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Theoretical study on the charge transfer through DNA induced by structural and solvent fluctuation

Research Project

Project/Area Number 25410021
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionKyushu University

Principal Investigator

YOSHIDA NORIO  九州大学, 高等研究院, 准教授 (10390650)

Co-Investigator(Renkei-kenkyūsha) NAKANO HARUYUKI  九州大学, 大学院理学研究院, 教授 (90251363)
WATANABE YOSHIHIRO  九州大学, 大学院理学研究院, 助教 (20315055)
NISHIYAMA KATSURA  島根大学, 教育学部, 教授 (40283725)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords電荷移動 / FMO / 3D-RISM / 理論化学 / 構造揺らぎ / 溶媒効果 / DNA / 電子移動 / フラグメント分子軌道法 / 3D-RISM理論 / 線形応答理論
Outline of Final Research Achievements

We developed a hybrid method of the fragment molecular orbital (FMO) method and the three-dimensional reference interaction site model (3D-RISM) theory, referred to as the FMO/3D-RISM method. We also derived its analytical free energy gradient formula, which allows us to evaluate the force on the solute biomolecule from the solvent distribution. We applied the method to a model system of DNA and demonstrated the validity of the method.
We investigated the mechanism of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase by the combinational use of the molecular dynamics simulation and the 3D-RISM method, and clarified the origin of the resistance. The methods used in this study can efficiently treat the structural fluctuation of biomolecule and the solvation thermodynamics.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (35 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (1 results) Journal Article (16 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 16 results,  Acknowledgement Compliant: 3 results) Presentation (15 results) (of which Int'l Joint Research: 3 results,  Invited: 15 results) Book (1 results) Remarks (2 results)

  • [Int'l Joint Research] Kasetsart university/Chulalongkorn University(タイ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Theoretical analysis of complex formation of p-carboxybenzeneboronic acid with a monosaccharide2016

    • Author(s)
      Yuki Seno, Norio Yoshida, Haruyuki Nakano
    • Journal Title

      J. Mol. Liq.

      Volume: 印刷中 Pages: 93-98

    • DOI

      10.1016/j.molliq.2015.12.063

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase2016

    • Author(s)
      Jiraphorn Phanich, Thanyada Rungrotmongkol, Daniel Sindhikara, Saree Phongphanphanee, Norio Yoshida, Fumio Hirata, Nawee Kungwan and Supot Hannongbua
    • Journal Title

      Protein science

      Volume: 25 Issue: 1 Pages: 147-158

    • DOI

      10.1002/pro.2718

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Three-Dimensional Reference Interaction Site Model Self-Consistent Field Analysis of Solvent and Substituent Effects on the Absorption Spectra of Brooker's Merocyanine2015

    • Author(s)
      Yuichi Tanaka, Norio Yoshida, Haruyuki Nakano
    • Journal Title

      J. Comput. Chem.

      Volume: 36 Issue: 22 Pages: 1655-1663

    • DOI

      10.1002/jcc.23980

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 続・生物工学基礎講座 バイオよもやま話「生体分子の溶媒和理論」2015

    • Author(s)
      吉田紀生
    • Journal Title

      生物工学会誌

      Volume: 8 Pages: 481-486

    • NAID

      110009985417

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method2014

    • Author(s)
      Norio Yoshida
    • Journal Title

      Journal of Chemical Physics

      Volume: 140 Issue: 21

    • DOI

      10.1063/1.4879795

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Water-meditated forces between the nucleotide binding domains generate the power stroke in an ABC transporter2014

    • Author(s)
      Furukawa-Hagiya T, Yoshida N, Chiba S, Hayashi T, Furuta T, Sohma Y, Sakurai M
    • Journal Title

      Chemical Physics Letters

      Volume: 616 - 617 Pages: 165-170

    • DOI

      10.1016/j.cplett.2014.10.038

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Distinct Configurations of Cations and Water in the Selective Filter of the KcsA Potasium Channel Probed by the 3D-RISM Theory2014

    • Author(s)
      Saree Phongphanphanee, Norio Yoshida, Shigetoshi Oiki, and Fumio Hirata
    • Journal Title

      J.Mol. Liq.

      Volume: 167 Pages: 578-584

    • DOI

      10.1016/j.molliq.2014.03.050

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical analysis of salt effect on intramolecular proton transfer reaction of glycine in NaCl aqueous solution2014

    • Author(s)
      Y. Kasai, N. Yoshida, H. Nakano
    • Journal Title

      J. Mol. Liq

      Volume: (in press) Pages: 32-37

    • DOI

      10.1016/j.molliq.2014.02.013

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] 液体の統計力学理論によるチャネルタンパクの透過現象解析2014

    • Author(s)
      吉田紀生
    • Journal Title

      膜

      Volume: 39 Pages: 379-384

    • NAID

      130005069453

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] The "ambivalent" snug-fit sites in the KcsA potassium channel probed by "3D-RISM microscopy"2014

    • Author(s)
      Phongphanphanee, S., Yoshida, N., Oiki, S. and Hirata, F
    • Journal Title

      Pure and Applied Chemistry

      Volume: 86 Issue: 2 Pages: 97-104

    • DOI

      10.1515/pac-2014-5018

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Characterization of the "Ridge" in the Supercritical Region in the Fluid Phase Diagram of Water2014

    • Author(s)
      Masaru Matsugami, Norio Yoshida, and Fumio Hirata
    • Journal Title

      J. Chem. Phys

      Volume: 140 Issue: 10 Pages: 1045-1045

    • DOI

      10.1063/1.4867974

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Extended Molecular Ornstein-Zernike Integral Equation for Fully Anisotropic Solute Molecules: Formulation in a Rectangular Coordinate System2013

    • Author(s)
      Ryosuke Ishizuka, Norio Yoshida
    • Journal Title

      Journal of Chemical Physics

      Volume: 139 Issue: 8

    • DOI

      10.1063/1.4819211

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Three-dimensional Reference Interaction Site Model Self-consistent Field Study of the Solvation and Electronic Structures of [Cr(H2O)6]3+ in Aqueous Solution2013

    • Author(s)
      S. Fujishige, Y. Kawashima, N. Yoshida, H. Nakano
    • Journal Title

      J. Phys. Chem. A

      Volume: 117 Issue: 34 Pages: 8314-8322

    • DOI

      10.1021/jp405876g

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solvent effect on excited states of merocyanines : A theoretical study using the RISM-SCF method2013

    • Author(s)
      Yuichi Tanaka, Norio Yoshida, Haruyuki Nakano
    • Journal Title

      Chem. Phys. Lett

      Volume: 583 Pages: 69-73

    • DOI

      10.1016/j.cplett.2013.08.004

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solvent dependence of Stokes shift for organic solute-solvent sysytems : A comparative study by spectroscopy and reference-interaction-site-model-self-consistent-field theory2013

    • Author(s)
      Katsura Nishiyama, Yasuhiro Watanabe, Norio Yoshida, and Fumio Hirata
    • Journal Title

      J. Chem., Phys

      Volume: 139 Issue: 9 Pages: 945-945

    • DOI

      10.1063/1.4819268

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Study of Salt Effects on Diels-Alder Reaction of Cyclopentadiene With Methyl Vinyl Ketone Using RISM-SCF Theory2013

    • Author(s)
      N. Yoshida, H. Tanaka, F. Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 117(45) Issue: 45 Pages: 1411-1411

    • DOI

      10.1021/jp4091552

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] プロトネーションと生体分子機能の予測:理論的アプローチ2016

    • Author(s)
      吉田紀生
    • Organizer
      2015年度第2回水和ナノ構造研究会
    • Place of Presentation
      秋湯温泉,宮城県仙台市
    • Year and Date
      2016-03-07
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Theoretical study of biological processes employing statistical mechanics of molecular liquids2016

    • Author(s)
      Norio Yoshida
    • Organizer
      Pure and Applied Chemistry International Conference 2016
    • Place of Presentation
      BITEC, Bangkok, Thai
    • Year and Date
      2016-02-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical study of ion transport in biological systems2016

    • Author(s)
      Norio Yoshida
    • Organizer
      Kasetsart University seminar
    • Place of Presentation
      Kasetsart university, Bangkok, Thai
    • Year and Date
      2016-02-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Multiscale implementation of 3D-RISM to the electronic structure theory being applicable for solvated biomolecules2015

    • Author(s)
      Norio Yoshida
    • Organizer
      Pacifichem2015
    • Place of Presentation
      Honolulu convention center, Honolulu, Hawaii
    • Year and Date
      2015-12-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] バイオマス利用に向けた酵素反応解析2015

    • Author(s)
      谷本勝一,東雅大,吉田紀生,中野晴之
    • Organizer
      第6回CMSI研究会
    • Place of Presentation
      東京大学本郷キャンパス,東京都文京区
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 液体の統計力学理論でみる膜チャネルタンパク質の物質輸送2015

    • Author(s)
      吉田紀生
    • Organizer
      「統合分析・生物化学研究特区」公開講演会 メンブレンサイエンス研究の新潮流
    • Place of Presentation
      九州大学箱崎キャンパス
    • Year and Date
      2015-03-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] チャネルロドプシンのイオン輸送経路の理論化学2014

    • Author(s)
      吉田紀生
    • Organizer
      柔らかな分子系第2回公開シンポジウム
    • Place of Presentation
      大阪大学会館,豊中市
    • Year and Date
      2014-11-28 – 2014-11-29
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 液体の統計力学理論でみる生体分子の溶媒和2014

    • Author(s)
      吉田紀生
    • Organizer
      奈良先端大生体分子セミナー
    • Place of Presentation
      奈良先端科学技術大学院大学,生駒市
    • Year and Date
      2014-11-18
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Efficient Implementation of 3D-RISM Theory to the FMO Method, and Its Applications2014

    • Author(s)
      Norio Yoshida
    • Organizer
      International Meeting on Applications of Statistical Mechanics of Molecular Liquid on Soft Matter
    • Place of Presentation
      Kasesart University, Bangkok, Thai
    • Year and Date
      2014-09-14 – 2014-09-17
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Molecular Recognition in Biomolecules Studied by Statistial-Mechanical Integral-Equation Theory of Liquids2014

    • Author(s)
      吉田紀生
    • Organizer
      兵庫県立大学大学院工学研究科物質系工学専攻・セミナー
    • Place of Presentation
      兵庫県立大学・姫路キャンパス,姫路市
    • Year and Date
      2014-04-21
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 3D-RISM理論の基礎と生体分子の分子認識への展開

    • Author(s)
      吉田紀生
    • Organizer
      構造活性フォーラム2013
    • Place of Presentation
      横浜市・理化学研究所横浜研究所交流棟ホール
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 液体の統計力学を用いた溶解液内化学過程の理論化学

    • Author(s)
      吉田紀生
    • Organizer
      2013年度九重分光関連セミナー
    • Place of Presentation
      大分県玖珠郡九重町,国立大学研修センター
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 液体の積分方程式理論による生体分子の分子認識の理論化学

    • Author(s)
      吉田紀生
    • Organizer
      第2回分子科学若手シンポジウム
    • Place of Presentation
      岡崎市・岡崎コンファレンスセンター
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 3D-RISMによるKcsAチャネル中のカチオン結合モード解析

    • Author(s)
      吉田紀生
    • Organizer
      第36回溶液化学シンポジウム
    • Place of Presentation
      札幌市・北海道大学学術交流会館
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Molecular recognition in biomolecules studied by statistical-mechanics theory

    • Author(s)
      吉田紀生
    • Organizer
      日本化学会第94回春期年会・アジア国際シンポジウム
    • Place of Presentation
      名古屋市・名古屋大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Book] "Theory of Molecular Recognition and Structural Fluctuation of Biomolecules", in Terazima et al.(Ed.) "Molecular Science of Fluctuations Toward Biological Functions", Chapter 82016

    • Author(s)
      Fumio Hirata, Norio Yoshida, Bongsoo Kim
    • Total Pages
      19
    • Publisher
      Springer Science
    • Related Report
      2015 Annual Research Report
  • [Remarks] Research Topics -Norio Yoshida

    • URL

      https://sites.google.com/site/norioyoshida1973/research-topics

    • Related Report
      2015 Annual Research Report
  • [Remarks] Research Topics

    • URL

      https://sites.google.com/site/norioyoshida1973/research-topics

    • Related Report
      2013 Research-status Report

URL: 

Published: 2014-07-25   Modified: 2019-07-29  

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