Updated on 2025/03/15

写真a

 
YOSHIDA Norio
 
Organization
Graduate School of Informatics Department of Complex Systems Science 3 Professor
Graduate School
Graduate School of Informatics
Undergraduate School
School of Informatics Department of Natural Informatics
Title
Professor
External link

Degree 1

  1. Doctor (Science) （ 2003.3   Kyoto University ） 

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Research Interests 26

  1. 電荷移動

  2. 電気伝導

  3. 部分モル圧縮率

  4. 部分モル体積

  5. 蛋白質

  6. 理論化学

  7. 溶媒効果

  8. 水分子

  9. 正孔移動

  10. 構造揺らぎ

  11. 分子認識

  12. リガンド

  13. プロトン

  14. イオンチャネル

  15. イオン

  16. アクアポリン

  17. Theoretical Chemistry

  18. Solution Chemistry

  19. RISM理論

  20. Quantum Chemistry

  21. QM

  22. Molecular Biology

  23. MM

  24. DNA

  25. 3D-RISM理論

  26. 3D-RISM-SCF

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Research Areas 4

  1. Life Science / Biophysics

  2. Natural Science / Biophysics, chemical physics and soft matter physics

  3. Nanotechnology/Materials / Bio chemistry

  4. Nanotechnology/Materials / Fundamental physical chemistry

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Research History 6

  1. National Institutes of Natural Sciences   Institute for Molecular Science   Visiting Professor

    2022.4

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  2. Nagoya University   Graduate School of Informatics   Professor

    2022.3

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    Country：Japan

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  3. Kyushu University   Graduate School of Science   Associate professor

    2017.1 - 2022.2

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  4. Kyushu University   Associate professor

    2012.2 - 2016.12

  5. National Institute of Natural Sciences, Institute of Molecular Science   Assistant Professor

    2007.7 - 2012.2

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Education 3

  1. Kyoto University

    1999.4 - 2003.3

  2. Kyoto University

    1997.4 - 1999.3

  3. Shinshu University

    1993.4 - 1997.3

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Professional Memberships 7

  1. 理論化学会

    2022.4

  2. 日本生物物理学会

    2022.4

  3. Biophysical Society

    2020.1

  4. 日本物理学会

    2012.12

  5. 分子科学会

    2012.4

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Committee Memberships 3

  1. 溶液化学研究会   運営委員  

    2025.4   

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    Committee type：Academic society

  2. 分子科学会   企画委員  

    2022 - 2023   

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    Committee type：Academic society

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  3. 日本化学会   九州支部会計幹事  

    2017.4 - 2018.3   

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Awards 1

  1. 溶液化学研究会奨励賞

    2011   溶液化学研究会  

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    Award type：International academic award (Japan or overseas) 

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Papers 31

  1. RISMiCal: a software package to perform fast rism/3d-rism calculations Reviewed

    Yutaka Maruyama, Norio Yoshida

    Journal of Computational Chemistry   Vol. 45   page： 1470 - 1482   2024.2

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    Solvent plays an essential role in a variety of chemical, physical, and biological pro- cesses that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMi- Cal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM pro- grams for single- and multi-GPU codes written in CUDA would enhance the availabil- ity of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.

    DOI： 10.1002/jcc.27340

  2. Implementation of solvent polarization in three-dimensional reference interaction-site model self-consistent field theory Reviewed International journal

    Yoshida N., Yamaguchi T., Nakano H.

    Chemical Physics Letters   Vol. 797   2022.6

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Chemical Physics Letters  

    The three-dimensional reference interaction-site model self-consistent field (3D-RISM-SCF) theory is an electronic structure theory of solvated molecules, which can handle the electronic polarization of the solute molecule induced by the interaction with the solvent, whereas the electronic polarization of solvent molecules is ignored. Here, the solvent-polarizable model is implemented to take into account the electronic polarization of solvent molecules. It is applied to the water molecule in an aqueous solution and the p-nitroaniline molecule in an aqueous solution, and the effects of the solvent polarization on the properties of these solutes are demonstrated.

    DOI： 10.1016/j.cplett.2022.139579

    Scopus

  3. QM/MM/3D-RISM study of an electronic structure change of benzimidazole derivative induced by molecular recognition of cucurbit[7]uril Reviewed

    Kodai Kanemaru, Keisuke Shiroshita, Haruyuki Nakano, Norio Yoshida

    IOP Conf. Series: Materials Science and Engineering   Vol. 1325   page： 012008   2025.3

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (international conference proceedings)  

    DOI： 10.1088/1757-899X/1325/1/012008

  4. Why is Dimeric 3D Domain Swapping in Antibody Light ChainsMissing from the Solution? Atomistic Insights Mechanisms Reviewed

    Lian Duan, Kowit Hengphasatporn, Takahiro Sakai, Ryo Fujiki, Norio Yoshida, Shun Hirota, Yasuteru Shigeta

    The Journal of Physical Chemistry B   Vol. 128   page： 9086 - 9093   2024.9

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    Language：English  

    Misfolding of antibody light chains can lead tosystemic light chain amyloidosis, which is associated withmisfolding and aggregation. The antibody light chain may engagein 3D domain swapping within the variable region (#4VL) throughhydrogen bonding (HB) interactions, potentially forming thetetramer, as revealed in solution and crystal structures. However,the 3D-domain swapping (3D-DS) dimers could not be detectedexperimentally. This study investigates the absence of 3D-DS usingcomputational approaches, focusing on structural dynamics,solvation effects, and stability relevant to the loss of 3D-DS.Microscale molecular dynamics simulations of #4VL and 3D-DSconfirm that native HB interactions are essential to maintain β-sheet structures in both #4VL and 3D-DS. A flickering native HBinteraction in the 3D-DS system, caused by repulsive interaction with water molecules in the hydrophobic region, leads tointramolecular breathing motions and oligomerization in another 3D-DS. Structural dynamics of the 3D-DS dimer in long-runsimulations were analyzed using the newly developed integrated solvation-based principal component analysis (3D-RISM/PCA) anddensity-based spatial clustering of applications with noise, confirm that if the 3D-DS cannot form the tetramer within the breathingmotion process, the 3D-DS will collapse. This finding provides insights into why the 3D-DS dimer is missing from the solution andcan be used to design and develop 3D-DS in other antibodies

    DOI： 10.1021/acs.jpcb.4c03234

  5. Redesign of a thioflavin-T-binding protein with a flat β-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity Reviewed

    Yuina Miura, Sae Namioka, Atsushi Iwai, Norio Yoshida, Hiroyuki Konno, Youhei Sohma, O Motomu Kanai, Koki Makabe

    International Journal of Biological Macromolecules   Vol. 269   page： 131992   2024.4

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    Language：English  

    Amyloids, proteinous aggregates with β-sheet-rich fibrils, are involved in several neurodegenerative diseases
    such as Alzheimer’s disease; thus, their detection is critically important. The most common fluorescent dye for
    amyloid detection is thioflavin-T (ThT), which shows on/off fluorescence upon amyloid binding. We previously
    reported that an engineered globular protein with a flat β-sheet, peptide self-assembly mimic (PSAM), can be
    used as an amyloid binding model. In this study, we further explored the residue-specific properties of ThT-
    binding to the flat β-sheet by introducing systematic mutations. We found that site-specific mutations at the
    ThT-binding channel enhanced affinity. We also evaluated the binding of a ThT-based photocatalyst, which
    showed the photooxygenation activity on the amyloid fibril upon light radiation. Upon binding of the photocatalyst
    to the PSAM variant, singlet oxygen-generating activity was observed. The results of this study expand
    our understanding of the detailed binding mechanism of amyloid-specific molecules.

    DOI： 10.1016/j.ijbiomac.2024.131992

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Books 2

  1. Self-Consistent Treatment of Solvation Structure with Electronic Structure Based on 3D-RISM Theory

    Yoshida N.

    Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability  2021.1  （ ISBN:9789811592355, 9789811592348 ）

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    The solvent effects on the electronic structure of biomolecules are essential for considering their functions and structures. The three-dimensional reference interaction site model (3D-RISM) theory is a statistical mechanics integral equation theory of molecular liquids. It is suitable for describing the solvation structure of large molecules, i.e., the main target of the fragment molecular orbital (FMO) approach. The hybrid method of FMO and 3D-RISM, referred to as FMO/3D-RISM, enables us to investigate the electronic structure of large molecules in solution as well as solvation thermodynamics at the molecular level. This chapter describes the theoretical background of the 3D-RISM theory, the formalism of the hybrid method of 3D-RISM and quantum chemical theory including the FMO, and the applications of these methods.

    DOI： 10.1007/978-981-15-9235-5_24

    Scopus

  2. Molecular basics of liquids and liquid-based materials

    Nishiyama Katsura, Yamaguchi Tsuyoshi, Takamuku Toshiyuki, Yoshida Norio

    Springer  2021  （ ISBN:9789811653940 ）

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    Language：English

    CiNii Books

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Presentations 30

  1. Recent development of the solvation theory of biomolecules International conference

    Norio Yoshida

    The Sugadaira Winter Workshop 2025 on the role of fluctuations and dynamics in bio and soft matter  2025.1.9 

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    Event date： 2025.1

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  2. Development of in-silico material design tool based on the molecular theory of solvation Invited International conference

    Norio Yoshida

    6th International Conference on Materials Research and Innovation  Kasetsart University

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    Event date： 2024.12

    Language：English   Presentation type：Oral presentation (invited, special)  

    Venue：Centra Grand Hotel, Bangkok   Country：Thailand  

  3. Theory of molecular solvation for bio/nano-material design Invited International conference

    Norio Yoshida

    Thailand-Japan Symposium for Chemistry  Chiang-mai University

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    Event date： 2024.11

    Language：English   Presentation type：Oral presentation (invited, special)  

    Venue：Chiang-mai University   Country：Thailand  

  4. Development of multi-scale theory for molecular liquids Invited International conference

    Norio Yoshida

    Chula Mini-Symposium on Protein Dynamics in Living System  2024.9.13 

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    Event date： 2024.9

    Language：English   Presentation type：Oral presentation (invited, special)  

    Venue：Chulalongkorn University, Bangkok   Country：Thailand  

  5. Development of multi-scale theory for molecular liquids International conference

    Norio Yoshida

    Workshop on Biomaterial design inspired by the origin of life caused by liquid-liquid phase separation in dynamic solution environment  2024.9.10 

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    Event date： 2024.9

    Language：English   Presentation type：Oral presentation (general)  

    Venue：Kasetsart University, Bangkok   Country：Thailand  

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Research Project for Joint Research, Competitive Funding, etc. 5

  1. DEVELOPMENT OF AN ADVANCED ALGORITHM FOR THE INTEGRAL EQUATION THEORY OF LIQUIDS BASED ON QUANTUM COMPUTER International coauthorship

    Grant number：AQC203  2025.1 - 2027.12

    National Research Council of Canada  COLLABORATIVE RESEARCH AND DEVELOPMENT  Applied Quantum Computing Challenge program

    Norio Yoshida

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\30448588 （ Direct Cost: \27680535 、 Indirect Cost：\2768053 ）

  2. 動的溶液環境のセンシングおよび液-液相分離の制御と予測

    2024.4 - 2026.3

    豊田理化学研究所  2024年度豊田理研スカラー共同研究Phase2 

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    Authorship：Coinvestigator(s)  Grant type：Competitive

    Grant amount：\1000000 （ Direct Cost: \1000000 ）

  3. アミロイド触媒に着想した人工蛋白質から明らかにする原始代謝系の起源

    2024.4 - 2025.3

    自然科学研究機構  生命創成探究センター ExCELLSプロジェクト研究 

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    Authorship：Coinvestigator(s)  Grant type：Competitive

    Grant amount：\600000 （ Direct Cost: \600000 ）

  4. 酸化還元状態と共役したタンパク質の液-液相分離の解析と制御を可能にする分子ツールの開発

    Grant number：R4-73  2023.4 - 2024.3

    豊田理化学研究所  2023年度豊田理研スカラー共同研究 

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\600000 （ Direct Cost: \600000 ）

  5. バイオ・高分子ビッグデータ駆動による完全循環型バイオアダプティブ材料の創出

    2023.4

    バイオ・高分子ビッグデータ駆動 データ創出・活用型マテリアル研究開発プロジェクト 

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    Authorship：Coinvestigator(s)  Grant type：Competitive

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KAKENHI (Grants-in-Aid for Scientific Research) 9

  1. 溶液環境による分子凝集制御機構の究明と分子設計ツールの創成

    Grant number：24K01434  2024.4 - 2028.3

    日本学術振興会  科学研究費助成事業   基盤研究(B)

    菅瀬謙治, 池田将, 山口毅

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\18720000 （ Direct Cost: \14400000 、 Indirect Cost：\4320000 ）

  2. 動的溶液環境における天然変性タンパク質自己凝縮過程の理論研究

    Grant number：22H05089  2022.5 - 2025.3

    日本学術振興会  科学研究費  学術変革領域研究(B)

    吉田紀生

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\23920000 （ Direct Cost: \18400000 、 Indirect Cost：\5520000 ）

  3. 高分子有機摩擦調整剤の最適設計－分子構造をマクロ摩擦特性につなぐ計算スキーム

    Grant number：24H00282  2024.3 - 2028.3

    日本学術振興会  科学研究費助成事業  基盤研究(A)

    張賀東, 塚本眞幸, 東直輝, 宋玉璽, 安田耕二

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    Authorship：Coinvestigator(s)  Grant type：Competitive

  4. 動的溶液科学の推進

    Grant number：22H05087  2022.5 - 2025.3

    科学研究費助成事業  学術変革領域研究(B)

    関山 直孝, 菅瀬 謙治, 吉田 紀生, 中村 秀樹, 山口 毅

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    Authorship：Coinvestigator(s) 

    本研究領域は、化学的・物理的な状態が時空間的に変動する動的溶液環境に着目し、動的溶液環境が天然変性タンパク質の自己凝縮過程を制御する機構の解明を目指す。そのために、各計画研究で得られた結果や知見を統合し相互循環させることで力強く領域を推進する。加えて、領域内で得られた研究成果や研究手法を幅広い分野に向けて発信し、同時に他分野の知見も積極的に取り入れることで、本研究領域の発展を目指す。

  5. アミロイド触媒型の原始酵素モデルに着想した人工酵素のデザインと応用

    Grant number： 22H01873  2022.4 - 2025.3

    日本学術振興会  科学研究費補助金  アミロイド触媒型の原始酵素モデルに着想した人工酵素のデザインと応用

    吉田紀生

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    Authorship：Coinvestigator(s)  Grant type：Competitive

    Grant amount：\2600000 （ Direct Cost: \2000000 、 Indirect Cost：\600000 ）

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Teaching Experience (On-campus) 1

  1. シミュレーション・サイエンス2

    2022

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Teaching Experience (Off-campus) 1

  1. バイオ・高分子マテリアルDX論

    2024.10 （Kyoto University）

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    Level：Postgraduate  Country：Japan

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