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Theoretical study on biomolecular functions: Effects of conformational fluctuations and changes

Research Project

Project/Area Number 16H02254
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionInstitute for Molecular Science

Principal Investigator

SAITO SHINJI  分子科学研究所, 理論・計算分子科学研究領域, 教授 (70262847)

Project Period (FY) 2016-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥45,370,000 (Direct Cost: ¥34,900,000、Indirect Cost: ¥10,470,000)
Fiscal Year 2020: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2019: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Fiscal Year 2018: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Fiscal Year 2017: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Keywords構造変化 / 生体分子系機能 / 励起エネルギー移動 / 概日リズム / 反応速度 / 動的乱れ / 機能発現 / 光合成系 / 時計タンパク質 / 一分子速度論 / 分子動力学シミュレーション / イオンチャネル / 化学反応 / 光合成タンパク質 / 酵素反応 / 拡散反応過程 / イオン透過 / 分子シミュレーション / 数理モデル / 水
Outline of Final Research Achievements

In biomolecules and liquids, conformations fluctuate and change over a wide range of spatiotemporal scales. In this project, we conducted theoretical studies on how chemical reactions and conformational changes proceed in biomolecular systems and how biomolecular functions are brought about under fluctuations. As a result, we revealed the presence of heterogeneous conformational changes and important prepared structures before reaction. We have also clarified the molecular mechanism of efficient excitation energy transfer in photosynthetic bacteria. In addition, we conducted theoretical studies on the dynamics of water and ionic aqueous solutions. As a result, we found a new dynamical transition at a very low temperature and revealed the low glass transition temperature of water. Furthermore, we investigated the molecular mechanism of ion and concentration dependence of collective orientation relaxation of water in aqueous solutions.

Academic Significance and Societal Importance of the Research Achievements

反応に関して、タンパク質の折れ畳みを例に構造変化の時間分布が従来の一次元理論では記述できないこと、異性化反応を例に反応前に構造変化に重要な構造励起状態の存在等を明らかにした。生体機能に関しては、光合成細菌における効率的励起エネルギー移動の分子機構を解明した。さらに、水に関する研究において、これまで見出されていなかった状態変化や低いガラス転移温度の起源等を解明した。これらの成果として、2018, 2019年におけるJ. Chem. Phys.のLiquids, Glasses, and Crystals分野のベスト論文に2報の論文が選ばれる等、国際的にも本研究課題の学術的意義が認知されている。

Report

(6 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (62 results)

All 2021 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (6 results) Journal Article (17 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 17 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (26 results) (of which Int'l Joint Research: 19 results,  Invited: 25 results) Book (1 results) Remarks (12 results)

  • [Int'l Joint Research] Sungkyunkwan University(韓国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Indian Institute of Technology Kanpur(インド)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University California Berkeley(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Indian Institute of Science(インド)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Indian Institute of Science/Indian Institute of Technology, Kanpur(インド)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Indian Institute of Science(インド)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Effects of interfaces on structure and dynamics of water droplets on a graphene surface: A molecular dynamics study2021

    • Author(s)
      MAURYA Manish、METYA Atanu K.、SINGH Jayant K.、SAITO Shinji
    • Journal Title

      The Journal of Chemical Physics

      Volume: 154 Issue: 16 Pages: 164704-164704

    • DOI

      10.1063/5.0046817

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Microscopic insights into dynamic disorder in the isomerization dynamics of the protein BPTI2021

    • Author(s)
      MATSUMURA Yoshihiro、SAITO Shinji
    • Journal Title

      The Journal of Chemical Physics

      Volume: 154 Issue: 22 Pages: 224113-224113

    • DOI

      10.1063/5.0055152

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase2020

    • Author(s)
      Mori Toshifumi、Saito Shinji
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 16 Issue: 5 Pages: 3396-3407

    • DOI

      10.1021/acs.jctc.9b01279

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins2020

    • Author(s)
      Koda Shin-ichi、Saito Shinji
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 10439-10439

    • DOI

      10.1038/s41598-020-67298-7

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tautomeric Effect of Histidine on β-Sheet Formation of Amyloid Beta 1?40: 2D-IR Simulations2020

    • Author(s)
      NAM Yeonsig、KALATHINGAL Mahroof、SAITO Shinji、LEE Jin Yong
    • Journal Title

      Biophysical Journal

      Volume: 119 Issue: 4 Pages: 831-842

    • DOI

      10.1016/j.bpj.2020.07.009

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular Mechanism of Acceleration and Retardation of Collective Orientation Relaxation of Water Molecules in Aqueous Solutions2020

    • Author(s)
      MORITSUGU Norifumi、NARA Takafumi、KODA Shin-ichi、TOMINAGA Keisuke、SAITO Shinji
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 124 Issue: 51 Pages: 11730-11737

    • DOI

      10.1021/acs.jpcb.0c10036

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inverse Kohn Sham Equations Derived from the Density Equation Theory2020

    • Author(s)
      T. Kato, K. Nobusada, and S. Saito
    • Journal Title

      J. Phys. Soc. Jpn

      Volume: 89 Issue: 2 Pages: 024301-024301

    • DOI

      10.7566/jpsj.89.024301

    • NAID

      40022155069

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Site-Dependent Fluctuations Optimize Electronic Energy Transfer in the Fenna?Matthews?Olson Protein2019

    • Author(s)
      Saito Shinji、Higashi Masahiro、Fleming Graham R.
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123 Issue: 46 Pages: 9762-9772

    • DOI

      10.1021/acs.jpcb.9b07456

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Theory of coherent two-dimensional vibrational spectroscopy2019

    • Author(s)
      Jansen Thomas la Cour、Saito Shinji、Jeon Jonggu、Cho Minhaeng
    • Journal Title

      The Journal of Chemical Physics

      Volume: 150 Issue: 10 Pages: 100901-100901

    • DOI

      10.1063/1.5083966

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Thermodynamic picture of vitrification of water through complex specific heat and entropy: A journey through “no man’s land”2019

    • Author(s)
      Saito Shinji、Bagchi Biman
    • Journal Title

      The Journal of Chemical Physics

      Volume: 150 Issue: 5 Pages: 054502-054502

    • DOI

      10.1063/1.5079594

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase2019

    • Author(s)
      Mori Toshifumi、Saito Shinji
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 10 Issue: 3 Pages: 474-480

    • DOI

      10.1021/acs.jpclett.8b03607

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crucial role of fragmented and isolated defects in persistent relaxation of deeply supercooled water2018

    • Author(s)
      Saito Shinji、Bagchi Biman、Ohmine Iwao
    • Journal Title

      The Journal of Chemical Physics

      Volume: 149 Issue: 12 Pages: 124504-124504

    • DOI

      10.1063/1.5044458

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study2018

    • Author(s)
      Kalathingal Mahroof、Sumikama Takashi、Mori Toshifumi、Oiki Shigetoshi、Saito Shinji
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 20 Issue: 5 Pages: 3334-3348

    • DOI

      10.1039/c7cp06299k

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Theoretical investigation on vibrational frequency fluctuations of SCN-derivatized vibrational probe molecule in water2018

    • Author(s)
      M. Okuda, M. Higashi, K. Ohta, S. Saito, K. Tominaga
    • Journal Title

      Chem. Phys.

      Volume: 印刷中 Pages: 82-87

    • DOI

      10.1016/j.chemphys.2018.03.012

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation2017

    • Author(s)
      M. Okuda, M. Higashi, K. Ohta, S. Saito, K. Tominaga
    • Journal Title

      Chem. Phys. Lett.

      Volume: 683 Pages: 547-552

    • DOI

      10.1016/j.cplett.2017.03.008

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed
  • [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 surface2016

    • 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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity2016

    • Author(s)
      Toshifumi Mori, Shinji Saito
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 120 Issue: 45 Pages: 11683-11691

    • DOI

      10.1021/acs.jpcb.6b08066

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Effect of ion on collective orientation relaxation of water2020

    • Author(s)
      SAITO Shinji
    • Organizer
      Dynamics of Chemical and Biological Systems
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Effect of ion on collective orientation relaxation of water2020

    • Author(s)
      SAITO Shinji
    • Organizer
      Department Seminar, SSCU, Indian Institute of Science
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Effect of ion on collective orientation relaxation of water2020

    • Author(s)
      S. Saito
    • Organizer
      Dynamics of Chemical and Biological Systems
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Excitation energy transfer in the Fenna-Matthews-Olson protein optimized by site-dependent fluctuations2019

    • Author(s)
      S. Saito
    • Organizer
      Indo-Japan workshop on "Frontiers in Molecular Spectroscopy: From Fundamentals to Applications in Chemistry and Biology"
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Circadian rhythm of Kai system: A reaction model considering reactions and conformational changes2019

    • Author(s)
      Shinji Saito
    • Organizer
      Dynamics at the Interface of Chemistry and Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure, dynamics, thermodynamics, and glass transition2019

    • Author(s)
      Shinji Saito
    • Organizer
      IMS workshop on Water at interfaces
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure, dynamics, thermodynamics, and glass transition2018

    • Author(s)
      Shinji Saito
    • Organizer
      Symposium on Spectroscopic and computational studies of complex chemical systems at different time and length scales
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure, dynamics, thermodynamics, and glass transition2018

    • Author(s)
      Shinji Saito
    • Organizer
      Conference on Local Structure and Dynamics of Hydrogen Bonds in Water: Super Cooled Water and Binary Mixture
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Excitation energy transfer in photosynthetic protein FMO2018

    • Author(s)
      Shinji Saito
    • Organizer
      Japan-Indo Seminar on Frontiers in Molecular Spectroscopy: From Fundamentals to Applications in Chemistry and Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure, dynamics, and glass transition2018

    • Author(s)
      Shinji Saito
    • Organizer
      Energy Landscape 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure and dynamics2018

    • Author(s)
      Shinji Saito
    • Organizer
      1st UJN-SKKU-IMS Symposium on Chemisrty and Materials
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercooled water: Structure, dynamics, and Kauzmann temperature2018

    • Author(s)
      Shinji Saito
    • Organizer
      7th JCS Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Circadian rhythm of Kai system: A reaction model considering reactions and conformational changes2018

    • Author(s)
      Shinji Saito
    • Organizer
      BK21plus Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 時計タンパク質概日リズムの反応モデル2017

    • Author(s)
      甲田信一、斉藤真司
    • Organizer
      第20回理論化学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Supercooled water: Fluctuation, glass transition, and quantum effects2017

    • Author(s)
      Shinji Saito
    • Organizer
      Korea-Japan Molecular Symposium 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Reaction model for circadian rhythm of Kai system considering elementary processes2017

    • Author(s)
      Shin-ichi Koda and Shinji Saito
    • Organizer
      ANSCSE21
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A reaction model for circadian rhythm of Kai systemconsidering reactions and conformational changes2017

    • Author(s)
      Shin-ichi Koda and Shinji Saito
    • Organizer
      APCTCC8
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 素過程に立脚した時計タンパク質概日リズムの反応モデル:反応から機能へ2017

    • Author(s)
      甲田信一
    • Organizer
      研究会「凝縮系の理論化学」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Structure and dynamics of supercooled water2016

    • Author(s)
      S. Saito
    • Organizer
      Indo-Japan bilateral seminar
    • Place of Presentation
      Kanpur, India
    • Year and Date
      2016-11-13
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 過冷却水の構造と動力学2016

    • Author(s)
      斉藤真司
    • Organizer
      Cryopreservation Conference 2016
    • Place of Presentation
      岡崎カンファレンスセンター、岡崎市、愛知県
    • Year and Date
      2016-11-10
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Structure and dynamics of supercooled water2016

    • Author(s)
      S. Saito
    • Organizer
      4th International Conference on Molecular Simulation
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2016-10-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structure and dynamics of supercooled water2016

    • Author(s)
      S. Saito
    • Organizer
      2016 annual meeting EMLG-JMLG
    • Place of Presentation
      Chania, Crete, Greece
    • Year and Date
      2016-09-11
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simulations of proton transfer and energy transfer in excited states2016

    • Author(s)
      S. Saito
    • Organizer
      9th International Meeting on Photodynamics and Related Aspects
    • Place of Presentation
      Mendoza, Argentina
    • Year and Date
      2016-05-09
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of water and proteins2016

    • Author(s)
      S. Saito
    • Organizer
      8th International Kasetsart University Science and Technology Annual Research Symposium
    • Place of Presentation
      Bangkok, Thailand
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 水の構造とダイナミクス:特異的性質の起源2016

    • Author(s)
      斉藤真司
    • Organizer
      琉球大学 化学系講演会
    • Place of Presentation
      琉球大学、中頭郡西原町、沖縄県
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 揺らぎから物性・機能機構の解明へ2016

    • Author(s)
      斉藤真司
    • Organizer
      第3回電子状態シンポジウム
    • Place of Presentation
      早稲田大学、新宿区、東京都
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Book] Coherent Multidimensional Spectroscopy2019

    • Author(s)
      M. Okuda, M. Higashi, K. Ohta, S. Saito and K. Tominaga
    • Total Pages
      394
    • Publisher
      Springer Singapore
    • ISBN
      9789811397530
    • Related Report
      2019 Annual Research Report
  • [Remarks] 斉藤真司

    • URL

      https://dyna.ims.ac.jp/shinji/index.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] 分子科学研究所 斉藤グループ

    • URL

      https://dyna.ims.ac.jp/index.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] 分子科学研究所 研究者詳細

    • URL

      https://www.ims.ac.jp/research/prof/saito.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] 分子研 斉藤グループ ホームページ

    • URL

      http://dyna.ims.ac.jp/index.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 分子研 斉藤真司 ホームページ

    • URL

      http://dyna.ims.ac.jp/shinji/index.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] Shinji Saito

    • URL

      http://dyna.ims.ac.jp/shinji/index.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] Saito Group

    • URL

      http://dyna.ims.ac.jp/index.html

    • Related Report
      2018 Annual Research Report
  • [Remarks]

    • URL

      http://dyna.ims.ac.jp/NewHP_Group/

    • Related Report
      2017 Annual Research Report
  • [Remarks]

    • URL

      http://dyna.ims.ac.jp/NewHP_Group/research.html

    • Related Report
      2017 Annual Research Report
  • [Remarks]

    • URL

      http://dyna.ims.ac.jp/shinji/index.html

    • Related Report
      2017 Annual Research Report
  • [Remarks] 斉藤真司 webpage

    • URL

      http://dyna.ims.ac.jp/shinji/index.html

    • Related Report
      2016 Annual Research Report
  • [Remarks] 斉藤グループ webpage

    • URL

      http://dyna.ims.ac.jp/NewHP_Group/

    • Related Report
      2016 Annual Research Report

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Published: 2016-04-21   Modified: 2023-01-30  

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