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2015 Fiscal Year Annual Research Report

Strucuter and Photochemical Reactions of Photoactive Yellow Proteins: Generality and diversity

Research Project

Project/Area Number 24247030
Research InstitutionNara Institute of Science and Technology

Principal Investigator

片岡 幹雄  奈良先端科学技術大学院大学, その他, 理事・副学長 (30150254)

Co-Investigator(Kenkyū-buntansha) 上久保 裕生  奈良先端科学技術大学院大学, 物質創成科学研究科, 准教授 (20311128)
山崎 洋一  奈良先端科学技術大学院大学, 物質創成科学研究科, 助教 (40332770)
Project Period (FY) 2012-04-01 – 2016-03-31
Keywordsイェロープロテイン / 低障壁水素結合 / 光反応 / 結晶構造解析 / アルギニン / FTIR / キメラ蛋白質 / 国際情報交換(アメリカ、デンマーク)
Outline of Annual Research Achievements

水溶性光受容蛋白質、イェロープロテイン(PYP)、を用いて、共通の構造基盤から機能や光反応の多様性を生む分子機構を明らかにすることを目的にしている。光反応サイクルの寿命が大きく異なるhPYP、RcPYP、存在形態の異なるPprPYPについての解析を進めてきた。
PYPの構造、光反応の共通基盤として、発色団とE46の間に形成される低障壁水素結合(LBHB)と呼ばれる特殊な水素結合とLBHBの形成に共役したR52の脱プロトン化の関係を精密FTIR測定と理論計算を組み合わせて解析した。その結果、光反応におけるLBHBの解消と共役したR52のプロトン化反応機構を明らかにした。PYPの基盤となる発色団の光反応におけるLBHBの役割を見出した。
光反応サイクルの寿命が極端に長く、光反応時の構造変化も小さいRcPYPの性質を生む領域をキメラタンパク質の解析から抽出した。これらの領域は活性中心となるLBHBから比較的離れたタンパク質表面に存在し、長距離の相互作用によって吸収スペクトルや構造変化に寄与していた。この際、RcPYPの相互作用に寄与する部位としてC末端領域が抽出されたが、これは、全長Pprの光反応の解析から得られたPYPドメインの働きに通じるものと考えれた。このため、RcPYPのC末端部位の局所構造変化と相互作用を検証するため部位特異的システインプローブを用いたFTIR測定を行った。その結果、RcPYPの相互作用に伴ってC末端βシート部位での局所構造変化が見出された。多様な機能を生む部位がC末端に共通に存在していることを示した。

Research Progress Status

27年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

27年度が最終年度であるため、記入しない。

  • Research Products

    (23 results)

All 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 4 results) Presentation (14 results) (of which Int'l Joint Research: 7 results) Book (3 results)

  • [Int'l Joint Research] Aarhus university(デンマーク)

    • Country Name
      DENMARK
    • Counterpart Institution
      Aarhus university
  • [Int'l Joint Research] NIDDK,National Institutes of Health(米国)

    • Country Name
      U.S.A.
    • Counterpart Institution
      NIDDK,National Institutes of Health
  • [Journal Article] Unambiguous Determination of the Ionization State of a Photoactive Protein Active Site Arginine in Solution by NMR Spectroscopy2016

    • Author(s)
      Y. Yoshimura, N. A.Oktaviani, K.Yonezawa, H.Kamikubo, F. A. A. Mulder
    • Journal Title

      Angewandte Chemie

      Volume: 56 Pages: 239-242

    • DOI

      10.1002/anie.201609605

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] VIPP1 has a disordered C-terminal tail necessary for protecting photosynthetic membranes against stress in Arabidopsis2016

    • Author(s)
      L. Zhang, H. Kondo, H. Kamikubo, M. Kataoka, W. Sakamoto
    • Journal Title

      Plant Physiology

      Volume: 171 Pages: 1983-1995

    • DOI

      10.1104/pp.16.00532

    • Peer Reviewed / Open Access
  • [Journal Article] Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein2015

    • Author(s)
      Y. Kanematsu, H. Kamikubo, M. Kataoka, M. Tachikawa
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 14 Pages: 16-19

    • DOI

      10.1016/j.csbj.2015.10.003

    • Peer Reviewed / Open Access
  • [Journal Article] Domain-Swapped Dimer of Pseudomonas aeruginosa Cytochrome c551: Structural Insights into Domain Swapping of Cytochrome c Family Proteins.2015

    • Author(s)
      S. Nagao, M. Ueda, H. Osuka, H. Komori, H. Kamikubo, M. Kataoka, Y. Higuchi, S. Hirota
    • Journal Title

      PLoS One

      Volume: 10 Pages: e0123653

    • DOI

      10.1371/journal.pone.0123653

    • Peer Reviewed / Open Access
  • [Presentation] Analysis of amyloid formation and inhibition mechanisms of human calcitonin2016

    • Author(s)
      Chiaki Ota, Hiroko Tanaka, Yoichi Yamazaki, Mikio Kataoka, Hironari Kamikubo
    • Organizer
      The Biophycial Society 60th Annual Meeting
    • Place of Presentation
      Los Angeles, (California, USA)
    • Year and Date
      2016-02-27 – 2016-03-02
    • Int'l Joint Research
  • [Presentation] Development of auto-sampling system designed for titration-saxs to investigate protein complexes under an equilibrium condition2016

    • Author(s)
      Hironari Kamikubo, Keito Yoshida, Nobutaka Shimizu, Yoichi Yamazaki, Mikio Kataoka
    • Organizer
      The Biophycial Society 60th Annual Meeting
    • Place of Presentation
      Los Angeles, (California, USA)
    • Year and Date
      2016-02-27 – 2016-03-02
    • Int'l Joint Research
  • [Presentation] Mechanism of amyloid formation of human calcitonin2015

    • Author(s)
      Mikio Kataoka, Hironari Kamikubo
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, (Hawaii, USA)
    • Year and Date
      2015-12-15 – 2015-12-20
    • Int'l Joint Research
  • [Presentation] Femtosecond time-resolved impulsive stimulated Raman study of the primary process of photoactive yellow protein2015

    • Author(s)
      Hikaru Kuramochi, Satoshi Takeuchi, Kento Yonezawa, Hironari Kamikubo, Mikio Kataoka, Tahei Tahara
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, (Hawaii, USA)
    • Year and Date
      2015-12-15 – 2015-12-20
    • Int'l Joint Research
  • [Presentation] Picosecond photobiology: Watching a signaling protein function in real time via 150-picosecond time-resolved X-ray diffraction and solution scattering2015

    • Author(s)
      Philip Anfinrud, Friedrich Schotte, Hyun Sun Cho, John Kyndt, Hironari Kamikubo, Mikio Kataoka
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, (Hawaii, USA)
    • Year and Date
      2015-12-15 – 2015-12-20
    • Int'l Joint Research
  • [Presentation] Structural investigation of direct interaction between Shootin1 and cortactin by the titration SAXS measurements2015

    • Author(s)
      Jyunko. Makino, Keito. Yoshida, Y. Kubo, K. Baba, Y. Yamazaki, N. Inagaki, Mikio. Kataoka, Hitonari. Kamikubo
    • Organizer
      The 4th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Place of Presentation
      西新プラザ(福岡県福岡市)
    • Year and Date
      2015-11-21 – 2015-11-23
    • Int'l Joint Research
  • [Presentation] Analysis of amyloid formation and inhibition mechanisms of human calcitonin2015

    • Author(s)
      Chiaki. Ota, Hiroko. Tanaka, T. Aizawa, Yoichi. Yamazaki, Mikio. Kataoka, Hironari. Kamikubo
    • Organizer
      The 4th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Place of Presentation
      西新プラザ(福岡県福岡市)
    • Year and Date
      2015-11-21 – 2015-11-23
    • Int'l Joint Research
  • [Presentation] Analysis of interaction sites on β-scaffold region of Rhodobacter capsulatus Photoactive Yellow Protein2015

    • Author(s)
      Yoichi Yamazaki, Atsuhiro Kawamura, Mikio Kataoka, Hironari Kamikubo
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] Protonation State of Arginine 52 in Photoactive Yellow Protein2015

    • Author(s)
      Kento Yonezawa, Hironari Kamikubo, Yusuke Kanematsu, Yoichi Yamazaki, Masanori Tachikawa, Mikio Kataoka
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] Effects of chromophores of PYP - Phytochrome Related Protein on the structure2015

    • Author(s)
      Keito Yoshida, Kento Yonezawa, Yoichi Yamazaki, Mikio Kataoka, Hironari Kamikubo
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] Intramolecular interaction as a determination factor for structure elements of proteins2015

    • Author(s)
      Yuji Konno, Takeshi Inagaki, Hironari Kamikubo, Mikio Kataoka
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] Interaction/Structure analysis of GGA-Ubiquitin complex by using titration SAXS Measurement2015

    • Author(s)
      Miho Shinohara, Hironari Kamikubo, Keito Yoshida, Yoichi Yamazaki, Kazuhisa Nakayama, Soichi Wakatsuki, Mikio Kataoka
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] Structural investigation of direct interaction between Shootin1 and cortactin by the titration SAXS measurements2015

    • Author(s)
      Junko Makino, Hironari Kamikubo, Yoichi Yamazaki, Mikio Kataoka, Keito Yoshida, Naoyuki Inagaki, Yusuke Kubo, Kentarou Baba
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Presentation] The role of N-terminal region of PYP binding protein at the formation of complex with Rc-PYP2015

    • Author(s)
      Tomoyuki Yasumuro, Yoichi Yamazaki, Mikio Kataoka, Hironari Kamikubo
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13 – 2015-09-15
  • [Book] 光と生命の事典2016

    • Author(s)
      片岡幹雄
    • Total Pages
      436(354-355)
    • Publisher
      朝倉書店
  • [Book] Molecular Science of Fluctuations Toward Biological Functions2016

    • Author(s)
      F. Schotte, H.-S. Cho, H. Kamikubo, M. Kataoka
    • Total Pages
      270(65-85)
    • Publisher
      Springer
  • [Book] Molecular Science of Fluctuations Toward Biological Functions2016

    • Author(s)
      M. Kataoka
    • Total Pages
      270(151-161)
    • Publisher
      Springer

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Published: 2018-01-16   Modified: 2022-01-27  

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