Target recognition and expression mechanism of intrinsically disordered protein/Results

Results

Lists

| A01 | A02 | A03 |

A01：Structural biology group

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

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

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. in press.

Sugase, K. Elucidating slow binding kinetics of a protein without observable bound resonances by longitudinal relaxation NMR spectroscopy. J. Biomol. NMR. in press.

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. in press.

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. In press.

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

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

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).

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

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. Adv. Chem. Phys. in press (2010).

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

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

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

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

Miyata, M., Sato, T., Kugimiya, M., Sho, M., Nakamura, T., Ikemizu, S., Chirifu, M., Mizuguchi, M., Nabeshima, Y., Suwa, Y., Morioka, H., Arimori, T., Suico, M.A., Shuto, T., Sako, Y., Momohara, M., Koga, T., Morino-Koga, S., Yamagata, Y. and Kai, H. Crystal structure of green tea polyphenol(-)-epigallocatechin gallate (EGCG)-transthyretin complex reveals novel binding site distinct from thyroxine binding site. Biochemistry 49, 6104-6114 (2010). PubMed

Miyata, M., Sato, T., Mizuguchi, M., Nakamura, T., Ikemizu, S., Nabeshima, Y., Susuki, S., Suwa, Y., Morioka, H., Ando, Y., Suico, M.A., Shuto, T., Koga, T., Yamagata, Y. and Kai. H. Role of the glutamic acid 54 residue in transthyretin stability and thyroxine binding. Biochemistry 49, 114-123 (2010). PubMed

Yamane, T., Okamura, H., Nishimura, Y., Kidera, A. and Ikeguchi, M. Side-Chain Conformational Changes of Transcription Factor PhoB upon DNA Binding: a Population-Shift Mechanism. J. Am. Chem. Soc. 132, 12653-12659 (2010). PubMed

Oda, T., Hashimoto, H., Kuwabara, N., Akashi, S., Hayashi, K., Kojima, C., Wong, HL., 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 (2009). PubMed

Miranda, FF., Iwasaki, K., Akashi, S., Sumitomo, K., Kobayashi, M., Yamashita, I., Tame, JR. and Heddle, JG. A Self-Assembled Protein Nanotube with High Aspect Ratio. Small. 5, 2077-2084 (2009). PubMed

Sekiguchi, T., Suzuki, N., Fujiwara, N., Aoyama, M., Kawada, T., Sugase, K., Murata, Y., Sasayama, Y., Ogasawara, M. and Satake, H. Calcitonin in a protochordate, Ciona intestinalis--the prototype of the vertebrate calcitonin/calcitonin gene-related peptide superfamily. FEBS J. 276, 4437-4447 (2009). PubMed

Takahashi, M., Mizuguchi, M., Shinoda, H., Aizawa, T., Demura, M., Okazawa, H. and Kawano, K. Polyglutamine tract binding protein-1 is an intrinsically unstructured protein. Biochim. Biophys. Acta. 1794, 936-943 (2009). PubMed

Kouno, T., Mizuguchi, M., Aizawa, T., Shinoda, H., Demura, M., Kawabata, S. and Kawano, K. A novel beta-defensin structure: big defensin changes its N-terminal structure to associate with the target membrane. Biochemistry 48, 7629-7635 (2009). PubMed

Oroguchi, T., Hashimoto, H., Shimizu, T., Sato, M. and Ikeguchi, M. Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis. Biophys. J. 96, 2808-2822 (2009). PubMed

Hishiki, A., Hashimoto, H., Kamei, K., Hanafusa, T., Ohashi, E., Shimizu, T., Ohmori, H. and Sato, M. Structural basis for novel interactions between human TLS polymerases and proliferating cell nuclear antigen. J. Biol. Chem. 282, 10552-10560 (2009). PubMed

Hara, K., Shimizu, T., Unzai, S., Akashi, S., Sato, M. and Hashimoto, H. Purification, crystallization and initial X-ray diffraction study of human REV7 in complex with REV3 fragment. Acta Cryst. F 65, 1302-1305 (2009). PubMed

Hashimoto, H., Kawaguchi, S., Hara, K., Nakamura, K., Shimizu, T., Tamaru, Y. and Sato, M. Purification, crystallization and initial X-ray diffraction study of the zinc-finger domain of zebrafish Nanos. Acta Cryst. F 65, 959-961 (2009). PubMed

Casuso, I., Kodera, N., Grimellec, C.L., Ando, T. and Scheuring, S. High-resolution high-speed contact mode atomic force microscopy movies of purple membrane. Biophys J. 97, 1354-1361 (2009). PubMed

Yamamoto, D., Nagura, N., Omote, S., Taniguchi, M. and Ando, T. Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy. Biophys. J. 97, 2358–2367 (2009). PubMed

Yamashita, H., Voïtchovsky, K., Uchihashi, T., Contera, S.A., Ryan, J.F. and Ando, T. Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy. J. Struct. Biol. 167, 153-158 (2009). PubMed

Shinohara, K., Kodera, N. and Ando, T. Single-molecule imaging of a micro-Brownian motion of a chiral helical π-conjugated polymer as a molecular spring driven by thermal fluctuations. Chem Lett. 38, 690-691 (2009).

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A02：Molecular biology group

Nakabayashi, Y., Kawashima, S., Sato, L., Enomoto, T., Seki, M. and Horikoshi, M. Roles of common subunits within distinct multisubunit complexes. Proc. Natl. Acad. Sci. U.S.A. 111, 699–704 (2014). PubMed

Horikoshi, M. Histone acetylation: From code to web and router via intrinsically disordered regions. Curr. Pharm. Design 19, 5019-5042 (2013). PubMed

Endo, H., Nakabayashi, Y., Kawashima, S., Enomoto, T., Seki, M. and Horikoshi, M. Nucleosome surface containing nucleosomal DNA entry/exit site regulates H3-K36me3 via association with RNA polymerase II and Set2. Genes Cells. 17, 65-81 (2012). PubMed

Ohno, M., Hiraoka, Y., Lichtenthaler, SF., Nishi, K., Saijo, S., Matsuoka, T., Tomimoto, H., Araki, W., Takahashi, R., Kita, T., Kimura, T. and Nishi, E. Nardilysin prevents amyloid plaque formation by enhancing α-secretase activity in an Alzheimer's disease mouse model. Neurobiol. Aging.35, 213-222 (2014). PubMed

Hiraoka, Y., Matsuoka, T., Ohno, M., Nakamura, K., Saijo, S., Matsumura, S., Nishi, K., Sakamoto, J., Chen, PM., Inoue, K., Fushiki, T., Kita, T., Kimura, T. and Nishi, E. Critical roles of nardilysin in the maintenance of body temperature homeostasis. Nat. Commun. 5, 3224 (2014). PubMed

Ichikawa, Y., Morohashi, N., Nishimura, Y., Kurumizaka, H. and Shimizu, M. Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res. 42, 1541-1552 (2014). Pubmed

Kagawa, W., Arai, N., Ichikawa, Y., Saito, K., Sugiyama, S., Saotome, M., Shibata, T. and Kurumizaka, H. Functional analyses of the C terminal half of the Saccharomyces cerevisiae Rad52 protein. Nucleic Acids Res. 42, 941-951 (2014). PubMed

Morozumi, Y., Ino, R., Ikawa, S., Mimida, N., Shimizu, T., Toki, S., Ichikawa, H., Shibata, T. and Kurumizaka, H. Homologous pairing activities of two rice RAD51 proteins, RAD51A1 and RAD51A2. PLoS ONE. 8, e75451 (2013). PubMed

Miura, T., Shibata, T. and Kusano, K. Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity. Proc Natl Acad Sci USA. 110, 16067-16072 (2013). PubMed

Takaoka, Y., Kioi, Y., Morito, A., Otani, J., Arita, K., Ashihara, E., Ariyoshi, M., Tochio, H., Shirakawa, M. and Hamachi, I. Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Chem Commun (Camb). 49, 2801-2803 (2013). PubMed

Otani, J., Arita, K., Kato, T., Kinoshita, M., Kimura, H., Suetake, I., Tajima, S., Ariyoshi, M. and Shirakawa, M. Structural basis of the versatile DNA recognition ability of the methyl CpG binding domain of methyl-CpG binding domain protein 4. J. Biol. Chem. 288, 6351-6362 (2013). PubMed

Unoki, M., Masuda, A., Dohmae, N., Arita, K., Yoshimatsu, M., Iwai, Y., Fukui, Y., Ueda, K., Hamamoto, R., Shirakawa, M., Sasaki, H. and Nakamura, Y. Lysyl 5-Hydroxylation, a Novel Histone Modification, by Jumonji Domain Containing 6 (JMJD6). J. Biol. Chem. 288, 6053-6062 (2013). PubMed

Arita, K., Isogai, S., Oda, T., Unoki, M., Sugita, K., Sekiyama, N., Kuwata, K., Hamamoto, R., Tochio, H., Sato, M., Ariyoshi, M. and Shirakawa, M. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. Proc Natl Acad Sci USA. 109, 12950-12955 (2012). PubMed

Miyata, Y., Nakamoto, H., and Neckers, L. The therapeutic target Hsp90 and cancer hallmarks. Current Pharmaceutical Design 19, 347-365 (2013). PubMed

Miyata, Y. The pivotal role of CK2 in the kinome-targeting Hsp90 chaperone machinery. "The Wiley-IUBMB Series on Biochemistry and Molecular Biology: Protein Kinase CK2", ed. L.A.Pinna, Wiley-Blackwell Publishing (John Wiley & Sons, Inc., Publication), pp.205-238, (2013).

Zanin, S., Borgo, C., Girardi, C., O'Brien, S.E., Miyata, Y., Pinna, L.A., Donella-Deana, A., and Ruzzene, M. Effects of the CK2 inhibitors CX-4945 and CX-5011 on drug-resistant cells. PLOS One 7, e49193 (2012). PubMed

Xu, W., Mollapour, M., Prodromou, C., Wang, S., Scroggins, B.T., Palchick, Z., Beebe, K., Siderius, M., Lee, M.-J., Couvillon, A., Trepel, J.B., Miyata, Y., Matts, R., and Neckers, L. Dynamic tyrosine phosphorylation modulates cycling of the Hsp90-p50Cdc37-Aha1 chaperone machine. Mol. Cell 47, 434-443 (2012). PubMed

Xavier, C.P., Rastetter, R.H., Blömacher, M., Stumpf, M., Himmel, M., Morgan, R.O., Fernandez, M.P., Wang, C., Osman, A., Miyata, Y., Gjerset, R.A., Eichinger, L., Hofmann, A., Linder, S., Noegel, A.A., and Clemen, C.S. Phosphorylation of CRN2 by CK2 regulates F-actin and Arp2/3 interaction and inhibits cell migration. Sci. Rep. 2, 241-254 (2012). PubMed

Handa, N., Yang, L., Dillingham, MS., Kobayashi, I., Wigley, DB. and Kowalczykowski, SC. Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, Chi, by RecBCD enzyme. PNAS 109, pp 8901–8906 (2012). PubMed

Yang, L., Handa, N., Liu, B., Dillingham, MS., Wigley, DB. and Kowalczykowski, SC. Alteration of Chi recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control. PNAS 109, pp 8907–8912 (2012). PubMed

Miura, T., Yamana, Y., Usui, T., Ogawa, H.I., Yamamoto, M-T. and Kusano, K. Homologous Recombination via Synthesis-Dependent Strand-Annealing in Yeast Requires the Irc20 and Srs2 DNA Helicases. Genetics 191, 65-78 (2012). PubMed

Yuzawa, S., Kamakura, S., Iwakiri, Y., Hayase, J. and Sumimoto, H. Structural basis for interaction between the conserved cell polarity proteins Inscuteable and Leu-Gly-Asn repeat-enriched protein (LGN). Proc Natl Acad Sci U S A. 108, 19210-19215 (2011). PubMed

Hirano, H. and Matsuura, Y. Sensing actin dynamics : Structural basis for G-actin-sensitive nuclear import of MAL. Biochem. Biophys. Res. Commun. 414, 373-378 (2011). PubMed

Kosako, H. and Nagano, K. Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways. Expert. Rev. Proteomics. 8, 81-94 (2011). PubMed

Ishikawa, K., Ohsumi, T., Tada, S., Natsume, R., Kundu, L.R., Nozaki, N., Senda, T., Enomoto, T., Horikoshi, M. and Seki, M. The roles of histone chaperone CIA/Asf1 in nascent DNA elongation during nucleosome replication. Genes Cells. 16, 1050-1062 (2011). PubMed

Abe, T., Sugimura, K., Hosono, Y., Takami, Y., Akita, M., Yoshimura, A., Tada, S., Nakayama, T., Murofushi, H., Okumura, K., Takeda, S., Horikoshi, M., Seki, M. and Enomoto, T. The histone chaperone FACT maintains replication fork rates. J.Biol.Chem. 286, 30504-30512 (2011). PubMed

Ogino, H., Ishino, S., Mayanagi, K., Haugland, G. H., Birkeland, N-K., Yamagishi, A. and Ishino Y. The GINS complex from the thermoacidophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication. Extremophiles. 15, in press (2011).

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

Ito, T., Tsuruta, S., Tomita, K., Kikuchi, K., Yokoi, T. and Aizawa, Y. Genes that integrated multiple adipogenic signaling pathways in human mesenchymal stem cells. Biochem. Biophys. Res. Commun. 409, 786-791 (2011). PubMed

Kato, K., Okuwaki, M. and Nagata, K. Involvement of Template Activating Factor-I as a chaperone in linker histone dynamics. J. Cell Sci. 124, 3254-3265 (2011). PubMed

Inoue, J., Nagae, T., Mishima, M., Ito, Y., Shibata, T. and Mikawa, T. A mechanism for SSB displacement from single-stranded DNA upon SSB-RecO interaction. J. Biol. Chem. 286, 6720-6732 (2011). PubMed

Ling, F., Mikawa, T. and Shibata, T. Enlightenment of yeast mitochondrial homoplasmy: diversified roles of gene conversion. Genes. 2, 169-190 (2011).

Oyama, T., Ishino, S., Fujino, S., Ogino, H., Shirai, T., Mayanagi, K., Saito, M., Nagasawa, N., Ishino, Y. and Morikawa, K. Architectures of archaeal GINS complexes, essential DNA replication initiation factors. BMC Biol. 9(1):28 (2011). PubMed

Liu, C., McKinney, M. C., Chen, Y. H., Earnest, T. M., Shi, X., Lin, L. J., Ishino, Y., Dahmen, K., Cann, I. K. and Ha, T. Reverse-Chaperoning Activity of an AAA+ Protein. Biophys. J. 100, 1344-1352 (2011). PubMed

Kawano, A., Hayashi, Y., Noguchi, S., Handa, H., Horikoshi, M. and Yamaguchi, Y. Global analysis for functional residues of histone variant Htz1 using the comprehensive point mutant library. Genes Cells. 16, 590-607 (2011). PubMed

Kundu, L.R., Seki, M., Murofushi, H., Furukohri, A., Waga, S., Score, A.J., Blow, J.J., Horikoshi, M., Enomoto, T. and Tada, S. Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication. Biochim Biophys Acta. 1813, 1129-36 (2011). PubMed

Nomura, W., Ohashi, N., Okuda, Y., Narumi, T., Ikura, T., Ito, N. and Tamamura, H. Fluorescence-quenching screening of protein kinase C ligands with an environmentally sensitive fluorophore. Bioconjugate Chem. 22, 923-930 (2011). PubMed

Gascoigne, KE., Takeuchi, K., Suzuki, A., Hori, T., Fukagawa, T. and Cheeseman, IM. Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes. Cell. 145, 410-422 (2011). PubMed

Suzuki, A., Hori, T., Nishino, T., Usukura, J., Miyagi, A., Morikawa, K. and Fukagawa, T. Spindle microtubules generate tension-dependent changes in the distribution of inner kinetochore proteins. Journal of Cell Biology. 193, 125-140 (2011). PubMed

Suzuki, A. and Fukagawa, T. Cell Biological Analysis of DT40 Knockout Cell Lines for Cell-Cycle Genes. Current Protocols in Cell Biology. 50, 8.7.1-8.7.17 (2011). PubMed

Kasahara, K., Ohyama, Y. and Kokubo, T. Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region. Nucleic Acids Res. 39, 4136-4150 (2011). PubMed

Torigoe, H., Rahman, S. M. A., Takuma, H., Sato, N., Imanishi, T., Obika. S. and Sasaki, K. 2'-O,4'-C-Aminomethylene bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH. Chemistry Eur. J. 17, 2742-2751 (2011). PubMed

Torigoe, H., Rahman, S. M. A., Takuma, H., Sato, N., Imanishi, T., Obika. S. and Sasaki, K. Interrupted 2'-O,4'-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition. Nucleosides Nucleotides Nucleic Acids. 30, 63-81 (2011). PubMed

Tohmonda, T., Miyauchi, Y., Ghosh, R., Yoda, M., Uchikawa, S., Takito. J., Morioka, H., Nakamura, M., Iwawaki, T., Chiba, K., Toyama, Y., Urano, F. and Horiuchi, K. The IRE1-XBP1 pathway is essential for osteoblast differentiation through promoting transcription of Osterix. EMBO Rep. 12, 451-457 (2011). PubMed

Thorp, E., Iwawaki, T., Miura, M. and Tabas, I. A reporter for tracking the UPR in vivo reveals patterns of temporal and cellular stress during atherosclerotic progression. J Lipid Res. 52, 1033-1038 (2011). PubMed

Miyazaki, Y., Kaikita, K., Endo, M., Horio, E., Miura, M., Tsujita, K., Hokimoto, S., Yamamuro, M., Iwawaki, T., Gotoh, T., Ogawa, H. and Oike, Y. C/EBP homologous protein deficiency attenuates myocardial reperfusion injury by inhibiting myocardial apoptosis and inflammation. Arterioscler Thromb Vasc Biol. 31, 1124-1132 (2011). PubMed

Hosoda, A., Maruyama, A., Oikawa, D., Oshima, Y., Komachi, Y., Kanai, G., Sato, H. and Iwawaki ,T. Detection of ER stress in vivo by Raman spectroscopy. Biochem Biophys Res Commun. 405, 37-41 (2011). PubMed

Arai, N., Kagawa, W., Saito, K., Shingu, Y., Mikawa, T., Kurumizaka, H. and Shibata, T. Vital roles of the second DNA binding site of Rad52 in yeast homologous recombination. J. Biol. Chem. 286, 17607-17617 (2011). PubMed

Mayanagi, K., Kiyonari, S., Nishida, H., Saito, M., Kohda, D., Ishino, Y., Shirai, T. and Morikawa, K. Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex. Proc. Natl. Acad. Sci. USA. 108, 1845-1849 (2010). PubMed

Fujikane, R., Ishino, S., Ishino, Y., and Forterre, P. Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. Genes Genet. Syst. 85, 243-257 (2010). PubMed

Hisaoka, M., Ueshima, S., Murano, K., Nagata, K. and Okuwaki, M. Regulation of nucleolar chromatin by B23/nucleophosmin jointly depends upon its RNA binding activity and transcription factor UBF. Mol Cell Biol. 30(20), 4952-64 (2010). PubMed

Miki, K., Shimizu, M., Fujii, M., Takayama, S., Hossain, M.N. and Ayusawa, D. 5-bromodeoxyuridine induces transcription of repressed genes with disruption of nucleosome positioning. FEBS J. 277, 4539-4548 (2010). PubMed

Inaba, Y., Nakabayashi, M., Itoh, T., Yoshimoto, N., Ikura, T., Ito, N., Shimizu, M. and Yamamoto, K. 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity. J. Steroid Biochem. Mol. Biol. 121, 146-150 (2010). PubMed

Ogawa, Y., Nonaka, Y., Goto, T., Ohnishi, E., Hiramatsu, T., Kii, I., Yoshida, M., Ikura, T., Onogi, H., Shibuya, H., Hosoya, T., Ito, N. and Hagiwara, M. Development of a novel selective inhibitor of the Down syndrome-related kinase Dyrk1A. Nat. Commun. 1, 1-9 (2010). PubMed

Sekiyama, N., Arita, K., Ikeda, Y., Hashiguchi, K., Ariyoshi, M., Tochio, H., Saitoh, H. and Shirakawa, M. Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45. Proteins. 78, 1491-1502 (2010). PubMed

Maehara, Y., Miyano, K., Yuzawa, S., Akimoto, R., Takeya, R. and Sumimoto, H. A conserved region between the TPR and activation domains of p67phox participates in activation of the phagocyte NADPH oxidase. J. Biol. Chem. 285, 31435-31445 (2010). PubMed

Ohyama, Y., Kasahara, K. and Kokubo, T. Saccharomyces cerevisiae Ssd1p promotes CLN2 expression by binding to the 5'-untranslated region of CLN2 mRNA. Genes Cells. 15, 1169-1188 (2010). PubMed

Iwawaki, T., Akai, R. and Kohno, K. IRE1 disruption causes histological abnormality of exocrine tissues, increase of blood glucose level, and decrease of serum immunoglobulin level. PLoS One. 5, e13052 (2010). PubMed

Lin, L-J., Yoshinaga, A., Lin, Y., Guzman, C., Chen, Y-H., Mei, S., Lagunas, A.M., Koike, S., Iwai, S., Spies, M.A., Nair, S.K., Mackie, R.I., Ishino, Y. and Cann, I.K.O. Molecular analyses of an unusual translesion DNA polymerase from Methanosarcina acetivorans C2A. J. Mol. Biol. 397, 13-30 (2010). PubMed

Akita, M., Adachi, A, Takemura, K., Yamagami, T., Matsunaga, F. and Ishino, Y. Cdc6/Orc1 from Pyrococcus furiosus may act as the origin recognition protein and Mcm helicase recruiter. Gens Cells 15, 537-552 (2010). PubMed

Tori, K., Dassa, B., Johnson, M.A., Southworth, M.W., Brace, L.E., Ishino, Y., Pietrokovski, S. and Perler, F.B. Splicing of the Mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate Block F nucleophile. J. Biol. Chem. 285, 2515-2526 (2010; on line は 2009年). PubMed

Tsukano, H., Gotoh, T., Endo, M., Miyata, M., Tazume, H., Kadomatsu, T., Yano, Y., Iwawaki, T., Kohno, K., Araki, K., Mizuta, H. and Oike, Y. The endoplasmic reticulum stress-CHOP pathway-mediated apoptosis in macrophages contributes to the instability of atherosclerotic plaques. Arterioscler. Thromb. Vasc. Biol. 30, 1925-1932 (2010). PubMed

Oikawa, D., Tokuda, M., Hosoda, A. and Iwawaki, T. Identication of a consensus element recognized and cleaved by IRE1alpha. Nucleic Acid Res. 38, 6265-6273 (2010). PubMed

Oikawa, D., Akai, R. and Iwawaki, T. Positive contribution of the IRE1alpha-XBP1 pathway to placental expression of CEA family genes. FEBS Lett. 584, 1066-1070 (2010). PubMed

Okuwaki, M., Kato, K. and Nagata, K. Functional characterization of human nucleosome assembly protein 1-like proteins as histone chaperones. Genes to Cells 15(1), 13-27 (2010). PubMed

Yamana, Y., Sonezaki, S., Ogawa, H.I. and Kusano, K. Mismatch-induced lethality due to a defect in Escherichia coli RecQ helicase in exonuclease-deficient background—Dependence on MutS and UvrD functions. Plasmid 63, 119-127 (2010). PubMed

Kosako, H. and Imamoto, N. Phosphorylation of nucleoporins: signal transduction-mediated regulation of their interaction with nuclear transport receptors. Nucleus 1, 309-313 (2010). PubMed

Sugihara, F., Kasahara, K. and Kokubo, T. Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. Nucleic Acids Res. 39, 59-75 (2010). PubMed

Ohtsuki, K., Kasahara, K., Shirahige, K. and Kokubo, T. Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters. Nucleic Acids Res. 38, 1805-1820 (2010). PubMed

Shingu, Y., Mikawa, T., Onuma, M., Hirayama, T. and Shibata, T. A DNA-binding surface of SPO11-1, an Arabidopsis SPO11 orthologue required for normal meiosis. FEBS J. 277, 2360-2374 (2010). PubMed

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

Tanase, J., Morohashi, N., Fujita, M., Nishikawa, J., Shimizu, M. and Ohyama, T. Highly efficient chromatin transcription induced by superhelically curved DNA segments: the underlying mechanism revealed by a yeast system. Biochemistry 49, 2351-2358 (2010). PubMed

Torigoe, H., Ono, A. and Kozasa T. HgII Ion Specifically Binds with T:T Mismatched Base Pair in Duplex DNA. Chmeistry European Journal 16, 13218-13225 (2010). PubMed

Endo, H., Kawashima, S., Sato, L., Lai, M.S., Enomoto, T., Seki, M. and Horikoshi, M. Chromatin dynamics mediated by histone modifiers and histone chaperones in post-replicative recombination. Genes Cells. 15, 945-958 (2010). PubMed

Sato, L., Noguchi, S., Hayashi, Y., Sakamoto, M. and Horikoshi, M. Global analysis of functional relationships between histone point mutations and the effects of histone deacetylase inhibitors. Genes Cells 15, 553-594 (2010). PubMed

Ohta, S., Bukowski-Wills, J.-C., Sanchez-Pulido L., de Lima Alves, F., Wood, L., Chen, Z., Platani, M., Fischer, L., Hudson D.F., Ponting, C.P., Fukagawa, T., Earnshaw, W.C. and Rappsilber. J. The protein composition of mitotic chromosomes determined using multi-classifier combinatorial proteomics. Cell. 142, 810-821 (2010). PubMed

Shang, W.-H., Hori, T., Toyoda, A., Kato, J., Popendorf, K., Sakakibara, Y., Fujiyama, A. and Tatsuo Fukagawa. T. Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences. Genome Research. 20, 1219-1228 (2010). PubMed

Ribeiro, S.A., Vagnarell, P., Dong, Y., Hori, T., McEwen, B.F., Fukagawa, T., Flors, C. and Earnshaw, W.C. A super-resolution map of the vertebrate kinetochore. Proc. Nat. Acad. Sci. USA 107, 10484-10489 (2010). PubMed

Johnston, K., Joglekar, A., Hori, T., Suzuki, A., Fukagawa, T. and Salmon, E.D. Vertebrate Kinetochore Protein Architecture: Protein Copy Number. J. Cell Biol. 189, 937-943. (2010). PubMed

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

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

Masuda, T., Ito, Y., Terada, T., Shibata, T. and Mikawa, T. A non-canonical DNA structure enables homologous recombination in various genetic systems. J. Biol. Chem. 284, 30230-30239 (2009). PubMed

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

Nishida, H., Mayanagi, K., Kiyonari, S., Sato, Y., Oyama, T., Ishino, Y. and Morikawa, K. Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex. Proc. Natl. Acad. Sci. USA. 106, 20693-20698 (2009). PubMed

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

Okada, M., Okawa, K., Isobe, T. and Fukagawa, T. CENP-H-containing complex facitates centromere deposition of CENP-A in cooperation with FACT and CHD1. Molecular Biology of the Cell. 20, 3986-3995 (2009). PubMed

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

Kawashima, T., Bao, YC., Minoshima, Y., Nomura, Y., Hatori, T., Hori, T., Fukagawa, T., Fukada, T., Takahashi, N., Nosaka, T., Inoue, M., Sato, T., Kukimoto-Niino, M., Shirouzu, M., Yokoyama, S. and Kitamura, T. A Rac GTPase activating protein MgcRacGAP is an NLS-containing nuclear chaperone in the activation of STAT transcription factors. Molecular and Cellular Biology. 29, 1796-1813 (2009). PubMed

Kong, X., Ball, AR, Jr., Sonoda, E., Feng, J., Takeda, S., Fukagawa, T., Yen, T, J. and Yokomori, K. Cohesin associates with spindle poles in a mitosis-specific manner and functions in spindle assemble in vertebrate cells. Molecular Biology of the Cell. 20, 1289-1301 (2009). PubMed

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A03：Biofinformatics group

Sharma, A., Dehzangi, A., Lyons, J., Imoto, S., Miyano, S., Nakai, K. and Patil, A. Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function. PLOS ONE 9, e89890 (2014). PubMed

Moesa, HA., Wakabayashi, S., Nakai, K. and Patil, A. Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Molecular BioSystems. 8, 3262-3273 (2012). PubMed

Sugihara, T., Higo, J. and Nakamura, H. Local representation of N-body Coulomb energy with path integrals. J. Phys. Soc. Jpn. (2014). In Press.

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

Nie, QM., Togashi,A., Sasaki, TN., Takano,M., Sasai, M. and Terada, TP. Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin. PLoS Comput Biol. 10, e1003552 (2014). PubMed

Matsushita, K.and Kikuchi, M. Short polypeptide with metastable structure. Interdisciplinary Information Sciences. 19 (2013).

Matsushita, K. and Kikuchi, M. Frustration-induced protein intrinsic disorder. J. Chem. Phys. 138, 105101 (2013). PubMed

Shirai, NC. and Kikuchi, M. Structural flexibility of intrinsically disordered proteins induces stepwise target recognition. J. Chem. Phys. 139, 225103 (2013). PubMed

Matsushita, K. and Kikuchi, M. Multicanonical simulation of coupled folding and binding of intrinsically disordered protein using an Ising-like protein model. J. Phys.: Conf. Ser. 454, 012034 (2013).

Higo, J., Umezawa, K. and Nakamura, H. 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. J. Chem. Phys. 138, 184106 (2013).

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).

Higo, J., Ikebe, J., Kamiya, N. and Nakamura, H. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophysical Rev. 4, 27–44 (2012). PubMed

Shirai, N.C. and Kikuchi, M. Structural flexibility of intrinsically disordered proteins induces stepwise target recognition. Journal of Chemical Physics. 139, 225103 (2013). PubMed

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

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

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, 10448-14458 (2011).

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

Fernandez, M., Ahmad, S. and Sarai, A. Proteochemometric recognition of stable kinase inhibition complexes using Topological Autocorrelation and Support Vector Machines. J. Chem. Inf. Model. 50, 1179-1188 (2010). PubMed

Umezawa, K., Morikawa, R., Nakamura, H. and Higo, J. Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: a molecular dynamics study. J. Chem. Phys. 132, 155103 (2010). PubMed

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

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

Sugawara, H., Ikeo, K., Fukuchi, S., Gojobori, T. and Tateno, Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 37, D16-D18 (2009). PubMed

Fukuchi, S., Homma, K., Sakamoto, S., Sugawara, H., Tateno, Y., Gojobori, T. and Nishikawa, K. The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res. 37, D333-D337 (2009). PubMed

Fukuchi, S., Homma, K., Minezaki, Y., Gojobori, T. and Nishikawa, K. Development of an Accurate Classification system of Proteins into Structured and Unstructured Regions that Uncovers Novel Structural Domains: Its Application to Human Transcription Factors. BMC Structural Biol. 9, 26 (2009). PubMed

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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