Publication / Paper

A01 | A02 | A03 


A03-1 Togashi-Team

  • Amartya Sarkar, Holger Flechsig and Alexander S. Mikhailov
    "Towards synthetic molecular motors: a model elastic-network study"
    New Journal of Physics, 18:043006, 2016
  • Yuichi Togashi
    "Screening for mechanical responses of proteins using coarse-grained elastic network models"
    Nonlinear Theory and Its Applications, IEICE, 7:190-201, 2016
  • Masaki Nakagawa and Yuichi Togashi
    "An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations"
    Frontiers in Physiology, 7:89, 2016
  • Holger Flechsig
    "Nucleotide-Induced Conformational Dynamics in ABC Transporters from Structure-Based Coarse Grained Modeling"
    Frontiers in Physics, 4:3, 2016
  • Soya Shinkai
    "Analytical theory of individual diffusion trajectories in living cells"
    Advances in Science, Technology and Environmentology (Waseda University), B11:167-169, 2015
  • Munenori Ishibashi, Yukihiro Miyanaga, Satomi Matsuoka, Jun Kozuka, Yuichi Togashi, Tatsuo Kinashi and Masahiro Ueda
    "Integrin LFA-1 Regulates Cell Adhesion via Transient Clutch Formation"
    Biochemical and Biophysical Research Communications, 464:459-466, 2015
  • Yuichi Togashi
    "Spying “Minorities” in the Cell"
    Dagstuhl Reports, 4:165-166, 2015
  • Radek Erban, Akira Funahashi, Mostafa Herajy, Tetsuya J. Kobayashi, Koichi Takahashi and Yuichi Togashi
    "DNA Structural Dynamics (Team 5)"
    Dagstuhl Reports, 4:191-194, 2015
  • J. Nicholas Taylor, Chun-Biu Li, David R. Cooper, Christy F. Landes and Tamiki Komatsuzaki
    "Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series"
    Scientific Reports, 5:9174-1-9174-9, 2015
  • Yuichi Togashi and Vanessa Casagrande
    "Spatiotemporal Patterns Enhanced by Intra- and Inter-molecular Fluctuations in Arrays of Allosterically Regulated Enzymes"
    New Journal of Physics, 17:33024, 2015
  • Takuma Akimoto, Masaki Nakagawa, Soya Shinkai and Yoji Aizawa
    "Generalized Lyapunov exponent as a unified characterization of dynamical instabilities"
    Physical Review E, 91:12926, 2015
  • Soya Shinkai
    "Dissipative heat decomposition in stochastic energetics: Implication of the instantaneous diffusion coefficient in nonequilibrium steady states"
    Journal of the Physical Society of Japan, 84:15001, 2015
  • Takuma Akimoto, Soya Shinkai and Yoji Aizawa
    "Distributional behavior of time averages of non-L1 observables in one-dimensional intermittent maps with infinite invariant measures"
    Journal of Statistical Physics, 158:476-493, 2015
  • Holger Flechsig
    "TALEs from a Spring – Superelasticity of Tal Effector Protein Structures"
    PLoS ONE, 9:e109919, 2014
  • Hideyuki Yaginuma, Shinnosuke Kawai, Kazuhito V. Tabata, Keisuke Tomiyama, Akira Kakizuka, Tamiki Komatsuzaki, Hiroyuki Noji and Hiromi Imamura
    "Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging"
    Scientific Reports, 4:42011, 2014
  • Hiroshi Teramoto, Mikito Toda and Tamiki Komatsuzaki
    "A New Method to Improve Validity Range of Lie Canonical Perturbation Theory: With a Central Focus on a Concept of Non Blow-Up Region"
    Theoretical Chemistry Accounts, 133:1571, 2014
  • Preetom Nag, Hiroshi Teramoto, Chun-Biu Li, Joseph Z. Terdik, Norbert F. Scherer and Tamiki Komatsuzaki
    "Local-heterogeneous responses and transient dynamics of cage breakingand formation in colloidal fluids"
    The Journal of Chemical Physics, 141:104907-1-12, 2014
  • Bo Shuang, David Cooper, J. Nick Taylor, Lydia Kisley, Jixin Chen, Wenxiao Wang, Chun Biu Li, Tamiki Komatsuzaki and Christy F. Landes
    "Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis"
    The Journal of Physical Chemistry Letters, 5:3157-3161, 2014
  • Soya Shinkai and Yuichi Togashi
    "Energetics of single active diffusion trajectories"
    Europhysics Letters, 105:30002, 2014
  • Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, and Tamiki Komatsuzaki
    "Non-Markovian properties and multiscale Hidden Markovian Network Buried in Single Molecule Time Series"
    The Journal of Chemical Physics, 139:245101, 2013
  • Yasuhiro Matsunaga, Akinori Baba, Chun Biu Li, John Straub, Mikito Toda, Tamiki Komatsuzaki and R. Stephen Berry
    "Spatio-temporal hierarchy in the dynamics of a minimalist protein model"
    The Journal of Chemical Physics, 139:215101, 2013
  • Hiroshi Teramoto, George Haller and Tamiki Komatsuzaki
    "Detecting invariant manifolds as stationary Lagrangian coherent structures in autonomous dynamical systems"
    Chaos, 23:43107, 2013
  • Chun-Biu Li and Tamiki Komatsuzaki
    "Aggregated Markov Model Using Time Series of Single Molecule Dwell Times with Minimum Excessive Information"
    Physical Review Letter, 111:58301, 2013
  • Shinnosuke Kawai, David Cooper, Christy F. Landes, Henning D. Mootz, Haw Yang, and Tamiki Komatsuzaki
    "Numerical Construction of Estimators for single-molecule fluorescence measurements"
    The Journal of Physical Chemistry B, 117(27):8061-8074, 2013
  • Shinnosuke Kawai and Tamiki Komatsuzaki
    "Effect of timescale on energy landscape: Distinction between free-energy landscape and potential of mean force"
    Phys. Rev. E (rapid communication), 87:30803, 2013
  • Tatyana Terentyeva, Johan Hofkens, Tamiki Komatsuzaki, Kerstin Blank, Chun-Biu Li
    "Time-Resolved Single Molecule Fluorescence Spectroscopy of an α-Chymotrypsin Catalyzed Reaction"
    The Journal of Physical Chemistry B, 117(5):1252-1260, 2013
  • Kiyoto Kamagata, Toshifumi Kawaguchi, Yoshitomo Iwahashi, Akinori Baba, Kazuya Fujimoto, Tamiki Komatsuzaki, Yoshihiro Sambongi, Yuji Goto and Satoshi Takahashi
    "Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes"
    Journal of American Chemical Society, 134(28):11525-32, 2012
  • Masatoshi Morimatsu, Yuichi Togashi, So Nishikawa, Mitsuhiro Sugawa, Atsuko H. Iwane and Toshio Yanagida
    "Spontaneous Structural Changes in Actin Regulate G-F Transformation"
    PLOS ONE, 7:e45864, 2012
  • Markus Düttmann, Markus Mittnenzweig, Yuichi Togashi, Toshio Yanagida and Alexander S. Mikhailov
    "Complex Intramolecular Mechanics of G-actin ― An Elastic Network Study"
    PLOS ONE, 7:e45859, 2012
  • Markus Düttmann, Yuichi Togashi, Toshio Yanagida and Alexander S. Mikhailov
    "Myosin-V as a Mechanical Sensor: An Elastic Network Study"
    Biophysical Journal, 102:542-551, 2012
  • Akinori Baba and Tamiki Komatsuzaki
    "Multidimensional Energy Landscapes in Single Molecule Biophysics"
    Advances in Chemical Physics, 146:299-328, 2012
  • Tatyana Terentyeva, Hans Engelkamp, Alan Rowan, Tamiki Komatsuzaki, Johan Hofkens, Chun Biu Li and Kerstin Blank
    "Dynamic Disorder in Single Enzyme Experiments: Facts and Artifacts"
    ACS Nano, 6(1):346-354, 2012
  • Shinnosuke Kawai and Tamiki Komatsuzaki
    "Why and how do systems react in thermally fluctuating environments?"
    Physical Chemistry Chemical Physics, 13:21217-21229, 2011
  • Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li and Tamiki Komatsuzaki
    "Decomposability of Multivariate Interactions"
    Complex Systems, 20(2):165-179, 2011
  • Carlos Echeverria, Yuichi Togashi, Alexander S. Mikhailov and Raymond Kapral
    "A Mesoscopic model for protein enzymatic dynamics in solution."
    Physical Chemistry Chemical Physics, 13:10527-10537, 2011

A03-2 Imada-Team

  • Katsumi Imada, Tohru Minamino, Yumiko Uchida, Miki Kinoshita and Keiichi Namba
    "Insight into the flagella type III export revealed by the complex structure of the type III ATPase and its regulator"
    Proc. Natl. Acad. Sci. USA., Epub ahead of print:pii: 201524025, 2016
  • Takamitsu J. Morikawa, Hideaki Fujita, Akira Kitamura, Takashi Horio, Johtaro Yamamoto, Masataka Kinjo, Akira Sasaki, Hiroaki Machiyama, Keiko Yoshizawa, Taro Ichimura, Katsumi Imada, Takeharu Nagai and Tomonobu M. Watanabe
    "Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it."
    Sci Rep., 6:22342, 2016
  • So-ichiro Nishiyama, Yohei Takahashi, Kentaro Yamamoto, Daisuke Suzuki, Yasuaki Itoh, Kazumasa Sumita, Yumiko Uchida, Michio Homma, Katsumi Imada and Ikuro Kawagishi
    "Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants."
    Sci Rep., 6:20866, 2016
  • Takuya Kuroda, Tomoko Kubori, Xuan Thanh Bui, Akihiro Hyakutake, Yumiko Uchida, Katsumi Imada and Hiroki Nagai
    "Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion."
    Sci Rep., 5:10912, 2015
  • Yasuhisa Fukuda, Asuka Abe, Takashi Tamura, Takahide Kishimoto, Atsushi Sogabe, Satoshi Akanuma, Shin-ichi Yokobori, Akihiko Yamagishi, Katsumi Imada, Kenji Inagaki
    "Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060."
    J Biosci Bioeng., 121:497-502, 2015
  • Marie Amano, Haruka Mizuguchi, Tadahisa Sano, Hiroki Kondo, Kengo Shinyashiki, Junko Inagaki, Takashi Tamura, Tatsuya Kawaguchi, Hitoshi Kusakabe, Katsumi Imada and Kenji Inagaki
    "Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, l-lysine α-oxidase from Trichoderma viride"
    J Biochem, 2015
  • Tohru Minamino and Katsumi Imada
    "The bacterial flagellar motor and its structural diversity"
    Trends Microbiol, 23:267-274, 2015
  • Shiwei Zhu, Masato Takao, Na Li, Mayuko Sakuma, Yuuki Nishino, Michio Homma, Seiji Kojima and Katsumi Imada
    "Conformational change in the periplamic region of the flagellar stator coupled with the assembly around the rotor"
    Proc Natl Acad Sci USA, 111:13523-13528, 2014
  • Takuma Fukumura, Yukio Furukawa, Tatsuya Kawaguchi, Yumiko Saijo-Hamano, Keiichi Namba, Katsumi Imada and Tohru Minamino
    "Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus"
    Acta Crystallogr F Struct Biol Commun, 70:1215-1218, 2014
  • Kiyohiko Igarashi, Takayuki Uchihashi, Taku Uchiyama, Hayuki Sugimoto, Masahisa Wada, Kazushi Suzuki, Shohei Sakuda, Toshio Ando, Takeshi Watanabe, Masahiro Samejima
    "Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin"
    Nature Communications, 5:3975, 2014
  • Yusuke Shibafuji, Akihiko Nakamura, Takayuki Uchihashi, Naohisa Sugimoto, Shingo Fukuda, Hiroki Watanabe, Masahiro Samejima, Toshio Ando, Hiroyuki Noji, Anu Koivula, Kiyohiko Igarashi, and Ryota Iino
    "Single-molecule Imaging Analysis of Elementary Reaction Steps of Trichoderma reesei Cellobiohydrolase I (Cel7A) Hydrolyzing Crystalline Cellulose Iα and IIII"
    The Journal of Biological Chemistry, 289:14056-14065, 2014
  • Akihiko Nakamura , Hiroki Watanabe , Takuya Ishida , Takayuki Uchihashi , Masahisa Wada , Toshio Ando , Kiyohiko Igarashi , and Masahiro Samejima
    "Trade-off between processivity and hydrolytic velocity of cellobiohydrolases at the surface of crystalline cellulose"
    Journal of American Chemical Society, 136 (12):4584–4592, 2014
  • Toshio Ando, Takayuki Uchihashi, and Simon Scheuring
    "Filming Biomolecular Processes by High-Speed Atomic Force Microscopy"
    Chemical Reviews, 114 (6):3120–3188, 2014
  • Hiroyuki Terashima, Na Li, Mayuko Sakuma, Masafumi Koike, Seiji Kojima, Michio Homma and Katsumi Imada
    "Insight into the assembly mechanism in the supramolecular rings of the sodium-driven Vibrio flagellar motor from the structure of FlgT"
    Proc. Natl. Acad. Sci., 110:doi:10.1073/pnas.1222655110, 2013
  • Miki Kinoshita Noritaka Hara Katsumi Imada Keiichi Namba and Tohru Minamino
    "Interactions of bacterial flagellar chaperone-substrate complexes with FlhA contribute to co-ordinating assembly of the flagellar filament"
    Mol Microbiol, 90:1249-1261, 2013
  • Neval Yilmaz, Taro Yamada, Peter Greimel, Takayuki Uchihashi, Toshio Ando, and Toshihide Kobayashi
    "Real-Time Visualization of Assembling of a Sphingomyelin-Specific Toxin"
    Biophysical Journal, 105:1397-1405, 2013
  • Tomonobu M. Watanabe, Katsumi Imada, Keiko Yoshizawa, Masayoshi Nishiyama, Chiaki Kato, Fumiyoshi Abe, Takamitsu J. Morikawa, Miki Kinoshita, Hideaki Fujita, Toshio Yanagida
    "Glycine Insertion Makes Yellow Fluorescent Protein Sensitive to Hydrostatic Pressure."
    PLoS One, 8:e73212, 2013
  • Shingi Fukuda, Takayuki Uchihashi, Ryota Iino, Yasuhiro Okazaki, Masashi Yoshida, Kiyohiko Igarashi, and Toshio. Ando
    "High-speed atomic force microscope combined with single-molecule fluorescence microscope"
    Review of Scientific Instruments, 84:073706(8pp), 2013
  • Jun-ichi Kishikawa, Tatsuya Ibuki, Shuichi Nakamura, Astuko Nakanishi, Tohru Minamino, Tomoko Miyata, Keiichi Namba, Hiroki Konno, Hiroshi Ueno, Katsumi Imada, Ken Yokoyama
    "Common evolutionary origin for the rotor domain of rotary ATPases and Flagellar protein export apparatus."
    PLoS One, 8:e64695, 2013
  • Toshio Ando, Takayuki Uchihashi and N. Kodera
    "High-speed AFM and applications to biomolecular systems"
    Annual Review of Biophysics, 42:393-414, 2013
  • Hiroki Watanabe, Takayuki Uchihashi, Toshihide Kobashi, Mikihiro Shibata, Jun Nishiyama, Ryohei Yasuda and Toshio Ando
    "Wide-area scanner for high-speed atomic force microscopy"
    Review of Scientific Instruments, 84:53702, 2013
  • Mayuko Sakuma, Katsumi Imada, Yoshiyuki Okumura, Kei-ichi Uchiya, Nobuo Yamashita, Kenji Ogawa, Atsushi Hijikata, Tsuyoshi Shirai, Michio Homma and Toshiaki Nikai
    "X-ray structure analysis and characterization of AFUEI, an elastase inhibitor from Aspergillus fumigatus"
    J Biol Chem, 288:17451-17459, 2013
  • Yumiko Saijo-Hamano, Hideyuki Matsunami, Keiichi Namba and Katsumi Imada
    "Expression, purification, crystallization and preliminary X-ray diffraction analysis of a core fragment of FlgG, a bacterial flagellar rod protein"
    Acta Crystallogr Sect F Struct Biol Cryst Commun, 69:547-50, 2013
  • Toshiaki Takei, Kazuya Hasegawa, Katsumi Imada, Keiichi Namba, Kouhei Tsumoto, Yukino Kuriki, Masakuni Yoshino, Kazumori Yazaki, Shuichi Kojima, Tsunetomo Takei, Takuya Ueda and Kin-ichiro Miura
    "Effects of Chain Length of an Amphipathic Polypeptide Carrying the Repeated Amino Acid Sequence (LETLAKA)n on α-Helix and Fibrous Assembly Formation"
    Biochemistry, 52:2810-2820, 2013
  • Hayato Yamashita, Keiichi Inoue, Mikihiro Shibata, Takayuki Uchihashi, Jun Sasaki, Hideki Kandori and Toshio Ando
    "Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy"
    Journal of Structural Biology, 84(1): 2-11, 2013
  • Tatsuya Ibuki, Yumiko Uchida, Yusuke Hironaka, Keiichi Namba, Katsumi Imada and Tohru Minamino
    "Interaction between FliJ and FlhA, components of the bacterial flagellar type III export apparatus."
    J. Bacteriol., 195:466-473, 2013
  • Yumiko Uchida, Tohru Minamino, Keiichi Namba and Katsumi Imada.
    "Crystallization and preliminary X-ray analysis of the FliH–FliI complex responsible for bacterial flagellar type III protein export."
    Acta Cryst. F, 68:1311-1314, 2012
  • Hayato Yamashita, Azuma Taoka, Takayuki Uchihashi, Tomoya Asano, Toshio Ando and Yoshihiro Fukumori
    "Single molecule imaging on living bacterial cell surface by high-speed AFM"
    J. Mol. Biol., 422(2):300-9, 2012
  • Reiko Murakami, Risa Mutoh, Ryo Iwase, Yukio Furukawa, Katsumi Imada, Kiyoshi Onai, Megumi Morishita, Satoshi Yasui, Kentaro Ishii, Jonathan S. Valencia, Tatsuya Uzumaki, Keiichi Namba , Masahiro Ishiura
    "The roles of the dimeric and tetrameric structures of the clock protein KaiB in the generation of circadian oscillations in cyanobacteria."
    J. Biol. Chem., 287:29506-29515, 2012
  • Toshio Ando, Takayuki Uchihashi and Noriyuki Kodera
    "High-speed atomic force microscopy"
    Jpn. J. Appl. Phys., 51: 08KA02 (15 pages), 2012
  • Jonathan S. Valencia, Kyohei Bitou, Kentaro Ishii, Reiko Murakami, Megumi Morishita, Kiyoshi Onai, Yukio Furukawa, Katsumi Imada, Keiichi Namba, Masahiro Ishiura.
    "Phase-dependent generation and transmission of time information by the KaiABC circadian clock oscillator through SasA-KaiC interaction in cyanobacteria."
    Genes to Cells, 17:398-419, 2012
  • Takayuki Uchihashi, Noriyuki Kodera and Toshio Ando
    "Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy"
    Nature Protocols, 7:1193-1206, 2012
  • Kiyohiko Igarashi, Takayuki Uchihashi, Anu. Koivula, Masahisa Wada, Satoshi Kimura, Merja Penttilä, Toshio Ando and Masahiro Samejima
    "Visualization of cellobiohydrolase I from Trichoderma reesei moving on crystalline cellulose using high-speed atomic force microscopy"
    Methods Enzymol., 510:169-182, 2012
  • Hideyuki Matsunami, Fadel S. Samatey, Shigehiro Nagashima, Katsumi Imada and Keiichi Namba
    "Crystallization and preliminary X-ray analysis of FlgA, a Periplasmic protein essential for flagellar P-ring assembly."
    Acta Cryst F, 68:310-313, 2012
  • Takayuki Uchihashi and Toshio Ando
    "High-speed atomic force microscopy and biomolecular processes"
    Methods Mol. Biol., 736:285-300, 2011
  • Tohru Minamino, Miki Kinoshita, Noritaka Hara,Shiori Takeuchi, Akira Hida, Satomi Koya,Helen Glenwright, Katsumi Imada,Phillip D. Aldridge and Keiichi Namba
    "Interaction of a bacterial flagellar chaperone FlgN with FlhAis required for efficient export of its cognate substrates"
    Molecular Microbiology, 83:775-788, 2011
  • Hirotaka Tajima, Katsumi Imada, Mayuko Sakuma, Fumiyuki Hattori, Toshifumi Nara, Naoki Kamo, Michio Homma and Ikuro Kawagishi
    "Ligand Specificity Determined by Differentially ArrangedCommon Ligand-binding Residues in Bacterial Amino AcidChemoreceptors Tsr and Tar"
    THE JOURNAL OF BIOLOGICAL CHEMISTRY, 286:42200-42210, 2011
  • Masafumi Shimada, Yumiko Saijo-Hamano, Yukio Furukawa,Tohru Minamino, Katsumi Imada and Keiichi Namba
    "Functional Defect and Restoration ofTemperature-Sensitive Mutants of FlhA, a Subunitof the Flagellar Protein Export Apparatus"
    Journal of Molecular Biology, 415:855-865, 2011
  • Tohru Minamino, Miki Kinoshita, Katsumi Imada and Keiichi Namba
    "Interaction between FliI ATPase and a flagellar chaperoneFliT during bacterial flagellar protein export"
    Molecular Microbiology, 83:168-178, 2011
  • Kiyohiko Igarashi, Takayuki Uchihashi, Anu Koivula, Masahisa Wada, Satoshi Kimura, Tetsuaki Okamoto, Merja Penttila, Toshio Ando and Masahiro Samejima
    "Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface"
    Science, 333:1279-1282, 2011