Updated on 2025/03/10

写真a

 
Shinoda Wataru
 
Organization
Research Institute for Interdisciplinary Science Professor
Position
Professor
External link

Degree

  • 博士(理学) ( 東京工業大学 )

Research Interests

  • Molecular simulation, multiscale modeling, lipid membrane, biological membrane, self-assembly, liposome, lipid nanoparticles, drug delivery carrier, virus capsid, polymer materials, polymer electrolytes

Research Areas

  • Natural Science / Biophysics, chemical physics and soft matter physics

  • Nanotechnology/Materials / Fundamental physical chemistry

Education

  • Tokyo Institute of Technology   総合理工学研究科   電子化学専攻 博士後期課程

    1995.4 - 1998.3

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    Country: Japan

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Research History

  • Okayama University   The Research Institute for Interdisciplinary Science   Professor

    2021.10

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  • Nagoya University   Graduate School of Engineering   Associate Professor

    2014.1 - 2021.9

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    Country:Japan

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  • University of Pennsylvania   Department of Chemistry   Visiting Scholar

    2005.4 - 2007.3

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    Country:United States

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  • National Institute of Advanced Industrial Science and Technology

    2001.4 - 2013.12

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  • National Institute of Materials and Chemical Research

    2000.4 - 2001.3

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Professional Memberships

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Papers

  • Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. Reviewed International journal

    Yuichi Umegawa, Tomoya Yamamoto, Mayank Dixit, Kosuke Funahashi, Sangjae Seo, Yasuo Nakagawa, Taiga Suzuki, Shigeru Matsuoka, Hiroshi Tsuchikawa, Shinya Hanashima, Tohru Oishi, Nobuaki Matsumori, Wataru Shinoda, Michio Murata

    Science advances   8 ( 24 )   eabo2658   2022.6

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

    Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.

    DOI: 10.1126/sciadv.abo2658

    PubMed

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  • Asymmetry and Heterogeneity in the Plasma Membrane

    Teppei Yamada, Wataru Shinoda

    2025.3

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    Publisher:Cold Spring Harbor Laboratory  

    Plasma membranes (PMs) exhibit asymmetry between their two leaflets in terms of phospholipid headgroups, unsaturation, and resulting membrane properties such as packing and fluidity. Lateral heterogeneity, including the formation of lipid domains, is another crucial aspect of PMs with significant biological implications. However, the nature and even the existence of lipid domains in the two leaflets of PMs remain elusive, hindering a complete understanding of the significance of lipid asymmetry. Using coarse-grained molecular dynamics simulation of the asymmetric PM, we find that the outer leaflet predominantly adopts a liquid-ordered state, whereas the inner leaflet separates into nanoscale (≈10 nm) liquid-ordered and liquid-disordered domains, exhibiting highly dynamic fusion and fission events. This structural asymmetry is further reinforced by asymmetric lateral stress resulting from a cholesterol bias toward the outer leaflet. These findings suggest distinct functional roles for the two leaflets, modulated by asymmetric lateral stress. Additionally, comparing the phase behavior of asymmetric and fully scrambled PMs reveals a key determinant of domain size: intact PMs maintain nanoscale domains, while cell-derived giant PM vesicles, which have lost the strict lipid asymmetry, exhibit microscale domains.

    DOI: 10.1101/2025.03.03.641122

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  • Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA

    Marina Musa, Zetao Zhu, Hiromi Takahashi, Wataru Shinoda, Yoshinobu Baba, Takao Yasui

    Lab on a Chip   2025

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/D4LC00893F

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  • NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using 13C and 19F labelling Invited Reviewed

    Yuichi Umegawa, Hiroshi Tsuchikawa, Wataru Shinoda, Michio Murata

    Organic & Biomolecular Chemistry   2025

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

    DOI: 10.1039/D4OB01468E

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  • Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation Reviewed

    Kevin A. Alberto, M. N. Hasna Begam, Hejian Xiong, Wataru Shinoda, Paul A. Slesinger, Zhenpeng Qin, Steven O. Nielsen

    Nanoscale   2025

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/D4NR02509A

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MISC

  • Elucidation of inter-leaflet coupling in asymmetric membranes induced by very long chain sphingomyelin based on solid-state NMR

    KEERATISAKULSITH Tanatchphong, UMEGAWA Yuichi, TSUCHIKAWA Hiroshi, HANASHIMA Shinya, MURATA Michio, SHINODA Wataru

    日本化学会春季年会講演予稿集(Web)   101st   2021

  • 分子動力学計算による界面活性剤含水ラメラの構造決定および分子挙動に関する研究

    武田康助, 安藤嘉倫, 篠田渉, 岡崎進, 岡崎進

    分子シミュレーション討論会講演要旨集   33rd   2019

  • B型肝炎ウイルス(HBV)への逆転写阻害薬剤分子の自由エネルギー計算によるカプシド内部への吸収・透過機構の解明

    浦野諒, 藤本和士, 安藤嘉倫, 吉井範行, 篠田渉, 岡崎進

    分子シミュレーション討論会講演要旨集   33rd   2019

  • B型肝炎ウイルス(HBV)への逆転写阻害薬剤分子のカプシド内部の自由エネルギー計算

    浦野諒, 藤本和士, 安藤嘉倫, 吉井範行, 篠田渉, 岡崎進

    分子科学討論会講演プログラム&要旨(Web)   13th   2019

  • Structure Elucidation of Ion Channel Assembly Formed by Amphotericin B and Sterol

    山本智也, 山本智也, 梅川雄一, 梅川雄一, 中川泰男, 鈴木大河, 山上正輝, 土川博史, 花島慎弥, 村田道雄, 村田道雄, 松森信明, 松森信明, SEO Sangjae, 篠田渉

    天然有機化合物討論会講演要旨集(Web)   60th   2018

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Presentations

  • Simulating Endosomal Escape of Lipid Nanoparticles Invited

    Wataru Shinoda

    The 6th International Conference on Molecular Simulation (ICMS2023)  2023.10.7 

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    Event date: 2023.10.6 - 2023.10.9

    Language:English   Presentation type:Oral presentation (keynote)  

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  • Coarse Grained Molecular Dynamics Study on Endosomal Escape of dsDNA Encapsulated in Lipid Nanoparticles using the SPICA Force Field Invited

    Wataru Shinoda

    CECAM workshop: Macromolecular complexes: from ab initio and integrative modelling to functional dynamics  2023.9.7 

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    Event date: 2023.9.5 - 2023.9.8

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

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  • 固体NMRを用いたリン脂質アシル鎖の平均配向解析

    梅川雄、齋藤宣樹、花島慎弥、篠田渉、村田道雄

    ケミカルバイオロジー学会 第17回年会  2023.5.29  日本ケミカルバイオロジー学会

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    Event date: 2023.5.29 - 2023.5.31

    Language:Japanese   Presentation type:Poster presentation  

    Venue:⼤阪⼤学会館(⼤阪⼤学 豊中キャンパス)   Country:Japan  

  • Exploring the Mechanism of Endosomal Escape of Lipid Nanoparticles: A Coarse-Grained Molecular Dynamics Study Invited International conference

    Wataru Shinoda

    Asia Pacific Conference of Theoretical and Computational Chemistry APATCC-10  2023.2.19 

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    Event date: 2023.2.19 - 2023.2.23

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

    Venue:The International Centre for Interdisciplinary Science and Education (ICISE)   Country:Viet Nam  

  • 分子動力学計算による Li 伝導機構解明に立脚した高 Li 輸率のための 電解液設計と最適化

    篠田 渉

    JST-ALCA SPRING Li-S電池チームミーティング  2023.1.8  JST

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    Event date: 2023.1.8 - 2023.1.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:静岡県   Country:Japan  

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Research Projects

  • Development of Applications of Engineered Lipid Particles

    Grant number:24H00038  2024.04 - 2029.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (S)

    渡慶次 学, 真栄城 正寿, 篠田 渉

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    Grant amount:\205400000 ( Direct expense: \158000000 、 Indirect expense:\47400000 )

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  • 膜透過の計算科学:膜モジュレータの作用と核酸透過機構の解明

    Grant number:24H00843  2024.04 - 2027.03

    日本学術振興会  科学研究費助成事業  学術変革領域研究(B)

    篠田 渉

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    Grant amount:\28340000 ( Direct expense: \21800000 、 Indirect expense:\6540000 )

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  • 細胞膜をゆらす核酸医薬の膜透過機構の総合理解と膜透過学の創成

    Grant number:24H00839  2024.04 - 2027.03

    日本学術振興会  科学研究費助成事業  学術変革領域研究(B)

    大澤 昂志, 三木 康嗣, 篠田 渉, 川口 祥正

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    Grant amount:\8320000 ( Direct expense: \6400000 、 Indirect expense:\1920000 )

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  • Average orientation of lipid acyl chains in the domain structure of model membranes

    Grant number:23K17373  2023.06 - 2026.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Pioneering)

    村田 道雄, 篠田 渉, 花島 慎弥, 杉山 成

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    Grant amount:\25740000 ( Direct expense: \19800000 、 Indirect expense:\5940000 )

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  • Molecular Dynamics of Intracellular Transport of Lipid Nanoparticles: Molecular mechanism of endosomal escape of nucleic acids

    Grant number:21H01880  2021.04 - 2025.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    篠田 渉, 浦野 諒

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    Grant amount:\17420000 ( Direct expense: \13400000 、 Indirect expense:\4020000 )

    脂質ナノ粒子(LNP)のエンドソーム脱出を分子動力学(MD)シミュレーションで解析し、その分子機構を明らかにすることを目的としており、当該年度においては、まず、核酸と脂質の複合構造であるLNPとエンドソーム膜の分子モデリングを中心に行った。dsDNAに標準系の脂質(1,2-dilinoleyloxy-3-dimethylaminopropane (DLin-MC3-DMA),コレステロール(Chol), ホスファチジルコリン(PC)脂質)を混合してできたLNPのMD計算を行った。カチオン性脂質(DLin-MC3-DMA)のpH変化に伴うイオン化状態の変化を考慮した粗視化(SPICA)力場を作成し、約30nmの直径のLNPのMD計算を実行した。DLin-MC3-DMAのイオン化状態の変化は、LNP構造を大きく変化させ、特にdsDNAのLNP内包状態が変化することがわかった。また、エンドソーム膜のモデリングを行い、実験情報に合わせた脂質組成を持つエンドソーム膜モデルをSPICA力場で作成した。コレステロールを含む5種の異なる脂質の混合膜としてモデルを作成し、大きなドメイン構造を持たないことを確認した。さらに、LNPとエンドソーム膜の相互作用を確認する分子動力学(MD)シミュレーションを行った。LNPは中性条件ではエンドソーム膜と積極的な相互作用を示さなかったが、酸性条件においては静電相互作用によってエンドソーム膜に強く吸着することがわかった。吸着後の融合プロセスは非常に長時間を要するため、律速段階であるLNPとエンドソーム膜間の吸着表面の脱水和を人工的にさせ、その後の融合の進展を観測した。現在、融合シミュレーションの途中であるが、数µs以上かけて構造緩和をしながら融合が進む様子が見られた。次年度以降にも継続して融合MD計算を実行する必要がある。

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Class subject in charge

  • Topics in Molecular Chemistry 1 (2024academic year) Concentration  - その他

  • Seminar in Molecular Science (2024academic year) Prophase  - その他

  • Seminar in Molecular Science (2024academic year) Year-round  - その他

  • Seminar in Molecular Science (Theoretical and Computational Chemistry) (2024academic year) Other  - その他

  • Seminar in Molecular Science (Theoretical and Computational Chemistry) (2024academic year) Year-round  - その他

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