天然変性タンパク質の分子認識機構と機能発現/成果

成果

業績リスト

| A01 | A02 | A03 |

A01：構造生物学グループ

Sugiyama, M., Arimura, Y., Shirayama, K., Fujita, R., Oba, Y., Sato, N., Inoue, R., Oda, T., Sato, M., Heenan, R. K. and Kurumizak, H. Distinct Features of the Histone Core Structure in Nucleosomes Containing the Histone H2A.B Variant. Biophysical J., 106, 2206-2213 (2014). PubMed

Walinda, E., Morimoto, D., Sugase, K., Konuma, T., Tochio, H. and Shirakawa, M. Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin. J. Biol. Chem. (2014). in press. PubMed

Nomura, K., Harada, E., Sugase, K. and Shimamoto, K. Solid-state NMR spectra of lipid-anchored proteins under magic angle spinning. J. Phys. Chem. B. 118, 2405-2413 (2014). PubMed

Sugase, K., Konuma, T., Lansing, JC. and , Wright, PE. Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE. J. Biomol. NMR. 56, 275-283 (2013). PubMed

Ando, T., Uchihashi, T. and Scheuring, S. Filming biomoleculear processes by high-speed atomic force microscopy. Chem. Rev. 114, 3120-3188 (2014). PubMed

Nakamura, A., Watanabe, H., Ishida, T., Uchihashi, T., Wada, M., Ando, T., Igarashi, K. and Samejima, M. Trade-off between processivity and hydrolytic velocity of cellobiohydrolases at the surface of crystalline cellulose. J. Am. Chem. Soc. 136, 4584-4592 (2014). PubMed

Igarashi, K., Uchihashi, T., Uchiyama, T., Sugimoto, H., Wada, M., Suzuki, K., Sakuda, S., Ando, T., Watanabe, T. and Samejima, M. Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin. Nature Communications. in press.

Kodera, N. and Ando, T. The path to visualization of walking myosin V by high-speed atomic force microscopy. Biophy. Rev. (accepted).

Noi, K., Yamamoto, D., Nishikori, S., Arita-Morioka, K., Ando, T. and Ogura, T. High-Speed atomic force microscopic observation of ATP-dependent rotation of the AAA+ chaperone p97. Structure 21, 1992-2002 (2013). PubMed

Yilmaz, N., Yamada, T., Greimel, P., Uchihashi, T., Ando, T. and Kobayashi, T. Real-time visualization of assembling of a sphingomyelin-specific toxin. Biophys. J. 105, 1397-1405 (2013). PubMed

Fukuda, S., Uchihashi, T., Iino, R., Okazaki, Y., Yoshida, M., Igarashi, K. and Ando, T. High-speed atomic force microscope combined with single-molecule fluorescence microscope. Rev. Sci. Instrum. 84, 073706 (2013). PubMed

Watanabe, H., Uchihashi, T., Kobashi, T., Shibata, M., Nishiyama, J., Yasuda, R. and Ando, T. Wide-area scanner for high-speed atomic force microscopy. Rev. Sci. Instrum. 84, 053702 (10 pp) (2013). PubMed

Hashimoto, M., Kodera, N., Tsunaka, Y., Oda, M., Tanimoto, M., Ando, T., Morikawa, K. and Tate, S. Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT. Biophys. J. 104, 2222-2234 (2013). PubMed

Yamashita, H., Inoue, K., Shibata, M., Uchihashi, T., Sasaki, J., Kandori, H. and Ando, T. Role of trimer-trimer interaction of bacteriorhodopsin studied by high-speed atomic force microscopy. J. Struct. Biol. 184, 2-11 (2013). PubMed

Ando, T. Molecular machines directly observed by high-speed atomic force microscopy. FEBS Lett. 587, 997-1007 (2013). PubMed

Ando, T., Uchihashi, T. and Kodera, N. High-speed AFM and applications to biomolecular systems. Annu. Rev. Biophys. 42, 393-414 (2013). PubMed

Ando, T. High-speed atomic force microscopy. Microscopy 62, 81-93 (2013). PubMed

Ando, T., Uchihashi, T. and Kodera, N. High-speed atomic force microscopy. Jpn. J. Appl. Phys. 51, 08KA02 (15 pp) (2012).

Yamashita, H., Taoka, A., Uchihashi, T., Asano, T., Ando, T. and Fukumori, Y. Single molecule imaging on living bacterial cell surface by high-speed AFM. J. Mol. Biol. 422, 300-309 (2012). PubMed

Ando, T. High-speed atomic force microscopy coming of age. Nanotechnology. 23, 062001 (27 pp) (2012). PubMed

Igarashi, K., Uchihashi, T., Koivula, A., Wada, M., Kimura, S., Penttilä, M., Ando, T. and Samejima, M. Visualization of cellobiohydrolase I from Trichoderma reesei moving on crystalline cellulose using high-speed atomic force microscopy. Methods Enzymol. 510, 169-182 (2012). PubMed

Uchihashi, T., Kodera, N. and Ando, T. Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy. Nature Protocols. 7, 1193-1206 (2012). PubMed

Ando, T. and Kodera, N. Visualization of mobility by atomic force microscopy. Methods Mol. Biol. 896, 57-69 (2012). PubMed

Uchihashi, T. and Ando, T. High-speed atomic force microscopy and biomolecular　processes. Methods Mol. Biol. 736, 285-300 (2011). PubMed

Igarashi, K., Uchihashi, T., Koivula, A., Wada, M., Kimura, S., Okamoto, T., Penttilä, M., Ando, T. and Samejima, M. Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface. Science. 333, 1279-1282 (2011). PubMed

Laisne, A., Ewald, M., Ando, T., Lesniewska, E. and Pompon, D. Self-assembly properties　and dynamic of synthetic proteo-nucleic building blocks in solution and on surfaces. Bioconjugate Chem. 22, 1824-1834 (2011). PubMed

Miyagi, A., Ando, T. and Lyubchenko, Y. L. Dynamics of nucleosomes assessed with time-lapse high speed atomic force microscopy. Biochemistry. 50, 7901-7908 (2011). PubMed

Uchihashi, T., Iino, R., Ando, T. and Noji, H. High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase. Science. 333, 755-758 (2011). PubMed

Shibata, M., Uchihashi, T., Yamashita, H., Kandori, H. Ando, T. Structural changes in bacteriorhodopsin in response to alternate illumination observed by high-speed atomic force microscopy. Angew. Chem. Int. Ed. 50, 4410-4413 (2011). PubMed

Lyubchenko, Y. L., Shlyakhtenko, L. S. and Ando, T. Imaging of nucleic acids with atomic force microscopy. Methods. 54, 274-283 (2011). PubMed

Inoue, S., Uchihashi, T., Yamamoto, D. and Ando, T. Direct Observation of Surfactant Aggregate Behavior on a Mica Surface using High-Speed Atomic Force Microscopy. Chem. Commun. 47, 4974–4976 (2011). PubMed

Ando, T. and Uchihashi, T. High-speed AFM and imaging of biomoleculr processes. pp. 713-742 in Nanoscale Liquid Interfaces: Wetting, Patterning, and Force Microscopy at the Molecular Scale. Thierry Ondarçuhu, Jean-Pierre Aimé Ed., Pan Stanford Publishing (2013).

Uchihashi, T., Kodera, N. and Ando, T. Nanovisualization of proteins in action using high-speed AFM. pp 119-147, in "Single-molecule Studies of Proteins. Biophysics for the Life Sciences Vol 2". Andres Oberhauser Ed., Springer (2013).

Ando, T. and Kodera, N. Visualization of mobility of atomic force microscopy. pp 57-69, in Springer series Methods in Molecular Biology, vol. 897, part 1 "Experimental Tools for the Intrinsically Disordered Protein Analysis": Vladimir N. Uversky and A. Keith Dunker Ed., Springer (2012).

Ando, T. Techniques for developing high-speed AFM. pp. 1-16 in "Control Technologies for Emerging Micro and Nanoscale Systems" (Lecture Notes in Control and Information Sceinces, Vol.413). Eleftheriou, Evangelos; Moheimani, S.O. Reza, Ed., Springer (2011).

Ando, T., Uchihashi, T., Kodera, N., Shibata, M., Yamamoto, D. and Yamashita, H. High-speed AFM for observing dynamic processes in liquid. pp.189-210, in "Atomic force microscopy in liquid", Arturo M Baró and Donald Refenberger Ed., Wiley-VCH Verlag GmbH (2011)

T. Uchihashi, T. Ando, High-speed atomic force microscopy for dynamic biological imaging. pp. 163-184, in "Life at the Nanoscale - Atomic force microscopy of live cells", Yves Dufrene Ed., Pan Stanford Publishing Pte. Ltd. (2011).

Yokoyama, T., Kosaka, Y. and Mizuguchi, M. Crystal structures of human transthyretin complexed with glabridin. Journal of Medicinal Chemistry. 57, 1090-1096 (2014). PubMed

Yokoyama, T., Ostermann, A., Mizuguchi, M., Niimura, N., Schrader, T. E. and Tanaka, I. Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate. Acta Crystallographica Section F. 70, 470-472 (2014). PubMed

Mizuguchi, M., Obita, T., Serita, T., Kojima, R., Nabeshima, Y. and Okazawa, H. Mutations in the PQBP1 gene prevent its interaction with the spliceosomal protein U5-15kD. Nature Communications. 5, 3822 (2014).

Hayashi, T., Oshima, H., Mashima, T., Nagata, T., Katahira, M. and Kinoshita, M. Binding of an RNA aptamer and a partial peptide of a prion protein: Crucial importance of water entropy in molecular recognition. Nucleic Acids Res. (2014). in press.

Furukawa, A., Sugase, K., Morishita, R., Nagata, T., Kodaki, T., Takaori-Kondo, A., Ryo, A. and Katahira, M. Quantitative Analysis of Location- and Sequence-Dependent Deamination by APOBEC3G Using Real-Time NMR Spectroscopy. Angew Chem Int Ed Engl. 53, 2349-2352 (2014). PubMed

Mashima, T., Nishikawa, F., Kamatari, O. Y., Fujiwara, H., Saimura, M., Nagata, T., Kodaki, T., Nishikawa, S., Kuwata, K. and Katahira, M. Anti-prion activity of an RNA aptamer and its structural basis. Nucleic Acids Res. 41, 1355-1362 (2013). PubMed

Furukawa, A., Okamura, H., Morishita, R., Matsunaga, S., Kobayashi, N., Ikegami, T.,Kodaki, T., Takaori-Kondo, A., Ryo, A., Nagata, T. and Katahira, M. NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir. Biochem. Biophys. Res. Commun. 425, 284-289 (2012). PubMed

Sugiyama, M., Yagi, H., Yamaguchi, T.,Kumoi, K., Hirai, M., Oba, Y., Sato, N., Porcar, L., Martel, A. and Kato, K. Conformational characterization of a protein complex involving intrinsically disordered protein by small-angle neutron scattering using the inverse contrast matching method: a case study of interaction between α-synuclein and PbaB tetramer as a model chaperone. Journal of Applied Crystallography. 47, 430-435 (2014).

Sugiyama, M., Sahashi, H., Kurimoto, E., Takata, S., Yagi, H., Kanai, K., Sakata, E., Minami, Y., Tanaka, K. and Kato, K. Spatial arrangement and functional role of α-subunits of proteasome activator PA28 in hetero-oligomer. Biochemical and Biophysical Research Communications. 432, 141-145 (2013). PubMed

Saikusa, K., Fuchigami, S., Takahashi, K., Asano, Y., Nagadoi, A., Tachiwana, H., Kurumizaka, H., Ikeguchi, M., Nishimura, Y. and Akashi, S. Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation. Anal. Chem. 85, 4165-4171 (2013). PubMed

Saikusa, K., Kuwabara, N., Kokabu, Y., Inoue, Y., Sato, M., Iwasaki, H., Shimizu, T., Ikeguchi, M. and Akashi, S. Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering. Analyst. 138, 1441-1449 (2013). PubMed

鎌形清人、「新規一分子蛍光観察法による蛋白質の構造変化の可視化」化学と生物 51, 22-27 (2013).

Kamagata, K., Kawaguchi, T., Iwahashi, Y., Baba, A., Fujimoto, K., Komatsuzaki, T., Sambongi, Y., Goto, Y., Takahashi, S. Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes. J. Am. Chem. Soc. 134, 11525-11532, (2012). PubMed

鎌形清人.「新技術によるタンパク質研究の新展開」生物物理 52, 104-105 (2012).

Downard, K.M., Maleknia, S.D. and Akashi, S. Impact of Limited Oxidation on Protein Ion Mobility and Structure of Importance to Footprinting by Radical Probe Mass Spectrometry. Rapid Commun. Mass Spectrom. 26, 226-230 (2012). PubMed

Kokabu, Y., Murayama, Y., Kuwabara, N., Oroguchi, T., Hashimoto, H., Tsutsui, Y., Nozaki, N., Akashi, S., Unzai, S., Shimizu, T., Iwasaki, H., Sato, M. and Ikeguchi, M. Fission yeast Swi5-Sfr1 complex, an activator of Rad51 recombinase, forms an extremely elongated Dogleg-shaped structure. J. Biol. Chem. 286, 43569-43576 (2011). PubMed

Downard, K.M., Kokabu, Y., Ikeguchi, M. and Akashi, S. Homology Modelled Structure of the βB2B3-Crystallin Heterodimer Studied by Ion Mobility and Radical Probe Mass Spectrometry. FEBS J. 278, 4044-4054 (2011). PubMed

Ikeda, K., Kameda, T., Harada, E., Akutsu, E. and Fujiwara, T. Combined use of replica-exchange molecular dynamics and magic-angle-spinning solid-state NMR spectral simulations for determining the structure and orientation of membrane-bound peptide. J. Phys. Chem. B. 115, 9327-9336 (2011). PubMed

Todokoro, Y., Kobayashi, M., Sato, T., Kawakami, T., Yumen, I., Aimoto, S., Fujiwara, T. and Akutsu, H. Structure analysis of membrane-reconstituted subunit c-ring of E. coli H+-ATP synthase by solid-state NMR under MAS. J. Biomol. NMR. 48, 1-11 (2010). PubMed

Iwasa, H., Meshitsuka, S., Hongo, K., Mizobata, T. and Kawata, Y. Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. J. Biol. Chem. 286 (24), 21796-21805 (2011). PubMed

Seki, Y., Shimbo, Y., Nonaka, T. and Soda, K. A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions Journal of Chemical Theory and Computation. American Chemical Society. 7, 2126-2136 (2011).

Tachiwana, H., Kagawa, W., Shiga, T., Osakabe, A., Miya, Y., Saito, K., Hayashi-Takanaka, Y., Oda, T., Sato, M., Park, S-Y., Kimura, H. and Kurumizaka, H. Crystal structure of the human centromeric nucleosome containing CENP-A. Nature. 476, 232-235 (2011). PubMed

Sugase, K. Elucidating slow binding kinetics of a protein without observable bound resonances by longitudinal relaxation NMR spectroscopy. J. Biomol. NMR. 50, 219-227 (2011). PubMed

Ikeda, K., Kameda, T., Harada, E., Akutsu, H. and Fujiwara, T. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B. 115, 9327-9336 (2011). PubMed

Higo, J., Nishimura, Y. and Nakamura, H. A Free-energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-atom Computations. J Am Chem Soc.133, 10448-10458 (2011). PubMed

Yoshizawa, T., Shimizu, T., Yamabe, M., Taichi, M., Nishiuchi, Y., Shichijo, N., Unzai, S., Hirano, H., Sato, M. and Hashimoto, H. Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase. FEBS J. 278, 1944-1954 (2011). PubMed

Oroguchi, T., Ikeguchi, M. and Sato, M. Towards the Structural Characterization of Intrinsically Disordered Proteins by SAXS and MD Simulation. J. Physics: Conference Series. 272, 012005 (2011).

Kawai, A., Hashimoto, H., Higuchi, S., Tsunoda M., Sato, M., Nakamura, KT. and Miyamoto, S. A novel heterotetrameric structure of the crenarchaeal PCNA2–PCNA3 complex. J. Struct. Biol. 174, 443-450 (2011). PubMed

苙口友隆, 池口満徳, 佐藤衛. 「天然変性タンパク質：タンパク質の構造・機能研究の新しいターゲット―Ｘ線小角散乱と分子動力学シミュレーションによる動的構造解析―」 実験医学. 29, 475-480 (2011).

Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W. and Kurumizaka, H. Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene. Acta Cryst. D 67, 112-118 (2011). PubMed

鎌形清人, 高橋聡. 「新しいタンパク質科学の可能性-新時代を切り拓くマルチタレントDavidBaker-」化学（化学同人）. 1, 68-69 (2011).

Nomura, K., Maeda, M., Sugase, K. and Kusumoto, S. Lipopolysaccharide induces raft domain expansion in membrane composed of a phospholipid-cholesterol-sphingomyelin ternary system. Innate Immun. 17, 256-268 (2011). PubMed

Kurahashi, H., Pack, CG., Shibata, S., Oishi, K., Sako, Y. and Nakamura, Y. [PSI(+)] aggregate enlargement in rnq1 nonprion domain mutants, leading to a loss of prion in yeast. Genes Cells. 16, 576-589 (2011). PubMed

Kataoka, M. and Nakagawa, H. Effect of hydration on protein dynamics In "Water, The Forgotten Biological Molecule" (Eds. Le Bihan, D., Fukuyama, H.), pp. 49-62, Pan Stanford Publishing, Singapore (2011).

Kataoka, M. and Nakagawa, H. Protein dynamics studied by neutron incoherent scattering In "Neutrons in Soft Matter" (Eds. Imae, T., Kanaya, T., Furusaka, M., Torikai, N.), pp. 517-538, John Wiley, New Jersey (2011).

中川洋，片岡幹雄. 「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」高分子. 60, 195-196 (2011).

Soda, K., Shimbo, Y., Seki, Y. and Taiji, M. Structural Characteristics of Hydration Sites in Lysozyme. Biophysical Chemistry. 156, 31-42 (2011). PubMed

Nakamura, S., Seki, Y., Katoh, E. and Kidokoro, S.-i. Thermodynamic and Structural Properties of the Acid Molten Globule State of Horse Cytochrome c. Biochemistry, American Chemical Society. 50, 3116-3126 (2011). PubMed

Kodera, N.,Yamamoto, D., Ishikawa, R. and Ando T. Video imaging of walking myosin V by high-speed atomic force microscopy. Nature. 468, 72-76 (2010). PubMed ( 補足：関連記事が朝日新聞に掲載されました。)

Ishikawa, T. and Kuwata, K. Interaction Analysis of the Native Structure of Prion Protein with Quantum Chemical Calculations. J. Chem. Theory Comput. 6, 538–547 (2010).

Ishikawa, T. and Kuwata, K. Accerelation of monomer self-consistent charge process in fragment molecular orbital method. Chem-Bio Inform. J. 10, 24-31 (2010).

Yamamoto, N. and Kuwata, K. Redox behaviors of the neurotoxic portion in human prion protein, HuPrP (106-126), Chemical Physics Letters. doi:10.1016 / j.cplett, 2010.08.041 (2010).

Endo, S., Matsunaga, T., Kuwata, K., Zhao, HT., El-Kabbani, O., Kitade, Y. and Hara, A. Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10. Bioorg. Med. Chem. 18, 2485-2490 (2010). PubMed

Takahashi, S. and Kamagata, K. Staring at a Protein: Ensemble and Single Molecule Investigations on Protein Folding Dynamics. Single-Molecule Biophysics : Experiment and Theory in Adv. Chem. Phys. 146, 3-22 (2012).

Oda, T., Hashimoto, H., Kuwabara, N., Akashi, S., Hayashi, K., Kojima, C., Kawasaki, T., Shimamoto, K., Sato M. and Shimizu, T. Structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications. J. Biol. Chem. 285, 1435-1445 (2010). PubMed

Yanagihara, I., Nakahira, K., Yamane, T., Kaieda, S., Mayanagi, K., Hamada, D., Fukui, T., Ohnishi, K., Kajiyama, S., Shimizu, T., Sato, M., Ikegami, T., Ikeguchi, M., Honda, T. and Hashimoto, H. Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin. J. Biol. Chem. 285, 16267-16274 (2010). PubMed

Hara, K., Hashimoto, H., Murakumo, Y., Kobayashi, S., Kogame, T., Unzai, S., Akashi, S., Takeda, S., Shimizu T. and Sato, M. Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase zeta and REV1. J. Biol. Chem. 285, 12299-12307 (2010). PubMed

Yamamoto, D., Taoka, A., Uchihashi, T., Sasaki, H., Watanabe, H., Ando, T. and Fukumori, Y. Visualization and structural analysis of the bacterial magnetic organelle magnetosome using atomic force microscopy. Proc. Natl. Acad. Sci. USA 107, 9382-9387 (2010). PubMed

Shimoyama, S., Nagadoi, A., Tachiwana, H., Yamada, M., Sato, M., Kurumizaka, H., Nishimura, Y. and Akashi, S. Deimination stabilizes histone H2A/H2B dimers as revealed by electrospray ionization mass spectrometry. J. Mass. Spectrom. 45, 900-908 (2010). PubMed

佐藤衛.「中性子溶液散乱法による生体高分子の構造解析」 RADIOISOTOPES. 59, 367-378 (2010).

Sugimoto, S., Yamanaka, K., Nishikori, S., Miyagi, A., Ando, T. and Ogura, T. AAA+ chaperone ClpX regulates dynamics of prokaryotic cytoskeletal protein FtsZ. J. Biol. Chem. 285, 6648-6657 (2010). PubMed

Giocondi, M.-C., Yamamoto, D., Lesniewska, E., Milhiet, P.-E., Ando, T. and Grimellec, C.L. Surface topography of membrane domains. Biochim. Biophys. Acta.-Biomembranes 1978, 703-718 (2010). PubMed

Shibata, M., Yamashita, H., Uchihashi, T., Kandori, H. and Ando, T. High-speed atomic force microscopy shows dynamic molecular processes in photo-activated bacteriorhodopsin. Nature Nanotechnology 5, 208-212 (2010). PubMed

Yagi, H., Takeuchi, H., Ogawa, S., Ito, N., Sakane, I., Hongo, K., Mizobata, T., Goto, Y. and Kawata, Y. Isolation of short peptide fragments from alpha-synuclein fibril core identifies a residue important for fibril nucleation: A possible implication for diagnostic applications. Biochim. Biophys. Acta / Proteins and Proteomics 1804, 2077-2087 (2010). PubMed

Hiroshima, M. and Sako, Y. Single-molecule kinetic analysis of receptor protein tyrosine kinases. "Cell Signaling Reactions: Single-molecule Kinetic Analyses". Sako, Y. and Ueda, M. ed. Springer in press (2010).

Hibino, K. and Sako, Y. Single-molecule analysis of molecular recognition between signaling proteins Ras and RAF. "Cell Signaling Reactions: Single-molecule Kinetic Analyses". Sako, Y. and Ueda, M. ed. Springer in press (2010).

Hashimoto, H., Hara, K., Hishiki, A., Kawaguchi, S., Shichijo, N., Nakamura, K., Unzai, S., Tamaru, Y., Shimizu, T. and Sato, M. Crystal structure of zinc-finger domain of Nanos and its functional implications. EMBO Rep. 11, 848-853 (2010). PubMed

Kuwabara, N., Hashimoto, H., Yamada, N., Unzai, S., Ikeguchi, M., Sato, M., Murayama, Y., Iwasaki, H. and Shimizu, T. Expression, purification and crystallization of Swi5 and the Swi5-Sfr1 complex from fission yeast. Acta Cryst. F 66, 1124-1126 (2010). PubMed

Milhiet, PE., Yamamoto, D., Berthoumieu, O., Dosset, P., Le, Grimellec, C., Verdier, JM., Marchal, S. and Ando, T. Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy. PLos One. 5, e13240 (8 pp) (2010). PubMed

Yamamoto, D., Uchihashi, T., Kodera, N., Yamashita, H., Nishikori, S., Ogura, T., Shibata, M. and Ando, T. High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. Methods Enzymol. 475 (B) 541-564 (2010). PubMed

安藤敏夫. 「歩くタンパク質 "ミオシンV" を捉えた!」化学. 66, 55-59 (2010).

安藤敏夫, 古寺哲幸. 「高速原子間力顕微鏡によるタンパク質の動態撮影」生物物理. 51, 22-25 (2010).

安藤敏夫. Visual Review「高速原子間力顕微鏡によるタンパク質の高解像・動画観察」感染・炎症・免疫. 40, 31-37 (2010).

安藤敏夫. 「生体分子の動態を捉える高速原子間力顕微鏡」表面科学. 31, 405-410 (2010).

安藤敏夫. 「生体分子の動的プロセスを直接可視化する高速AFM」顕微鏡. 45, 22-30 (2010).

Domann, PJ., Akashi, S., Barbas, C., Huang, L., Lau, W., Legido-Quigley, C., McClean, S., Neusüss, C., Perrett, D., Quaglia, M., Rapp, E., Smallshaw, L., Smith, NW., Smyth, WF. and Taylor, CF. Minimum Information About a Proteomics Experiment (MIAPE). Guidelines for reporting the use of capillary electrophoresis in proteomics. Nat Biotechnol. 28, 654-655 (2010). PubMed

Tanaka, S., Kawata, Y., Otting, G., Dixon, NE., Matsuzaki, K. and Hoshino, M. Chaperonin-encapsulation of proteins for NMR. Biochim Biophys Acta. 1804, 866-8671 (2010). PubMed

日比野佳代, 白燦基, 佐甲靖志. 「細胞内1分子計測とシステムズバイオロジー」細胞工学. 29, 344-348 (2010).

Nakagawa, H. and Kataoka, M. Percolation of hydration water as a control of protein dynamics. J. Phys. Soc. Jpn. 79, 083801 (2010).（補足：この研究は科学新聞、日系産業新聞、日刊工業新聞で取り上げられました。）

Takahashi, M., Mizuguchi, M., Shinoda, H., Aizawa, T., Demura, M., Okazawa, H. and Kawano, K. Polyglutamine tract-binding protein-1 binds to U5-15kD via a continuous 23-residue segment of the C-terminal domain. Biochim. Biophys. Acta. 1804, 1500-1507 (2010). PubMed

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Kawashima, S., Nakabayashi, Y., Matsubara, K., Sano, N., Enomoto, T., Tanaka, K., Seki, M. and Horikoshi, M. Global analysis of core histones reveals nucleosomal surfaces required for chromosome bi-orientation. EMBO J. 30, 3353-3367 (2011). PubMed

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Oikawa, D. and Kimata, Y. Experimental approaches to elucidate stress-sensing mechanism of Ire1 family proteins. Methods Enzymol. in press (2010).

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Cheng, Y., Geng, H., Cheng, S.H., Liang, P., Bai, Y., Li, J., Srivastava, G., Ng, M.H., Fukagawa, T., Wu, X., Chan, A.T. and Tao, Q. The KRAB zinc finger protein ZNF382 is a general, proapoptotic tumor suppressor repressing multiple oncogenes and frequently silenced in multiple carcinomas. Cancer Research. 70, 6516-6526 (2010). PubMed

Welburn, J.P.I., Vleugel, M., Liu, D., Yates III, J.R., Lampson, M.A., Fukagawa, T. and Cheeseman, I.M. Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface. Molecular Cell 38, 383-392 (2010). PubMed

Akai, Y., Adachi, N., Hayashi, Y., Eitoku, M., Sano, N., Natsume, R., Kudo, N., Tanokura, M., Senda T. and Horikoshi, M. Structure of the histone chaperone CIA/ASF1-double bromodomain complex connecting histone modifications and site-specific histone eviction. Proc. Natl. Acad. Sci. U.S.A. 107, 8153-8158 (2010). PubMed　（補足：この研究は科学新聞、日経産業新聞、日刊工業新聞、化学工業新聞で取り上げられました。）

Schmidt, JC., Kiyomitsu, T., Hori, T., Backer, CB., Fukagawa, T. and Cheeseman, IM. Aurora B kinase controls the targeting of the Astrin/SKAP complex to bi-oriented kinetochores. Journal of Cell Biology. 191, 269-280 (2010). PubMed

Matsuda, R., Hori, T., Kitamura, H., Takeuchi, K., Fukagawa, T. and Harata, M. Identification and characterization of two isoforms of the vertebrate H2A.Z histone variant. Nucleic Acids Research. 38, 4263-4273 (2010). PubMed

Masuda, T., Ling, F., Shibata, T. and Mikawa, T. Analysis of DNA-binding sites on Mhr1, a yeast mitochondrial ATP-independent homologous pairing protein. FEBS J. 277, 1440-1452 (2010). PubMed

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Ling, F., Yoshida, M. and Shibata, T. Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase. J. Biol. Chem. 284, 9341-9353 (2009). PubMed

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Matsunaga, F., Takemura, K., Akita, M., Adachi, A., Yamagami, T. and Ishino, Y. Localized melting of duplex DNA by Cdc6/Orc1 at the DNA replication origin in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 14, 21-31 (2009). PubMed

Liu, D., Vleugel, M., Backer, CB., Hori, T., Fukagawa, T., Cheeseman, IM. and Lampson, MA. Regulated targeting of protein phosphatase 1 to the outer kinetochore by KNL1 opposes Aurora B kinase. Journal of Cell Biology. 188, 809-820 (2010). PubMed

Xu, Z., Ogawa, H., Vagnarelli, P., Bergmann, JH., Hudson, DF., Fukagawa, T., Earnshaw, WC. and Samejima, K. INCENP -aurora B interactions modulate kinase activity and chromosomal passenger complex localization. Journal of Cell Biology. 187, 637-653 (2009). PubMed

Nishimura, T., Fukagawa, T., Takisawa, H., Kakimoto, T. and Kanemaki, M. An auxin-based degron system for the rapid deletion of proteins in nonplant cells. Nature Methods. 6, 917-922 (2009). PubMed

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Amano, M., Suzuki, A., Hori, T., Backer, C., Okawa, K., Cheeseman, IM. and Fukagawa, T. The CENP-S complex is essential for the stable assembly of outer kinetochore structure. Journal of Cell Biology. 186, 173-182 (2009). PubMed

Iwamoto, M., Mori, C., Kojidani, T., Bunai, F., Hori, T., Fukagawa, T., Hiraoka, Y. and Haraguchi, T. Two Distinct Repeat Sequences of Nup98 Nucleoporins Characterize Dual Nuclei in the Binucleated Ciliate Tetrahymena. Current Biology. 19, 843-847 (2009). PubMed

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A03：情報生物学グループ

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Shirai, H., Ikeda, K., Yamashita, K., Tsuchiya, Y., Sarmiento, K., Liang, S., Morokata, T., Mizuguchi, K., Higo, J., Standley, DM. and Nakamura. High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations. Proteins. (2014). PubMed

Higo, J. and Umezawa, K. Free-energy landscape of Intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics. Chapter 14 in "Protein Conformational Dynamics" (Han, K., Zhang, X., and Yang, M. eds.). Springer. Advances in Experimental Medicine and Biology. 805, 331-351 (2014). PubMed

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Higo, J. and Nakamura, H. Virtual states introduced for overcoming entropic barriers in conformational space. Biophysics. 8, 139–144 (2012).

Umezawa, K., Ikebe, J., Takano, M., Nakamura, H. and Higo, J. Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics. Biomolecules. 2, 104-121 (2012).

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Arai, R., Fukui, S., Kobayashi, N. and Sekiguchi, J. Solution structure of IseA, an inhibitor protein of DL-endopeptidases from Bacillus subtilis, reveals a novel fold with a characteristic inhibitory loop. J. Biol. Chem. 287, 44736-44748 (2012). PubMed (解説は信州大学のプレリリースサイトへ)

Arai, R., Kobayashi, N., Kimura, A., Sato, T., Matsuo, K., Wang, A.F., Platt, J.M., Bradley, L.H. and Hecht, M.H. Domain-Swapped Dimeric Structure of a Stable and Functional De Novo 4-Helix Bundle Protein, WA20. J. Phys. Chem. B. 116, 6789-6797 (2012). PubMed （解説は信州大学のプレリリースサイトへ）

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高松敦子, 高野光則, 山崎義弘, 宮口智成, 柳谷晃.「コンプレックス・ダイナミクスの挑戦」共立出版. in press.

Nishi, H., Koike, R. and Ota, M. Cover and spacer insertions: Small nonhydrophobic accessories that assist protein oligomerization. Proteins. in press (2011).

Fukuchi, S., Hosoda, K., Homma, K., Gojobori,T. and Nishikawa. K. Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC Structural Biol. In press.

Tsuruta, T., Goda, N., Umetsu, Y., Iwaya, N., Kuwahara, Y. and Hiroaki, H. 1H, 13C, and 15N resonance assignment of the SPFH domain of human stomatin. Biomol NMR Assign. in press.

Umetsu, Y., Goda, N., Taniguchi, R., Satomura, K., Ikegami, T., Furuse, M. and Hiroaki, H. 1H, 13C, and 15N resonance assignment of the first PDZ domain of mouse ZO-1. Biomol NMR Assign. in press.

Ikebe, J., Standley, D. M., Nakamura, H. and Higo, J. Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Sci. 20, 187-196 (2011). PubMed

Ikebe, J., Umezawa, K., Kamiya, N., Sugihara, T., Yonezawa, Y., Takano, Y., Nakamura, H. and Higo, J. Theory for Trivial Trajectory Parallelization of Multicanonical Molecular Dynamics and Application to a Polypeptide in Water. J. Comput. Chem. 32, 1286–1297 (2011). PubMed

Takeda, S., Koike, R., Nitanai, Y., Minakata, S., Maéda, Y. and Ota, M. Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function. Phys. Biol. 8, 035005 (2011). PubMed

Amemiya, T., Koike, R., Fuchigami, S., Ikeguchi, M. and Kidera, A. Classification and annotation of the relationship between protein structural change and ligand binding. J. Mol. Biol. 408, 568-584 (2011). PubMed

Nonomura, K., Eiguchi, M., Nakano, M., Takashima, K., Komeda, N., Fukuchi, S., Miyazaki, S., Miyano, A., Hirochika, H. and Kurata, N. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in Rice. PLoS Genet. 7, e1001265 (2011). PubMed

Umetsu, Y., Tenno, T., Goda, N., Shirakawa, M., Ikegami, T. and Hiroaki, H. Structural difference of vasoactive intestinal peptide in two distinct membrane-mimicking environments. Biochim Biophys Acta. 1814, 724-730 (2011) . PubMed

Hasegawa, J., Tokuda, E., Tenno, T., Tsujita, K., Sawai, H., Hiroaki, H., Takenawa, T. and Itoh, T. SH3YL1 regulates dorsal ruffle formation by a novel phosphoinositide-binding domain. J Cell Biol. 193, 901-916 (2011). PubMed

Fujiwara, Y., Fujiwara, K., Goda, N., Iwaya, N., Tenno, T., Shirakawa, M. and Hiroaki, H. Structure and Function of the N-terminal Nucleolin Binding Domain of Nuclear Valosin-containing Protein-like 2 (NVL2) Harboring a Nucleolar Localization Signal. J Biol Chem. 286, 21732-21741 (2011). PubMed

Matsuura, Y., Ota, M., Tanaka, T., Takehira, M., Ogasahara, K., Bagautdinov, B., Kunishima, N. and Yutani, K. Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design. J. Biochem. 148, 449-458 (2010) . PubMed

Nishi, H. and Ota, M. Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state. Proteins. 78, 1563-1574 (2010). PubMed

Nishikawa, I., Nakajima, Y., Ito, M., Fukuchi, S., Homma, K. and Nishikawa, K. Computational prediction of O-linked glycosylation sites that preferentially map on intrinsically disordered regions of extracellular proteins. Int. J. Mol. Sci. 11, 4991-5008 (2010). PubMed

Iwaya, N., Kuwahara, Y., Fujiwara, Y., Goda, N., Tenno, T., Akiyama, K., Mase, S., Tochio, H., Ikegami, T., Shirakawa, M. and Hiroaki, H. A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. J Biol Chem. 285, 16822-16829 (2010). PubMed

Jee, J., Mizuno, T., Kamada, K., Tochio, H., Chiba, Y., Yanagi, K., Yasuda, G., Hiroaki, H., Hanaoka, F. and Shirakawa, M. 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. J Biol Chem. 285, 15931-15940 (2010). PubMed

Takano, M., Terada, T.P. and Sasai, M. Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor. Proc. Natl. Acad. Sci. USA. 107, 7769-7774 (2010). PubMed

Ohnishi, H., Tochio, H., Kato, Z., Kimura, T., Hiroaki, H., Kondo, N. Shirakawa, M. 1H, 13C, and 15N resonance assignment of the TIR domain of human MyD88. Biomol NMR Assign. 4, 123-125 (2010). PubMed

Takeda, S., Minakata, S., Koike, R., Kawahata, I., Narita, A., Kitazawa, M., Ota, M., Yamakuni T., Maéda, Y. and Nitanai, Y. Two Distinct Mechanisms for Actin Capping Protein Regulation—Steric and Allosteric Inhibition. PLoS Biol. 8, e1000416 (2010). PubMed

Guo, R., Hirano, T., Kawakami, T., Gong, Y., Nomura, M., Yamaguchi, G., Saji, H., Kakihana, M., Ohira, T. and Ikeda, N. Proteins secreted by lung adenocarcinoma cells: Identification of candidate diagnosis markers from culture supernatants of dissected tumor tissue. Japanese Journal of Lung Cancer. 50, 141-150 (2010).

Gromiha, M.M. and Sarai, A. Thermodynamic Database for Proteins: Features and Applications. Biological Data Mining, Methods Mol. Biol. 609, 97-112 (2010). PubMed

Fernandez, M., Caballero, J., Fernandez, L. and Sarai, A. Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Mol. Divers. 15, 269-289 DOI 10.1007/s11030-010-9234-9 (2010). PubMed

Ahmad, S., Keskin, O., Mizuguchi, K., Sarai, A. and Nussinov, R. CCR XP: Exploring clusters of conserved residues in protein structures. Nucleic Acids Res. 38, 398-401 (2010). PubMed

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果然, 平野隆, 川上隆雄, 龚雲波, 野村将春, 山口学, 佐治久, 垣花昌俊, 大平達夫, 池田徳彦. 「肺腺癌細胞の分泌蛋白質群：外科的切除組織の培養上清に含まれる診断バイオマーカー候補の同定」肺癌. 50, 141-150 (2010).

Hayashi, A., Hino, N., Kobayashi, T., Arai, R., Shirouzu, M., Yokoyama, S. and Sakamoto, K. Dissecting Cell Signaling Pathways with Genetically Encoded 3-Iodo-L-tyrosine. Chem Bio Chem. 12, 387-389 (2010). PubMed

Nishimasu, R., Komori, H., Higuchi, Y., Nishimasu, H. and Hiroaki, H. Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3. Kobe J Med Sci. 56, E125-E139 (2010). PubMed

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Morita, H. and Takano, M. Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster. Phys. Rev. E, 79, 020901(R) (2009). PubMed

Ohnishi, H., Tochio, H., Kato, Z., Orii, K. E., Li, A., Kimura, T., Hiroaki, H., Kondo, N. and Shirakawa, M. Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling. Proc Natl Acad Sci U S A. 106, 10260-10265 (2009). PubMed

Ito, J., Sonobe, Y., Ikeda, K., Tomii, K. and Higo, J. Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. BMC Struct. Biol. 9, 34 (2009). PubMed

Sugihara, T., Higo, J. and Nakamura, H. Parallelization of Markov chain generation and its application to the multicanonical method. J. Phys. Soc. Jpn. 78, 074003 (2009).

Higo, J., Kamiya, N., Sugihara, T., Yonezawa, Y. and Nakamura, H. Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water. Chem. Phys. Lett. 473, 326–329 (2009).

Kuwahara, Y., Unzai, S., Nagata, T., Hiroaki, Y., Yokoyama, H., Matsui, I., Ikegami, T., Fujiyoshi, Y. and Hiroaki, H. Unusual thermal disassembly of the SPFH domain oligomer from Pyrococcus horikoshii. Biophys J. 97, 2034-2043 (2009). PubMed

Inomata, K., Ohno, A., Tochio, H., Isogai, S., Tenno, T., Nakase, I., Takeuchi, T., Futaki, S., Ito, Y., Hiroaki, H. and Shirakawa, M. High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature. 458, 106-109 (2009). PubMed

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Umezawa, K., Ikebe, J., Nomizu, M., Nakamura, H. and Higo, J. Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities. Biopolymers: Peptide Science. 92, 124-131 (2009). PubMed

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