-11-17
• [Presentation] 光化学系IIタンパク質における混合原子価Mn4CaO5クラスターの結晶構造解析 (2016)
  • Author(s): 梅名泰史, 川上恵典, 神谷信夫, 沈建仁
  • Organizer: 第55回電子スピンサイエンス学会年会
  • Place of Presentation: 大阪市立大学、大阪
  • Year and Date: 2016-11-10
  • Invited
• [Presentation] Crystallographic studies of the valence of four Mn atoms in photosystem II using anomalous diffraction technique (2016)
  • Author(s): Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen
  • Organizer: The 42nd Naito Conference
  • Place of Presentation: 札幌、北海道（ポスター）
  • Year and Date: 2016-10-04
• [Presentation] Estimation of valences and radiation damage of four Mn atoms in photosystem II crystals using anomalous diffraction analysis (2016)
  • Author(s): Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen
  • Organizer: The 12th International Conference on Biology and Synchrotron Radiation (BSR 2016)
  • Place of Presentation: Menlo Park, CA, USA
  • Year and Date: 2016-08-21
  • Int'l Joint Research
• [Presentation] Crystal structure of the oxygen evolving photosystem II in the intermediate state revealed by femtosecond X-ray free electron lasers (2016)
  • Author(s): M. Suga, F. Akita, M. Kubo, Y. Nakajima, K. Yamashita, T. Nakane, M. Nakabayashi, Y. Umena, M. Suzuki, E. Nango, R. Tanaka, S. Inoue, T. Masuda, K. Tono, T. Kimura, Y. Joti, M. Yamamoto, O. Nureki, M. Yabashi, T. Ishikawa, S.o Iwata, M. Sugawara, J.-R Shen
  • Organizer: The 17th International Congress on Photosynthesis Research
  • Place of Presentation: Maastricht, Netherland
  • Year and Date: 2016-08-07
  • Int'l Joint Research
• [Presentation] Valences and radiation damage of four Mn atoms in photosystem II crystals revealed by anomalous diffraction analysis (2016)
  • Author(s): Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen,
  • Organizer: The 17th International Congress on Photosynthesis Research
  • Place of Presentation: Maastricht, Netherland（ポスター）
  • Year and Date: 2016-08-07
  • Int'l Joint Research
• [Presentation] Crystal structure analysis of photosystem II complex from an SQDG-deficient mutant of Thermosynechococcus elongatu (2016)
  • Author(s): Y. Nakajma, Y. Umena, K. Endo, H. Wada, J.-R. Shen
  • Organizer: The 17th International Congress on Photosynthesis Research
  • Place of Presentation: Maastricht, Netherland（ポスター）
  • Year and Date: 2016-08-07
  • Int'l Joint Research
• [Presentation] X-ray crystallographic studies of active sites in oxygen-evolving photosystem II (2016)
  • Author(s): Y. Umena
  • Organizer: 13th International Workshop on Supermolecular Nanoscience of Chemically Programmed Pigment (SNCPP13)
  • Place of Presentation: Ritsumeikan University, Shiga, Japan
  • Year and Date: 2016-06-17
  • Int'l Joint Research / Invited
• [Presentation] スルフォキノボシルジアシルグリセロール欠損T.elongatus変異体由来PSⅡ複合体ダイマーの結晶構造 (2016)
  • Author(s): 中島芳樹、梅名泰史、遠藤嘉一郎、和田元、沈建仁
  • Organizer: 第７回日本光合成学会年会
  • Place of Presentation: 東京理科大学、日本（ポスター）
  • Year and Date: 2016-05-27
• [Presentation] 光化学系IIの４つのMnの価数とＸ線による還元作用の検証 (2016)
  • Author(s): 梅名泰史、川上恵典、神谷信夫、沈建仁
  • Organizer: 第７回日本光合成学会年会
  • Place of Presentation: 東京理科大学、日本（ポスター）
  • Year and Date: 2016-05-27
• [Presentation] X-ray crystal structure and functional alteration of PsbZ-deleted photosystem II (2016)
  • Author(s): Yuri Kitashita, Kouhei Ueda, Keisuke Kawakami, Tomoyasu Noji, Yasufumi Umena, Masako Iwai, Masahiko Ikeuchi, Jian-Ren Shen, Nobuo Kamiya
  • Organizer: 第57回日本植物生理学会年会
  • Place of Presentation: 岩手、日本（ポスター）
  • Year and Date: 2016-03-18
• [Presentation] Crystallographic study for estimation of the valence of four Mn atoms in oxygen-evolving Photosystem II using anomalous absorption techniques (2016)
  • Author(s): Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya (Invited)
  • Organizer: 7th OCARINA Annual International Meeting
  • Place of Presentation: Osaka City University, Osaka, Japan
  • Year and Date: 2016-03-17
  • Int'l Joint Research / Invited
• [Presentation] Estimation of the valences and radiation damage of four Mn atoms in photosystem II crystals using anomalous diffraction techniques (2016)
  • Author(s): Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya
  • Organizer: 9th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
  • Place of Presentation: Lund, Sweden
  • Year and Date: 2016-03-09
  • Int'l Joint Research / Invited
• [Presentation] ヨウ素イオンによるシアノバクテリア由来光化学系IIの酸素発生阻害機構 (2015)
  • Author(s): 川上恵典，萩原大介, 梅名泰史, 福島佳優, 伊藤亮孝, 手木芳男, 沈建仁, 神谷信夫
  • Organizer: 日本結晶学会2015年度年会
  • Place of Presentation: 大阪、日本（口頭発表）
  • Year and Date: 2015-10-17
  • Invited
• [Presentation] 光化学系II のMn4CaO5クラスターにおけるX線還元と吸収端波長X線結晶構造解析 (2015)
  • Author(s): 梅名泰史, 川上恵典, 沈建仁 ,神谷信夫
  • Organizer: 日本結晶学会2015年度年会
  • Place of Presentation: 大阪、日本（口頭発表）
  • Year and Date: 2015-10-17
  • Invited
• [Presentation] Proton transfer mechanisms of photosystem II: Hybrid ab inito quantum mechanics study (2015)
  • Author(s): A. Nakamura, J. Kang, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya, M. Tateno
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 金沢、日本、（ポスター）
  • Year and Date: 2015-09-13
• [Presentation] Proton transfer mechanisms of photosystem II: Hybrid ab inito quantum mechanics study (2015)
  • Author(s): Atsushi Nakamura, Jiyong Kang, Yasufumi Umena, Keisuke Kawakami, Shen Jian-Ren, Nobuo Kamiya, and Masaru Tateno
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 金沢、日本
  • Year and Date: 2015-09-13
• [Presentation] Crystallographic study for estimation of the valence of four Mn atoms in oxygen-evolving Photosystem II using anomalous absorption techniques (2015)
  • Author(s): Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya
  • Organizer: The 65th Annual Meeting of the American Crystallographic Association
  • Place of Presentation: Philadelphia, USA（口頭発表）
  • Year and Date: 2015-07-25
  • Int'l Joint Research / Invited
• [Presentation] Crystal mounting method using humid air and hydrophilic glue coating for ambient and cryogenic experiments (2015)
  • Author(s): T. Kumasaka, S. Baba, N. Yagi, Y. Umena, N. Kamiya, F. Shima, T. Kataoka, M. Yamamoto
  • Organizer: The 65th Annual Meeting of the American Crystallographic Association
  • Place of Presentation: Philadelphia, USA（口頭発表）
  • Year and Date: 2015-07-25
  • Invited
• [Presentation] Crystallographic study for estimation of the valence of four Mn atoms in Photosystem II using anomalous absorption techniques (2015)
  • Author(s): Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya
  • Organizer: Symposium "Metals in Biology"
  • Place of Presentation: 和光理研、埼玉、日本、（ポスター）
  • Year and Date: 2015-06-16
  • Int'l Joint Research
• [Presentation] 光化学系IIの酸素発生中心Mn4CaO5クラスターの吸収端波長Ｘ線結晶構造解析 (2015)
  • Author(s): 梅名泰史, 川上恵典, 沈建仁, 神谷信夫
  • Organizer: 第6回日本光合成学会年会
  • Place of Presentation: 岡山、日本（ポスター）
  • Year and Date: 2015-05-22