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2017

Yanagida T, Ishii Y. gSingle molecule detection, thermal fluctuation and life.h, Proc Jpn Acad Ser B Phys Biol Sci. , (2017)

Kitagawa H, Sugo N, Morimatsu M, Arai Y, Yanagida T, Yamamoto N. gActivity-Dependent Dynamics of the Transcription Factor of cAMP-Response Element Binding Protein in Cortical Neurons Revealed by Single-Molecule Imaging.h, J Neurosci., (2017)

2016

Fujita K., Iwaki M., Yanagida T. "Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA.h, Nat. Commun., (2016)

Iwaki M., Wickham S., Ikezaki K., Yanagida T., Shih W. "A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.h, Nat. Commun., (2016)

Kitagawa H, Sugo N, Morimatsu M, Arai Y, Yanagida T, Yamamoto N. "Activity-Dependent Dynamics of the Transcription Factor CREB in Cortical Neurons Revealed by Single-Molecule Imaging", J Neurosci., (2016)

Marcucci L, Washio T, Yanagida T. "Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling.", PLoS Comput Biol. , (2016)

2015

Sugo N, Morimatsu M, Arai Y, Kousoku Y, Ohkuni A, Nomura T, Yanagida T, Yamamoto N. "Single-Molecule Imaging Reveals Dynamics of CREB Transcription Factor Bound to Its Target Sequence.", Sci Rep., (2015)

Noguchi TQ, Morimatsu M, Iwane AH, Yanagida T, Uyeda TQ. "The role of structural dynamics of actin in class-specific myosin motility.", PLoS One, (2015)

Iwaki M, Iwane AH, Ikezaki K, Yanagida T. "Local heat activation of single myosins based on optical trapping of gold nanoparticles.", Nano Lett., (2015)

Ikezaki K, Komori T, Arai Y, Yanagida T. "Lever arm extension of myosin VI is unnecessary for the adjacent binding state.h, Biophysics, (2015)

2014

Murata T, Hamada T, Shimokawa T, Tanifuji M, Yanagida T. "Stochastic process underlying emergent recognition of visual objects hidden in degraded images.", PLoS One, (2014)

Yanagida T. "Single molecule imaging expanded to macroscopic level by computer simulation.", Microscopy, (2014)

Karagiannis P, Ishii Y, Yanagida T. "Molecular machines like myosin use randomness to behave predictably.", Chem Rev., (2014)

Ichimura T, Chiu LD, Fujita K, Kawata S, Watanabe TM, Yanagida T, Fujita H. "Visualizing cell state transition using Raman spectroscopy.", PLoS One, (2014)

2013

Watanabe TM, Imada K, Yoshizawa K, Nishiyama M, Kato C, Abe F, Morikawa TJ, Kinoshita M, Fujita H, Yanagida T. "Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure.", PLoS One, (2013)

Watanabe TM, Fujii F, Jin T, Umemoto E, Miyasaka M, Fujita H, Yanagida T. "Four-dimensional spatial nanometry of single particles in living cells using polarized quantum rods.", Biophys J., (2013)

Yasuhara N, Yamagishi R, Arai Y, Mehmood R, Kimoto C, Fujita T, Touma K, Kaneko A, Kamikawa Y, Moriyama T, Yanagida T, Kaneko H, Yoneda Y. "Importin alpha subtypes determine differential transcription factor localization in embryonic stem cells maintenance.", Dev Cell, (2013)

Kong SG, Arai Y, Suetsugu N, Yanagida T, Wada M. "Rapid serving and motility of chloroplast-actin filaments are required for the chloroplast avoidance response in Arabidopsis.", Plant Cell, (2013)

K. Ikezaki, T. Komori, T. Yanagida. gBackward step of myosin-VI is generated by the spontaneous detachment of the leading headh PLoS One (2013)

2012

Yanagida T, Ishii Y. "Muscle contraction mechanism based on single molecule measurements.", J Muscle Res Cell Motil. ., (2012)

Duttmann M, Mittnenzweig M, Togashi Y, Yanagida T, Mikhailov AS. "Complex Intramolecular Mechanics of G-actin - An Elastic Network Study.", PLoS One., (2012)

Marcucci L, Yanagida T. "From Single Molecule Fluctuations to Muscle Contraction: A Brownian Model of A.F. Huxley's Hypotheses", PLoS One., (2012)

M. Morimatsu, Y. Togashi, S. Nishikawa, M. Sugawa, A. Iwane, T. Yanagida. "Spontaneous Structural Change in Actin Regulate G-F Transformation", PLoS One., (2012)

M. Iwaki, L. Marcucci, Y. Togashi, T. Yanagida. "Single molecule and collective dynamics of motor proteins coupled with mechano-sensitive chemical reaction", Engineering of Chemical Complexity, (World Scinetific Lecture Notes in Complex Systems - Vol. 11), (2012)

K. Fujita, M. Iwaki, A. H. Iwane, L. Marcucci, T. Yanagida "Switching of myosin-V motion between the lever-arm swing and Brownian search-and-catch", Nat. Commun., (2012)

T.Q.P. Noguchi, T. Komori, N. Umeki, N. Demizu, K. Ito, A. H. Iwane, K. Tokuraku, T. Yanagida, T.Q.P. Uyeda "SG146V mutation at the hinge region of actin reveals a myosin class-specific requirement of actin conformations for motility", J. Bio. Chem.,(2012)

K. Ikezaki, T. Komori, M. Sugawa, Y. Arai, S. Nishikawa, A. H. Iwane, T. Yanagida. "Simultaneous Observation of the Lever Arm and Head Explains Myosin VI Dual Function", Small, (2012)

Takahashi M, Shibata T, Yanagida T, Sako Y. "A protein switch with tunable steepness reconstructed in Escherichia coli cells with eukaryotic signaling proteins.", Biochem Biophys Res Commun., (2012)

Ohmachi M, Komori Y, Iwane AH, Fujii F, Jin T, Yanagida T. "Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rod-tagged myosin V.", Proc Natl Acad Sci U S A., (2012)

Matsuoka S, Miyanaga Y, Yanagida T, Ueda M, "Visualizing single molecules in living Dictyostelium cells using total internal reflection fluorescent microscopy (TIRFM)., (2012)

Matsuoka S, Miyanaga Y, Yanagida T, Ueda M, "Preparation of an imaging chamber for visualizing single molecules in living Dictyostelium cells.", Cold Spring Harb Protoc., (2012)

Matsuoka S, Miyanaga Y, Yanagida T, Ueda M, "Preparation of chemotactically competent Dictyostelium cells.", Cold Spring Harb Protoc., (2012)

Matsuoka S, Miyanaga Y, Yanagida T, Ueda M, "Single-molecule imaging of stochastic signaling events in living cells.", Cold Spring Harb Protoc., (2012)

Duttmann M, Togashi Y, Yanagida T, Mikhailov AS, "Myosin-V as a mechanical sensor: an elastic network study.", Biophys J., ,(2012)


2011

Yanagida T, "Single molecule meets brain: a new concept to understand complex bio-system.", Rinsho Shinkeigaku. [Japanese], (2011)

Hirano M, Onishi Y, Yanagida T, Ide T. "Role of the KcsA channel cytoplasmic domain in pH-dependent gating.", Biophys J., (2011)

Kayo Hibino, Tatsuo Shibata, Toshio Yanagida, and Yasushi Sako, "Activation kinetics of RAF in the ternary complex of RAF, RASGTP, and kinase on the plasma membrane of living cells: single-molecule imaging analysis.", J Biol Chem., (2011)

Mitsunori Kitta, Toru Ide, Minako Hirano, Hiroyuki Tanaka, Toshio Yanagida, and Tomoji Kawai, "Direct Manipulation of a Single Potassium Channel Gate with an Atomic Force Microscope Probe.", Small., 7,(2011)



2010

T. Ide, "Simultaneous optical and electronical recording of single molecule binding to single chennel proteins.", ChemPhysChem., 11, 3408-11 (2010)


T.M. Watanabe, A.H. Iwane, H. Tanaka, M. Ikebe, T. Yanagida, "Mechanical characterization of one-headed myosin-V using optical tweezers.", PLoS One, 5, e12224 (2010)

T.M. Watanabe, S. Fukui, T. Jin, F. Fujii, T. Yanagida, "Real-time Nanoscopy by using Blinking Enhanced Quantum Dots", Biophys. J., 99, L50-2 (2010)

H. Fujita, H. Hatakeyama, T.M. Watanabe, M. Sato, H. Higuchi, M. Kanzaki, "Identification of Three Distinct Functional Sites of Insulin-mediated GLUT4 Trafficking in Adipocytes Using Quantitative Single Molecule Imaging.", Mo. Biol. Chem., 21, 2721-31 (2010)

T.M. Watanabe, H. Tokuo, K. Gonda, H. Higuchi, M. Ikebe, "Dynamics of myosin-X during filopodia protrusion ", J Biol Chem, 285, 19605-14 (2010)

K. Gonda, T.M. Watanabe, N. Ouchi, H. Higuchi, "In Vivo nano-imaging of membrane dynamics in metastatic tumor cells using quantum dots", J Biol Chem, 285, 2750-57 (2010)

K. Amano, T. Yoshidome, M. Iwaki, M. Suzuki, M. Kinoshita, "Entropic potential field formed for a linear-motor protein near a filament: Statistical mechanical analyses using simple models.", The Journal of Chemical Physics, 133, 045103 (2010)

S. Nishikawa, I. Arimoto, K. Ikezaki, M. Sugawa, H. Ueno, T. Komori, A. H Iwane, T. Yanagida., "Switch between large hand-over-hand and small inchworm-like steps in myosin VI", Cell, 142, 879-88 (2010)

T. Fujii, A.H. Iwane, T. Yanagida, K. Namba., "Direct visualization of secondary structures of F-actin by electron cryomicroscopy.", Nature, 467, 724-8 (2010)

Y. Arai, T. Shibata, S. Matsuoka, M. J. Sato, T. Yanagida, M. Ueda, "Self-organization of the phosphatidylinositol lipids signaling for random cell migration.", Proc. Natl. Acad. Sci. USA, 107, 12399-404 (2010)

T.M. Watanabe, T. Yanagida, A.H. Iwane, "Single molecular observation of self-regulated kinesin motility.", Biochemistry, 49, 4654-61 (2010)

Y. Togashi, T. Yanagida, A.S. Mikhailov, "Nonlinearity of Mechanochemical Motions in Motor proteins", PLoS Comput. Biol., 6, e1000814 (2010)

H. Ueno, S. Nishikawa, R. Iino, K.V. Tabata, S. Sakakihara, T. Yanagida, H. Noji , "Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution.", Biophys. J.98, 2014-23 (2010)

Y. Tsuchiya, T. Komori, M. Hirano, T. Shiraki, A. Kakugo, T. Ide, J, -P. Gong, S. Yamada, T. Yanagida, S. Shinkai, "A Polysaccharide-Based Container Transportaion System Powered by Molecular Motors", Angew. Chem. Int. Ed. , 49, 724-7 (2010)

M. Yamada, S. Toba, T. Takitoh, Y. Yoshida, D. Mori, T. Nakamura, A.H. Iwane, T. Yanagida, H. Imai, L.Y. Yu-Lee, T. Schroer, A. Wynshaw-Boris, S. Hirotsune, "mNUDC is required for plus-end-directed transport of cytoplasmic dynein and dynactins by kinesin-1", EMBO J., 29, 517-31 (2010)

M. Sugawa,S. Nishikawa, A. H. Iwane, V. Biju, T. Yanagida, "Single-Molecule FRET imaging for Enzymatic Reactions at High Ligand Concentrations", Small, 6, 346-50 (2010)

T. Ide, Y. Takeuchi, H. Noji, K. Tabata, "Simultaneous optical and electrical single channel recordings on aPEG glass", Langmuir, 26, 8540-3 (2010)

M. Hirano, Y. Takeuchi, T. Aoki, T. Yanagida, T. Ide, "Rearrangements in the KcsA cytoplasmic domain underlie its gaiting.", J.Biol. Chem., 285, 3777-83 (2010)



2009

A. H. Iwane, M. Morimatsu, T. Yanagida, "Recombinant -actin for specific fluorescent labeling", Proc. Jpn. Acad., Ser. B, 85, 491-9 (2009)

T. Ide, Y. Takeuchi, H. Noji, K. Tabata, "Simultaneous optical and electrical single channel recordings on aPEG glass", Langmuir, in press

K. V. Tabata, K. Sato, T. Ide, T. Nishizaka, A. Nakano, H.Noji, "Visualization of carge concentration by COPII minimal machinery in a plannar lipid membrane.", EMBO J., 28, 3279-89 (2009)

Y. Miyanaga, S. Matsuoka, M. Ueda, "Single-molecule imaging techniques to visualize chemotactic signaling events on the membrane of living Dictyostelium cells.", Methods Mol. Biol., 571, 417-35 (2009)

S. Matsuoka, T. Shibata, M. Ueda,, Statistical analysis of lateral diffusion and multi-state kinetics in single-molecule imaging, Biophys. J., 97(4), 1115-1124 (2009)

M. Iwaki, A. H. Iwane, T. Shimokawa, R. Cooke, T. Yanagida, Brownian search-and-catch mechanism for myosin-VI steps, Nat. Chem. Biol., 5(6), 403-405 (2009)

M. Hirano, Y. Takeuchi, T. Aoki, T. Yanagida, T. Ide,, Current recordings of ion channel proteins immobilized on resin beads, Anal. Chem., 81(8), 3151-3154 (2009)

M. J. Sato, H. Kuwayama, W. N. van Egmond, A. L. K. Takayama, H. Takagi, P. J. M. van Haastert, T. Yanagida, M. Ueda, Swithching direction in electric-signal-induced cell migration by cyclic guanosine monophosphate and phosphatidylinositol signaling, Proc. Natl. Acad. Sci. USA, 106(16), 6667-6672 (2009)

S. I. Nishimura, M. Ueda, M. Sasai Cortical factor feedback model for cellular locomotion and cytofission. PLoS Comput. Biol., 5(3), e1000310 (2009)

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, T. Yanagida, Simultaneous measurement of nucleotide occupancy and mechanical displacement in myosin-V, a processive molecular motor, Biophys. J., 96(1), L04-06 (2009)