Mechanism of allosteric dissociation by regulator proteins of actin filament elongation

• Project/Area Number: 19K12217
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 62010:Life, health and medical informatics-related
• Research Institution: Nagoya University
• Principal Investigator: Koike Ryotaro 名古屋大学, 情報学研究科, 助教 (20381577)
• Project Period (FY): 2019-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2022: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2021: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000); Fiscal Year 2020: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000); Fiscal Year 2019: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
• Keywords: 動的構造 / 分子シミュレーション / アクチン

Outline of Research at the Start

アクチンフィラメントの伸び縮みは，細胞の変形や運動という生命にとって普遍的な現象と密接に関わる．本研究では，フィラメントの伸縮に関わるCARMIL蛋白質とキャッピング蛋白質（CP）に着目し，CARMILによるCPのフィラメントからの引きはがし（結合解離）の分子メカニズムを調査する．まず解離過程の分子シミュレーションを行う．このときフィラメントの代わりにV-1蛋白質を用いる．得られたシミュレーションのデータを，独自に開発した計算機ツールMotion Treeを用いて調査し，特徴的な分子運動を特定する．分子運動と結合の関係を探り，結合解離の分子メカニズムを調査する．

Outline of Final Research Achievements

Actin filament elongation is regulated by a number of proteins. Actin capping protein (CP) binds to the end of filament and inhibits their elongation, whereas CARMIL protein binds to CP and can dissociate it from filament. Structural flexibility of CP is expected to be the key to this dissociation. In this study, using molecular dynamics simulation and elastic network model, we comprehensively investigated the effect of binding of CARMIL on the flexibility of CP. As a result, we clarified which part of CARMIL significantly changes the flexibility of CP. We also clarified the characteristics binding patterns of the parts that change the flexibility.

Academic Significance and Societal Importance of the Research Achievements

アクチンフィラメントの伸長は細胞の変形や運動という普遍的な生命現象に直結している．フィラメントを制御する蛋白質の研究は，細胞の変形・運動といったマクロな現象が，分子レベルでどのように実現されているのかを理解するために欠かせなない．制御蛋白質の働きには揺らぎが関わっている．蛋白質間の結合と揺らぎがどのように関係するか，分子シミュレーションや弾性ネットワークモデルを使って網羅的に解析し，結合と揺らぎの関係を明らかにした．結合と揺らぎに関する知見は，フィラメントの伸長を制御する蛋白質の働きをコトンロールするための基盤となる．

Research Products

• [Journal Article] Structures and mechanisms of actin ATP hydrolysis (2022)
  • Author(s): Kanematsu Yusuke、Narita Akihiro、Oda Toshiro、Koike Ryotaro、Ota Motonori、Takano Yu、Moritsugu Kei、Fujiwara Ikuko、Tanaka Kotaro、Komatsu Hideyuki、Nagae Takayuki、Watanabe Nobuhisa、Iwasa Mitsusada、Ma?da Yuichiro、Takeda Shuichi
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 119 Issue: 43
  • DOI: 10.1073/pnas.2122641119
  • Peer Reviewed / Open Access
• [Journal Article] Structural insights into the regulation of actin capping protein by twinfilin C-terminal tail (2021)
  • Author(s): Shuichi Takeda, Ryotaro Koike, Ikuko Fujiwara, Akihiro Narita, Makoto Miyata, Motonori Ota and Yuichiro Maeda
  • Journal Title: J Mol Biol Volume: 433 Issue: 9 Pages: 166891-166891
  • DOI: 10.1016/j.jmb.2021.166891
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of human V-1 in the apo form (2021)
  • Author(s): Shuichi Takeda, Ryotaro Koike, Takayuki Nagae, Ikuko Fujiwara, Akihiro Narita, Yuichiro Maeda, Motonori Ota
  • Journal Title: Acta Crystallogr F Struct Biol Commun Volume: 77 Issue: 1 Pages: 13-21
  • DOI: 10.1107/s2053230x20016829
  • Peer Reviewed
• [Journal Article] Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins (2019)
  • Author(s): Koike Ryotaro、Amano Mutsuki、Kaibuchi Kozo、Ota Motonori
  • Journal Title: Protein Science Volume: 29 Issue: 2 Pages: 564-571
  • DOI: 10.1002/pro.3789
  • Peer Reviewed / Open Access
• [Journal Article] All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins (2019)
  • Author(s): Koike Ryotaro、Ota Motonori
  • Journal Title: Biophysics and Physicobiology Volume: 16 Issue: 0 Pages: 280-286
  • DOI: 10.2142/biophysico.16.0_280
  • NAID: 130007752770
  • ISSN: 2189-4779
  • Peer Reviewed / Open Access
• [Presentation] Structural changes of ATPase complexes in the PDB (2022)
  • Author(s): Ryotaro Koike
  • Organizer: 第60回日本生物物理学会
• [Presentation] 天然変性タンパク質データベース：IDEAL (2022)
  • Author(s): ANBO Hiroto, SAKUMA Koya, KADO Yumiko, SAKAMOTO Shigetaka, HOSODA Kazuo, SHIKAMA Noriko, DAIYASU Hiromi, TAKAGI Daisuke, YAMAGUCHI Atsuko, HATANAKA Hideki, KOIKE Ryotaro, HIROAKI Hidekazu, FUKUCHI Satoshi, OTA Motonori
  • Organizer: トーゴーの日シンポジウム2022
• [Presentation] 異なる機能状態にあるアクチンの構造ゆらぎとその相関関係 (2021)
  • Author(s): 小池亮太郎，森次圭，太田元規
  • Organizer: 第21回日本蛋白質科学会年会
• [Presentation] Elastic network model analysis shows distinct flexibilities of capping protein bound to CARMIL or twinfilin (2021)
  • Author(s): Ryotaro Koike, Motonori Ota
  • Organizer: 第59回日本生物物理学会
• [Presentation] Structural flexibility of actin in molecular dynamics simulation (2021)
  • Author(s): Ryotaro Koike, Motonori Ota
  • Organizer: 環太平洋国際化学会議2021
  • Int'l Joint Research
• [Presentation] Structural flexibility of actin studied by molecular dynamics simulation (2020)
  • Author(s): Ryotaro Koike, Motonori Ota
  • Organizer: 第58回日本生物物理学会
• [Presentation] 全原子Motion Treeとドメイン運動に伴う側鎖の運動 (2019)
  • Author(s): 小池亮太郎，太田元規
  • Organizer: 第19回日本蛋白質科学会年会
• [Presentation] タンパク質ータンパク質間相互作用の有向ネットワークが示す細胞内情報伝達 (2019)
  • Author(s): 葉山雄揮，小池亮太郎，太田元規
  • Organizer: 第19回日本蛋白質科学会年会
• [Presentation] Full-atom Motion Tree detects side-chain motions and their coupling with domain motions (2019)
  • Author(s): Ryotaro Koike, Motonori Ota
  • Organizer: 第57回日本生物物理学会
• [Presentation] Structural flexibility of actin monomer in molecular dynamics simulation (2019)
  • Author(s): Ryotaro Koike, Motonori Ota
  • Organizer: 11th Toyota Riken International Workshop, Actin Workshop
  • Int'l Joint Research
• [Book] Protein Structural Changes Based on Structural Comparison (Chapter 8 of eBook "Practical Guide to Life Science Databases" edited by Imad Abugessaisa, Takeya Kasukawa) (2022)
  • Author(s): Koike Ryotaro, Ota Motonori
  • Total Pages: 224
  • Publisher: Springer Nature
  • ISBN: 9789811658129