Excited states of bio-molecules and their dynamics : Electronic-structure theoretical approach

• Project/Area Number: 18770130
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: Kyoto University
• Principal Investigator: HASEGAWA Jun-ya Kyoto University, 大学院工学研究科, 講師 (30322168)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥3,680,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥180,000); Fiscal Year 2008: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2007: ¥2,200,000 (Direct Cost: ¥2,200,000); Fiscal Year 2006: ¥700,000 (Direct Cost: ¥700,000)
• Keywords: 光生物学 / 励起状態理論 / QM / MM法 / SAC-CI法 / 生体分子 / 光化学 / 励起状態 / 光合成反応中心 / レチナールたんぱく質 / 蛍ルシフェラーゼ / 励起生体分子 / 電子状態理論

Research Abstract

電子励起した生体分子がどのような挙動を示すかを研究するために、励起状態のポテンシャルエネルギー面を計算する方法を整備した。巨大な蛋白質-色素複合体を計算するために、量子-古典ハイブリッド法であるQM/MM 法のプログラムを開発した。その応用として、レチナール蛋白質、ホタルルシフェラーゼなどの励起状態を計算した。その結果、ヒト色覚で見られるレチナールのスペクトル制御メカニズムやホタルの黄緑色発光の起源などを明らかにし、人工的な発光色チュ-ニングの提案などを行った。また、ヘムにおける酸素分子吸着過程を明らかにした。

Research Products

• [Journal Article] Charge-polarized coordination space for H2 adsorption (2009)
  • Author(s): J. Hasegawa, M. Higuchi, Y. Hijikata, and S. Kitagawa
  • Journal Title: Chem. Mater.
  • Peer Reviewed
• [Journal Article] Artificial Color Tuning of Firefly Luminescence : Theoretical Mutation by Tuning Electrostatic (2009)
  • Author(s): N. Nakatani, J. Hasegawa, and H. Nakatsuji
  • Journal Title: Cheni. Phys. Letters 469 Pages: 191-194
  • Peer Reviewed
• [Journal Article] Photocyclization of 2, 4, 6-Triethylbenzophenones in the Solid State (2009)
  • Author(s): Y. Ito, H. Takahashi, J. Hasegawa, and N. J. Turro
  • Journal Title: Tetrahedron 65 Pages: 677-689
  • Peer Reviewed
• [Journal Article] A multi-core QM/MM approach for the geometry optimization of chromophore aggregate in protein (2009)
  • Author(s): Y. Kiyota, J. Hasegawa, K. Fujimoto, B. Swerts, and H.
  • Journal Title: J. Comp. Chem.
  • Peer Reviewed
• [Journal Article] 分子間相互作用の解析と分子設計への展望 (2009)
  • Author(s): 長谷川淳也
  • Journal Title: 配位空間の化学-最新技術と応用-
• [Journal Article] Origin of color tuning in human red, green, and blue cone visual pigments : SAC-CI and QM/MM study (2008)
  • Author(s): K. Fujimoto, J. Hasegawa, and H. Nakatsuji
  • Journal Title: Chem. Phys. Letters 462 (4-6) Pages: 318-320
• [Journal Article] Spectral Tuning Mechanism in Photofunctional Proteins : ASAC-CI Theoretical Study (2008)
  • Author(s): L Hasegawa, K. Fujimoto, Nakatani, H. Nakatsuji
  • Journal Title: Frontiers of Computational Science 2008 1 Pages: 1-8
  • Peer Reviewed
• [Journal Article] Origin of color tuning in human red, green, and blue cone visual pigments: SAC-CI and QM/MM study (2008)
  • Author(s): K. Fujimoto, J. Hasegawa, and H. Nakatsuji
  • Journal Title: Chem. Phys. Letters 462 Pages: 318-320
  • Peer Reviewed
• [Journal Article] 紅色細菌光合成反応中心における励起状態と電子移動の量子化学 (2008)
  • Author(s): 長谷川淳也
  • Journal Title: 光合成研究 18 Pages: 53-59
• [Journal Article] 光合成・視覚・生物発光の初期過程 : SAC-CI法による研究 (2008)
  • Author(s): 長谷川淳也、中辻博
  • Journal Title: 固体物理 43 Pages: 147-155
• [Journal Article] Exploring Photo-Biology and Bio-Spectroscopy with the SAC-CI (Symmetry-Adapted Cluster-Configuration (2008)
  • Author(s): 長谷川淳也、中辻博
  • Journal Title: Radiation Induced Molecular Phenomena in Nucleic Acid : A Comprehensive Theoretical and Pages: 93-123
  • Peer Reviewed
• [Journal Article] Exploring Photo-Biology and Bio-Spectroscopy with the SAC-CI (Symmetry-Adapted Cluster-Configuration Interaction) Method (2008)
  • Author(s): J. Hasegawa and H. Nakatsuji
  • Journal Title: Radiation Induced Molecular Phenomena in Nucleic Acid: A Comprehensive Theoretical and Experimental Analysis (印刷中)
  • Peer Reviewed
• [Journal Article] A Review of the SAC-CI Applications to the Excited States of Porohyrin Compounds: How Q-band absorptions are controlled? (2008)
  • Author(s): J. Hasegawa and H. Nakatsuji
  • Journal Title: Computing Lett. (印刷中)
  • Peer Reviewed
• [Journal Article] Red Light in Chemiluminescence and Yellow-green Light in Bioluminescence : Color-tuning Mechanism of Firefly, Photinus pyralis, studied by the SAC-CI method (2007)
  • Author(s): N. Nakatani, J. Hasegawa, and H. Nakatsuji, J
  • Journal Title: Am. Chem. Soc 129 Pages: 8756-8765
• [Journal Article] Excited States of GFP Chromophore and Active Site Studied by the SAC-CI method : Effect of Protein-environment and Mutation (2007)
  • Author(s): J. Hasegawa, K. Fujimoto, B. Swerts, T. Miyahara, and H. Nakatsuji
  • Journal Title: J. Comp. Chem 28 Pages: 2443-2452
• [Journal Article] Red Light in Chemiluminescence and Yellow-green Light in Bioluminescence: Color-tuning Mechanism of Firefly, Photinus pyralis, studied by the SAC-CI (2007)
  • Author(s): Naoki Nakatani, Jun-ya Hasegawa, Hiroshi Nakatsuji
  • Journal Title: J. Am. Chem. Soc. 129 Pages: 8756-8765
  • Peer Reviewed
• [Journal Article] Excited States of GFP Chromophore and Active Site Studied by the SAC-CI method: Effect of Protein-environment and Mutations (2007)
  • Author(s): J. Hasegawa, K. Fujimoto, B. Swerts, T. Miyahara, and H. Nakatsuji
  • Journal Title: J. Comp. Chem 28 Pages: 2443-2452
  • Peer Reviewed
• [Journal Article] SAC-CI Theoretical Study on the Excited States of Lumiflavin: Structure, Excitation Spectrum, and Solvation Effect (2007)
  • Author(s): J. Hasegawa, S. Bureekaew, and H. Nakatsuji
  • Journal Title: J. Photochem.Photobiology A: Chemistry 189 Pages: 205-210
  • Peer Reviewed
• [Journal Article] Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins (2007)
  • Author(s): K. Fujimoto, S. Hayashi, J. Hasegawa, and H. Nakatsuji
  • Journal Title: J. Chem. Theory Comput 3 Pages: 605-618
  • Peer Reviewed
• [Journal Article] Excited and ionized states of ozone studied by the MEG (multi-exponentially generated)/EX (excited)-MEG method (2007)
  • Author(s): Y. Ohtsuka, J. Hasegawa, and H. Nakatsuji
  • Journal Title: Chem. Phys. 332 Pages: 262-270
  • Peer Reviewed
• [Journal Article] SAC-CI Theoretical Study on the Excited States of Lumiflavin : Structure, Excitation Spectrum, and Solvation Effect (2007)
  • Author(s): J.Hasegawa, S.Bureekaew, H.Nakatsuji
  • Journal Title: J.Photochem.Photobiology A : Chemistry (印刷中)
• [Journal Article] Excited and ionized states of ozone studied by the MEG (multi-exponentially generated)/EX(excited)-MEG method (2007)
  • Author(s): Y.Ohtsuka, J.Hasegawa, H.Nakatsuji
  • Journal Title: Chemical Physics (印刷中)
• [Journal Article] Excited States of GFP Chromophore and Active Site Studied by the SAC-CI method : Effect of Protein-environment and Mutations (2007)
  • Author(s): J.Hasegawa, K.Fujimoto, B.Swerts, T.Miyahara, H.Nakatsuji
  • Journal Title: J.Computational Chemistry (印刷中)
• [Journal Article] Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins (2007)
  • Author(s): K.Fujimoto, S.Hayashi, J.Hasegawa, H.Nakatsuji
  • Journal Title: J.Chem.Theory Comput. 3 Pages: 605-618
• [Journal Article] On the reversible O2 birding of the Fe-porphyrin complex (2006)
  • Author(s): H. Nakashima, J. Hasegawa, and H. Nakatsuji
  • Journal Title: J. Comp. Chem 27 Pages: 426-433
• [Journal Article] On the color-tuning mechanism of Human-Blue visual pigment : SAC-CI and QM/MM study (2006)
  • Author(s): K.Fujimoto, J.Hasegawa, S.Hayashi, H.Nakatsuji
  • Journal Title: Chem.Phys.Lett. 423 Pages: 252-256
• [Journal Article] On the O2 binding of Fe-porphyrin, Fe-porphycene, and Fe-corrphycene complexes (2006)
  • Author(s): H.Nakashima, J.Hasegawa, H.Nakatsuji
  • Journal Title: J.Comp.Chem. 27 Pages: 1363-1372
• [Journal Article] Electronic Circular Dichroism Spectrum of Uridine Studied by the SAC-CI method (2006)
  • Author(s): S.Bureekaew, J.Hasegawa, H.Nakatsuji
  • Journal Title: Chem.Phys.Lett. 425 Pages: 367-37
• [Journal Article] On the reversible O2 binding of the Fe-porphyrin complex (2006)
  • Author(s): H.Nakashima, J.Hasegawa, H.Nakatsuji
  • Journal Title: J.Comp.Chem. 27 Pages: 426-433
• [Presentation] 光機能性蛋白質にみられるカラーチューニングの起源に関する物理と化学と生物学 (2009)
  • Author(s): 長谷川淳也
  • Organizer: 第1回生物物質科学フォーラム
  • Place of Presentation: 名古屋大学
  • Year and Date: 2009-03-17
• [Presentation] ヒト網膜の光受容体におけるスペクトル・チューニング (2008)
  • Author(s): 長谷川淳也
  • Organizer: 量子化学研究協会シンポジウム「革新的量子化学の展開」
  • Place of Presentation: キャンパスプラザ京都
  • Year and Date: 2008-05-31
• [Presentation] SAC-CI study on the primary events in photobiological processes (Invited lecture) (2008)
  • Author(s): J. Hasegawa
  • Organizer: 第88回日本化学会春季年会アジア国際シンポジウム
  • Place of Presentation: 立教大学
  • Year and Date: 2008-03-28
• [Presentation] SAC-CI study on the primary events in photobiological processes(招待講演) (2008)
  • Author(s): J. Hasegawa
  • Organizer: 第88回日本化学会春季年会アジア国際シンポジウム
  • Place of Presentation: 立教大学東京
  • Year and Date: 2008-03-28
• [Presentation] Spectral Tuning Mechanism in Photofunctional Proteins : ASAC-CI Theoretical Study (2008)
  • Author(s): J. Hasegawa
  • Organizer: International Symposium on Frontiers of Computatinal Science 2008
  • Place of Presentation: 北陸先端大東京サテライトキャンパス
• [Presentation] 光生物学における分子理論の展開 : 励起状態理論の開発を基盤とし (2008)
  • Author(s): 長谷川淳也
  • Organizer: 特定領域研究「実在系の分子理論」平成20年度成果報告会
  • Place of Presentation: 北海道大学
• [Presentation] 光機能性蛋白質にみられるカラーチューニング機構に関する理論的研究 (2008)
  • Author(s): 長谷川淳也
  • Organizer: 研シンポジウム「分子アンサンブル2008」
  • Place of Presentation: 理化学研究所
• [Presentation] 紅色光合成細菌の反応中心の励起状態と電子移動:電子理論による研究(依頼講演) (2008)
  • Author(s): 長谷川淳也
  • Organizer: 分子研研究会「分子の視点から見る光合成」
  • Place of Presentation: 分子科学研究所
• [Presentation] Quantum Chemical Approach to Photobiology: Excited States of Photosynthetic Reaction Centers, Fluorescent Proteins, and Human Visual Cone Pigments(招待講演) (2007)
  • Author(s): J. Hasegawa
  • Organizer: Photosynthesis and Enzyme Reactions
  • Place of Presentation: 大阪市立大学
  • Year and Date: 2007-11-29
• [Presentation] Exploring Photobiology with the SAC-CI method (2007)
  • Author(s): J. Hasegawa
  • Organizer: Molecular Response to Electronic Excitation, Bad Munstereifel
  • Place of Presentation: Germany
• [Presentation] 光合成細菌の反応中心における励起状態と電子移動:量子化学の視点から(招待講演) (2007)
  • Author(s): 長谷川淳也
  • Organizer: 有機固体冬の学校
  • Place of Presentation: 箱根
• [Presentation] Color-tuning mechanism of human visual cone pigments(招待講演) (2007)
  • Author(s): J. Hasegawa
  • Organizer: The 2-nd Japan-Czeck-Slovakia Joint Symposium for Theoretical/Computational Chemistry
  • Place of Presentation: 京都大学
• [Presentation] SAC-CI study of the Color-tuning Mechanism in Photobiology(招待講演) (2007)
  • Author(s): J. Hasegawa
  • Organizer: The Third Asian-Pacific Conference of Theoretical and Computational Chemistry (APCTCC)
  • Place of Presentation: Beijing
• [Presentation] Color-tuning in Photobiology: A SAC-CI study(招待講演) (2007)
  • Author(s): J. Hasegawa
  • Organizer: International Symposium on Molecular Theory for Real Systems, Kyoto
  • Place of Presentation: 京都大学
• [Presentation] Exploring Photobiology with the SAC-CI method(招待講演) (2007)
  • Author(s): J. Hasegawa
  • Organizer: Molecular Response to Electronic Excitation
  • Place of Presentation: ドイツ
• [Presentation] SAC-CI applied to photobiology and biospectroscopy (2006)
  • Author(s): J. Hasegawa
  • Organizer: The XII-th International Congress of Quantum Chemistry, Satellite Symposium「Reactions in Solution and Biological Systems : Potential Energy Surface and Dynamics」
  • Place of Presentation: Fukui Institute for Fundamental Chemistry
• [Book] Radiation Induced Molecular Phenomena in Nucleic Acid : A Comprehensive Theoretical and Experimental Analysis, (Ed., by M. Shukla and J. Leszczynsk), (Exploring Photo-Biology and Bio-Spectroscopy with the SAC-CI (Symmetry-Adapted Cluster-Configuration Interaction) Method) (2008)
  • Author(s): J. Hasegawa and H. Nakatsuji
  • Publisher: Springer