2016

D. Yamamoto and T. Ando

Chaperonin GroEL-GroES functions as both alternating and non-alternating engines, J. Mol. Biol. 428, 3090-3101 (2016). DOI: 10.1016/j.jmb.2016.06.017 (PDF) (Movie S1)

Hayashi Yamamoto, Yuko Fujioka, Sho W. Suzuki, Daisuke Noshiro, Hironori Suzuki, Chika Kondo-Kakuta, Yayoi Kimura, Hisashi Hirano, Toshio Ando, Nobuo N. Noda, Yoshinori Ohsumi

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes, Dev. Cell 38:86-99 (2016). DOI: 10.1016/j.devcel.2016.06.015. (PDF) (Open Access)

T. Watanabe-Nakayama, M. Itami, N. Kodera, T. Ando and H. Konno

High-speed atomic force microscopy reveals strongly polarized movement of clostridial collagenase along collagen fibrils, Sci. Rep. 6:28975 (2016). DOI: 10.1038/srep28975. (Link) 

T. Uchihashi, H. Watanabe, S. Fukuda, M. Shibata and T. Ando

"Functional extension of high-speed atomic force microscopy", Ultramicroscopy 160, 182-196 (2016). DOI: 10.1016/j.ultramic.2015.10.017 (Link) (PDF)

Wilaiwan Sriwimol, Aratee Aroonkesorn, Somsri Sakdee, Chalermpol Kanchanawarin, Takayuki Uchihashi, Toshio Ando and Chanan Angsuthanasombat

"Potential pre-pore trimer formation by the Bacillus thuringiensis mosquito-specific toxin: Molecular insights into a critical prerequisite of membrane-bound monomers",  J. Biol. Chem. 290 (34), 20793-20803 (2015). DOI: 10.1074/jbc.M114.627554 (Link)

Shingo Fukuda, Takayuki Uchihashi, Toshio Ando

"Method of mechanical holding of cantilever chip for tip-scan high-speed atomic force microscopy", Rev. Sci. Instrum. 86, 063703 (2015). DOI: 10.1063/1.4922381 (Link) (PDF)

Kouta Takeda, Takayuki Uchihashi, Hiroki Watanabe, Takuya Ishida, Kiyohiko Igarashi, Nobuhumi Nakamura, Hiroyuki Ohno,

"Real-time dynamic adsorption processes of cytochrome c on an electrode observed through electrochemical high-speed atomic force microscopy", PLoS One (in press) DOI:10.1371/journal.pone.0116685 (Link)

M. Shibata, T. Uchihashi, T. Ando and R. Yasuda

"Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells"

Scientific Reports 5, 8724 (7 pp) (2015). DOI:10.1038/srep08724 (Link) (PDF)

M. Imamura, T. Uchihashi, T. Ando, A. Leifert, U. Simon, A. D. Malay and J. G. Heddle

"Probing structural dynamics of an artificial protein cage using high-speed atomic force microscopy", Nano Lett. 15 (2): 1331–1335 (2015). DOI: 10.1021/nl5045617 (Link)

Kien Xuan Ngo, Noriyuki Kodera, Eisaku Katayama, Toshio Ando and Taro Q.P. Uyeda

"Cofilin-induced unidirectional cooperative conformational changes in actin filaments revealed by high-speed AFM", e-Life 4:e04806 (2015) DOI: 10.7554/eLife.04806#sthash.zRRaKrcb.dpuf (Link) (PDF) (Supplements)

N. Kodera, K. Uchida, T. Ando, and S. Aizawa

"Two-ball structure of the flagellar hook-length control protein FliK as revealed by high-speed atomic force microscopy", J. Mol. Biol.  427, 406-414 (2015) doi: 10.1016/j.jmb.2014.11.007 (Link) 

S. Ishino, T. Yamagami, M. Kitamura, N. Kodera, T. Mori, S. Sugiyama, T. Ando, N. Goda, T. Tenno, H. Hiroaki, and Y. Ishino

"Multiple Interactions of the Intrinsically Disordered Region between the N-terminal Helicase and C-terminal Nuclease Domains

 of the Archaeal Hef Protein", J. Biol. Chem. 289: 21627-21639 (2014). DOI:10.1074/jbc.M114.554998 (Link)

"IgGs are made for walking on bacterial and viral surfaces", Nature Communications 5: 4394 (8 pp) (2014) DOI:10.1038/ncomms5394 (Link)

4.

N. Kodera and T. Ando, "The path to visualization of walking myosin V by high-speed atomic force microscopy", Biophys. Rev. 6:237-260 (2014). DOI: 10.1007/s12551-014-0141-7(PDF) (Link) (Open access)

5.

Y. Shibafuji, A. Nakamura, T. Uchihashi, N. Sugimoto, S. Fukuda, H. Watanabe, M. Samejima, T. Ando, H. Noji, A. Koivula, K. Igarashi, and R. Iino, Single-molecule imaging analysis of elementary reaction steps of Trichoderma Reesei cellobiohydrolase I (Cel7A) hydrolyzing crystalline cell. J. Biol. Cherm.289:14056-14065 (2014). Doi: 10.1074/jbc.M113.546085.

6.

T. Ando, T. Uchihashi, and S. Scheuring, "Filming biomoleculear processes by high-speed atomic force microscopy", Chem. Rev. 114(6):3120-3188 (2014). DOI:0.1021/cr4003837. (Link)  (PDF Ile)

7.

A. Nakamura, H. Watanabe, T. Ishida, T. Uchihashi, M. Wada, T. Ando, K. Igarashi, and M. Samejima, "Trade-off between processivity and hydrolytic velocity of cellobiohydrolases at the surface of crystalline cellulose", J. Am. Chem. Soc. 136:4584-4592 (2004) DOI: 10.1021/ja4119994. (Link) (PDF File)

8.

K. Igarashi, T. Uchihashi, T. Uchiyama, H. Sugimoto, M. Wada, K. Suzuki, S. Sakuda, T. Ando, T. Watanabe, and M. Samejima, "Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin", Nature Communications 5: 3975 (2014).  

1.

Kentaro Noi, Daisuke Yamamoto, Shingo Nishikori, Ken-ichi Arita-Morioka, Toshio Ando and Teru Ogura, "High-speed atomic force microscopic observation of ATP-dependent rotation of the AAA+ chaperone p97", Structure 21: 1992-2002 (2013). DOI: 10.1016/j.str.2013.08.017 (Link) (PDF File)

2.

Neval Yilmaz, Taro Yamada, Peter Greimel, Takayuki Uchihashi, Toshio Ando, and Toshihide Kobayashi, "Real-Time Visualization of Assembling of a Sphingomyelin-Specific Toxin", Biophys. J. 105, 1397-1405 (2013). DOI: 10.1016/j.bpj.2013.07.052  (Link)  (PDF File)

3.

S. Fukuda, T. Uchihashi, R. Iino, Y. Okazaki, M. Yoshida, K. Igarashi, and T. Ando, "High-speed atomic force microscope combined with single-molecule fluorescence microscope", Rev. Sci. Instrum. 84, 073706 (2013). DOI: 10.1063/1.4813280  (Link) (PDF File)

4.

M. Hashimoto, N. Kodera, Y. Tsunaka, M. Oda, M. Tanimoto, T. Ando, K. Morikawa, and S. Tate, "Phosphorylation-Coupled Intramolecular Dynamics of Unstructured Regions in Chromatin Remodeler FACT", Biophys. J. 104: 2222-2234 (2013) DOI: 10.1016/j.bpj.2013.04.007  (Link) (PDF File)

5.

H. Watanabe, T. Uchihashi, T. Kobashi, M. Shibata, J. Nishiyama, R. Yasuda, and T. Ando, "Wide-area scanner for high-speed atomic force microscopy", Rev. Sci. Instrum. 84: 053702 (2013).  DOI: 10.1063/1.4803449  (Link)  (PDF File) 

6.

T. Ando, "High-speed atomic force microscopy of protein dynamics: myosin on actin and rotary enzyme F1-ATPase", Microscopy & Analysis 27(3):10-13 (2013). (Link) (PDF File)

7.

H. Yamashita, K. Inoue, M. Shibata, T. Uchihashi, J. Sasaki, H. Kandori, and T. Ando, "Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy", J. Struct. Biol. 184: 2-11 (2013). DOI: 10.1016/j.jsb.2013.02.011  (Link) (PDF File)

8.

T. Ando, "Molecular Machines directly observed by high-speed atomic force microscopy", FEBS Lett. 587: 997-1007 (2013). DOI: 10.1016/j.febslet.2012.12.024, (Link)  (PDF File)

9.

T. Ando, T. Uchihashi, and N. Kodera, "High-speed AFM and applications to biomolecular systems", Annu. Rev. Biophys. 42: 393-414(2013).DOI: 10.1146/annurev-biophys-083012-130324  (Link)  (PDF File) 

10.

T. Ando, "High-speed atomic force microscopy", Microscopy 62(1):81-93 (2013). DOI: 10.1093/jmicro/dfs093 (PDF File)

1.

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

2.

H. Yamashita, A. Taoka, T. Uchihashi, T. Asano, T. Ando, and Y. Fukumori, "Single molecule imaging on living bacterial cell surface by high-speed AFM", J. Mol. Biol. 422(2) 300-309 (2012).  (Link) (Movie1, Movie2, Movie3, Movie4, Supplementary data)  (PDF File).

3.

T. Uchihashi, N. Kodera, and T. Ando, "Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy", Nature Protocols 7(6): 1193-1206 (2012). (Link) (PDF File)

4.

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

5.

T. Nojima, H. Konno, N. Kodera, K. Seio, H. Taguchi, M. Yoshida, “Nano-scale alignment of proteins on a flexible DNA backbone”, PLoS One 7(12): e52534 (5 pp) (2012).

6.

T. Ando, "High-speed atomic force microscopy coming of age", Nanotechnology 23: 062001 (27 pp)  (2012). (Link) (Editorial) (PDF File)

7.

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

1.

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

2.

K. Igarashi, T. Uchihashi, A. Koivula, M. Wada, S. Kimura, T. Okamoto, M. Penttilä, T. Ando, and M. Samejima, "Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface", Science 333:1279-1282 (2011). (Link) (Supplementary Info) (Movie 1) (Movie 2) (Movie 3) (Movie 4) (Movie 5) (Movie 6) (Movie 7) (Movie 8) (Movie 9) (Science Japan) (PDF File)

3.

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

4.

A. Miyagi, T. Ando and Y. L. Lyubchenko, "Dynamics of nucleosomes assessed with time-lapse high speed atomic force microscopy", Biochemistry 50: 7901-7908 (2011). (this paper is highlighted in Biochemistry) (Link)  (PDF File) 

5.

T. Uchihashi, R. Iino, T. Ando, and H. Noji, "High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase, Science 333, 755-758 (2011). (Link) (Supplementary_Inf) (Movie 1) (Movie 2) (Movie 3) (Movie 4) (Movie 5) (Movie 6) (Movie 7) (Movie 8) (perspectives) (Science Japan)  (PDF File) 

6.

M. Shibata, T. Uchihashi, H. Yamashita, H. Kandori, and T. Ando, "Structural changes in bacteriorhodopsin in response to alternate illumination observed by high-speed atomic force microscopy",  Angewande Chemie International edition 50: 4410–4413 (2011). (Link) (Supplementary_Info)  (Movie 1) (Movie 2) (Movie 3) (Movie 4) (PDF File)

7.

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

8.

S. Inoue, T. Uchihashi, D. Yamamoto, and T. Ando, Direct observation of surfactant aggregate behavior on a mica surface using high-speed atomic force microscopy, Chem. Commun. 47: 4974–4976 (2011) (Link)  (PDF File)

1.

N. Kodera, D. Yamamoto, R. Ishikawa, and T. Ando, Video imaging of walking myosin V by high-speed atomic force microscopy. Nature 468: 72-76 (2010). (Link) (Movie 1) (Movie 2) (Movie 3) (Movie 4) (Movie 5) (Movie 6) (supplementary info) (News & View)  (PDF File) 

2.

P.-E. Milhiet, D. Yamamoto, O. Berthoumieu, P. Dosset, Ch. Le Grimellec, J.-M. Verdier, S. Marchal, and T. Ando, “Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy”, PLos One 5 (11): e13240 (8 pp) (2010). (Link) (Movie S1, Movie S2, Movie S3) (supplementary info) (PDF File)

3.

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

4.

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

5.

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

6.

M.-C. Giocondi, D. Yamamoto, E. Lesniewska, P.-E. Milhiet, T. Ando, and Ch. Le Grimellec, Surface topography of membrane domains, Biochim. Biophys. Acta.-Biomembranes 1798: 703-718 (2010).  (Link)  (PDF File)

7.

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

1.

I. Casuso, N. Kodera, C. Le Grimellec, T. Ando, and S. Scheuring, Contact mode high-resolution high-speed  atomic force microscopy movies of purple membrane, Biophys J, 97 (5): 1354-1361 (2009). (Link) (PDF File)　

2.

D. Yamamoto, N. Nagura, S. Omote, M. Taniguchi, and T. Ando, Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy, Biophys. J. 97(8): 2358–2367 (2009). (Link)  (PDF File)

3.

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

4.

K. Shinohara, N. Kodera, and T. Ando, 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(7): 690-691 (2009). (Link) (PDF File)

1.

T. Ando, T. Uchihashi, and T. Fukuma, High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes, Progr. Surf. Sci. 83: 337-437 (2008). (Link) (PDF file)　

2.

D. Yamamoto, T. Uchihashi, N. Kodera, and T. Ando, Anisotropic diffusion of point defects in two-dimensional crystal of streptavidin observed by high-speed atomic force microscopy, Nanotechnology 19: 384009 (9 pp) (2008). (Link) (Supplementary Movie)  (PDF file)

3.

A. Miyagi, Y. Tsunaka, T. Uchihashi, K. Mayanagi, S. Hirose, K. Morikawa, and T. Ando, Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy, Chem. Phys. Chem. 9(13):1859-1866 (2008). (Link)  (PDF file)

4.

T. Fukuma, Y. Okazaki, N. Kodera, T. Uchihashi, and T. Ando, High resonance frequency force microscope scanner using inertia balance support, Appl. Phys. Lett. 92:243119 (2008). (Link) (PDF file) 

5.

T. Ando, T. Uchihashi, N. Kodera, D. Yamamoto, M. Taniguchi, A. Miyagi, and H. Yamashita, High-speed AFM and nano-visualization of biomolecular processes, Pflügers Archiv -Eur. J. Physiol. 456:211-225 (2008). (Link)  (PDF file)  　

6.

T. Ando, Control techniques in high-speed atomic force microscopy, Proceedings of the American Control Conference, art. no. 4586984, pp. 3194-3200 (2008). (PDF File) 

7.

H. Iwase, H. Choi, M. Akabori, T. Suzuki, S. Yamada, D. Yamamoto and T. Ando, Fabrication of 3D micro-cantilevers based on MBE-grown strained semiconductor layers, Physica E: Low-dimensional Systems and Nanostructures 40(6): 2210-2213 (2008). 

1.

T. Ando, T. Uchihashi, N. Kodera, D. Yamamoto, M. Taniguchi, A. Miyagi, and H. Yamashita, High-speed atomic force microscopy for observing dynamic biomolecular processes, J. Mol. Recognit. 20:448-458 (2007). (Link) (PDF file)   

2.

H. Yamashita, T. Uchihashi, N. Kodera, A. Miyagi, D. Yamamoto, T. Ando, Tip-sample distance control using photo-thermal actuation of a small cantilever for high-speed atomic force microscopy, Rev. Sci. Instrum. 78:083702 (5 pages) (2007). (Link)  (PDF file) 

3.

K. Shinohara, N. Kodera, and T. Ando, Single molecular imaging of a micro-Brownian motion and a bond scission of a supramolecular chiral π-conjugated, Chem. Lett. 36: 1378-1379 (2007).  (PDF file)

4.

S. Morita, H. Yamada, and T. Ando, Japan AFM roadmap 2006, Nanotechnology 18:08401 (10 pages) (2007).  (Link) (PDF file)  

1.

T. Uchihashi, H. Yamashita, and T. Ando, Fast phase imaging in liquids using a rapid scan atomic force microscope, Appl. Phys. Lett. 89:213112 (3 pages) (2006). (Link)  (PDF file)

2.

N. Kodera, M. Sakashita, and T. Ando, Dynamic proportional-integral-differential controller for high-speed atomic force microscopy, Rev. Sci. Instrum. 77(8):083704 (7 pages) (2006). (Link) (PDF file)

3.

H. Koide, T. Kinoshita, Y. Tanaka, S. Tanaka, N. Nagura, G. Meyer zu Hörste, A. Miyagi, and T. Ando, Identification of the specific IQ motif of myosin V from which calmodulin dissociates in the presence of Ca²⁺, Biochemistry 45(38):11598-11604 (2006). (Link)  (PDF file)  

4.

M. Yokokawa, C. Wada, T. Ando, N. Sakai , A. Yagi, S.H. Yoshimura, and K. Takeyasu, Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL, EMBO J. 25:4567-4576 (2006). (Link) (PDF File) 

5.

M. Yokokawa, S.H. Yoshimura, Y. Naito, T. Ando, A. Yagi, N. Sakai, and K. Takeyasu, Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease, IEE Proc Nanobiotechnol. 153(4):60-66 (2006). 

6.

T. Ando, T. Uchihashi, N. Kodera, A. Miyagi, R. Nakakita, H. Yamashita, and M. Sakashita, High-speed atomic force microscopy for studying the dynamic behavior of protein molecules at work, Jpn. J. Appl. Phys. 45(3B):1897-1903 (2006). (Link)  (PDF file)

7.

T. Uchihashi, N. Kodera, H. Itoh, H. Yamashita, and T. Ando, Feed-forward control for high-speed AFM imaging of biomolecules, Jpn. J. Appl. Phys. 45(3B):1904-1908 (2006). (Link) (PDF file) 

1.

T. Ando, T. Uchihashi, N. Kodera, A. Miyagi, R. Nakakita, H. Yamashita, and K. Matada, High-speed AFM for studying the dynamic behavior of protein molecules at work, e-J. Surf. Sci. Nanotechnol. 3:384-392 (2005). (Link)  (Supplementary Movies) (PDF file) 

2.

N. Kodera, H. Yamashita, and T. Ando, Active damping of the scanner for high-speed atomic force microscopy, Rev. Sci. Instrum. 76: 053708 (5pages) (2005). (Link)   (PDF file)

1.

N. Kodera, T. Kinoshita, T. Ito, and T. Ando, High-resolution imaging of myosin motor in action by a high-speed atomic force microscope, Adv. Exp. Med. Biol. 538:119-127 (2003). 

2.

R. Ishikawa, T. Sakamoto, T. Ando, S. Higashi-Fujime, and K. Kohama, Polarized actin bundles formed by human fascin-1: Their sliding and disassembly on myosin II and myosin V in vitro, J. Neurochem. 87:676-685 (2003). (Link) (PDF file)

3.

T. Ando, N. Kodera, Y. Naito, T. Kinoshita, K. Furuta, and Y.Y. Toyoshima, A high-speed atomic force microscope for studying biological macromolecules in action, ChemPhysChem 4:1196-1202 (2003). (Link) (PDF file)

4.

T. Ando, N. Kodera, D. Maruyama,  E. Takai, K. Saito, and A. Toda, A High-speed atomic force microscope for studying biological macromolecules in action, Jpn. J. Appl. Phys. 41:4851-4856 (2002). (Link) (PDF file)

5.

T. Ando, N. Kodera, E. Takai, D. Maruyama,  K. Saito, and A. Toda, A High-speed atomic force microscope for studying biological macromolecules, Proc. Natl. Acad. Sci. USA  98:12468-12472 (2001). (Link) (PDF file)

6.

I. Amitani, T. Sakamoto, and T. Ando, Link between the enzymatic and mechanical behavior in an actomyosin motor, Biophys. J. 80:379-397 (2001). (Link) (PDF file)

7.

T. Sakamoto, I. Amitani, E. Yokota, and T. Ando, Direct observation of processive movement by individual myosin V molecules, Biochem. Biophys. Res. Commun. 272:586-590 (2000). (Link)  (PDF file)