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2017 Fiscal Year Annual Research Report

Elucidation of the mechanism by which virus inhibits the function of human anti-virus enzymes and molecular basis of drug discovery

Research Project

Project/Area Number 26440026
Research InstitutionKyoto University

Principal Investigator

永田 崇  京都大学, エネルギー理工学研究所, 准教授 (10415250)

Project Period (FY) 2014-04-01 – 2018-03-31
KeywordsVif / APOBEC / アプタマー / NMR
Outline of Annual Research Achievements

APOBEC3ファミリータンパク質の中で、APOBEC3F(A3F)とAPOBEC3G(A3G)は、HIV-1に対する防御機構を担っている。これらはそれぞれ一本鎖DNA (ssDNA)上に存在するシトシンをウラシルに変換する脱アミノ化酵素である。HIV-1は自身の持つVifタンパク質を使い、A3FとA3Gをユビキチン・プロテアソーム経路に導き、これらを分解する。Vifを阻害し、A3FとA3Gを働かせることは、治療戦略として近年注目されている。我々はこれまで、A3Gについて機能解析を行ってきた。今年度は当初計画通り、A3Fのキャラクテリゼーションを行い、論文に報告した(Phys Chem Chem Phys, 2018)。A3FはssDNA上のTCを標的とすることが知られていたが、TC前後の配列や、配列の長さの指向性などについては研究が進んでいなかった。A3Fの機能解析が困難だった理由として、A3Fの溶解度が低いことが挙げられる。まず我々は、溶液条件を最適化し、また各種解析には低濃度のA3F (1 μM程度)を使うことで問題を克服した。そして、A3Fのシトシン脱アミノ化反応は、ウラシルDNAグリコシラーゼアッセイ法を、A3FとssDNAの結合は蛍光偏光解消法を用いた。複数の異なる配列をもつssDNAを用いて解析した結果、A3FはTCに隣接する塩基も識別し、TTCA/G配列を好むことが明らかとなった。鎖長については、長いssDNA (>20 nt)を短いものよりも好むことが明らかとなった。さらに、複数の変異体やpHの異なる溶液を使うことにより、脱アミノ化活性及びDNA結合を担うアミノ酸残基を明らかにした。先述のVifはヒトのCBFβ、EloB/EloC、Cul5などと複合体を形成して、A3F及びA3Gを分解に導く。我々はSELEX法を用いてVif複合体に結合するRNAアプタマーの取得を試みてきた。今年度は、当初計画通り、より親和性の高いRNAアプタマーの獲得に成功した

  • Research Products

    (45 results)

All 2018 2017 Other

All Int'l Joint Research (1 results) Journal Article (13 results) (of which Peer Reviewed: 13 results,  Open Access: 13 results) Presentation (31 results) (of which Int'l Joint Research: 10 results)

  • [Int'l Joint Research] Goethe University Frankfurt am Main(Germany)

    • Country Name
      Germany
    • Counterpart Institution
      Goethe University Frankfurt am Main
  • [Journal Article] Mechanism of protein-RNA recognition: analysis based on the statistical mechanics of hydration2018

    • Author(s)
      Hayashi Tomohiko, Matsuda Tomoaki, Nagata Takashi, Katahira Masato, Kinoshita Masahiro
    • Journal Title

      Phys Chem Chem Phys

      Volume: 20 Pages: 9167~9180

    • DOI

      10.1039/C8CP00155C

    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of the glutathione S-transferases that belong to the GSTFuA class in Ceriporiopsis subvermispora : Implications in intracellular detoxification and metabolism of wood-derived compounds2018

    • Author(s)
      Osman Wan Hasnidah Wan、Lin Meng-I、Kondo Keiko、Nagata Takashi、Katahira Masato
    • Journal Title

      Int J Biol Macromol

      Volume: 113 Pages: 1158~1166

    • DOI

      10.1016/j.ijbiomac.2018.03.029

    • Peer Reviewed / Open Access
  • [Journal Article] Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses2018

    • Author(s)
      Takada Kenta、Amano Ryo、Nomura Yusuke、Tanaka Yoichiro、Sugiyama Shigeru、Nagata Takashi、Katahira Masato、Nakamura Yoshikazu、Kozu Tomoko、Sakamoto Taiichi
    • Journal Title

      FEBS Open Bio

      Volume: 8 Pages: 264~270

    • DOI

      10.1002/2211-5463.12368

    • Peer Reviewed / Open Access
  • [Journal Article] Plastic roles of phenylalanine and tyrosine residues of TLS/FUS in complex formation with the G-quadruplexes of telomeric DNA and TERRA2018

    • Author(s)
      Kondo Keiko、Mashima Tsukasa、Oyoshi Takanori、Yagi Ryota、Kurokawa Riki、Kobayashi Naohiro、Nagata Takashi、Katahira Masato
    • Journal Title

      Sci Rep

      Volume: 8 Pages: 2864

    • DOI

      10.1038/s41598-018-21142-1

    • Peer Reviewed / Open Access
  • [Journal Article] High yield production of fungal manganese peroxidases by E. coli through soluble expression, and examination of the activities2018

    • Author(s)
      Lin Meng-I、Nagata Takashi、Katahira Masato
    • Journal Title

      Protein Expr Purif

      Volume: 145 Pages: 45~52

    • DOI

      10.1016/j.pep.2017.12.012

    • Peer Reviewed / Open Access
  • [Journal Article] The first successful observation of in-cell NMR signals of DNA and RNA in living human cells2018

    • Author(s)
      Yamaoki Yudai、Kiyoishi Ayaka、Miyake Masayuki、Kano Fumi、Murata Masayuki、Nagata Takashi、Katahira Masato
    • Journal Title

      Phys Chem Chem Phys

      Volume: 20 Pages: 2982~2985

    • DOI

      10.1039/c7cp05188c

    • Peer Reviewed / Open Access
  • [Journal Article] The C-terminal cytidine deaminase domain of APOBEC3G itself undergoes intersegmental transfer for a target search, as revealed by real-time NMR monitoring2018

    • Author(s)
      Kamba Keisuke、Nagata Takashi、Katahira Masato
    • Journal Title

      Phys Chem Chem Phys

      Volume: 20 Pages: 2976~2981

    • DOI

      10.1039/c7cp05171a

    • Peer Reviewed / Open Access
  • [Journal Article] Influence of the DNA sequence/length and pH on deaminase activity, as well as the roles of the amino acid residues around the catalytic center of APOBEC3F2018

    • Author(s)
      Wan Li、Nagata Takashi、Katahira Masato
    • Journal Title

      Phys Chem Chem Phys

      Volume: 20 Pages: 3109~3117

    • DOI

      10.1039/c7cp04477a

    • Peer Reviewed / Open Access
  • [Journal Article] Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain2017

    • Author(s)
      Nomura Yusuke、Yamazaki Kaori、Amano Ryo、Takada Kenta、Nagata Takashi、Kobayashi Naohiro、Tanaka Yoichiro、Fukunaga Junichi、Katahira Masato、Kozu Tomoko、Nakamura Yoshikazu、Haishima Yuji、Torigoe Hidetaka、Sakamoto Taiichi
    • Journal Title

      J Biochem

      Volume: 162 Pages: 431~436

    • DOI

      10.1093/jb/mvx049

    • Peer Reviewed / Open Access
  • [Journal Article] Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B2017

    • Author(s)
      Wan Li、Nagata Takashi、Morishita Ryo、Takaori-Kondo Akifumi、Katahira Masato
    • Journal Title

      ACS Chem Biol

      Volume: 12 Pages: 2704~2708

    • DOI

      10.1021/acschembio.7b00662

    • Peer Reviewed / Open Access
  • [Journal Article] Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA2017

    • Author(s)
      Iwaoka Ryo、Nagata Takashi、Tsuda Kengo、Imai Takao、Okano Hideyuki、Kobayashi Naohiro、Katahira Masato
    • Journal Title

      Biomol NMR Assign

      Volume: 11 Pages: 265~268

    • DOI

      10.1007/s12104-017-9760-9

    • Peer Reviewed / Open Access
  • [Journal Article] Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA2017

    • Author(s)
      Iwaoka Ryo、Nagata Takashi、Tsuda Kengo、Imai Takao、Okano Hideyuki、Kobayashi Naohiro、Katahira Masato
    • Journal Title

      Molecules

      Volume: 22 Pages: 1207~1207

    • DOI

      10.3390/molecules22071207

    • Peer Reviewed / Open Access
  • [Journal Article] Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions2017

    • Author(s)
      Yamaoki Yudai、Nagata Takashi、Mashima Tsukasa、Katahira Masato
    • Journal Title

      Chem Commun (Camb)

      Volume: 53 Pages: 7056~7059

    • DOI

      10.1039/c7cc03312e

    • Peer Reviewed / Open Access
  • [Presentation] セルラーゼ糖質結合モジュールとリグニン間相互作用部位のNMRによる解析2018

    • Author(s)
      徳永有希、大城理志、永田崇、近藤敬子、西村裕志、片平正人、渡辺隆司
    • Organizer
      第68回日本木材学会
  • [Presentation] The effect of different target nucleic acids on the structural change of TLS2017

    • Author(s)
      Nesreen Hamad, Tsukasa Mashima, Hiroki Watanabe, Takayuki Uchihashi, Riki Kurokawa, Takashi Nagata, Masato Katahira
    • Organizer
      第40回日本分子生物学会年会
  • [Presentation] Modeling of the tandem RNA-binding domains of a neural and oncogenic protein, Musashi1, engaging the minimum target RNA2017

    • Author(s)
      Ryo Iwaoka, Takashi Nagata, Kengo Tsuda, Takao Imai, Hideyuki Okano, Naohiro Kobayashi, Masato Katahira
    • Organizer
      第40回日本分子生物学会年会
  • [Presentation] Studies on lytic polysaccharide monooxygenase (LPMO) from the selective white rot fungus, Ceriporiposis subvermispora2017

    • Author(s)
      Yuu Iseki, Satoshi Oshiro, Takashi Nagata, Keiko Kondo, Hiroshi Nishimura, Masato Katahira, Takashi Watanabe
    • Organizer
      Humanosphere Science School 2017
    • Int'l Joint Research
  • [Presentation] Analysis of Adsorption Mechanism between Carbohydrate Binding Module of Cellulase and Lignin by NMR2017

    • Author(s)
      Yuki Tokunaga, Satoshi Oshiro, Takashi Nagata, Keiko Kondo, Hiroshi Nishimura, Masato Katahira, Takashi Watanabe
    • Organizer
      Humanosphere Science School 2017
    • Int'l Joint Research
  • [Presentation] Analysis of Lignin-Carbohydrate Complexes in Woody Biomass by Using NMR2017

    • Author(s)
      Shizuka Sakon, Hiroshi Nishimura, Misato Yamada, Yukari Ohta, Keiko Kondo, Yudai Yamaoki, Takashi Nagata, Masato Katahira, Takashi Watanabe
    • Organizer
      Humanosphere Science School 2017
    • Int'l Joint Research
  • [Presentation] Characterization of the cytidine deamination properties of human APOBEC3B by real-time NMR, which are quite different from those of APOBEC3G2017

    • Author(s)
      Li Wan, Takashi Nagata, Ryo Morishita, Akifumi Takaori-Kondo, Masato Katahira
    • Organizer
      The 44th International Symposium on Nucleic Acids Chemistry, The 1st Annual Meeting of Japan Society of Nucleic Acids Chemistry
    • Int'l Joint Research
  • [Presentation] 翻訳開始前複合体において形成される翻訳開始因子間の結合ネットワークの役割2017

    • Author(s)
      永田崇、吉田尚志、雲財悟、浦野健、浅野桂、尾林栄治
    • Organizer
      第56回NMR討論会
  • [Presentation] In-cell NMR法によるヒト細胞内DNAおよびRNAの観測2017

    • Author(s)
      山置 佑大, 清石 彩華, 三宅雅之, 加納 ふみ, 村田 昌之, 永田 崇, 片平 正人
    • Organizer
      第56回NMR討論
  • [Presentation] RNA結合タンパク質Musashi-1のRBD2:r(GUAGU)複合体溶液構造決定と標的RNA選択メカニズムの解明2017

    • Author(s)
      岩岡諒,永田崇,津田健吾,今井貴雄,岡野栄之,小林直宏,片平正人
    • Organizer
      第56回NMR討論
  • [Presentation] 深層学習により強化されたNMR立体構造解析2017

    • Author(s)
      小林直宏、永田崇、服部良一、新家粧子、Julia M. Wurz、Peter Guntert、児嶋長次郎、藤原敏道
    • Organizer
      第56回NMR討論
  • [Presentation] Analysis of peroxidase activity, lignin model degradation of heterologous expressed soluble fungal ligninolytic enzymes2017

    • Author(s)
      Meng-I Lin, Keiko Kondo, Takashi Nagata, Masato Katahira
    • Organizer
      2017 Taiwan-Japan Biomedical Symposium on Magnetic Resonance
    • Int'l Joint Research
  • [Presentation] Sphingombium sp. YG1由来guaiacylglycerol-β-guaiacyl ether - Cα位酸化酵素の酵素学的解析と利用2017

    • Author(s)
      前田亜鈴悠、宋晶、西真郎、黒澤佳奈子、市川淳子、 塩谷美夏、山置佑大、永田崇、片平正人、山田美沙登、渡辺隆司、大田ゆかり
    • Organizer
      第62回リグニン討論会
  • [Presentation] フラグメント分子軌道法を活用したリグニンβ-O-4還元開裂酵素の機能改変2017

    • Author(s)
      嶋根康弘、黒澤佳奈子、市川淳子、前田亜鈴悠、布浦拓郎、山置佑大、永田崇、片平正人、高谷光、吉田亮太、中村正治、渡辺隆司、大田ゆかり
    • Organizer
      第62回リグニン討論会
  • [Presentation] Kinetic studies of the two fungal glutathione-dependent enzymes and their potential roles in the intracellular detoxification and wood-derived compound metabolism2017

    • Author(s)
      Wan Hasnidah Wan Osman, Meng-I Lin, Keiko Kondo, Takashi Nagata, Masato Katahira
    • Organizer
      第62回リグニン討論会
  • [Presentation] 18-crown-6を用いるヒドロニウム溶媒和イオン液体の基礎物性2017

    • Author(s)
      北田敦、竹岡駿、近都康平、深見一弘、才村正幸、永田崇、片平正人、邑瀬邦明
    • Organizer
      2017年電気化学会秋季大会
  • [Presentation] Development of the artificial multi-domain enzymes immobilized on the curdlan sheet at low cost.2017

    • Author(s)
      Masataka Horiuchi, Takashi Nagata, Masato Katahira, Yoshihiro Kobashigawa, Yasuhiko Suzuki, Masanori Ochiai
    • Organizer
      The 8th International Symposium of Advanced Energy Science
    • Int'l Joint Research
  • [Presentation] Structure-function relationship of Epstein-Barr Virus EBNA3C NLS and transport receptor2017

    • Author(s)
      Go Matsuda, Takashi Nagata, Masato Katahira, Ken-ichi Imadome
    • Organizer
      The 8th International Symposium of Advanced Energy Science
    • Int'l Joint Research
  • [Presentation] Development of RNA binding peptides based on tertiary structural information2017

    • Author(s)
      Natsuki Watanabe, Tomoaki Kinase, Takashi Nagata, Masato Katahira, Kazuo Harada, and Taiichi Sakamoto
    • Organizer
      The 8th International Symposium of Advanced Energy Science
    • Int'l Joint Research
  • [Presentation] テロメア長短縮をもたらすTLS/FUS蛋白質とテロメアDNAおよびTERRAのグアニン四重鎖との複合体に関するNMR解析2017

    • Author(s)
      近藤 敬子、 真嶋 司、大吉 崇文、黒川 理樹、小林直宏、永田 崇、片平 正人
    • Organizer
      第55回生物物理学会
  • [Presentation] Influences of length and concentration of the DNA substrate, as well as the location of the target sequence, on deamination by APOBEC3F2017

    • Author(s)
      Li Wan, Takashi Nagata, Masato Katahira
    • Organizer
      第55回生物物理学会
  • [Presentation] An anti-prion aptamer inhibits the formation of prion protein-amyloid β oligomer complex that is related to Alzheimer's disease2017

    • Author(s)
      Mamiko IIDA, Tsukasa MASHIMA, Yudai YAMAOKI, Takashi NAGATA, Masato KATAHIRA
    • Organizer
      第55回生物物理学会
  • [Presentation] NMR Analysis of Interaction Mechanism between Carbohydrate Binding Module of Cellulase and Lignin2017

    • Author(s)
      Yuki Tokunaga, Satoshi Oshiro, Keiko Kondo, Takashi Nagata, Hiroshi Nishimura, Masato Katahira, Takashi Watanabe
    • Organizer
      The 2nd Asia Research Node Symposium on Humanosphere Science
    • Int'l Joint Research
  • [Presentation] TLS/FUSの非コードRNAの認識機構の構造学的研究2017

    • Author(s)
      真嶋司, 小澤 駿介, Nesreen Hamad, 米田竜馬, 黒川 理樹, 永田崇, 片平 正人
    • Organizer
      第19回日本RNA学会年会
  • [Presentation] Conformational change detection of translocated in liposarcoma, TLS, upon binding to various RNAs2017

    • Author(s)
      Nesreen Hamad, Tsukasa Mashima,Yudai Yamaoki, Keiko Kondo, Takashi Nagata, Masato Katahira
    • Organizer
      第19回日本RNA学会年会
  • [Presentation] NMR法によるセルラーゼ糖質結合モジュール-リグニン間相互作用の解明2017

    • Author(s)
      徳永有希、大城理志、永田崇、近藤敬子、西村裕志、片平正人、渡辺隆司
    • Organizer
      第31回セルラーゼ研究会
  • [Presentation] Highly automated NMR signal assignments using peak-noise recognition assisted by Deep Neural Networks2017

    • Author(s)
      Kobayashi, N., Nagata, T., Kojima, C., and Fujiwara, T.
    • Organizer
      Gordon Research Conference. Computational Aspects-Biomol NMR
    • Int'l Joint Research
  • [Presentation] TLS/FUSのRNA認識機構と結合に伴うコンフォーメーション変化の研究2017

    • Author(s)
      真嶋 司, 小澤 駿介, Nesreen Hamad, 米田 竜馬, 黒川 理樹, 永田 崇, 片平 正人
    • Organizer
      第17回日本蛋白質科学会年会
  • [Presentation] High yield production, activity analysis, and homologous modeling of soluble fungal peroxidases expressed in E. coli2017

    • Author(s)
      Meng-I Lin, Keiko Kondo, Takashi Nagata, Masato Katahira
    • Organizer
      第17回日本蛋白質科学会年会
  • [Presentation] APOBEC3Gのストランド間移動の実時間NMR法検出2017

    • Author(s)
      神庭圭佑,永田崇,片平正人
    • Organizer
      第17回日本蛋白質科学会年会
  • [Presentation] HIV-1 RRE由来のRNA断片と人工ペプチドの相互作用の解析2017

    • Author(s)
      渡邊 なつき,木名瀬智章,永田崇,片平正人,原田和雄,坂本泰一
    • Organizer
      平成29年度日本生化学会関東支部例会

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Published: 2018-12-17  

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