最近の研究業績

2018年

• Teikichi Ikura1, Naoya Tochio, Ryosuke Kawasaki, Mizuki Matsuzaki, Akihiro Narita, Mahito Kikumoto, Naoko Utsunomiya-Tate, Shin-ichi Tate and Nobutoshi Ito "The trans isomer of Tau peptide is prone to aggregate, and the WW domain of Pin1 drastically decreases its aggregation." FEBS Letters, https://doi.org/10.1002/1873-3468.13218, 2018.
• Shunsuke Tanaka, Kingo Takiguchi, Masahito Hayashi "Repetitive stretching of giant liposomes utilizing the nematic alignment of confined actin." Communications Physics, 1, Article number 18, 2018.
• Kingo Takiguchi, Masahito Hayashi, Yuki Kazayama, Taro Toyota, Yoshie Harada, Masayoshi Nishiyama "Morphological Control of Microtubule-Encapsulating Giant Vesicles by Changing Hydrostatic Pressure." Biological and Pharmaceutical Bulletin, 41 (3), 288-293, 2018.
• S. Kawano, Y. Tamura, R. Kojima, S. Bala, E. Asai, A.H. Michel, B. Kornmann, I. Riezman, H. Riezman, Y. Sakae, Y. Okamoto, and T. Endo, Structure-function insights into phospholipid transfer by Mmm1-Mdm12 of ERMES between membranes Journal of Cell Biology 217, 959-974 (2018).
• S. Tsukamoto, Y. Sakae, Y. Itoh, T. Suzuki, and Y. Okamoto, Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations The Journal of Chemical Physics 148, 125102 (6 pages) (2018).
• S. Ito, D.G. Fedorov, Y. Okamoto, and S. Irle, Implementation of replica-exchange umbrella sampling in GAMESS Computer Physics Communications 228, 152-162 (2018).
• Kojima S, Takao M, Almira G, Kawahara I, Sakuma M, Homma M, Kojima C, Imada K., The Helix Rearrangement in the Periplasmic Domain of the Flagellar Stator B Subunit Activates Peptidoglycan Binding and Ion Influx. Structure 2018 Apr 3;26(4):590-598.e5.
• Onoue Y, Takekawa N, Nishikino T, Kojima S, Homma M., The role of conserved charged residues in the bidirectional rotation of the bacterial flagellar motor. Microbiologyopen 2018 Mar 24:e00587.
• Liew CW, Hynson RM, Ganuelas LA, Shah-Mohammadi N, Duff AP, Kojima S, Homma M, Lee LK. , Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem Biophys Res Commun 2018 Jan 8;495(2):1614-1619.
• Ohmae, E., Hamajima, Y., Nagae, T., Watanabe, N., Kato, C. (2018) "Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1" Biochem. Biophys. Acta 1866 (5-6): 680-691
• Popp, D., Koh, F., Scipion, C. P. M., Ghoshdastider, U., Narita, A., Holmes, K. C. & Robinson, R. C. (2018). Advances in Structural Biology and the Application to Biological Filament Systems. Bioessays 40, e1700213.
• Tanaka, K., Takeda, S., Mitsuoka, K., Oda, T., Kimura-Sakiyama, C., Maeda, Y. & Narita, A. (2018). Structural basis for cofilin binding and actin filament disassembly. Nat Commun 9, 1860.
• Mizuno, H., Tanaka, K., Yamashiro, S., Narita, A. & Watanabe, N. (2018). Helical rotation of the diaphanous-related formin mDia1 generates actin filaments resistant to cofilin. Proc Natl Acad Sci U S A 115, E5000-E5007.
• Matsuo, N., Goda, N., Shimizu, K., Tenno, T., Fukuchi, F., Ota, M. and Hiroaki, H.*, 2018, Discovery of Cryoprotective Activity of Human-genome derived Intrinsically Disordered Proteins. Int J Mol Sci,, 19(2), 401
• Hiroaki, H., Kohda, D*. Chapter 21: Protein-ligand interactions studied by NMR, in “Experimental Approaches of NMR Spectroscopy ‐ Methodology and Application to Life Science and Materials Science” (Springer), edited by The NMR Society of Japan, 2018, 579-600 (invited review).
• Shigemitsu, Y., Hiroaki, H*. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis, 2018, J Biochemistry, 163(1), 11–17 (invited review)
• Takayuki Uchihashi#, Yo-hei Watanabe#*, Yosuke Nakazaki, Takashi Yamasaki, Hiroki Watanabe, Takahiro Maruno, Kentaro Ishii, Susumu Uchiyama, Chihong Song, Kazuyoshi Murata, Ryota Iino*, Toshio Ando*, "Dynamic structural states of ClpB involved in its disaggregation function", Nature Communications 9, Article number: 2147 (2018).
• Mikihiro Shibata#, Keiichi Inoue#, Kento Ikeda, Masae Konno, Manish Singh, Chihiro Kataoka, Rei Abe-Yoshizumi, Hideki Kandori*, Takayuki Uchihashi*, "Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy", Scientific Reports 8, Article number: 8262 (2018).(#equal contribution)
• akahiro Maruno, Hiroki Watanabe, Takayuki Uchihashi, Satoru Adachi, Kunihito Arai, Taichi Sawaguchi and Susumu Uchiyama*, "Sweeping of adsorbed therapeutic proteins on prefillable syringe enhances subvisible particles generation", Journal of Pharmaceutical Sciences 107, pp. 1521-1529 (2018).
• Takayuki Umakoshi, Hikari Udaka, Takayuki Uchihashi, Toshio Ando, Miho Suzuki, Takeshi Fukuda*, "Quantum-dot antibody conjugation visualized at the single-molecule scale with high-speed atomic force microscopy", Colloids and Surfaces B: Biointerfaces 167, pp. 264-274 (2018).
• Naoya Terahara, Yumi Inoue, Noriyuki Kodera, Yusuke V. Morimoto, Takayuki Uchihashi, Katsumi Imada, Toshio Ando, Keiichi Namba, and Thoru Minamino*, "Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export", Science Advances 4, eaao7054 (2018).
• Hisao Tsukamoto, Masahiro Higashi, Hideyoshi Motoki, Hiroki Watanabe, Christian Ganser, Koichi Nakajo, Yoshihiro Kubo, Takayuki Uchihashi and Yuji Furutani*, "Structural properties determining low K+ affinity of the selectivity filter in the TWIK1 K+ channel", Journal of Biological Chemistry 293, pp. 6969-6984 (2018).
• Akiya Oda, Satoshi Nagao, Masaru Yamanaka, Hiroki Watanabe, Takayuki Uchihashi, Ikki Ueda, Naoki Shibata, Yoshiki Higuchi, and Shun Hirota*, "Construction of a Triangle-Shaped Trimer and a Tetrahedral Structure Using an α-Helix-Inserted Circular Permutant of Cytochrome c555", Chemistry - An Asian Journal 13, pp. 964-967 (2018).
• Takamitsu Haruyama, Takayuki Uchihashi, Yutaro Yamada, Noriyuki Kodera, Toshio Ando and Hiroki Konno*, "Negatively charged lipids are essential for functional and structural switch of human 2-Cys peroxiredoxin II", Journal of Molecular Biology 430, pp. 602-610 (2018).
• Tetsuya Takeda*, Toshiya Kozai, Huiran Yang, Daiki Ishikuro, Kaho Seyama, Yusuke Kumagai, Tadashi Abe, Hiroshi Yamada, Takayuki Uchihashi, Toshio Ando* and Kohji Takei*, "Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis", e-Life 7, e3024 (2018).
• Maho Yagi-Utsumi, Arunima Sikdar, Toshiya Kozai, Rintaro Inoue, Masaaki Sugiyama, Takayuki Uchihashi, Tadashi Satoh and Koichi Kato*, "Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation", Protein engineering design & selection 31, 29-36 (2018).
• Akihiko Nakamura, Tomoyuki Tasaki, Yasuko Okuni, Chihong Song, Kazuyoshi Murata, Toshiya Kozai, Mayu Hara, Hayuki Sugimoto, Kazushi Suzuki, Takeshi Watanabe, Takayuki Uchihashi, Hiroyuki Noji and Ryota Iino*, "Rate constants, processivity, and productive binding ratio of chitinase A revealed by single-molecule analysis", Physical Chemistry Chemical Physics 20, 3010-3018 (2018).
• Takayuki Uchihashi* and Simon Scheuring, "Review: Applications of high-speed atomic force microscopy to real-time visualization of dynamic biomolecular processes", BBA General Subjects 1862, 229-240 (2018).
• Masanori Hosoyamada, Nobuhiro Yanai*, Keisuke Okumura, Takayuki Uchihashi and Nobuo Kimizuka*, "Translating MOF chemistry into supramolecular chemistry: soluble coordination nanofibers showing efficient photon upconversion", Chemical Communications (in press)
• Shindo A, Audrey A, Takagishi M, Takahashi M, Wallingford JB, Kinoshita M. Septin-dependent remodeling of cortical microtubule drives cell reshaping during epithelial wound healing. Journal of Cell Science in press
• Ageta-Ishihara N, Konno K, Yamazaki M, Abe M, Sakimura K, Watanabe M, Kinoshita M. CDC42EP4, a perisynaptic scaffold protein in Bergmann glia, is required for glutamatergic tripartite synapse configuration. Neurochemistry International in press
• Naoki Nakatani, Hiroki Sakuta, Masahito Hayashi, Shunsuke Tanaka, Kingo Takiguchi, Kanta Tsumoto, Kenichi Yoshikawa "Specific Spatial Localization of Actin and DNA in a Water/Water Microdroplet: Self‐Emergence of a Cell‐Like Structure." ChemBioChem, 19 (13), 2018. 1370-1374

2017年

• Kobayashi, J., *Matsuura, Y. Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae. Protein Science, 26: 2105-2112 (2017).
• Koyama, M., Hirano, H., Shirai, N., *Matsuura, Y. Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p. Genes Cells, 22: 861-875 (2017).
• Koyama, M., *Matsuura, Y. Crystal structure of importin-a3 bound to the nuclear localization signal of Ran-binding protein 3. Biochem Biophys Res Commun, 491: 609-613 (2017).
• Koyama, M., Sasaki, T., Sasaki, N., *Matsuura, Y. Crystal structure of human WBSCR16, an RCC1-like protein in mitochondria. Protein Science, 26: 1870-1877 (2017).
• Nakada, R., *Matsuura, Y. Crystal structure of importin-a bound to the nuclear localization signal of Epstein-Barr virus EBNA-LP protein. Protein Science, 26: 1231-1235 (2017).
• Nakada, R., Hirano, H., *Matsuura, Y. Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal. Biochem Biophys Res Commun, 484: 113-117 (2017).
• Misako Nishigami, Takaaki Mori, Masahiro Tomita, Kingo Takiguchi, Kanta Tsumoto "Membrane fusion between baculovirus budded virus-enveloped particles and giant liposomes generated using a droplet-transfer method for the incorporation of recombinant membrane proteins." Colloids and Surfaces B: Biointerfaces, 155, 248-256, 2017.
• Shota Kobayashi, Takuya Terai, Yuki Yoshikawa, Ryoya Ohkawa, Mika Ebihara, Masahito Hayashi, Kingo Takiguchi, Naoto Nemoto "In vitro selection of random peptides against artificial lipid bilayers: a potential tool to immobilize molecules on membranes." Chemical Communications, 53 (24), 3458-3461, 2017.
• Y. Mori and Y. Okamoto, Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study, Journal of Computational Chemistry 38, 1167-1173 (2017).
• Y. Sakae, T. Satoh, H. Yagi, S. Yanaka, T. Yamaguchi, Y. Isoda, S. Iida, Y. Okamoto, and K. Kato, Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa Scientific Reports 7, 13780 (10 pages) (2017).
• Kojima S. Mechanism of stator assembly and incorporation into the flagellar motor. Methods Mol. Biol. 2017 1593, 147-159. doi: 10.1007/978-1-4939-6927-2_11.
• Kondo S, Homma M, Kojima S., Analysis of the GTPase motif of FlhF in the control of the number and location of polar flagella in Vibrio alginolyticus. Biophys Physicobiol. 2017 Dec 5;14:173-181.
• Rad MA, Ahmad MR, Nakajima M, Kojima S, Homma M, Fukuda T., Application of Environmental Scanning Electron Microscope-Nanomanipulation System on Spheroplast Yeast Cells Surface Observation. Scanning 2017 Apr 27;2017:8393578.
• Zhu S, Nishikino T, Hu B, Kojima S, Homma M & Liu J., Molecular architecture of the sheathed polar flagellum in Vibrio alginolyticus. Proc Natl Acad Sci U S A 2017 Sep 25. pii: S201712489.
• Miyanoiri Y, Hijikata A, Nishino Y, Gohara M, Onoue Y, Kojima S, Kojima C, Shirai T, Kainosho M, Homma M. , Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na+-Driven Flagella. Structure 2017 Sep 6. pii: S0969-2126(17)30263-0.
• Inaba S, Nishigaki T, Takekawa N, Kojima S, Homma M., Localization and domain characterization of the SflA regulator of flagellar formation in Vibrio alginolyticus.Genes Cells 2017 Jul;22(7):619-627.
• Onoue Y, Homma M., Structure of the Sodium-Driven Flagellar Motor in Marine Vibrio. Methods Mol Biol 2017;1593:253-258
• Kumar A, Isumi M, Sakuma M, Zhu S, Nishino Y, Onoue Y, Kojima S, Miyanoiri Y, Imada K, Homma M, Biochemical characterization of the flagellar stator-associated inner membrane protein FliL from Vibrio alginolyticus J. Biochem. 161 (4): 331-337 (2017)
• Takekawa N, Kojima S, and Homma M., Mutational analysis and overproduction effects of MotX, an essential component for motor function of Na+-driven polar flagella of Vibrio J. Biochem. 161 (2): 159-166 (2017)
• Kikumoto M, Oosawa I. Thermodynamic measurements of actin polymerization with various cation species. Cytoskeleton (2017) 74(12) 465-471
• Usukura E, Narita A, Yagi A, Sakai N, Uekusa Y, Imaoka Y, et al. A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM). Scientific reports. 2017;7:6462.
• Fujiwara I, Narita A. Keeping the focus on biophysics and actin filaments in Nagoya: A report of the 2016 "now in actin" symposium. Cytoskeleton (Hoboken). 2017.
• Kobayashi S, Terai T, Yoshikawa Y, Ohkawa R, Ebihara M, Hayashi M, Takiguchi K, Nemoto N. In vitro selection of random peptides against artificial lipid bilayers: a potential tool to immobilize molecules on membranes. Chem. Commun. (2017) 53: 3458-3461.
• Nishigami M, Mori T, Tomita M, Takiguchi K, Tsumoto K. Membrane fusion between baculovirus budded virus-enveloped particles and giant liposomes generated using a droplet-transfer method for the incorporation of recombinant membrane proteins. Colloids Surf. B Biointerfaces. (2017) 155: 248-256.
• Shimasaki, T., Ohtsuka, H., Naito, C., Tenno, T., Hiroaki, H., Murakami, H., Hirofumi Aiba, H*. 2017, Ecl1 is a zinc binding protein that is involved in the zinc-limitation dependent extension of chronological lifespan in fission yeast. Molecular Genetics and Genomics, 292(2):475-481.
• Niwa, N., Shimizu, S., Maeda, Y., Hiroaki, H. and Ueno, Y.*, 2017, Benzene-Glycol Nucleic Acid (BGNA)-DNA Chimeras: Synthesis, Binding Properties, and Ability to Elicit Human RNase H Activity. RSC Advances., 7, 25378-25386.
• Toshiya Kozai, Taichiro Sekiguchi, Tadashi Satoh, Hirokazu Yagi, Koichi Kato* and Takayuki Uchihashi*, "Two-step process for disassembly mechanism of proteasome α7 homo-tetradecamer by α6 revealed by high-speed atomic force microscopy", Scientific Reports 7 article number: 15373 (2017).
• Naoya Terahara, Noriyuki Kodera, Takayuki Uchihashi, Toshio Ando, Keiichi Namba* and Tohru Minamino*, "Na+-induced structural transition of MotPS for stator assembly of Bacillus flagellar motor", Science Advances 3, eaao4119 (2017).
• Mikihiro Shibata*, Hiroki Watanabe, Takayuki Uchihashi, Toshio Ando, and Ryohei Yasuda, "High-speed atomic force microscopy imaging of live mammalian cells", Biophysics and Physicobiology 14, 127-135 (2017).
• Mikihiro Shibata*, Hiroshi Nishimasu*, Noriyuki Kodera, Seiichi Hirano, Toshio Ando, Takayuki Uchihashi and Osamu Nureki*, "Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy", Nature Communications 8, article number: 1430 (2017).
• Tadashi Satoh*, Chihong Song, Tong Zhu, Takayasu Toshimori, Kazuyoshi Murata, Yugo Hayashi, Hironari Kamikubo, Takayuki Uchihashi and Koichi Kato*, "Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT", Scientific Reports 7, Article Number: 12142 (2017).
• Hirofumi Harada, Akira Onoda*, Takayuki Uchihashi*, Hiroki Watanabe, Naoki Sunagawa, Masahiro Samejima, Kiyohiko Igarashi*, and Takashi Hayashi, "Interdomain Flip-flop Motion Visualized in Flavocytochrome Cellobiose Dehydrogenase Using High-speed Atomic Force Microscopy during Catalysis", Chemical Science 8, 6561-6565 (2017).
• Shusuke Matsui, Takuma Kureha, Seina Hiroshige, Mikihiro Shibata,Takayuki Uchihashi*, and Daisuke Suzuki*, "Fast Adsorption of Soft Hydrogel Microspheres on Solid Surfaces in Aqueous Solution", Angewandte Chemie International Edition (Communication) 56, 12146-12149 (2017).
• Jakia Jannat Keya, Daisuke Inoue, Yuki Suzuki, Toshiya Kozai, Daiki Ishikuro, Noriyuki Kodera, Takayuki Uchihashi, Arif Md. Rashedul Kabir, Masayuki Endo, Kazuki Sada, Akira Kakugo, "High-Resolution Imaging of a Single Gliding Protofilament of Tubulins by HS-AFM", Scientific Reports 7, 6166 (2017).
• Mahmoud Mohamed, Akiko Kobayashi, Azuma Taoka, Takahiro Watanabe-Nakayama, Yosuke Kikuchi, Masaharu Hazawa, Toshinari Minamoto, Yoshihiro Fukumori, Noriyuki Kodera, Takayuki Uchihashi, Toshio Ando and Richard Wong*, "High-Speed Atomic Force Microscopy Reveals Loss of Nuclear Pore Resilience as a Dying Code in Colorectal Cancer Cells", ACS Nano 11, 5567-5578 (2017).
• Ayumi Sumino, Takayuki Uchihashi and Shigetoshi Oiki*, "Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging ", J. Phy. Chem. Lett. 8, 785-793 (2017).
• Moé Yamada, Yohko Tanaka-Takiguchi, Masahito Hayashi, Momoko Nishina, Gohta Goshima. "Multiple kinesin-14 family members drive microtubule minus end–directed transport in plant cells." J. Cell Biol., 216 (6), 1705-1714, 2017.