Management for Molecular Science of Fluctuations toward Biological Functions

• Project Area: Molecular Science of Fluctuations toward Biological Functions
• Project/Area Number: 20107001
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Kyoto University
• Principal Investigator: TERAZIMA Masahide 京都大学, 理学(系)研究科(研究院), 教授 (00188674)
• Co-Investigator(Kenkyū-buntansha): KATAOKA Mikio 奈良先端科学技術大学院大学, 物質創成科学研究科 (30150254) ; UEOKA Ryuichi 崇城大学, 生物生命学部, 教授 (70099076) ; OKAMOTO Yuko 名古屋大学, 大学院・理学研究科, 教授 (70185487) ; KATO Koichi 大学共同利用機関法人自然科学研究機構, 岡崎統合バイオサイエンスセンター, 教授 (20211849) ; HOHSAKA Takahiro 北陸先端科学技術大学院大学, マテリアルサイエンス研究科, 教授 (30263619) ; HIRATA Fumio 分子科学研究所, 理論・計算分子科学研究領域, 教授 (90218785) ; KUWAJIMA Kunihiro 大学共同利用機関法人自然科学研究機構, 岡崎統合バイオサイエンスセンター, 教授 (70091444)
• Project Period (FY): 2008-11-13 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥119,600,000 (Direct Cost: ¥92,000,000、Indirect Cost: ¥27,600,000); Fiscal Year 2013: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2012: ¥24,310,000 (Direct Cost: ¥18,700,000、Indirect Cost: ¥5,610,000); Fiscal Year 2011: ¥24,310,000 (Direct Cost: ¥18,700,000、Indirect Cost: ¥5,610,000); Fiscal Year 2010: ¥24,310,000 (Direct Cost: ¥18,700,000、Indirect Cost: ¥5,610,000); Fiscal Year 2009: ¥24,310,000 (Direct Cost: ¥18,700,000、Indirect Cost: ¥5,610,000); Fiscal Year 2008: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
• Keywords: 揺らぎ / ダイナミクス / 生体分子 / 機能 / 反応 / 分子科学

Research Abstract

本研究の研究代表者（寺嶋）と総括班メンバーを中心とし、新学術領域研究で培った分野融合の成果を国内の学生や研究者によりよく知っていただくために、基礎から先端研究までをまとめた日本語解説書籍（揺らぎと生体機能）を出版した。本書籍を関係研究者へ配布し、成果の広報に努めた。
領域研究メンバーの中から代表的な講演者を選び、「揺らぎが機能を決める生命分子の科学」と題する公開ワークショップを開催し、新学術領域研究の成果を発信した。このワークショップは広く関心を呼び、学部生も含めた多くの参加者が集まった。揺らぎに関する多くの議論が行われ、これからの発展すべき方向性が検討された。
また、広く一般市民に成果を解説する、市民講座を京都にて開催した。

Current Status of Research Progress

Reason

25年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

25年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] High hydrostatic pressure induces CCW to CW reversals of the Escherichia coli flagellar motor (2013)
  • Author(s): M.Nishiyama, Y.Sowa, Y.Kimura, M. Homma, A. Ishijima, M. Terazima
  • Journal Title: J.Bacterio. Volume: １９５ Issue: 8 Pages: 1809-1814
  • DOI: 10.1128/jb.02139-12
  • Peer Reviewed
• [Journal Article] Anomalous diffusion of TePixD and identification of the photoreaction product (2013)
  • Author(s): K.Kuroi, K.Tanaka, K.Okajima, M. Ikeuchi, S. Tokutomi, M.Terazim
  • Journal Title: Photochem.Photobiol.Sci. Volume: １２ Issue: 7 Pages: 1180-1186
  • DOI: 10.1039/c3pp25434h
  • Peer Reviewed
• [Journal Article] Photochemistry of Arabidopsis phototropin 1 LOV1: transient tetramerization (2013)
  • Author(s): Y. Nakasone, K. Zikihara, S. Tokutomi,M. Terazima
  • Journal Title: Photochem.Photobiol.Sci. Volume: １２ Issue: 7 Pages: 1171-1179
  • DOI: 10.1039/c3pp50047k
  • Peer Reviewed
• [Journal Article] The molten globule of β(2)-microglobulin accumulated at pH 4 and its role in protein folding (2013)
  • Author(s): A. Mukaiyama, T. Nakamura, K. Makabe, K. Maki, Y. Goto, K. Kuwajima
  • Journal Title: J. Mol. Biol. Volume: 425 Issue: 2 Pages: 273-291
  • DOI: 10.1016/j.jmb.2012.11.002
  • Peer Reviewed
• [Journal Article] Time-Resolved Tracking of Interprotein Signal Transduction: Synechocystis PixD-PixE complex as a Sensor of Light Intensity (2012)
  • Author(s): K. Tanaka, Y. Nakasone, K. Okajima, M. Ikeuchi, S. Tokutomi, M. Terazima
  • Journal Title: J.Am.Chem.Soc Volume: 134 Issue: 20 Pages: 8336-8339
  • DOI: 10.1021/ja301540r
  • Peer Reviewed
• [Journal Article] temperature and pressure dependence of complex systems (2012)
  • Author(s): Generalized-ensemble algorithms for studying Y. Mori, Y. Okamoto
  • Journal Title: Molecular Simulation Volume: 38 Issue: 5 Pages: 452-457
  • DOI: 10.1080/08927022.2011.651139
  • Peer Reviewed
• [Journal Article] Protein encapsulation within synthetic molecular hosts (2012)
  • Author(s): D. Fujita, K. Suzuki, S. Sato, M. Yagi-Utsumi, Y. Yamaguchi, N. Mizuno, T. Kumasaka, M. Takata, M. Noda, S. Uchiyama, K. Kato, and M. Fujita
  • Journal Title: Nature Communications Volume: 3 Issue: 1 Pages: 1093-1093
  • DOI: 10.1038/ncomms2093
  • Peer Reviewed
• [Journal Article] Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography (2012)
  • Author(s): F. Schotte, H. Sun Cho, V. R. I. Kaila, H. Kamikubo, N. Dashdorj, E. R. Henry, T. J. Graber, M. Kataoka, P. A. Anfinrud
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 109 Issue: 47 Pages: 19256-19261
  • DOI: 10.1073/pnas.1210938109
  • NAID: 120005716810
  • Peer Reviewed
• [Journal Article] Selective accumulation and growth inhibition of hybrid liposomes to human hepatocellular carcinoma cells in relation to fluidity of plasma membranes (2012)
  • Author(s): Y. Komizu, H. Ueoka, R. Ueoka, Biochem
  • Journal Title: Biophys. Res. Commun Volume: 418 Issue: 1 Pages: 81-86
  • DOI: 10.1016/j.bbrc.2011.12.134
  • Peer Reviewed
• [Journal Article] NMR characterization of the interaction between the PUB domain of peptide: N-glycanase and ubiquitin-like domain of HR23. (2012)
  • Author(s): Y.Kamiya, Y.Uekusa, A.Sumiyoshi, H.Sasakawa, T.Hirao, T.Suzuki, and K.Kato
  • Journal Title: FEBS Lett. Volume: 586 Issue: 8 Pages: 1141-1146
  • DOI: 10.1016/j.febslet.2012.03.027
  • Peer Reviewed
• [Journal Article] Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations (2012)
  • Author(s): B. A. Berg
  • Journal Title: Molecular Simulation Volume: 38 Issue: 11 Pages: 856-860
  • DOI: 10.1080/08927022.2011.651140
  • Peer Reviewed
• [Journal Article] Amber Codon-Mediated Expanded Saturation Mutagenesis of Proteins using a Cell-Free Translation System (2012)
  • Author(s): Naoki Shozen, Takayoshi Watanabe, Takahiro Hohsaka
  • Journal Title: J.Biosci.Bioeng. Volume: (印刷中) Issue: 6 Pages: 704-709
  • DOI: 10.1016/j.jbiosc.2012.01.018
  • Peer Reviewed
• [Journal Article] Anti-tumor Effects of Cationic Hybrid Liposomes against Colon Carcinoma along with Apoptosis <i>in Vitro</i> (2012)
  • Author(s): M. Hino, H. Ichihara, Y. Matsumoto, R. Ueoka
  • Journal Title: Biological and Pharmaceutical Bulletin Volume: 35 Issue: 11 Pages: 2097-2101
  • DOI: 10.1248/bpb.b12-00633
  • NAID: 130001872276
  • ISSN: 0918-6158, 1347-5215
  • Peer Reviewed
• [Journal Article] Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone (2012)
  • Author(s): J. Chen
  • Journal Title: FEBS Lett. Volume: 586 Pages: 1120-1127
  • Peer Reviewed
• [Journal Article] Solvent and Salt Effects on Structural Stability of Human Telomere (2011)
  • Author(s): Y. Maruyama, T. Matsushita, R. Ueoka, F. Hirata
  • Journal Title: J. Phys. Chem. B Volume: 115 Issue: 10 Pages: 2408-2416
  • DOI: 10.1021/jp1096019
  • Peer Reviewed
• [Journal Article] Macromolecular Crowding Effects on Reactions of TePixD (T110078) (2011)
  • Author(s): T.Toyooka, K.Tanaka, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Journal Title: Photochem.Photobiol. Volume: 87 Issue: 3 Pages: 584-584
  • DOI: 10.1111/j.1751-1097.2010.00849.x
  • Peer Reviewed
• [Journal Article] Light-induced conformational change and product release in DNA repair by (6-4) photolyase (2011)
  • Author(s): M.Kondoh, K.Hitomi, J.Yamamoto, T.Todo, S.Iwai, E.D.Getzoff, M.Terazima
  • Journal Title: J.Am.Chem.Soc. Volume: 133 Issue: 7 Pages: 2183-2191
  • DOI: 10.1021/ja107691w
  • Peer Reviewed
• [Journal Article] Light-Induced Conformational Change and Transient Dissociation Reaction of the BLUF Photoreceptor Synechocystis PixD (Slr1694) (2011)
  • Author(s): K.Tanaka, Y.Nakasone, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Journal Title: J.Mol.Biol. Volume: 409 Issue: 5 Pages: 773-785
  • DOI: 10.1016/j.jmb.2011.04.032
  • NAID: 120003203917
  • Peer Reviewed
• [Journal Article] A way to sense light intensity : multiple-excitation of the BLUF photoreceptor TePixD suppresses confogrmational change (2011)
  • Author(s): K.Tanaka, Y.Nakasone, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Journal Title: FEBS Lett. Volume: 585 Pages: 786-790
  • Peer Reviewed
• [Journal Article] Macromolecular Crowding Effects on Reactions of TePixD (TI10078) (2011)
  • Author(s): T.Toyooka, K.Tanaka, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Journal Title: Photochem.Photobiol. Volume: 87 Pages: 584-584
  • Peer Reviewed
• [Journal Article] Kinetics of conformational changes of the FKF1-LOV domain upon photoexcitation (2010)
  • Author(s): Y.Nakasone, K.Zikihara, S.Tokutomi, M.Terazima
  • Journal Title: Biophys.J. 99 Pages: 3831-3839
  • NAID: 120002709547
  • Peer Reviewed
• [Journal Article] When is the helix conformation restored after the reverse reaction of Phototropin (2010)
  • Author(s): Y.Kawaguchi, Y.Nakasone, K.Zikihara, S.Tokutomi, M.Terazima
  • Journal Title: J.Am.Chem.Soc. 132 Pages: 8838-8839
  • Peer Reviewed
• [Journal Article] Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching (2009)
  • Author(s): I. Iijima, T. Hohsaka
  • Journal Title: Chem Bio Chem Volume: 10 Issue: 6 Pages: 999-1006
  • DOI: 10.1002/cbic.200800703
  • Peer Reviewed
• [Journal Article] Oligomeric State-Dependent Conformational Change of a BLUF Protein TePixD (Tll0078) (2009)
  • Author(s): K.Tanaka, Y.Nakasone, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Journal Title: J.Mol.Biol. 386 Pages: 1290-1300
  • Peer Reviewed
• [Journal Article] Raman spectroscopic study on solvation of p-aminobenzonitrile in supercritical water end methanol. (2009)
  • Author(s): K.Osawa
  • Journal Title: J.Phys.Chem.A Volume: 113 Pages: 3143-3164
  • Peer Reviewed
• [Journal Article] Diffusion of gold ions and gold particles during photoreduction processes probed by_the transient grating method. (2009)
  • Author(s): M.Harada
  • Journal Title: J.Collo.Inter.Sci. Volume: 332 Pages: 373-381
  • Peer Reviewed
• [Journal Article] Low barrier hydrogen bond in photoactive yellow protein. (2009)
  • Author(s): S.Yamaguchi
  • Journal Title: Proc.Natl.Acad.Sci.USA Volume: 106 Pages: 440-444
  • Peer Reviewed
• [Journal Article] Raman spectroscopic study on solvation of p-aminobenzonitrile in supercritical water and methanol (2009)
  • Author(s): K.Osawa, et al.
  • Journal Title: J.Phys.Chem.A 113 Pages: 3143-3154
  • Peer Reviewed
• [Journal Article] Diffusion of gold ions and gold particles during photoreduction processes probed by the transient grating (2009)
  • Author(s): M.Harada, et al.
  • Journal Title: J.Collo.Inter.Sci. 332 Pages: 373-381
  • Peer Reviewed
• [Journal Article] Low barrier hydrogen bond in photoactive yellow protein (2009)
  • Author(s): S.Yamaguchi, et al.
  • Journal Title: Proc.Natl.Acad.Sci.USA 106 Pages: 440-444
  • Peer Reviewed
• [Presentation] 揺らぎと分子間相互作用の時間分解検出 (2013)
  • Author(s): 寺嶋正秀
  • Organizer: 分子基盤に基づく生体機能への揺らぎとダイナミックネットワークの解明
  • Place of Presentation: 国際高等研究所
  • Invited
• [Presentation] 複合糖質の構造生物学： 創薬標的としての糖鎖 (2012)
  • Author(s): 加藤晃一
  • Organizer: 第40回構造活性相関シンポジウム
  • Place of Presentation: 愛知県岡崎市
  • Year and Date: 2012-11-30
  • Invited
• [Presentation] Generalized-ensemble algorithms for classical and quantum simulations (2012)
  • Author(s): Y. Okamoto
  • Organizer: International Workshop on Recent Advances in Computational and Theoretical Chemistry
  • Place of Presentation: Nagoya, Japan
  • Year and Date: 2012-11-09
• [Presentation] Protein dynamics and hydration water (2012)
  • Author(s): M. Kataoka
  • Organizer: 10th International Conference on Quasielastic Neutron Scattering
  • Place of Presentation: Nikko, Japan
  • Year and Date: 2012-10-04
• [Presentation] 非天然アミノ酸の導入によるタンパク質の部位特異的PEG化 (2012)
  • Author(s): 渡邉 貴嘉・山口 純・芳坂 貴弘
  • Organizer: 第6回バイオ関連化学シンポジウム
  • Place of Presentation: 札幌, 日本
  • Year and Date: 2012-09-06
• [Presentation] NMR analysis of specific carbohydrate-carbohydrate interaction between gangliosides (2012)
  • Author(s): Y. Uekusa, S. Sonnino, K. Kato
  • Organizer: 26 International Carbohydrate Symposium
  • Place of Presentation: Madrid, スペイン
  • Year and Date: 2012-07-25
• [Presentation] Molecular mechanisms of cytotoxicity of HAMLET and other protein-oleic acid complexes (2012)
  • Author(s): K. Kuwajima
  • Organizer: 12th KIAS Conference on Protein Structure
  • Place of Presentation: Seoul, Korea
• [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope (2012)
  • Author(s): F. Hirata
  • Organizer: The ACS Symposium on "Continuum Solvation Modeling in Biological Systems
  • Place of Presentation: Philadelphia, USA
• [Presentation] Membrane-Targeted Nanotherapy with Hybrid Liposomes for Cancer Cells Leading to Apoptosis (2012)
  • Author(s): Y. Matsumoto, R. Ueoka
  • Organizer: The International Conference on Statistical Mechanics of Liquids: From Water to Biomolecules
  • Place of Presentation: 岡崎,日本
• [Presentation] A strange reaction of a photosensor protein: PixD (2011)
  • Author(s): M.Terazima
  • Organizer: Third Korea-Japan Seminars on Biomolecular Sciences
  • Place of Presentation: Jeju, Korea
• [Presentation] Spectrally silent photochemistry is important for biological reactions (2011)
  • Author(s): M.Terazima
  • Organizer: Gordon Research Conference on Photochemistry
  • Place of Presentation: Easton, USA
• [Presentation] タンパク質反応における時間分解揺らぎ検出の試み (2010)
  • Author(s): 寺嶋正秀
  • Organizer: 日本物理学会
  • Place of Presentation: 大阪府立大学(招待)
  • Year and Date: 2010-09-23
• [Presentation] Role of water-protein interaction for the function of biological proteins (2010)
  • Author(s): M.Terazima
  • Organizer: Pacifichem
  • Place of Presentation: Honolulu, USA
• [Presentation] タンパク質反応における時間分解揺らぎ検出の試み (2010)
  • Author(s): 寺嶋正秀
  • Organizer: 日本物理学会年会
  • Place of Presentation: 大阪府立大学
• [Presentation] Time-resolved observation of protein-protein interaction between blue-light receptor PixD and response regulator PixE (2010)
  • Author(s): K.Tanaka, Y.Nakasone, K.Okajima, M.Ikeuchi, S.Tokutomi, M.Terazima
  • Organizer: 生物物理学会年会
  • Place of Presentation: 仙台
• [Presentation] 光センサータンパク質Phot2LOV1の光反応の解明 (2010)
  • Author(s): 川口雄輝
  • Organizer: 第4回分子科学討論会
  • Place of Presentation: 大阪大学
• [Presentation] 光センサータンパク質フォトトロピンの光反応と隠された機能 (2009)
  • Author(s): 中曽根祐介
  • Organizer: 分子科学討論会
  • Place of Presentation: 名古屋大学東山キャンパス
• [Book] 揺らぎ・ダイナミクスと生体機能―物理化学的視点から見た生体分子― (2013)
  • Author(s): 寺嶋正秀編
  • Total Pages: 347
  • Publisher: 化学同人
• [Book] アミロイド蓄積開始機構の解明と治療薬開発への展開 (2012)
  • Author(s): 柳澤勝彦, 松崎勝巳, 加藤晃一
  • Publisher: 最新医学, 67
• [Book] Generalized-ensemble algorithms for simulations of complex molecular systems (2012)
  • Author(s): Hisashi Okumura
  • Total Pages: 33
  • Publisher: Prac. Aspe.of Comp. Chem. II
• [Book] バイオ／抗体医薬品の開発・製造プロセス (2012)
  • Author(s): 加藤晃一
  • Total Pages: 11
  • Publisher: 情報機構
• [Book] 最新医学 (2012)
  • Author(s): 柳澤勝彦
  • Total Pages: 21
  • Publisher: 最新医学社
• [Book] Protein dynamics studied by neutron incoherent scattering (2011)
  • Author(s): M. Kataoka, H.Nakagawa
  • Publisher: Neutrons in Soft Matter
• [Book] 揺らぎと生体機能総論, メディカルバイオ別冊 (2010)
  • Author(s): 寺嶋正秀、揺らぎと生体機能、寺嶋正秀監修
  • Publisher: オーム社
• [Book] 揺らぎと生体機能(生体分子の反応中の揺らぎをとらえる分子科学手法)(寺嶋正秀監修)メディカルバイオ別冊 (2010)
  • Author(s): 寺嶋正秀
  • Publisher: オーム社
• [Book] メディカルバイオ別冊(揺らぎと生体機能) (2010)
  • Author(s): 寺嶋正秀
  • Total Pages: 4
  • Publisher: オーム社
• [Book] 人工タンパク質の合成と応用, 超分子サイエンス&テクノロジー (2009)
  • Author(s): 芳坂貴弘
  • Publisher: エヌティーエス
• [Book] 可視・紫外分光法 (2009)
  • Author(s): 寺嶋正秀・馬場正昭・冨宅喜代一・星野幹雄・松本剛昭・宮崎芳雄・西澤潔 共著
  • Publisher: 講談社サイエンティフィック
• [Book] Water and Biomolecules(Time-resolved detection of intermolecular interaction of photosensor proteins, Physical Chemistry of Life Phenomena)(Eds.K.Kuwajima, Y.Goto, F.Hirata, M.kataoka, M.Terazima) (2009)
  • Author(s): M.Terazima
  • Publisher: Springer
• [Book] Water and Biomolecules, Physical Chemistry of Life Phenomena (Eds.K.Kuwajima, Y.Goto, F.Hirata, M.kataoka, M.Terazima) (2009)
  • Author(s): M.Terazima
  • Total Pages: 23
  • Publisher: Springer
• [Remarks] 光物理化学研究室
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/yuragi/
• [Remarks] 揺らぎが機能を決める生命分子の科学
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/yuragi/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/yuragi/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/yuragi/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/hikari/yuragi/
• [Patent(Industrial Property Rights)] 焼酎蒸留粕からのエタノール抽出残さ、エタノール抽出物及びそれらの製造方法 (2012)
  • Inventor(s): 上岡龍一、家藤治幸、廣瀬茂
  • Industrial Property Rights Holder: 上岡龍一、家藤治幸、廣瀬茂
  • Acquisition Date: 2012-06-29
• [Patent(Industrial Property Rights)] 残余双極子相互作用の解析法及び残余双極子相互作用解析用試薬 (2009)
  • Inventor(s): 藤田誠、佐藤宗太、諸原理、加藤晃一、山口芳樹
  • Industrial Property Rights Holder: 藤田誠、佐藤宗太、諸原理、加藤晃一、山口芳樹
  • Industrial Property Number: 2009-057080
  • Filing Date: 2009-03-10