Target recognition and expression mechanism of intrinsically disordered protein

2013 Fiscal Year Final Research Report

• Project Area: Target recognition and expression mechanism of intrinsically disordered protein
• Project/Area Number: 21113001
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Yokohama City University
• Principal Investigator: SATO Mamoru 横浜市立大学, その他の研究科, 教授 (60170784)
• Co-Investigator(Kenkyū-buntansha): SHIBATA Takehiko 理化学研究所, 遺伝制御科学特別研究ユニット, ユニットリーダー (70087550) ; OTA Motonori 名古屋大学, 大学院情報科学研究科, 教授 (40290895) ; AKASHI Satoko 横浜市立大学, 大学院生命医科学研究科, 准教授 (10280728) ; ISHONO Yoshizumi 九州大学, 大学院農学研究院, 教授 (30346837) ; HIGO Jyunichi 大阪大学, 蛋白質研究所, 特任研究員 (80265719) ; NISHIMURA Yoshifumi 横浜市立大学, 大学院生命医科学研究科, 教授 (70107390)
• Co-Investigator(Renkei-kenkyūsha): FUJII Yoshiaki 東北大学/東京医科歯科大学, 難治疾患研究所, 名誉教授/客員教授 (00098146) ; ISHIKAWA Fuyuki 京都大学, 大学院生命科学研究科, 教授 (30184493) ; NAKAMURA Haruki 大阪大学, 蛋白質研究所, 教授 (80134485) ; MORIKAWA Kousuke 国際高等研究所, チーフリサーチフェロー (80012665)
• Project Period (FY): 2009-07-23 – 2014-03-31
• Keywords: 天然変性タンパク質 / Ｘ線小角散乱 / 高速AFM / NMR / 核内タンパク質

Research Abstract

The management group has supported with every aspect so that scientists in the fields of structure biology, molecular biology and bioinformatics within this innovated research project can work together to elucidate the structures and properties of intrinsically disordered proteins. In fact, the group has annually held several management and research meetings, and has given appropriate advice to all the research groups within this research project. Also, the management group has planned special workshops for young researcher resource development within the research duration of five years as well as international symposia and open symposia in annual meetings of several scientific societies.

Research Products

• [Journal Article] Distinct Features of the Histone Core Structure in Nucleosomes Containing the Histone H2A.B Variant (2014)
  • Author(s): M.Sugiyama, Y.Arimura, K.Shirayama, R.Fujita, Y.Oba, N.Sato, R.Inoue, T.Oda, M. Sato, R.K.Heenan, and H.Kurumizak
  • Journal Title: Biophysical J. Volume: 106 Pages: 2206-2213
  • DOI: 10.1016/j.bpj.2014.04.007
• [Journal Article] Functional analyses of the C terminal half of the Saccharomyces cerevisiae Rad52 protein (2014)
  • Author(s): Kagawa, W., Arai, N., Ichikawa, Y., Saito, K., Sugiyama, S., Saotome, M., Shibata, T. and Kurumizaka, H.
  • Journal Title: Nucleic Acids Res Volume: 42 Pages: 941-951
  • DOI: 10.1093/nar/gkt986
  • Peer Reviewed
• [Journal Article] IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners (2014)
  • Author(s): Fukuchi, S., Amemiya, T., Sakamoto, S., Nobe, Y., Hosoda, K., Kado, Y., Murakami, S.D., Koike, R., Hiroaki, H., and Ota, M.
  • Journal Title: Nucleic Acids Res. Volume: 42 Pages: D320-D325
  • DOI: 10.1093/nar/gkt1010
  • Peer Reviewed
• [Journal Article] Hierarchical description and extensive classification of protein structural changes by Motion Tree (2014)
  • Author(s): Koike, R., Ota, M., and Kidera, A.
  • Journal Title: J. Mol. Biol Volume: 426 Pages: 752-762
  • DOI: 10.1016/j.jmb.2013.10.034
  • Peer Reviewed
• [Journal Article] Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin (2013)
  • Author(s): Y.Arimura, H.Kimura, T.Oda, K.Sato, A.Osakabe, H.Tachiwana, Y.Sato, Y.Kinugasa, T.Ikura, M.Sugiyama, M.Sato, and H.Kurumizaka
  • Journal Title: Sci. Rep Volume: 3 Pages: 3510
  • DOI: 10.1038/srep03510
• [Journal Article] Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity (2013)
  • Author(s): Miura, T., Shibata, T. and Kusano, K.
  • Journal Title: Proc Natl Acad Sci USA Volume: 110 Pages: 16067-16072
  • DOI: 10.1073/pnas.1303111110
  • Peer Reviewed
• [Journal Article] Report of the wwPDB Small-Angle Scattering Task Force : Data Requirements for Biomolecular Modeling and the PDB (2013)
  • Author(s): J.Trewhella, W.A.Hendrickson, G.J.Kleywegt, A.Sali, M.Sato, T.Schwede, D.I.Svergun, J.A.Tainer, J.Westbrook, and H.M.Berman
  • Journal Title: Structure Volume: 21 Pages: 875-881
  • DOI: 10.1016/j.str.2013.04.020
  • Peer Reviewed
• [Journal Article] Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening (2013)
  • Author(s): Tenno, T., Goda, N., Umetsu, Y., Ota, M., Kinoshita, K., and Hiroaki, H.
  • Journal Title: Molecules Volume: 18 Pages: 9567-9581
  • DOI: 10.3390/molecules18089567
  • Peer Reviewed
• [Journal Article] Conclusive evidence of the reconstituted hexasome proven by native mass spectrometry (2013)
  • Author(s): Azegami, N., Saikusa, K., Todokoro, Y., Nagadoi, A., Kurumizaka, H., Nishimura, Y., and Akashi, S.
  • Journal Title: Biochemistry Volume: 52 Pages: 5155-5157
  • DOI: 10.1021/bi4005655
  • Peer Reviewed
• [Journal Article] Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation (2013)
  • Author(s): Saikusa, K., Fuchigami, S., Takahashi, K., Asano, Y., Nagadoi, A., Tachiwana, H., Kurumizaka, H., Ikeguchi, M., Nishimura, Y., and Akashi, S.
  • Journal Title: Anal. Chem Volume: 85 Pages: 4165-4171
  • DOI: 10.1021/ac400395j
  • Peer Reviewed
• [Journal Article] A virtual-system coupled multicanonical molecular dynamics simulation : Principle and its application to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent (2013)
  • Author(s): Higo, J., Umezawa, K., and Nakamura, H.
  • Journal Title: J. Chem. Phys Volume: 138 Pages: 184106
  • DOI: 10.1063/1.4803468
  • Peer Reviewed
• [Journal Article] Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1 (2012)
  • Author(s): K.Arita, S.Isogai, T.Oda, M.Unoki, K.Sugita, N.Sekiyama, K.Kuwata, R.Hamamoto, H.Tochio, M.Sato, M.Ariyoshi, and M.Shirakawa
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 109 Pages: 12950-12955
  • DOI: 10.1073/pnas.1203701109
• [Journal Article] Virtual states introduced for overcoming entropic barriers in conformational space (2012)
  • Author(s): Higo, J. and Nakamura, H
  • Journal Title: Biophys Volume: 8 Pages: 139-144
  • DOI: 10.1021/ac400395j
  • Peer Reviewed
• [Journal Article] Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling (2012)
  • Author(s): Okuwaki, M., Sumi, A., Hisaoka, M., Saotome-Nakamura, A., Akashi, S., Nishimura, Y., and Nagata, K.
  • Journal Title: Nucleic Acid Res. Volume: 40 Pages: 4861-4878
  • DOI: 10.1093/nar/gks162
  • Peer Reviewed
• [Journal Article] Homologous recombination via synthesis-dependent strand annealing in yeast requires the Irc20 and Srs2 DNA helicases (2012)
  • Author(s): Miura, T., Yamana Y, Usui, T., Ogawa, H.I., Yamamoto, M.T., and Kusano, K.
  • Journal Title: Genetics Volume: 191 Pages: 65-78
  • DOI: 10.1534/genetics
  • Peer Reviewed
• [Journal Article] Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2, and NPM3 during sperm chromatin remodeling (2011)
  • Author(s): Okuwaki, M., Sumi, A.,Hisaoka, M., Saotome-Nakamura, A., Akashi, S., Nishimura, Y., and Nagata, K.
  • Journal Title: Nucleic Acid Res. Volume: 286 Pages: 17607-17617
  • DOI: 10.1093/nar/gks162
  • Peer Reviewed
• [Journal Article] Vital roles of the second DNA-binding site of Rad52 in yeast homologous recombination (2011)
  • Author(s): Arai, N., Kagawa, W., Saito, K., Shingu, Y., Mikawa, T., Kurumizaka, H., and Shibata, T.
  • Journal Title: J. Biol. Chem Volume: 286 Pages: 17607-17617
  • DOI: 10.1074/jbc.M110.216739
  • Peer Reviewed
• [Presentation] Protein dynamics investigated by SAXS and MD simulation (2013)
  • Author(s): Mamoru Sato
  • Organizer: International Conference on Structural Genomics-Structural Life Science-
  • Place of Presentation: Keio Plaza Hotel Sapporo
  • Year and Date: 20130729-0801
• [Presentation] 天然変性領域をターゲットにした抗体医薬の創成を目指して (2013)
  • Author(s): 佐藤 衛
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: とりぎん文化会館
  • Year and Date: 20130612-14
• [Presentation] 神経疾患における天然変性タンパク質の認識と創薬 (2013)
  • Author(s): 西村善文
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: とりぎん文化会館
  • Year and Date: 20130612-14
• [Presentation] REV7-REV3 複合体構造から示唆されるREV7/Mad2L2 と赤痢菌タンパク質IpaB との相互作用 (2013)
  • Author(s): 菊池壮太郎、原幸大、清水敏之、佐藤 衛、橋本 博
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: とりぎん文化会館
  • Year and Date: 20130612-14
• [Presentation] RecA のL1 loop 領域はDNA結合を制御する (2013)
  • Author(s): 篠原魁、井川粛子、岩崎わかな、美川務、柴田武彦
  • Organizer: 第36回日本分子生物学会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2013-12-05
• [Presentation] Behavior of intrinsically disordered regions within a protein complex of Swi5-Sfr1 characterized by ion mobility mass spectroscopy (2012)
  • Author(s): Saikusa K., Kuwabara N., Kokabu Y., Sato M., Iwasaki H., Ikeguchi M. and Akashi S.
  • Organizer: The 60^<th> ASMS Conference of Mass Spectrometry and Allied Topics
  • Place of Presentation: Vancouver Convention Center, Canada
  • Year and Date: 20120520-24
• [Presentation] Intrinsically disordered regions of the proteins related to stalled replication fork repair (2011)
  • Author(s): Ishino, Y.
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] Toward the structural characterization of intrinsically disordered proteins by SAXS and MD simulation (2011)
  • Author(s): Sato, M.
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] Database for the research of intrinsically disordered proteins (2011)
  • Author(s): Ota, M.
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] NMR studies on chromatin-related proteins (2011)
  • Author(s): Nishimura, Y.
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] Local folding of the N-terminal domain of RecA upon protein-protein/protein-DNA interactions and its role (2011)
  • Author(s): Mikawa, T., Ito, Y., Shibata, T.
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] 天然変性タンパク質研究 : タンパク質の構造・機能研究の新しいパラダイム (2010)
  • Author(s): 佐藤 衛
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] 相同組換え開始制御に働く天然変性タンパク質の機能 (2010)
  • Author(s): 柴田武彦
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] DNA 複製フォーク進行停止の修復に関わる天然変性タンパク質 (2010)
  • Author(s): 石野良純
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] NMR モデルを利用した天然変性領域のアサインメント (2010)
  • Author(s): 太田元規
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] 天然変性タンパク質の認識機構の多様性と創薬への道 (2010)
  • Author(s): 西村善文
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] 天然変性蛋白質NRSF とパートナー蛋白質Sin3 の結合/折り畳みの自由エネルギー地形 (2010)
  • Author(s): 肥後順一
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 20100616-18
• [Presentation] 天然変性タンパク質による転写調節機構 (2009)
  • Author(s): 西村善文
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 20091209-12
• [Presentation] X線小角散乱法と分子動力学シミュレーションを組み合わせた天然変性タンパク質動的構造解析法の開発 (2009)
  • Author(s): 佐藤 衛
  • Organizer: 第82回日本生化学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 20091021-24
• [Presentation] 相同DNA 組換えにおける天然変性領域の機能 (2009)
  • Author(s): 柴田武彦, 新井直人, 凌 楓, 香川 亘, 胡桃坂 仁志, 井上 仁, 新宮 良宣, 美川務
  • Organizer: 第82回日本生化学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 20091021-24
• [Presentation] 天然変性タンパク質のデータベース構築と解析 (2009)
  • Author(s): 太田元規、福地佐斗志
  • Organizer: 第82回日本生化学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 20091021-24
• [Presentation] マルチカノニカル分子動力学シミュレーションによる天然変性蛋白質の自由エネルギー地形 (2009)
  • Author(s): 肥後順一
  • Organizer: 第82回日本生化学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 20091021-24
• [Presentation] 天然変性転写関連タンパク質 (2009)
  • Author(s): 西村善文
  • Organizer: 第82回日本生化学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 20091021-24
• [Book] Protein Conformational Dynamics in Advances in Experimental Medicine and Biology Vol.805 (2014)
  • Author(s): Higo J., Umezawa K.
  • Total Pages: 21
  • Publisher: Springer
• [Book] Protein conformational dynamics : Free-energy land scope of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics (2012)
  • Author(s): Higo J.
  • Total Pages: 10
  • Publisher: Springer
• [Remarks]
  • URL: http://www.tsurumi.yokohama-cu.ac.jp/IDP/results.html