Synthetic and Structural Biology Approach for Understanding Mechanism of AAA-ATPase

• Project/Area Number: 22570118
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Nagoya University (2011-2012); Kobe University (2010)
• Principal Investigator: HIROAKI Hidekazu 名古屋大学, 創薬科学研究科, 教授 (10336589)
• Co-Investigator(Renkei-kenkyūsha): TENNO Takeshi 名古屋大学, 大学院・創薬科学研究科, 助教 (70381663) ; FUJIWARA Yoshie 京都大学, 物質-細胞統合システム拠点, 研究員 (90423095)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: 分子認識及び相互作用 / マルチドメインタンパク質 / 天然変性タンパク質 / ATPase / AAA-ATPase / 膜輸送 / 細胞骨格 / 膜骨格 / マルチドメイン蛋白質 / AAAドメイン / MITドメイン / 微小管切断酵素 / ESCRT-III複合体 / ドミナントネガティブ変異体 / タウタンパク質 / ヒストンフォールド

Research Abstract

We extensively used the 3D structural information of the N-terminal domains which were isolated from the other part of AAA-ATPases (Class I and II). We succeeded in determining the tubulin binding site on Katanin p^60 N-terminal domain. Subsequently we found a novel Ca^2+-dependent regulatory mechanism of Katanin’s ATPase activity. For NVL2, the solution structure as well as binding target of N-terminal domain were determined. We thus proposed two hypothesis, one is for the molecular mechanisms on microtubule severing, and another is for the cellular function of NVL2.We extensively used the 3D structural information of the N-terminal domains which were isolated from the other part of AAA-ATPases (Class I and II). We succeeded in determining the tubulin binding site on Katanin p60 N-terminal domain. Subsequently we found a novel Ca2+-dependent regulatory mechanism of Katanin’s ATPase activity. For NVL2, the solution structure as well as binding target of N-terminal domain were determined. We thus proposed two hypothesis, one is for the molecular mechanisms on microtubule severing, and another is for the cellular function of NVL2.

Research Products

• [Journal Article] An assignment of intrinsically disordered regions of proteins based on NMR structures. (2013)
  • Author(s): Ota, M*., Koike, R., Amemiya, T., Tenno, T., Romero, P.R., Hiroaki, H., Dunker, A.K., and Fukuchi, S.
  • Journal Title: J Structural Biol Volume: 181 Pages: 29-36
  • Peer Reviewed
• [Journal Article] MIT domain of Vps4 is a Ca^2+-dependent phosphoinositide-binding domain. (2013)
  • Author(s): Iwaya, N., Takasu, H., Goda, N., Shirakawa, M., Tanaka, T., Hamada, D., and Hiroaki, H*.
  • Journal Title: J. Biochem. Volume: 153(5) Pages: 473-481
  • Peer Reviewed
• [Journal Article] MIT domain of Vps4 is a Ca^<2+>-dependent phosphoinositide-binding domain (2013)
  • Author(s): Naoko Iwaya, Hirotoshi Takasu, Natsuko Goda, Masahiro Shirakawa, Toshiki Tanaka, Daizo Hamada, Hidekazu Hiroaki
  • Journal Title: The Journal of Biochemistry Volume: 153巻 Issue: 5 Pages: 473-481
  • DOI: 10.1093/jb/mvt012
  • Peer Reviewed
• [Journal Article] Recent applications of isotopic labeling for protein NMR in drug discovery. invited review (2013)
  • Author(s): Hiroaki, H* (Hiroaki, H.)
  • Journal Title: Expert Opinion on Drug Discovery Volume: 8 Issue: 5 Pages: 523-536
  • DOI: 10.1517/17460441.2013.779665
  • Peer Reviewed
• [Journal Article] IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature. (2012)
  • Author(s): Fukuchi, S*., Sakamoto, S., Nobe, Y., Murakami, D. S., Amemiya, T., Hosoda, K., Koike, R. Hiroaki, H., and Ota, M*.
  • Journal Title: Nucleic Acids Research (database issue) Volume: 40 (1)
  • Peer Reviewed
• [Journal Article] Effect of Ca^2+ on microtubule severing enzyme katanin p60; insight into the substrate dependent activation mechanism. (2012)
  • Author(s): Iwaya, N., Akiyama, K., Goda, N., Tenno, T., Fujiwara, Y., Hamada, D., Ikura, T., Shirakawa, M., and Hiroaki, H*.
  • Journal Title: FEBS J Volume: 279 Pages: 1339-1352
  • Peer Reviewed
• [Journal Article] IDEAL : intrinsically disordered proteins with extensive annotations and literature (2012)
  • Author(s): S.Fukuchi.H.Hiroaki, M.Ota, et al.
  • Journal Title: Nucleic Acids Res. Volume: 40巻 Issue: D1 Pages: D507-D511
  • DOI: 10.1093/nar/gkr884
  • Peer Reviewed
• [Journal Article] Effect of Ca^<2+> on microtubule severing enzyme katanin p60 ; insight into the substrate dependent activation mechanism (2012)
  • Author(s): N.Iwaya, et al
  • Journal Title: FEBS J. Volume: 279 Issue: 7 Pages: 1339-1352
  • DOI: 10.1111/j.1742-4658.2012.08528.x
  • Peer Reviewed
• [Journal Article] A Simplified Recipe for Assigning Amide NMR Signals Using Combinatorial 14N Amino Acid Inverse-Labeling. (2011)
  • Author(s): Hiroaki, H*., Umetsu, Y., Hoshi, M., Nabeshima, Y. and Kohda, D.
  • Journal Title: J Structural Functional Genomics Volume: 12 (3) Pages: 167-174
  • Peer Reviewed
• [Journal Article] Structure and function of the N-terminal nucleolin binding domain of nuclear Valocin containing protein like 2 (NVL2) harboring a nucleolar localization signal (2011)
  • Author(s): Fujiwara, Y., Fujiwara, K., Goda, N., Iwaya, N., Tenno, T., Shirakawa, M., Hiroaki, H*.
  • Journal Title: J Biol Chem Volume: 286 (24) Pages: 21732-21741
  • Peer Reviewed
• [Journal Article] Structure and function of the N-terminal nucleolin binding domain of nuclear Valocin containing protein like 2 (NVL2) harboring a nucleolar localization signal (2011)
  • Author(s): Y.Fujiwara, et al
  • Journal Title: J Biol Chem Volume: 286 Issue: 24 Pages: 21732-21741
  • DOI: 10.1074/jbc.m110.174680
  • Peer Reviewed
• [Journal Article] A Simplified Recipe for Assigning Amide NMR Signals Using Combinatorial 14N Amino Acid Inverse-Labeling (2011)
  • Author(s): H.Hiroaki, et al.
  • Journal Title: J Structural Functional Genomics. Volume: 12巻 Issue: 3 Pages: 167-174
  • DOI: 10.1007/s10969-011-9116-0
  • Peer Reviewed
• [Journal Article] SAHG, a comprehensive database of predicted structures of all human proteins. (2010)
  • Author(s): Motono, C., Nakata, J., Koike, R., Shimizu, K., Shirota, M., Amemiya, T., Tomii, K., Nagano, N., Sakaya, N., Misoo, K., Sato, M., Kidera, A., Hiroaki, H., Shirai, T., Kinoshita, K., Noguchi, T., and Ota, M.
  • Journal Title: Nucleic Acids Res Volume: 39(suppl 1)
  • Peer Reviewed
• [Journal Article] A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. (2010)
  • Author(s): Iwaya, N., Kuwahara, Y., Fujiwara, Y., Goda, N., Tenno, T., Akiyama, K., Mase, S., Tochio, H., Ikegami, T., Shirakawa, M., and Hiroaki, H*.
  • Journal Title: J Biol Chem Volume: 285 Pages: 16822-16829
  • Peer Reviewed
• [Journal Article] Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins. (2010)
  • Author(s): Jee, J., Mizuno, T., Kamada, K., Tochio, H., Chiba, Y., Yanagi, K., Yasuda, G., Hiroaki, H., Hanaoka, F., and Shirakawa, M.
  • Journal Title: J Biol Chem Volume: 285 Pages: 15931-15940
  • Peer Reviewed
• [Journal Article] SAHG, a comprehensive database of predicted structures of all human proteins. (2010)
  • Author(s): Motono, C., Hiroaki, H., Ota, M, 他
  • Journal Title: Nucleic Acids Research Volume: 39 (suppl 1)
  • Peer Reviewed
• [Journal Article] Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3. (2010)
  • Author(s): Nishimasu, R., Komori, H., Higuchi, Y., Nishimasu, H., Hiroaki, H.
  • Journal Title: Kobe Journal of Medical Sciences Volume: 56
  • NAID: 110009824994
  • Peer Reviewed
• [Journal Article] A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. (2010)
  • Author(s): Iwaya, N., Kuwahara, Y., Fujiwara, Y., Goda, N., Tenno, T., Hiroaki, H., 他
  • Journal Title: Jounrnal of Biologicl Chemistry Volume: 285 Pages: 16822-16829
  • Peer Reviewed
• [Journal Article] Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins. (2010)
  • Author(s): Jee, J., Hiroaki, H., Hanaoka, F., Shirakawa, M, 他
  • Journal Title: Jounrnal of Biologicl Chemistry Volume: 285 Pages: 15931-15940
  • Peer Reviewed
• [Journal Article] Recent applications of isotopic labeling for protein NMR in drug discovery
  • Author(s): Hiroaki, H*.
  • Journal Title: Expert Opinion on Drug Discovery Volume: 8(5) Pages: 523-536
  • Peer Reviewed
• [Presentation] I型AAA-ATPaseのN末端ドメインに存在するCa^2+結合部位の機能比較 (2013)
  • Author(s): 岩谷奈央子、合田名都子、高須博敏、白川昌宏、田中俊樹、〓田大三、廣明秀一
  • Organizer: 日本薬学会第133年会
  • Place of Presentation: パシフィコ横浜(横浜市)
  • Year and Date: 2013-03-28
• [Presentation] IDEAL: the collection and visualization of knowledge regarding intrinsically disordered proteins verified by experiments (2013)
  • Author(s): 雨宮崇之、坂本盛宇、野辺由紀子、村上聖子、嘉戸裕美子、細田和男、小池亮太郎、廣明秀一、太田元規、福地佐斗志
  • Organizer: The 2nd Internatiional Symposium on Intrinsically Disordered Proteins
  • Place of Presentation: 理化学研究所横浜研究所
  • Year and Date: 2013-01-23
• [Presentation] IDEAL: the collection and visualization of knowledge regarding intrinsically disordered proteins verified by experiments (2013)
  • Author(s): 雨宮崇之、坂本盛宇、野辺由紀子、村上聖子、嘉戸裕美子、細田和男、小池亮太郎、廣明秀一、太田元規、福地佐斗志 (福地)
  • Organizer: The 2nd Internatiional Symposium on Intrinsically Disordered Proteins
  • Place of Presentation: 理化学研究所横浜研究所(横浜市）
• [Presentation] I型AAA-ATPaseのN末端ドメインに存在するCa2+結合部位の機能比較 (2013)
  • Author(s): 岩谷奈央子、合田名都子、高須博敏、白川昌宏、田中俊樹、濵田大三、廣明秀一 (廣明)
  • Organizer: 日本薬学会第133年会
  • Place of Presentation: パシフィコ横浜(横浜市）
• [Presentation] 天然変性タンパク質データベースIDEALの開発 (2012)
  • Author(s): 雨宮崇之、坂本盛宇、野辺由紀子、村上聖子、細田和男、小池亮太郎、廣明秀一、太田元規、福地佐斗志
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2012-06-22
• [Presentation] 微小管切断酵素p60-kataninに対するCa^2+の効果 (2012)
  • Author(s): 岩谷奈央子、合田名都子、天野剛志、藤原芳江、〓田大三、伊倉貞吉、白川昌宏、廣明秀一
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2012-06-22
• [Presentation] 創薬標的としてのAAA-ATPaseとNMR構造生物学 (2012)
  • Author(s): 廣明秀一
  • Organizer: 第一回岐阜構造生物学・医学・論理的創薬研究会シンポジウム:構造生物学・医学・論理的創薬の拠点構築を目指して
  • Place of Presentation: 岐阜大学医学部(岐阜市)
  • Year and Date: 2012-03-23
• [Presentation] 創薬標的としてのAAA-ATPaseとNMR構造生物学 (2012)
  • Author(s): 廣明秀一
  • Organizer: 第一回岐阜構造生物学・医学・論理的創薬研究会シンポジウム:構造生物学・医学・論理的創薬の拠点構築を目指して
  • Place of Presentation: 岐阜大学医学部多目的室(岐阜市)
  • Year and Date: 2012-03-23
• [Presentation] 天然変性タンパク質データベースIDEALの開発 (2012)
  • Author(s): 雨宮崇之、坂本盛宇、野辺由紀子、村上聖子、細田和男、小池亮太郎、廣明秀一、太田元規、福地佐斗志 (福地)
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場（名古屋市）
• [Presentation] 微小管切断酵素p60-kataninに対するCa2+の効果 (2012)
  • Author(s): 岩谷奈央子、合田名都子、天野剛志、藤原芳江、濵田大三、伊倉貞吉、白川昌宏、廣明秀一(岩谷）
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場（名古屋市）
• [Presentation] 核小体に局在するAAA ATPase, NVL2のN末端ドメインの解析 (2011)
  • Author(s): 藤原芳江、合田名都子*、岩谷奈央子*、天野剛志*、白川昌宏、廣明秀一
  • Organizer: 第34回日本分子生物学学会年会
  • Place of Presentation: パシフィコ横浜(横浜市)
  • Year and Date: 2011-12-13
• [Presentation] 核小体に局在するAAAATPase,NVL2のN末端ドメインの解析 (2011)
  • Author(s): 藤原芳江、合田名都子、岩谷奈央子、天野剛志、白川昌宏、廣明秀
  • Organizer: 第34回日本分子生物学学会年会
  • Place of Presentation: パシフィコ横浜(横浜市)
  • Year and Date: 2011-12-13
• [Presentation] Contribution of NMR studies to constructing SAHG, a database of predicted protein structures from human genome (2011)
  • Author(s): 廣明秀一、合田(天野)名都子*、天野剛志、本野千恵子、富井健太郎、清水佳奈、木下賢吾、太田元規
  • Organizer: ISNMR2011-第50回記念NMR討論会国際シンポジウム
  • Place of Presentation: 横浜大桟橋ホール(横浜市)
  • Year and Date: 2011-11-15
• [Presentation] Structure and Function of the Two N-Terminal Domains of AAA-ATPases, p60 Katanin and Nuclear Valosin Containing Protein Like 2 (NVL2) (2011)
  • Author(s): 廣明秀一
  • Organizer: 9th International Conference on AAA proteins
  • Place of Presentation: 熊本市国際交流センター(熊本市)
  • Year and Date: 2011-11-06
• [Presentation] NVL2のN末端にある新規ヌクレオリン結合ドメインの構造と機能 (2010)
  • Author(s): 藤原芳江, 藤原健一郎, 合田名都子, 岩谷奈央子, 天野剛志, 廣明秀一
  • Organizer: 第49回NMR討論会
  • Year and Date: 2010-11-16
• [Remarks] 研究室ホームページ(名古屋大学創薬科学研究科構造分子薬理学分野)
  • URL: http://presat-vector.org/hiroaki-lab/?p=54
• [Remarks] 神戸大学膜生物学グローバルCOEホームページ
  • URL: http://www.research.kobe-u.ac.jp/fmed-gcoe/index_j.html