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

• Project Area: Dynamical 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 Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: University 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: ¥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。

Research Products

• [Journal Article] Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach (2018)
  • Author(s): Yoshida Norio、Higashi Masahiro、Motoki Hideyoshi、Hirota Shun
  • Journal Title: The Journal of Chemical Physics Volume: 148 Issue: 2 Pages: 025102-025102
  • DOI: 10.1063/1.5009785
  • 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: Journal of Computer Chemistry, Japan Volume: 17 Issue: 1 Pages: 8-13
  • DOI: 10.2477/jccj.2018-0006
  • NAID: 130006528632
  • ISSN: 1347-1767, 1347-3824
  • Peer Reviewed / Open Access
• [Journal Article] Structural properties determining low K+affinity of the selectivity filter in the TWIK1 K+channel (2018)
  • Author(s): Tsukamoto Hisao、Higashi Masahiro、Motoki Hideyoshi、Watanabe Hiroki、Ganser Christian、Nakajo Koichi、Kubo Yoshihiro、Uchihashi Takayuki、Furutani Yuji
  • Journal Title: Journal of Biological Chemistry Volume: 293 Issue: 18 Pages: 6969-6984
  • DOI: 10.1074/jbc.ra118.001817
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Theoretical approaches for dynamical ordering of biomolecular systems (2018)
  • Author(s): Okumura Hisashi、Higashi Masahiro、Yoshida Yuichiro、Sato Hirofumi、Akiyama Ryo
  • Journal Title: Biochimica et Biophysica Acta(BBA) - General Subjects Volume: 1862 Issue: 2 Pages: 212-228
  • DOI: 10.1016/j.bbagen.2017.10.001
  • Peer Reviewed
• [Journal Article] Cinchona-Based Primary Amine Catalyzed a Proximal Functionalization of Dienamines: Asymmetric α-Fluorination of α-Branched Enals (2017)
  • Author(s): Arimitsu Satoru、Yonamine Tsunaki、Higashi Masahiro
  • Journal Title: ACS Catalysis Volume: 7 Issue: 7 Pages: 4736-4740
  • DOI: 10.1021/acscatal.7b01178
  • Peer Reviewed
• [Journal Article] Two Furanosesterterpenoids from the Sponge Luffariella variabilis (2017)
  • Author(s): Ahmadi Peni、Higashi Masahiro、Voogd Nicole J. de、Tanaka Junichi
  • Journal Title: Marine Drugs Volume: 15 Issue: 8 Pages: 249-249
  • DOI: 10.3390/md15080249
  • 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: Marine Drugs Volume: 15 Issue: 4 Pages: 117-117
  • DOI: 10.3390/md15040117
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Theoretical Study on Photoexcitation Dynamics of a Bis-diimine Cu(I) Complex in Solutions (2017)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] The ion-dependence of carbohydrate binding of CBM36: MD and 3D-RISM study (2016)
  • Author(s): Shoichi Tanimoto, Masahiro Higashi, Norio Yoshida, Haruyuki Nakano
  • Journal Title: Journal of Physics: Condensed Matter Volume: 28 Issue: 34 Pages: 344005-344005
  • DOI: 10.1088/0953-8984/28/34/344005
  • 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 Point (2016)
  • Author(s): K. Watanabe, N. Nakatani, A. Nakayama, M. Higashi, and J. Hasegawa
  • Journal Title: Inorg. Chem. Volume: 55 Issue: 16 Pages: 8082-8090
  • DOI: 10.1021/acs.inorgchem.6b01187
  • 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 surface (2016)
  • Author(s): Masahiro Higashi, Shinji Saito
  • Journal Title: Journal of Chemical Theory and Computation Volume: 12 Issue: 8 Pages: 4128-4137
  • DOI: 10.1021/acs.jctc.6b00516
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] One-pot synthesis and theoretical calculation for trifluoromethylated pyrrolizidines by 1,3-dipolar cycloaddition with azomethine ylides and β-trifluoromethyl acrylamides (2016)
  • 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
  • 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
  • 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 surface (2018)
  • Author(s): Masahiro Higashi, Shinji Saito
  • Organizer: 255 th ACS National Meeting & Exposition
  • Int'l Joint Research
• [Presentation] Anion Effects on the Dimer Stability of Cytochrome c Revealed by MD Simulation and 3D-RISM Theory (2018)
  • 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
  • Int'l Joint Research
• [Presentation] Theoretical Study on Correlation between Ion Selectivity and IR Spectrum of Ion Channels (2018)
  • 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
  • Int'l Joint Research
• [Presentation] Anion effects on oligomer formation of cytochrome c with MD simulation and 3D-RISM theory (2018)
  • Author(s): Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
  • Organizer: 255th ACS National Meeting & Exposition
  • Int'l Joint Research
• [Presentation] Theoretical investigation of excited states of pigments in the light-harvesting antenna (2017)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Theoretical understanding of the self-organization process of the light-harvesting B820 subunits (2017)
  • 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
  • Int'l Joint Research
• [Presentation] Theoretical analysis of regio- and stereoselectivity of new organic reactions (2017)
  • Author(s): Masahiro Higashi
  • Organizer: International Symposium on Pure & Applied Chemistry 2017
  • Int'l Joint Research / Invited
• [Presentation] Theoretical investigation of excited-state reactions and properties in condensed phases (2017)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Toward quantitative understanding of excitation energy transfer in light-harvesting complexes (2017)
  • Author(s): Masahiro Higashi
  • Organizer: The 9th Conference of the Asian Consortium on Computational Materials Science
  • 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
  • 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
  • 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
• [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
• [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
• [Presentation] Theoretical study on domain-swapped oligomer formation of cytochrome c (2017)
  • 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
  • Int'l Joint Research
• [Presentation] MD and 3D-RISM Study on the Domain-Swapped Cytochrome c Oligomer (2017)
  • Author(s): Hideyoshi Motoki, Norio Yoshida, Shun Hirota, Masahiro Higashi
  • Organizer: The 9th Conference of the Asian Consortium on Computational Materials Science
  • 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
• [Presentation] Theoretical study of the self- organization process of the light-harvesting complexes with molecular dynamics simulation (2016)
  • 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
• [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
  • Invited
• [Presentation] Theoretical analysis of site energies and their fluctuations of pigments in the light-harvesting antenna (2016)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Theoretical study on the self-organization process of light-harvesting complexes with molecular dynamics simulations (2016)
  • 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
  • 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