Development of model systems for intrinsically disordered protein and understanding of the role of fluctuation on molecular recognition and folding

2012 Fiscal Year Final Research Report

• Project Area: Molecular Science of Fluctuations toward Biological Functions
• Project/Area Number: 20107006
• 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: Nara Institute of Science and Technology
• Principal Investigator: KATAOKA Mikio 奈良先端科学技術大学院大学, 物質創成科学研究科, 教授 (30150254)
• Co-Investigator(Renkei-kenkyūsha): KAMIKUBO Hironari 奈良先端科学技術大学院大学, 物質創成科学研究科, 准教授 (20311128) ; YAMAZAKI Yoichi 奈良先端科学技術大学院大学, 物質創成科学研究科, 助教 (40332770) ; YAMAGUCHI Mariko 奈良先端科学技術大学院大学, 物質創成科学研究科, 助教 (50521738) ; SHIBA Rumi 奈良先端科学技術大学院大学, 物質創成科学研究科, 博士研究員 (70617133) ; ENDO Hitoshi 日本原子力研究開発機構, 量子ビーム応用研究部門, 研究員 (40447313)
• Project Period (FY): 2008 – 2012
• Keywords: 天然変性蛋白質 / 誘導折り畳み / 分子認識 / 変性構造 / 結晶構造解析 / Staphylococcal nuclease

Research Abstract

We created various mutants of functional proteins which do not take stable native conformations but possess enzymatic activity as well as the mutants which take native structure without enzymatic activity. The ligand-induced folding of the former mutants and the crystal structure analysis of the latter mutants brought the conclusion that fluctuations or structure dynamics facilitate the ligand recognition and that fluctuations controls the catalytic activity. We also revealed that the hydration water network via hydrogen bond encircled the protein whole molecule is essential for the control of fluctuations.

Research Products

• [Journal Article] Preferential domain orientation of HMGB2 determined by weak intramolecular interactions mediated by the interdomain linker (2013)
  • Author(s): J. Uewaki, H. Kamikubo, J. Kurita, N. Hiroguchi, H. Moriuchi, M. Yoshida, M. Kataoka, N. U.-Tate, S. Tate
  • Journal Title: Chem.Phys
  • DOI: doi:10.1016/j.chemphys.2013.02.004
  • Peer Reviewed
• [Journal Article] Fingerprint signatures of lanthanide circularly polarized luminescence from proteins covalently labeled by a β -diketonate europium(III) chelate (2013)
  • Author(s): J.Yuasa, T. Ohno, H. Tsumatori, R. Shiba, H. Kamikubo, M. Kataoka, Y. Hasegawa, T. Kawai
  • Journal Title: Chem. Commn
  • Peer Reviewed
• [Journal Article] 働いているタンパク質の構造を実時間で見た!-次世代構造生物科学への期待 (2013)
  • Author(s): 上久保裕生,片岡幹雄
  • Journal Title: 化学 Volume: 68 Pages: 74-75
• [Journal Article] 1H, 13C, and 15N resonance assignment of photoactive yellow protein (2012)
  • Author(s): T. J. Pool, N. A. Oktaviani, H. Kamikubo, M. Kataoka, F. A. A. Mulder
  • Journal Title: Biomol. NMR Assign Volume: 7 Pages: 97-100
  • Peer Reviewed
• [Journal Article] Maintenance of the secondary structure ofhorse cytochrome c during the conversion process of monomers to oligomers byaddition of ethanol (2012)
  • Author(s): S. Hirota, M. Ueda, Y. Hayashi, S. Nagao, H. Kamikubo, M. Kataoka
  • Journal Title: J. Biochem Volume: 152 Pages: 521-529
  • Peer Reviewed
• [Journal Article] Time-resolved observation of chiral-index-selective wrapping on single-walled carbon nanotube with non-aromatic polysilane (2012)
  • Author(s): W. Chung, K. Nobusawa, H. Kamikubo, M. Kataoka, M. Fujiki, M. Naito
  • Journal Title: J. Am. Chem. Soc Volume: 135 Pages: 2374-2383
  • Peer Reviewed
• [Journal Article] Theoretical analysis of the geometrical isotope effect on the hydrogen bonds in photoactive yellow protein with multi-component density functional theory (2012)
  • Author(s): Y. Kita, H. Kamikubo, M. Kataoka, M. Tachikawa
  • Journal Title: Chem. Phys
  • DOI: doi:10.1016/j.chemphys.2012.11.022
  • Peer Reviewed
• [Journal Article] Watching asignaling protein function in real time via100-ps time-resolved Laue crystallography (2012)
  • Author(s): F. Schotte, H. S. Cho, V. R. I. Kaila, H. Kamikubo, N. Dashdorj, E. R. Henry, T. J. Graber, R. Henning, M. Wulff, G. Hummer, M. Kataoka, P. A. Anfinrud
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 109 Pages: 19256-19261
  • Peer Reviewed
• [Journal Article] Structural basis for Arf6.MKLP1 complexformation on the Flemming bodyresponsible for cytokinesis (2012)
  • Author(s): H. Makyio, M. Ohgi, T. Takei, S. Takahashi, H. Takatsu, Y. Katoh, A. Hanai, T. Ueda, Y. Kanaho, Y. Xie, H.-W. Shin, H. Kamikubo, M. Kataoka, M. Kawasaki, R. Kato, S. Wakatsuki, K. Nakayama
  • Journal Title: EMBO J Volume: 31 Pages: 2590-2603
  • Peer Reviewed
• [Journal Article] 中性子生物物理学の展開 (2012)
  • Author(s): 片岡幹雄
  • Journal Title: 波紋 Volume: 22 Pages: 132-138
• [Journal Article] Comprehensivedetermination of protein tyrosine pKavalues for photoactive yellow protein usingindirect 13C NMR spectroscopy (2011)
  • Author(s): N. A. Oktaviani, T. J. Pool, H. Kamikubo, J. Slager, R. M. Scheek, M. Kataoka, F. A.A. Mulder
  • Journal Title: Biophys. J Volume: 102 Pages: 579-586
  • Peer Reviewed
• [Journal Article] 生物研究における中性子 (2011)
  • Author(s): 片岡幹雄
  • Journal Title: 波紋 Volume: 21 Pages: 243-246
  • Peer Reviewed
• [Journal Article] Solvent penetration in photoactive yellow protein R52Q mutant: a theoretical study (2011)
  • Author(s): D. J. Sindhikara, N. Yoshida, M. Kataoka, F. Hirata
  • Journal Title: J. Mol. Liq Volume: 164 Pages: 120-122
  • Peer Reviewed
• [Journal Article] Changes in the hydrogen-bondnetwork around the chromophore of photoactive yellow protein in the groundand excited states (2011)
  • Author(s): M. Mizuno, H. Kamikubo, M. Kataoka, Y. Mizutani
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 9306-9310
  • Peer Reviewed
• [Journal Article] 中性子非弾性散乱による生体高分子ダイナミックスの研究 (2011)
  • Author(s): 中川洋,片岡幹雄
  • Journal Title: 高分子 Volume: 60 Pages: 195-196
• [Journal Article] Systematic alanine insertion reveals the essential regions that encode structure formation and activity of dihydrofolate reductase (2010)
  • Author(s): R. Shiba, M. Umeyama, S. Tsukasa, H. Kamikubo, Y. Yamazaki, M. Yamaguchi, M.Iwakura, M. Kataoka
  • Journal Title: Biophysics Volume: 7 Pages: 1-10
  • Peer Reviewed
• [Journal Article] Percolation of hydration water as a control of protein dynamics (2010)
  • Author(s): H. Nakagawa, M. Kataoka
  • Journal Title: J. Phys. Soc. Jpn Volume: 79 Pages: 083801
  • Peer Reviewed
• [Journal Article] Size-controlled aggregation of cube-shaped EuS nanocrystals with magneto-opticproperties in solution phase (2010)
  • Author(s): A. Tanaka, H. Kamikubo, M. Kataoka, Y. Hasegawa, T. Kawai
  • Journal Title: Langmuir Volume: 27 Pages: 104-108
  • Peer Reviewed
• [Journal Article] Cytochrome c polymerization by successive domain swapping at the C-terminal helix (2010)
  • Author(s): S. Hirota, Y. Hattori, S. Nagao, M.Taketa, H. Komori, H. Kamikubo, Z. Wang, I. Takahashi, S. Negi, Y. Sugiura, M. Kataoka, Y. Higuchi
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 107 Pages: 12854-12859
  • Peer Reviewed
• [Journal Article] フォトアクティブイェロープロテインの中性子結晶構造解析 (2010)
  • Author(s): 上久保裕生,山口繁生,片岡幹雄
  • Journal Title: Radioisotopes Volume: 59 Pages: 289-297
  • Peer Reviewed
• [Journal Article] Effect of conformational states on protein dynamical transition (2009)
  • Author(s): H. Nakagawa, H. Kamikubo, M. Kataoka
  • Journal Title: Biochim. Biophys. Acta Volume: 1804 Pages: 27-33
  • Peer Reviewed
• [Journal Article] Self-assembly and enhanced magnetic properties of three-dimensional superlattice structures composed of cube-shaped EuS nanocrystals (2009)
  • Author(s): A. Tanaka, H. Kamikubo, Y. Doi, Y. Hinatsu, M. Kataoka, T. Kawai, Y. Hasegawa
  • Journal Title: Chem. Mater Volume: 22 Pages: 1776-1781
  • Peer Reviewed
• [Journal Article] Nonlocal interactions are responsible for tertiary structure formation in staphylococcalnuclease (2009)
  • Author(s): S. Kato, H. Kamikubo, S. Hirano, Y.Yamazaki, M. Kataoka
  • Journal Title: Biophys. J Volume: 98 Pages: 678-7861Tanaka, Y. Hasegawa, H. Kamikubo, M. Kataoka, T. Kawai
  • Peer Reviewed
• [Journal Article] Self-aggregation of magnetic semiconductor EuS nanocrystals (2009)
  • Author(s): Tanaka, Y. Hasegawa, H. Kamikubo, M. Kataoka, T. Kawai
  • Journal Title: Thin Solid Films Volume: 518 Pages: 870-872
  • Peer Reviewed
• [Journal Article] Structural effects on the ultrafast photoisomerization of photoactive yellowprotein. Transient absorption spectroscopy of two point mutants (2009)
  • Author(s): P. Changenet-Barret, P. Plaza, M. M. Martin, H. Chosrowjan, S. Taniguchi, N. Mataga, Y. Imamoto, M. Kataoka
  • Journal Title: J. Phys. Chem. C Volume: 113 Pages: 11605-11613
  • Peer Reviewed
• [Journal Article] 非干渉性中性子非弾性散乱で観るタンパク質ダイナミクスの水和効果 (2009)
  • Author(s): 中川洋,片岡幹雄
  • Journal Title: 波紋 Volume: 19 Pages: 91-94
  • Peer Reviewed
• [Journal Article] Nucleotide-dependentconformational changes and assembly of the AAA ATPase SKD1/VPS4B (2008)
  • Author(s): M. Inoue, H. Kamikubo, M. Kataoka,Ryuichi Kato, T. Yoshimori, S. Wakatsuki, M. Kawasaki
  • Journal Title: Traffic Volume: 9 Pages: 2180-2189
  • Peer Reviewed
• [Journal Article] Low-barrier hydrogen bond in photoactiveyellow protein (2008)
  • Author(s): S. Yamaguchi, H. Kamikubo, K. Kurihara, R. Kuroki, N. Niimura, N. Shimizu, Y. Yamazaki, M. Kataoka
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 106 Pages: 440-444
  • Peer Reviewed
• [Presentation] Is the protein tertiary structure necessary for a specificfunction? (2013)
  • Author(s): M. Kataoka
  • Organizer: American Physical Society (APS)March Meeting 2013
  • Place of Presentation: Baltimore, MD, USA
  • Year and Date: 20130317-22
• [Presentation] Protein dynamics and hydration water (2012)
  • Author(s): M. Kataoka
  • Organizer: The 10th International Conference on Quasi Elastic Neutron Scattering
  • Place of Presentation: Nikko
  • Year and Date: 20120930-1004
• [Presentation] Is tertiary structure required for a specific function? (2011)
  • Author(s): M. Kataoka
  • Organizer: Telluride Science Research Center (TSRC) Workshopon Protein Dynamics 2011
  • Place of Presentation: Telluride, CO,USA
  • Year and Date: 20110801-05
• [Presentation] High resolution neutron crystal structure of photoactive yellow protein: Discovery of low barrierhydrogen bond (2011)
  • Author(s): M. Kataoka
  • Organizer: The 7th Asian BiophysicsAssociation (ABA) Symposium
  • Place of Presentation: New Delhi,India
  • Year and Date: 20110130-0202
• [Presentation] Low barrier hydrogenbond in photoactive yellow protein and itsrole in photoreaction (2010)
  • Author(s): M. Kataoka
  • Organizer: International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2010)
  • Place of Presentation: Honolulu, U. S. A.
  • Year and Date: 20101217-21
• [Presentation] Effect of hydration water on protein dynamics (2010)
  • Author(s): M. Kataoka
  • Organizer: The 4th Shangai International Conference on Biophysics and Molecular Biology(2010SICBM)
  • Place of Presentation: Shanghai-Jiashan, China
  • Year and Date: 20100808-12
• [Presentation] Effect of hydration on protein dynamics (2010)
  • Author(s): M. Kataoka
  • Organizer: Leopoldina-Symposium on the ComplexityConnecting Biomolecular Structure and Solvation Dynamics
  • Place of Presentation: Bochum, Germany
  • Year and Date: 20100526-27
• [Presentation] Low barrier hydrogen bond in photoactive yellow protein and its role in photoreaction (2009)
  • Author(s): M. Kataoka
  • Organizer: Telluride Science Research Center (TSRC) Workshop on Protein Dynamics 2009
  • Place of Presentation: Telluride, CO, USA
  • Year and Date: 20090731-0804
• [Book] ひかりエネルギー革命-グリーンフォトニクス-(NAISTグリーンフォトニクス研究チーム編著) (2012)
  • Author(s): 片岡幹雄
  • Total Pages: 91-96
  • Publisher: 化学同人,京都
• [Book] Neutrons in Soft Matter (Eds.T. Imae, T. Kanaya, M.Furusaka, N. Torikai) (2011)
  • Author(s): M. Kataoka, H. Nakagawa
  • Total Pages: 517-538
  • Publisher: John Wiley, NewJersey
• [Book] 揺らぎと生体機能 (MedicalBio 10月別冊)(寺嶋正秀監修) (2010)
  • Author(s): 片岡幹雄
  • Total Pages: 27-31
  • Publisher: オーム社,東京
• [Book] 光ナノ科学への招待(長谷川靖哉、細川陽一郎、中嶋琢也編) (2010)
  • Author(s): 片岡幹雄
  • Total Pages: 36-45
  • Publisher: 化学同人,京都
• [Book] Water, The Forgotten Biological Molecule (Eds. D. LeBihan, H. Fukuyama) (2010)
  • Author(s): M. Kataoka, H. Nakagawa
  • Total Pages: 49-62
  • Publisher: Pan Stanford Publishing, Singapore
• [Book] Water andBiomolecules (Eds. K. Kuwajima, Y. Goto, F.Hirata, M. Kataoka, M. Terazima) (2009)
  • Author(s): M. Kataoka, H. Kamikubo
  • Total Pages: 137-148
  • Publisher: Springer-Verlag, Berlin
• [Book] 光科学研究の最前線 2(「光科学研究の最前線 2」編集委員会編 (2009)
  • Author(s): 片岡幹雄
  • Total Pages: 208
  • Publisher: 強光子場科学研究懇談会,東京
• [Remarks] (1)光センサータンパク質の構造変化を世界最高レベルの分解能で可視化することに成功(MSN産経ニュース「ベテラン記者のデイリーコラム・坂口至徳の科学の現場を歩く」2012年11月6日、日刊工業新聞 2012年11月7日、日経新聞 2012年11月27日)
• [Remarks] (2)日本中性科学会第 9回学会賞を受賞(科学新聞 2011年11月18日)
• [Remarks] (3) M. Terazima, M. Kataoka and R. Ueoka, "Molecular Science of Fluctuations toward Biological Functions",(Science, 333, 1329. 2011年9月2日)
• [Remarks] (4)タンパク質動力学に対する水和水の役割を解明(科学新聞 2010年8月6日、日経産業新聞 2010年8月16日、日刊工業新聞 2010年8月23日)
• [Remarks] (5)世界で初めてタンパク質に低障壁水素結合を発見(時事通信 2008年12月30日、産経新聞2008年12月31日、奈良日日新聞2009年1月5日、日刊工業新聞2009年1月6日、フジサンケイビジネスアイ2009年1月6日、科学新聞 2009年1月16日)