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Theoretical investigation on self-organization and function of light-harvesting complexes

Publicly

Project AreaDynamical ordering of biomolecular systems for creation of integrated functions
Project/Area Number 16H00778
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionUniversity of the Ryukyus

Principal Investigator

東 雅大  琉球大学, 理学部, 助教 (20611479)

Project Period (FY) 2016-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2017: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2016: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords自己組織化 / 光捕集複合体 / MDシミュレーション / シトクロムc / ドメインスワッピング / 液体の積分方程式理論 / 機能発現 / 分子動力学シミュレーション / 励起エネルギー / 光捕集アンテナ
Outline of Annual Research Achievements

本年度は昨年度に引き続き、分子動力学シミュレーションを用いて、紅色光合成細菌の光捕集複合体のサブユニットB820の物性や自己組織化過程の解析を行った。昨年度に開発した、静電相互作用を減衰させた仮想的な状態を導入して結合自由エネルギーを計算する手法を様々な菌種由来のサブユニットB820に適用し、ポリペプチドの構造を壊すことなく結合自由エネルギーを計算することができた。現在、手法に由来する統計誤差の評価を行っている。また、自己組織化の過程についても引き続き解析を進めている。
また、本年度はシトクロムcのドメインスワッピング機構の解析も行った。シトクロムcは、ミトコンドリア内の呼吸に関わる反応において電子を伝達する役割を担うヘムタンパク質である。シトクロムcは、互いのC末端ヘリックスを交換するドメインスワッピングにより多量体を形成し、電子伝達の機能を失うことが知られているが、多量体形成のメカニズムは未だはっきりしていない。この多量体形成メカニズムの解明を目指して、分子動力学シミュレーションと液体の積分方程式理論を用いてシトクロムcの単量体と二量体の熱力学安定性の解析を行った。得られた計算結果は、実験とよく一致し、タンパク質の構造変化が二量体の不安定化に、また水和が二量体の安定化に寄与することを明らかにした。また、単量体と二量体の自由エネルギーの差を各残基ごとの寄与に分解にすることにより、正の電荷と負の電荷を持つ残基が、それぞれ二量体の安定化と不安定化に寄与することを明らかにした。さらに、2つのユニットをつなぐヒンジループも二量体の安定化に寄与することも明らかにしている。

Research Progress Status

29年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

29年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2017 Annual Research Report
  • 2016 Annual Research Report

Research Products

(35 results)

All 2019 2018 2017 2016

All Journal Article Presentation

  • [Journal Article] Structural properties determining low K+ affinity of the selectivity filter in the TWIK1 K+ channel.2019

    • Author(s)
      Tsukamoto Hisao、Higashi Masahiro、Motoki Hideyoshi、Watanabe Hiroki、Ganser Christian、Nakajo Koichi、Kubo Yoshihiro、Uchihashi Takayuki、Furutani Yuji
    • Journal Title

      J. Biol. Chem.

      Volume: 293 Pages: 6969-6984

    • DOI
      10.1074/jbc.ra118.001817
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Theoretical Analysis of the Domain-Swapped Dimerization of Cytochrome c: An MD and 3D-RISM Approach2018

    • Author(s)
      Norio Yoshida, Masahiro Higashi, Hideyoshi Motoki, Shun Hirota
    • Journal Title

      J. Chem. Phys.

      Volume: 148 Pages: 025102-025102

    • DOI
      10.1063/1.5009785
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Theoretical Study on Oligomerization of Cytochrome <i>c</i>2018

    • Author(s)
      根木秀佳, 吉田紀生, 廣田俊, 東雅大
    • Journal Title

      J. Comput. Chem. Jpn.

      Volume: 17 Issue: 1 Pages: 8-13

    • DOI
      10.2477/jccj.2018-0006
    • NAID
      130006528632
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Theoretical approaches for dynamical ordering of biomolecular systems2018

    • Author(s)
      Okumura Hisashi、Higashi Masahiro、Yoshida Yuichiro、Sato Hirofumi、Akiyama Ryo
    • Journal Title

      BBA - General Subjects

      Volume: 1862 Pages: 212-228

    • DOI
      10.1016/j.bbagen.2017.10.001
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cinchona-Based Primary Amine Catalyzed a Proximal Functionalization of Dienamines: Asymmetric α-Fluorination of α-Branched Enals2017

    • Author(s)
      Arimitsu Satoru、Yonamine Tsunaki、Higashi Masahiro
    • Journal Title

      ACS Catalysis

      Volume: 7 Pages: 4736-4740

    • DOI
      10.1021/acscatal.7b01178
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Two Furanosesterterpenoids from the Sponge Luffariella variabilis2017

    • Author(s)
      Ahmadi Peni、Higashi Masahiro、Voogd Nicole J. de、Tanaka Junichi
    • Journal Title

      Marine Drugs

      Volume: 15

    • DOI
      10.3390/md15080249
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia.2017

    • Author(s)
      Idam Hermawan, Atsushi Furuta, Masahiro Higashi, Yoshihisa Fujita, Nobuyoshi Akimitsu, Atsuya Yamashita, Kohji Moriishi, Satoshi Tsuneda, Hidenori Tani, Masamichi Nakakoshi, Masayoshi Tsubuki, Yuji Sekiguchi, Naohiro Noda, Junichi Tanaka
    • Journal Title

      Mar Drugs

      Volume: 15 Pages: 117-117

    • DOI
      10.3390/md15040117
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Theoretical Study on Photoexcitation Dynamics of a Bis-diimine Cu(I) Complex in Solutions2017

    • Author(s)
      Asaka Agena, Satoru Iuchi, Masahiro Higashi
    • Journal Title

      Chemical Physics Letters

      Volume: 679 Pages: 60-65

    • DOI
      10.1016/j.cplett.2017.04.082
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The ion dependence of carbohydrate binding of CBM36: an MD and 3D-RISM study2016

    • Author(s)
      Shoichi Tanimoto, Masahiro Higashi, Norio Yoshida, Haruyuki Nakano
    • Journal Title

      J. Phys. Condens.

      Volume: 28 Pages: 344005-344005

    • DOI
      10.1088/0953-8984/28/34/344005
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Spin-blocking effect in CO and H2 binding reactions to molybdenocene and tungstenocene: a theoretical study on the reaction mechanism via the minimum energy intersystem crossing point2016

    • Author(s)
      K. Watanabe, N. Nakatani, A. Nakayama, M. Higashi, and J. Hasegawa
    • Journal Title

      Inorganic Chemistry

      Volume: 55 Pages: 8082-8090

    • DOI
      10.1021/acs.inorgchem.6b01187
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Quantitative Evaluation of Site Energies and Their Fluctuations of Pigments in the Fenna-Matthews-Olson Complex with an Efficient Method for Generating a Potential Energy Surface2016

    • Author(s)
      Masahiro Higashi, Shinji Saito
    • Journal Title

      J. Chem. Theor. Comput.

      Volume: 12 Pages: 4128-4137

    • DOI
      10.1021/acs.jctc.6b00516
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] One-pot synthesis and theoretical calculation for trifluoromethylated pyrrolizidines by 1,3-dipolar cycloaddition with azomethine ylides and beta-trifluoromethyl acrylamides2016

    • Author(s)
      Yoshiki Toma, Masataka Kunigami, K-jiro Watanabe, Masahiro Higashi, Satoru Arimitsu
    • Journal Title

      Journal of Fluorine Chemistry

      Volume: 189 Pages: 22-32

    • DOI
      10.1016/j.jfluchem.2016.07.013
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 凝縮系の励起状態反応ダイナミクスの定量的理解を目指して2018

    • Author(s)
      東雅大
    • Organizer
      第32回量子系分子科学研究セミナー
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Quantitative evaluation of site energies and their fluctuations of pigments in the light-harvesting complex with an efficient method for generating a potential energy surface2018

    • Author(s)
      Masahiro Higashi, Shinji Saito
    • Organizer
      255 th ACS National Meeting & Exposition
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Anion Effects on the Dimer Stability of Cytochrome c Revealed by MD Simulation and 3D-RISM Theory2018

    • Author(s)
      Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
    • Organizer
      新学術領域研究「動的秩序と機能」第6回国際シンポジウム
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical Study on Correlation between Ion Selectivity and IR Spectrum of Ion Channels2018

    • Author(s)
      Hideyoshi Motoki, Yuji Furutani, Masahiro Higashi
    • Organizer
      新学術領域研究「動的秩序と機能」第6回国際シンポジウム
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Anion effects on oligomer formation of cytochrome c with MD simulation and 3D-RISM theory2018

    • Author(s)
      Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
    • Organizer
      255th ACS National Meeting & Exposition
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical investigation of excited states of pigments in the light-harvesting antenna2017

    • Author(s)
      Masahiro Higashi
    • Organizer
      Kickoff To Explore The New Field Of Molecular Soft Matter
    • Place of Presentation
      Kasetsart University (Bangkok, Thailand)
    • Year and Date
      2017-03-14
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical understanding of the self-organization process of the light-harvesting B820 subunits2017

    • Author(s)
      Marie Yamauchi, Shinji Saito, Masahiro Higashi
    • Organizer
      新学術領域研究「動的秩序と機能」第5回国際シンポジウム
    • Place of Presentation
      東京大学数理科学研究棟(東京都目黒区)
    • Year and Date
      2017-01-21
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical analysis of regio- and stereoselectivity of new organic reactions2017

    • Author(s)
      Masahiro Higashi
    • Organizer
      International Symposium on Pure & Applied Chemistry 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical investigation of excited-state reactions and properties in condensed phases2017

    • Author(s)
      Masahiro Higashi
    • Organizer
      國立交通大學應用化學系106年 前瞻跨領域基礎科學中心 尖端生物分子探測 専題演講
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Toward quantitative understanding of excitation energy transfer in light-harvesting complexes2017

    • Author(s)
      Masahiro Higashi
    • Organizer
      The 9th Conference of the Asian Consortium on Computational Materials Science
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 高効率ポテンシャル関数生成手法による光捕集アンテナ中の色素の励起エネルギーの大きさと揺らぎの定量的評価2017

    • Author(s)
      東雅大
    • Organizer
      レア・イベントの計算科学
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 凝縮系の反応ダイナミクスを記述可能な計算手法の開発と応用2017

    • Author(s)
      東雅大
    • Organizer
      北大理論化学研究会:実践理論化学の最前線
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] シンコナアルカロイド触媒を用いた α,β-不飽和アルデヒドの高立体選択的フッ素化反応に関する理論的研究2017

    • Author(s)
      東雅大,喜屋武茜,亀井翔矢,與那嶺綱希,有光暁
    • Organizer
      第20回理論化学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによる光捕集複合体サブユニットB820の構造および自己組織化過程の解明2017

    • Author(s)
      山内真梨江, 斉藤真司, 東雅大
    • Organizer
      北大理論化学研究会:実践理論化学の最前線
    • Related Report
      2017 Annual Research Report
  • [Presentation] 溶液中のクロロフィルaとフィオフィチンaの励起状態に関する理論的研究2017

    • Author(s)
      水谷亮, 東雅大
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Theoretical study on domain-swapped oligomer formation of cytochrome c2017

    • Author(s)
      Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
    • Organizer
      國立交通大學應用化學系106年 前瞻跨領域基礎科學中心 尖端生物分子探測 専題演講
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MD and 3D-RISM Study on the Domain-Swapped Cytochrome c Oligomer2017

    • Author(s)
      Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
    • Organizer
      The 9th Conference of the Asian Consortium on Computational Materials Science
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MDシミュレーションと3D-RISM 理論を用いたシトクロムcの多量体形成に関する理論的研究2017

    • Author(s)
      根木秀佳,吉田紀生,廣田俊,東雅大
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Theoretical study of the self- organization process of the light-harvesting complexes with molecular dynamics simulation2016

    • Author(s)
      山内 真梨江, 斉藤 真司, 東 雅大
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-26
    • Related Report
      2016 Annual Research Report
  • [Presentation] 新規有機反応における立体・位置選択性の理論的解明2016

    • Author(s)
      東 雅大
    • Organizer
      IQCE講演会「量子化学で探る化学の最先端2016」
    • Place of Presentation
      東京大学山上会館(東京都文京区)
    • Year and Date
      2016-11-19
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Theoretical analysis of site energies and their fluctuations of pigments in the light-harvesting antenna2016

    • Author(s)
      Masahiro Higashi
    • Organizer
      The 9th Korea-Japan Seminars on Biomolecular Science
    • Place of Presentation
      Commodore Hotel Gyeongju (Gyeongju, Korea)
    • Year and Date
      2016-11-14
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical study on the self-organization process of light-harvesting complexes with molecular dynamics simulations2016

    • Author(s)
      Marie Yamauchi, Shinji Saito, Masahiro Higashi
    • Organizer
      52nd Symposium on Theoretical Chemistry
    • Place of Presentation
      Ruhr University Bochum (Bochum, Germany)
    • Year and Date
      2016-09-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 光捕集複合体サブユニットB820の構造および自己組織化過程の理論的解明2016

    • Author(s)
      山内 真梨江, 斉藤 真司, 東 雅大
    • Organizer
      第10回分子科学討論会2016神戸
    • Place of Presentation
      神戸ファッションマート(兵庫県神戸市)
    • Year and Date
      2016-09-14
    • Related Report
      2016 Annual Research Report

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Published: 2016-04-26   Modified: 2018-12-17  

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