構造と環境の柔らかさが相関した光駆動イオン輸送の解明

• Project Area: Science on Function of Soft Molecular Systems by Cooperation of Theory and Experiment
• Project/Area Number: 16H00842
• 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: Kyushu University
• Principal Investigator: 吉田 紀生 九州大学, 理学研究院, 准教授 (10390650)
• Project Period (FY): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2017: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2016: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• Keywords: 光駆動チャネル / ロドプシン / ３D-RISM / MDシミュレーション / QM/MM / 理論化学 / チャネル / 液体の積分方程式理論

Outline of Annual Research Achievements

MDシミュレーションと3D-RISMにより、チャネルロドプシンの閉状態および初期開状態の構造探索及びチャネル内の水分布に関する研究を行った。得られた研究結果は現在論文として国際誌に投稿準備中である。
また、3D-RISM理論とストリング法を組み合わせた効率的なチャネル内イオン輸送経路探索手法を開発した。この手法では、与えられたタンパク質構造（たとえばMDなどで求める）に対して、3D-RISM理論を用いて、イオンの平均場ポテンシャルを求め、その平均場ポテンシャル曲面上の自由エネルギー最小経路をストリング法で決定するというものである。この手法をチャネルロドプシンの閉構造の細胞外側チャネルに適用し、解離性残基のプロトン化状態に依存したイオン透過の自由エネルギープロファイルの変化を明らかにした。この成果はChemical Physics Letters誌に掲載された。
さらに、本新学術領域から旅費援助を受けて、タイ・カセサート大学との共同研究を行った。共同研究では3D-RISM理論を用いてプルシアンブルーによるセシウムイオンの吸着過程を明らかにした。この成果もChemical Physics Letters誌に掲載された。

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

• [Int'l Joint Research] Kasetart University(タイ)
• [Int'l Joint Research] Kasetsart University(タイ)
• [Journal Article] A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method (2018)
  • Author(s): Norio Yoshida
  • Journal Title: Chemical Physics Letters Volume: 699 Pages: 22-27
  • DOI: 10.1016/j.cplett.2018.03.034
  • Peer Reviewed
• [Journal Article] Size-dependent adsorption sites in a Prussian blue nanoparticle: A 3D-RISM study (2017)
  • Author(s): Nirun Ruankaew, Norio Yoshida, Yoshihiro Watanabe, Haruyuki Nakano, Saree Phongphanphanee
  • Journal Title: Chemical Physics Letters Volume: 684 Pages: 117-125
  • DOI: 10.1016/j.cplett.2017.06.053
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Solvatochromism and Preferential Solvation of Brooker's Merocyanine in Water-Methanol Mixtures (2017)
  • Author(s): Yuichi Tanaka, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano
  • Journal Title: J. Comput. Chem. Volume: 38 Issue: 28 Pages: 2411-2419
  • DOI: 10.1002/jcc.24902
  • Peer Reviewed
• [Journal Article] Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids (2017)
  • Author(s): Norio Yoshida
  • Journal Title: Journal of Chemical Information and Modeling Volume: 57 Issue: 11 Pages: 2646-2656
  • DOI: 10.1021/acs.jcim.7b00389
  • Peer Reviewed
• [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
• [Presentation] pKa Prediction in Biological Systems Based on the Statistical Mechanics Theory of Liquids combined with the electronic structure theory (2018)
  • Author(s): Norio Yoshida
  • Organizer: PACCON2018
  • Int'l Joint Research / Invited
• [Presentation] An MD and 3D-RISM Approach to the Ion Transport of Channel Rhodopsin (2018)
  • Author(s): Norio Yoshida
  • Organizer: American Chemical Society Meeting 2018 spring
  • Int'l Joint Research
• [Presentation] 芳香族化合物における磁気遮蔽効果に関する理論的研究 (2018)
  • Author(s): 大古場渉，井上頌基，渡邉祥弘，中野 晴之
  • Organizer: 凝縮系の理論化学2018
• [Presentation] pKaの理論的予測手法の開発 (2018)
  • Author(s): 藤木涼，笠井友佳子，妹尾裕貴，松井亨，重田育照，吉田紀生，中野晴之
  • Organizer: 凝縮系の理論化学2018
• [Presentation] 擬縮退摂動論に基づいた相対論2成分法の評価 (2018)
  • Author(s): 金丸恒大，井上頌基，東雅大，渡邉祥弘，中野晴之
  • Organizer: 凝縮系の理論化学2018
• [Presentation] pKa Prediction in Biological Systems Based on the Statistical Mechanics Theory of Liquids combined with the electronic structure theory (2017)
  • Author(s): Norio Yoshida
  • Organizer: Computer aided drug design 2017
  • Int'l Joint Research / Invited
• [Presentation] Statistical mechanics theory of solvation of biomolecules (2017)
  • Author(s): Norio Yoshida
  • Organizer: The 9th Conference of the Asian Consortium on Computational Materials Science
  • Int'l Joint Research / Invited
• [Presentation] pKa Prediction in Biological Systems Based on the Statistical Mechanics Theory of Liquids (2017)
  • Author(s): Norio Yoshida
  • Organizer: The 21th international annual symposium on computational science and engineering (ANSCSE20)
  • Int'l Joint Research / Invited
• [Presentation] Theoretical study of ion transportation of light-driven channel (2017)
  • Author(s): Norio Yoshida
  • Organizer: Joint EMLG/JMLG Annual Meeting 2017
  • Int'l Joint Research
• [Presentation] Theoretical study of ion transportation of light-driven channel (2017)
  • Author(s): Norio Yoshida
  • Organizer: "KAKENHI International Symposium on “Studying the Function of Soft Molecular Systems”"
  • Int'l Joint Research
• [Presentation] 液体の積分方程式理論による膜イオン輸送の解析 (2017)
  • Author(s): 吉田紀生
  • Organizer: 大阪大学蛋白質研究所セミナー「膜イオン輸送の学際研究：計算科学から医学まで」
  • Invited
• [Presentation] New solvation free energy expression for the three-dimensional reference interaction site model combined with the distributed partial wave expansion correction (2017)
  • Author(s): Shoichi TANIMOTO, Norio YOSHIDA, Haruyuki NAKANO
  • Organizer: "KAKENHI International Symposium on “Studying the Function of Soft Molecular Systems”"
  • Int'l Joint Research
• [Presentation] 部分波展開法と3D-RISM法の結合による新たな溶媒和自由エネルギー計算式の提案 (2017)
  • Author(s): 谷本 勝一、吉田 紀生、中野 晴之
  • Organizer: 分子科学討論会
  • Int'l Joint Research
• [Presentation] 部分波展開法と3D-RISM法の結合による新たな溶媒和自由エネルギー計算式の提案 (2017)
  • Author(s): Shoichi Tanimoto, Norio Yoshida, Haruyuki Nakano
  • Organizer: 生物物理年会
  • Int'l Joint Research
• [Presentation] Theoretical study of Zinc affinity for VHH antibody (2017)
  • Author(s): Kentaro Handa, Shoichi Tanimoto, Norio Yoshida, Koki Makabe, Mitsuo Umetsu, Haruyuki Nakano
  • Organizer: "KAKENHI International Symposium on “Studying the Function of Soft Molecular Systems”"
  • Int'l Joint Research
• [Presentation] Development of a theoretical prediction method for pKa (2017)
  • Author(s): Ryo Fujiki, Yukako Kasai, Norio Yoshida, Toru Matsui, Yasuteru Shigeta, Haruyuki Nakano
  • Organizer: "KAKENHI International Symposium on “Studying the Function of Soft Molecular Systems”"
  • Int'l Joint Research
• [Presentation] pKaの理論的予測手法の開発 (2017)
  • Author(s): 藤木涼, 笠井友佳子, 妹尾裕貴, 松井亨, 重田育照, 吉田紀生, 中野晴之
  • Organizer: 柔らかな分子系全体合宿会議
  • Int'l Joint Research
• [Presentation] Theoretical study of biological processes based on integral equation of molecular liquids (2016)
  • Author(s): Norio Yoshida
  • Organizer: 4th International Conference on Computation for Science and Technology
  • Place of Presentation: Langkawi, Malaysia
  • Year and Date: 2016-11-03
  • Int'l Joint Research / Invited
• [Presentation] "Role of calcium ion in molecular recognition process of calcium-dependent carbohydrate-binding module " (2016)
  • Author(s): Shoichi Tanimoto, Masahiro Higashi, Norio Yoshida, Haruyuki Nakano
  • Organizer: Joint EMLG/JMLG Annual Meeting 2016
  • Place of Presentation: Platanias, Creta, Greece
  • Year and Date: 2016-09-12
  • Int'l Joint Research
• [Presentation] FMO法と3D-RISM法の連成による生体分子の溶媒和理論 (2016)
  • Author(s): 吉田紀生
  • Organizer: 第12回FMO研究会
  • Place of Presentation: 神戸大学統合研究拠点, 神戸市
  • Year and Date: 2016-09-07
  • Invited
• [Presentation] Selective ion adsorption of Prussian blue nanoparticle: A 3D-RISM study (2016)
  • Author(s): Nirun Ruankaew, Norio Yoshida, Yoshihiro Watanabe, Haruyuki Nakano, Saree Phongphanphanee
  • Organizer: ISSPIC XVIII - International Symposium on Small Particles and Inorganic Clusters
  • Place of Presentation: Congress Centre Paviljonki, Jyvaskyla, Finland
  • Year and Date: 2016-08-09
  • Int'l Joint Research
• [Presentation] Theoretical study of biological processes by molecular theory of solvation (2016)
  • Author(s): Norio Yoshida
  • Organizer: The 20th international annual symposium on computational science and engineering
  • Place of Presentation: Kasetsart University, Bangkok, Thai
  • Year and Date: 2016-07-29
  • Int'l Joint Research / Invited
• [Book] "Molecular Aspects of Solvation Investigated using Statistical Mechanics", in Leszczynski (Ed.) "Handbook of Computational Chemistry", 2nd edn (2016)
  • Author(s): Norio Yoshida, Katsura Nishiyama
  • Total Pages: 17
  • Publisher: Springer Science
• [Remarks] Research Topics -Norio Yoshida-
  • URL: https://sites.google.com/site/norioyoshida1973/research-topics-eng
• [Remarks] Research Topics - Norio Yoshida
  • URL: https://sites.google.com/site/norioyoshida1973/research-topics