Theoretical investigation of excitation energy transfer in biomolecular systems with molecular simulation

• Project/Area Number: 26810008
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Physical chemistry
• Research Institution: University of the Ryukyus
• Principal Investigator: HIGASHI Masahiro 琉球大学, 理学部, 助教 (20611479)
• Research Collaborator: SAITO Shinji 分子科学研究所, 理論・計算分子科学研究領域 理論分子科学第一研究部門, 教授
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2017: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 励起エネルギー移動 / 光捕集複合体 / 分子シミュレーション / 理論解析 / EETダイナミクス / 理論化学 / 光捕集アンテナ / 分子動力学シミュレーション / FMOタンパク / 励起子相互作用 / MDシミュレーション

Outline of Final Research Achievements

Our purpose is to investigate the roles of protein structures and fluctuations on the efficient light-energy transfer in light-harvesting antennas by developing efficient methods combining quantum chemical method and molecular dynamics simulation. We developed a method for analyzing excitation energies and their fluctuations of pigments in the light-harvesting antennas. By using the method, we succeeded in reproducing excitation energies and their fluctuations of seven pigments in the light-harvesting FMO protein. We also developed a method for analyzing exciton couplings and their fluctuations between pigments.

Research Products

• [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
• [Journal Article] Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment (2014)
  • Author(s): Masahiro Higashi, Takahiro Kosugi, Shigehiko Hayashi, and Shinji Saito
  • Journal Title: Journal of Physical Chemistry B Volume: 118 Issue: 37 Pages: 10906-10918
  • DOI: 10.1021/jp507259g
  • Peer Reviewed
• [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] Quantitative Analysis of Site Energies and Their Fluctuations of Pigments in the FMO Complex (2017)
  • Author(s): Masahiro Higashi, Shinji Saito
  • 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: 2017-01-22
  • Int'l Joint Research
• [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] Quantitative Analysis of Site Energies and Their Fluctuations of Pigments in the Light-Harvesting Antenna (2016)
  • Author(s): Masahiro Higashi, Shinji Saito
  • Organizer: International Symposium on Multi-scale Simulation of Condensed-phase Reacting Systems
  • Place of Presentation: Nagoya University (Nagoya, Japan)
  • Year and Date: 2016-10-11
  • Int'l Joint Research
• [Presentation] Quantitative Analysis of Site Energies and Their Fluctuations of Pigments in the Light-Harvesting Antenna (2016)
  • Author(s): Masahiro Higashi, Shinji Saito
  • Organizer: 52nd Symposium on Theoretical Chemistry
  • Place of Presentation: Ruhr University Bochum (Bochum, Germany)
  • Year and Date: 2016-09-26
  • Int'l Joint Research
• [Presentation] 光捕集複合体FMOタンパク 中の色素の励起状態に関する理論的研究 (2016)
  • Author(s): 東 雅大，斉藤 真司
  • 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: 2016-09-13
• [Presentation] 分子シミュレーションによる光捕集アンテナ中の色素の励起状態の理論的解明 (2016)
  • Author(s): 東 雅大，斉藤 真司
  • Organizer: 第19回理論化学討論会
  • Place of Presentation: 早稲田大学西早稲田キャンパス（東京都新宿区）
  • Year and Date: 2016-05-25
• [Presentation] 分子シミュレーションによる光捕集アンテナ中の色素の励起状態の理論的解明 (2016)
  • Author(s): 東 雅大，斉藤 真司
  • Organizer: 第19回 理論化学討論会
  • Place of Presentation: 東京
  • Year and Date: 2016-05-23
• [Presentation] 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理論的解明 (2016)
  • Author(s): 東 雅大，斉藤 真司
  • Organizer: 日本化学会第96春季年会
  • Place of Presentation: 京都
  • Year and Date: 2016-03-24
• [Presentation] Toward quantitative analysis of excitation energy transfer in light-harvesting antennas (2015)
  • Author(s): Masahiro Higashi
  • Organizer: Pacifichem 2015
  • Place of Presentation: Honolulu, HI, USA
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] 分子シミュレーション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導出と解析 (2015)
  • Author(s): 東 雅大，斉藤 真司
  • Organizer: 第9回分子科学討論会2015東京
  • Place of Presentation: 東京
  • Year and Date: 2015-09-16
• [Presentation] Toward molecular understanding of excitation energy transfer in light-harvesting antennas (2015)
  • Author(s): Masahiro Higashi
  • Organizer: Asian International Symposium -Interplay between Theory and Experiment in Physical Chemistry-
  • Place of Presentation: Chiba, Japan
  • Year and Date: 2015-03-27
  • Invited
• [Presentation] 揺らぎを露わに考慮可能な計算手法による凝縮相中の化学反応の理論的解明 (2015)
  • Author(s): 東 雅大
  • Organizer: 日本化学会第95春季年会（2015），若い世代の特別講演会
  • Place of Presentation: 千葉
  • Year and Date: 2015-03-26 – 2015-03-29
• [Presentation] 光捕集アンテナにおける励起エネルギー移動ダイナミクスの分子論的理解を目指して (2015)
  • Author(s): 東 雅大
  • Organizer: 理研シンポジウム「生体分子系量子化学計算の最前線」
  • Place of Presentation: 埼玉
  • Year and Date: 2015-01-22 – 2015-01-23
  • Invited
• [Presentation] 光捕集アンテナにおける色素の励起エネルギーの揺らぎに関する理論的研究 (2014)
  • Author(s): 東 雅大，斉藤 真司
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] Theoretical studies on excitation energy fluctuations of pigments in a light-harvesting complex (2014)
  • Author(s): Masahiro HIgashi and Shinji Saito
  • Organizer: 248th ACS National Meeting
  • Place of Presentation: San Francisco, CA, USA
  • Year and Date: 2014-08-10 – 2014-08-14
• [Presentation] 分子シミュレーションによる凝縮相中の励起状態反応ダイナミクスの定量的理解を目指して (2014)
  • Author(s): 東 雅大
  • Organizer: 第344回触媒化学研究センターコロキウム
  • Place of Presentation: 札幌
  • Year and Date: 2014-05-12
  • Invited