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Theoretical Study on Catalytic Mechanism of Metalloenzyme including Manganese Ions at Active Site

Research Project

Project/Area Number 22550010
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionMie University

Principal Investigator

YOSHIOKA Yasunori  三重大学, 大学院・工学研究科, 教授 (00291451)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2012: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2010: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords生物物理科学 / 金属酵素 / マンガンイオン / 酸素発生複合体 / Mn/Fe2核系 / 光化学系II / ホスファターゼ / B3LYP / 自然軌道解析 / Mn/Fe2核系 / リボヌクレオチド還元酵素 / 光科学系II
Research Abstract

Oxygen-Evolving Complex (OEC), which is one of metalloenzymes including manganese ions at active site, catalyzes four-electron oxidation of two water molecules to give oxygen. The catalytic mechanism of OEC is unclear and has been investigated intensively based on theoretical and experimental viewpoints. We have determined the molecular and electronic structures of five oxidative states, S0, S1, S2, S3,and S4 proposed as Kok cycle using theoretical study. We have also proposed the catalyticmechanism. It is expected that our results will be basis to develop a new unit producing oxygen and hydrogen as next-generation energy.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (51 results)

All 2013 2012 2011 2010

All Journal Article (16 results) (of which Peer Reviewed: 16 results) Presentation (35 results)

  • [Journal Article] Theoretical Study on the Mechanism of Dioxygen Evolution in Photosystem II. I. Molecular and Electronic Structures at the S0, S1, and S2 States of Oxygen-Evolving Complex2013

    • Author(s)
      T. Ichino and Y. Yoshioka
    • Journal Title

      Bull. Chem. Soc. Jpn

      Volume: 86 Issue: 4 Pages: 479-491

    • DOI

      10.1246/bcsj.20120223

    • NAID

      10031162154

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Nature of chemical bonds of the CaMn4O5cluster in oxygen evolving complex of photosystem II. Jahn-Teller distortion and its suppression by Ca doping in cubane structures2013

    • Author(s)
      K. Yamaguchi, S. Yamanaka, H. Isobe, T. Saito, K. Kanda, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura, H. Nakamura, M. Shoji and Y. Yoshioka
    • Journal Title

      Internat. J. Quantum Chem

      Volume: 113 Issue: 4 Pages: 453-473

    • DOI

      10.1002/qua.24280

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Which oxidation state is preferable at S0 state in oxygen-evolving complex2012

    • Author(s)
      T. Ichino and Y. Yoshioka
    • Journal Title

      Chem. Phys. Lett.

      Volume: 545 Pages: 107-111

    • DOI

      10.1016/j.cplett.2012.07.029

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A B3LYP Study on Electronic structures of [(X)_mMn(m-oxo)_2 Mn(Y)_n]q+ (X, Y = H_2 O, OH and O) as a Mn cluster model of OEC2012

    • Author(s)
      M. Katsuda, E. Hishikawa, M. Mitani and Y.Yoshioka
    • Journal Title

      J. Biophys. Chem.

      Volume: 3 Pages: 111-126

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Effectiveness of optimizing geometry for CaMn4O5 cluster at 1.9 A resolved OEC and proposal for oxidation mechanism from S0 to S3 states2012

    • Author(s)
      T. Ichino, K. Yamaguchi and Y. Yoshioka
    • Journal Title

      Chem. Lett

      Volume: 41 Issue: 1 Pages: 18-20

    • DOI

      10.1246/cl.2012.18

    • NAID

      130004426307

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathway Revealed for CaMn4O5 Cluster of PSII Refined to 1.9 A X-Ray Resolution2012

    • Author(s)
      T. Saito, S. Yamanaka, K. Kanda, H. Isobe, Y. Takano, Y. Shigeta, Y. Umeda, K. Kawakami, J.-R. Shen, N. Kamiya, M. Okumura, M. Shoji, Y. Yoshioka and K. Yamaguchi
    • Journal Title

      Internat. J. Quantum. Chem

      Volume: 112 Pages: 253-276

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A B3LYP Study on Electronic structures of [(X)mMn(-oxo)2Mn(Y)n]q+ (X, Y = H2O, OH and O) as a Mn cluster model of OEC2012

    • Author(s)
      M. Katsuda, E. Hishikawa, M. Mitani and Y. Yoshioka
    • Journal Title

      J. Biophys. Chem.

      Volume: 3 Pages: 111-126

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Numerical integration of atomic electron density with double exponential formula for density functional calculation2012

    • Author(s)
      M. Mitani and Y. Yoshioka
    • Journal Title

      Theoret. Chem. Acc.

      Volume: 131 Issue: 3

    • DOI

      10.1007/s00214-012-1169-z

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A B3LYP study on electronic structures of [(X)_mMn(μ-oxo)_2Mn(Y)_n]^<q+> (X,Y=H_2O, OH and O) as a Mn cluster model of OEC2012

    • Author(s)
      M.Katsuda, E.Hishikawa, M.Mitani, Y.Yoshioka
    • Journal Title

      J.Biophys.Chem.

      Volume: (印刷中)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Numerical integration of atomic electron density with double exponential formula for density functional calculation2012

    • Author(s)
      M.Mitani, Y.Yoshioka
    • Journal Title

      Theor.Chem.Acta

      Volume: 131(印刷中)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathway Revealed for CaMn_4O_5 Cluster of PSII Refined to 1.9 Å X-Ray Resolution2012

    • Author(s)
      T.Saito, S.Yamanaka, K.Kanda, H.Isobe, Y.Takano, Y.Shigeta, Y.Umeda, K.Kawakami, J.-R.Shen, N.Kamiya, M.Okumura, M.Shoji, Y.Yoshioka, K.Yamaguchi
    • Journal Title

      Internat.J.Quantum.Chem.

      Volume: 112 Pages: 253-276

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A B3LYP Study on repair of guanyl and 8-oxoguanyl radical by simultaneous proton- and electron-transfer reaction2011

    • Author(s)
      M.Yamamura, T.Ichino, Y.Yoshioka
    • Journal Title

      Bull.Chem.Soc.Jpn.

      Volume: 84 Pages: 181-190

    • NAID

      10027814087

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] B3 LYP Study on Reduction Mechanisms from O2 to H2O at the Active Site of Fully Reduced and Mixed-Vale nce Bovine Cytochrome cOxidases2010

    • Author(s)
      Y. Yoshioka and M. Mitani
    • Journal Title

      Bioinorg. Chem. Appl

      Volume: Volume 2010 Issue: 1 Pages: 18-18

    • DOI

      10.1155/2010/182804

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of electronic structures of [(H_2O)_3(O-)Mn(m-oxo)_2Mn(OH_2)_4]q+(q = 2 or 3) with Mn-O bond2010

    • Author(s)
      M. Katsuda, E. Hishikawa, M. Mitani and Y. Yoshioka
    • Journal Title

      Phys. Chem. Chem. Phys

      Volume: 12 Pages: 2730-2739

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of electronic structures of [(H_2O)_3(O-)Mn(μ-oxo)_2Mn(O-H_2))4]^<q+> (q=2 or 3) with M-O bond2010

    • Author(s)
      M.Katsuda, E.Hishikawa, M.Mitani, Y.Yoshioka
    • Journal Title

      Phys.Chem.Chem.Phys.

      Volume: 12 Pages: 2730-2739

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] B3LYP Study on reduction mechanisms from O_2 to H_2O at the active site of fully reduced and mixed-valence bovine cytochrome c oxidase2010

    • Author(s)
      Y.Yoshioka, M.Mitani
    • Journal Title

      Bioinorg.Chem.Appl.

      Volume: 2010

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] OECのS2からS3状態遷移での一電子酸化およびプロトン移動に関する理論的研究2013

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第93 春季年会, 1PA-092
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス, 草津
    • Related Report
      2012 Final Research Report
  • [Presentation] 16個の水分子を考慮したKcsAカリウムチャンネルの金属イオン水和構造に関する密度汎関数計算2013

    • Author(s)
      伊藤瑞紀, 伊藤駿, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第93春季年会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] OECのS2からS3状態遷移での一電子酸化およびプロトン移動に関する理論的研究2013

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第93春季年会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] 密度汎関数計算によるEcClC対向輸送体のプロトン輸送経路の対するモデル系の検討2013

    • Author(s)
      三谷昌輝, 秋山由衣, 吉岡泰規
    • Organizer
      日本化学会第93春季年会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] Theoretical study on mechanism of water oxidation from S0 to S3 states catalyzed by OEC2012

    • Author(s)
      T. Ichino M. Mitani, Y. Yoshioka
    • Organizer
      International Symposium for Sustainability by Engineering at MIU, EP-29
    • Place of Presentation
      Mie University, Tsu, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] OECによるS_0からS_4状態までの水分子酸化機構に関する理論的研究2012

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      第6回分子科学討論会2012東京
    • Place of Presentation
      東京大学本郷キャンパス, 東京
    • Related Report
      2012 Final Research Report
  • [Presentation] OECによるS_0からS_3状態までの水分子酸化機構に関する理論的研究2012

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス, 横浜
    • Related Report
      2012 Final Research Report
  • [Presentation] ホスファターゼ(PAP)とリン酸エステルおよびリン酸との複合体の電子状態に関する理論的研究2012

    • Author(s)
      清水智也, 市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      第43回中部化学関係学協会支部連合秋季大会
    • Place of Presentation
      名古屋工業大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] OECによるS0からS4状態までの水分子酸化機構に関する理論的研究2012

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      第6回分子科学討論会2012東京
    • Place of Presentation
      東京大学本郷キャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] 密度汎関数計算による第2水和殻を考慮したKcsAカリウムチャンネルの金属イオン水和構造の検討2012

    • Author(s)
      伊藤瑞紀, 三谷昌輝, 吉岡泰規
    • Organizer
      第6回分子科学討論会2012東京
    • Place of Presentation
      東京大学本郷キャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] 二重指数関数型公式による2原子分子の電子密度の数値積分2012

    • Author(s)
      三谷昌輝, 吉岡泰規
    • Organizer
      第6回分子科学討論会2012東京
    • Place of Presentation
      東京大学本郷キャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] 二重指数関数型公式による原子の電子密度の数値積分2012

    • Author(s)
      三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] 12個の水分子を考慮したKcsAカリウムチャンネルの金属イオン水和構造に関する密度汎関数計算2012

    • Author(s)
      伊藤瑞紀, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] ホスファターゼ(PAP)とリン酸エステル複合体の電子状態と安定性に関する理論化学計算2012

    • Author(s)
      吉岡泰規, 市野智也, 三谷昌輝
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mn/Fe2核系RNRの2電子酸化機能に関する理論化学計算2012

    • Author(s)
      清水智也, 市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] OECによるS_0からS_3状態までの水分子酸化機構に関する理論的研究2012

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第92春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mn/Fe2核系RNRの酸化還元状態の電子状態に関する理論化学計算2011

    • Author(s)
      吉岡泰規, 三谷昌輝
    • Organizer
      分子科学討論会2011
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2011-09-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] OECの高解像度X線構造におけるCaMn_4O_5クラスターの電子状態に対する構造最適化の効果2011

    • Author(s)
      市野智也, 吉岡泰規
    • Organizer
      分子科学討論会2011
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2011-09-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] KcsAカリウムチャンネルの金属イオン水和構造に関する密度汎関数計算2011

    • Author(s)
      三谷昌輝, 杉本知美, 吉岡泰規
    • Organizer
      分子科学討論会2011
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2011-09-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] S_0からS_1状態への遷移に対するOECの反応活性部位と電子状態に関する理論化学計算2011

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス
    • Year and Date
      2011-03-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Mn/Fe2核系RNRの活性部位の分子構造と電子状態に関する理論化学計算2011

    • Author(s)
      吉岡泰規, 三谷昌輝
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス
    • Year and Date
      2011-03-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] 密度汎関数計算によるKcsAカリウムチャンネルのキャビティーにおける金属イオン水和構造の検討2011

    • Author(s)
      三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス
    • Year and Date
      2011-03-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Theoretical Study on Electronic Structures at S0 and S1 States of the OEC in Photosystem II2011

    • Author(s)
      T. Ichino, Y. Yoshioka
    • Organizer
      International Symposium for Sustainability by Engineering at MIU
    • Place of Presentation
      Mie University, Tsu, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] OECの高解像度X線構造におけるCaMn_4O_5 クラスターの電子状態に対する構造最適化の効果2011

    • Author(s)
      市野智也, 吉岡泰規
    • Organizer
      分子科学討論会2011 札幌
    • Place of Presentation
      札幌コンベンションセンター, 札幌
    • Related Report
      2012 Final Research Report
  • [Presentation] Development of Broken Symmetry Methods-Application to the CaMn_4O_5 Cluster at OEC of PSII Refined to 1.9 AX-Ray Resolution-2011

    • Author(s)
      K. Kanda, S. Yamanaka, T. Saito, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, Y. Yoshioka, K. Yamaguchi
    • Organizer
      7-th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
    • Place of Presentation
      Waseda University, Tokyo, Japan.
    • Related Report
      2012 Final Research Report
  • [Presentation] Theoretical Study on Intermediates from S0to S1 States of OEC in Photosystem II2011

    • Author(s)
      Y. Yoshioka, T. Ichino, and M. Mitani
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemist (WATOC 2011)
    • Place of Presentation
      University of Santiago, Santiago de Compostela, Spin
    • Related Report
      2012 Final Research Report
  • [Presentation] S_0からS1状態への遷移に対するOECの反応活性部位と電子状態に関する理論化学計算2011

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      日本化学会第91 春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス, 横浜
    • Related Report
      2012 Final Research Report
  • [Presentation] Theoretical Study on Intermediates from S_0 to S_1 States of OEC in Photosystem II2011

    • Author(s)
      Y.Yoshioka, T.Ichino, M.Mitani
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemist (WATOC 2011)
    • Place of Presentation
      University of Santiago, Santiago de Compostela, Spin
    • Related Report
      2011 Annual Research Report
  • [Presentation] A B3LYP Study on Hydration of K^+ and Na^+ ions in the Cavity of the KcsA Potassiun Channel2011

    • Author(s)
      M.Mitani, T.Sugimoto, Y.Yoshioka
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemist (WATOC 2011)
    • Place of Presentation
      University of Santiago, Santiago de Compostela, Spin
    • Related Report
      2011 Annual Research Report
  • [Presentation] Development of Broken Symmetry Methods-Application to the CaMn_4O_5 Cluster at OEC of PSII Refined to 1.9 Å X-Ray Resolution2011

    • Author(s)
      K.Kanda, S.Yamanaka, T.Saito, Y.Umena, K.Kawakami, J.R.Shen, N.Kamiya, M.Okumura, Y.Yoshioka, K.Yamaguchi
    • Organizer
      7-th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
    • Place of Presentation
      Waseda University, Tokyo, Japan
    • Related Report
      2011 Annual Research Report
  • [Presentation] Theoretical Study on Electronic Structures at S_0 and S_1 States of the OEC in Photosystem II2011

    • Author(s)
      T.Ichino, Y.Yoshioka
    • Organizer
      International Symposium for Sustainability by Engineering at MIU
    • Place of Presentation
      Mie University, Tsu, Japan
    • Related Report
      2011 Annual Research Report
  • [Presentation] KcsAカリウムチャンネルの金属イオン結合サイトに関する密度汎関数計算2010

    • Author(s)
      三谷昌輝, 吉岡泰規
    • Organizer
      分子科学討論会2010
    • Place of Presentation
      大阪大学豊中キャンパス
    • Year and Date
      2010-09-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] Mn/Fe系RNRにおける酸素分子による酵素活性化の初期状態に関する理論化学計算2010

    • Author(s)
      吉岡泰規, 徳松めぐみ, 三谷昌輝
    • Organizer
      分子科学討論会2010
    • Place of Presentation
      大阪大学豊中キャンパス
    • Year and Date
      2010-09-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] S_0およびS_1状態にあるOECの反応活性部位の構造と電子状態に関する理論化学計算2010

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      分子科学討論会2010
    • Place of Presentation
      大阪大学豊中キャンパス
    • Year and Date
      2010-09-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] S_0およびS1状態にあるOECの反応活性部位の構造と電子状態に関する理論化学計算",分子科学討論会20102010

    • Author(s)
      市野智也, 三谷昌輝, 吉岡泰規
    • Organizer
      分子科学討論会2010
    • Place of Presentation
      大阪大学豊中キャンパス, 豊中
    • Related Report
      2012 Final Research Report

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Published: 2010-11-30   Modified: 2019-07-29  

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