High-speed atomic force microscopy

Journal of Electron Microscopy

Volumn 62, Issue 1, 2013, Pages 81-93

  Ando, Toshio ^a  

^a KANAZAWA UNIVERSITY   (Japan)

Author keywords

Atomic force microscopy; Bioimaging; Biomolecular processes; Dynamics of proteins; High speed AFM; Realtime imaging

Indexed keywords

BACTERIORHODOPSIN; MYOSIN V;

ANIMAL; ATOMIC FORCE MICROSCOPY; CHEMISTRY; IMAGE PROCESSING; ISOLATION AND PURIFICATION; MAMMAL; METHODOLOGY; MOLECULAR DYNAMICS; REVIEW; ULTRASTRUCTURE;

ANIMALS; BACTERIORHODOPSINS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAMMALS; MICROSCOPY, ATOMIC FORCE; MOLECULAR DYNAMICS SIMULATION; MYOSIN TYPE V;

ATOMIC FORCE MICROSCOPY; DYNAMICS; MOLECULAR BIOLOGY; MOLECULES; PROTEINS;

ATOMIC-FORCE-MICROSCOPY; BIO-IMAGING; BIOMOLECULAR PROCESS; DYNAMIC BEHAVIORS; DYNAMIC OF PROTEIN; DYNAMIC VISUALIZATION; HIGH SPEED; HIGH-SPEED AFM; REALTIME IMAGING; VISUALIZATION TECHNIQUE;

BIOIMAGING;

EID: 84876954136     PISSN: 00220744     EISSN: 14779986     Source Type: Journal    
DOI: 10.1093/jmicro/dfs093     Document Type: Review

References (85)

1. Huang B, Bates M, and Zhuang X (2009) Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78: 993-1016.
2. De Jonge N and Ross F M (2011) Electron microscopy of specimens in liquid. Nat. Nanotechnol. 6: 695-704.
3. Binnig G, Quate C F, and Gerber Ch (1986) Atomic force microscope. Phys. Rev. Lett. 56: 930-933.
4. Müller D J and Dufrêne Y F (2008) Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology. Nat. Nanotechnol. 3: 261-269.
5. Müller D J, Helenius J, Alsteens D, and Dufrêne Y F (2009) Force probing surfaces of living cells to molecular resolution. Nat. Chem. Biol. 5: 383-390.
6. Müller D J, Janovjak H, Lehto T, Kuerschner L, and Anderson K (2002) Observing structure, function and assembly of single proteins by AFM. Progr. Biophys. Mol. Biol. 79: 1-43.
7. Scheuring S and Sturgis J N (2005) Chromatic adaptation of photosynthetic membranes. Science 309: 484-487.
8. Nakajima H, Kunioka Y, Nakano K, Shimizu K, Seto M, and Ando T (1997) Scanning force microscopy of the interaction events between a single molecule of heavy meromyosin and actin. Biochem. Biophys. Res. Commun. 234: 178-182.
9. Williams P M, Fowler S B, Best R B, Toca-Herrera J L, Scott K A, Steward A, and Clarke J (2003) Hidden complexity in the mechanical properties of titin. Nature 422: 446-449.
10. Dague E, Alsteens D, Latgé J-P, Verbelen C, Raze D, Baulard A R, and Dufrêne Y F (2007) Chemical force microscopy of single live cells. Nano Lett. 7: 3026-3030.
11. Touhami A, Nysten B, and Dufrêne Y F (2003) Nanoscale mapping of the elasticity of microbial cells by atomic force microscopy. Langmuir 19: 4539-4543.
12. Stewart M P, Helenius J, Toyoda Y, Ramanathan S P, Müller D J, and Hyman A A (2011) Hydrostatic pressure and the actomyosin cortex drive mitotic cell rounding. Nature 469: 226-230.
13. Drake B, Prater C B, Weisenhorn A L, Gould S A C, Albrecht T R, Quate C F, Cannell D S, Hansma H G, and Hansma P K (1989) Imaging crystals, polymers, and processes in water with the atomic force microscope. Science 243: 1586-1589.
14. Häberle W, Höber J K H, Ohnesorge F, Smith D P E, and Binnig G (1992) In situ investigations of single living cells infected by viruses. Ultramicroscopy 42-44: 1161-1167.
15. Ohnesorge F, Heckl W M, Häberle W, Pum D, Sara M, Schindler H, Schilcher K, Kiener A, Smith D P E, Sleytr U B, and Binnig G (1992) Scanning force microscopy studies of the S-layers from Bacillus coagulans E38-66, Bacillus sphaericus CCM2177 and of an antibody binding process. Ultramicroscopy 42-44: 1236-1242.
16. Binnig G (1992) Force microscopy. Ultramicroscopy 42-44: 7-15.
17. Ando T, Uchihashi T, and Fukuma T (2008) High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes. Progr. Surf. Sci. 83: 337-437.
18. Walters D A, Cleveland J P, Thomson N H, Hansma P K, Wendman M A, Gurley G, and Elings V (1996) Short cantilevers for atomic force microscopy. Rev. Sci. Instrum. 67: 3583-3590.
19. Kitazawa M, Shiotani K, and Toda A (2003) Batch fabrication of sharpened silicon nitride tips. Jpn. J. Appl. Phys. 42: 4844-4847.
20. Ando T, Kodera N, Takai E, Maruyama D, Saito K, and Toda A (2001) A high-speed atomic force microscope for studying biological macromolecules. Proc. Natl. Acad. Sci. USA 98: 12468-12472.
21. Viani M B, Schäffer T E, Paloczi G T, Pietrasanta L I, Smith B L, Thompson J B, Richter M, Rief M, Gaub H E, Plaxco K W, Cleland N, Hansma H G, and Hansma P K (1999) Fast imaging and fast force spectroscopy of single biopolymers with a new atomic force microscope designed for small cantilevers. Rev. Sci. Instrum. 70: 4300-4303.
22. Ando T, Uchihashi T, Kodera N, Miyagi A, Nakakita R, Yamashita H, and Matada K (2005) High-speed AFM for studying the dynamic behavior of protein molecules at work. e-J. Surf. Sci. Nanotechnol. 3: 384-392.
23. Fukuma T, Okazaki Y, Kodera N, Uchihashi T, and Ando T (2008) High resonance frequency force microscope scanner using inertia balance support. Appl. Phys. Lett. 92: 243119 (3 pp).
24. Kodera N, Yamashita H, and Ando T (2005) Active damping of the scanner for high-speed atomic force microscopy. Rev. Sci. Instrum. 76: 053708 (5 pp).
25. Kodera N, Sakashita M, and Ando T (2006) Dynamic proportional-integral- differential controller for high-speed atomic force microscopy. Rev. Sci. Instrum. 77: 083704 (7 pp).
26. Shibata M, Yamashita H, Uchihashi T, Kandori H, and Ando T (2010) High-speed atomic force microscopy shows dynamic molecular processes in photo-activated bacteriorhodopsin. Nat. Nanotechnol. 5: 208-212 (2010).
27. Kodera N, Yamamoto D, Ishikawa R, and Ando T (2010) Video imaging of walking myosin V by high-speed atomic force microscopy. Nature 468: 72-76.
28. Uchihashi T, Iino R, Ando T, and Noji H (2011) High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase. Science 333: 755-758.
29. Igarashi K, Uchihashi T, Koivula K, Wada M, Kimura S, Okamoto T, Penttilä M, Ando T, and Samejima M (2011) Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface. Science 333: 1279-1282.
30. Casuso I, Khao J, Paul-Gilloteaux P, Husain M, Duneau J-P, Stahlberg H, Sturgis J N, and Scheuring S (2012) Characterization of the motion of membrane proteins using high-speed atomic force microscopy. Nat. Nanotechnol. 7: 525-529.
31. Ando T (2012) High-speed atomic force microscopy coming of age. Nanotechnology 23: 062001 (27 pp).
32. Uchihashi T, Kodera N, and Ando T (2012) Guide to video recording of structure dynamics and dynamic processes of proteins by highspeed atomic force microscopy. Nat. Protocols 7: 1193-1206.
33. Zhong Q, Inniss D, Kjoller K, and Elings V B (1993) Fractured polymer/silica fiber surface studied by tapping mode atomic force microscopy. Surf. Sci. 290: L688-L692.
34. 4 receptors. PLoS Biol. 7: e1000103 (12 pp).
35. Shibata M, Uchihashi T, Yamashita H, Kandori, and Ando T (2011) Structural changes in bacteriorhodopsin in response to alternate illumination observed by high-speed atomic force microscopy. Angew. Chem. Int. Ed. 50: 4410-4413.
36. Yokokawa M and Takeyasu K (2011) Motion of the Ca2+-pump captured. FEBS J. 278: 3025-3031.
37. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, and Ando T (2008) Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy. Chem. Phys. Chem. 9: 1859-1866.
38. Milhiet P-E, Yamamoto D, Berthoumieu O, Dosset P, Le Grimellec Ch, Verdier J-M, SMarchal S, and Ando T (2010) Deciphering the structure, growth and assembly of amyloid-like fibrils using highspeed atomic force microscopy. PLoS ONE 5: e13240 (8 pp).
39. Giocondi M-C, Yamamoto D, Lesniewska E, Milhiet P-E, Ando T, and Le Grimellec Ch (2010) Surface topography of membrane domains. Biochim. Biophys. Acta. Biomembranes 1798: 703-718.
40. Casuso I, Sens P, Rico F, and Scheuring S (2010) Experimental evidence for membrane-mediated protein-protein interaction. Biophys. J. 99: L47-L49.
41. Casuso I, Kodera N, Le Grimellec Ch, Ando T, and Scheuring S (2009) High-resolution high-speed contact mode atomic force microscopy movies of purple membrane. Biophys. J. 97: 1354-1361.
42. Yamashita H, Voïtchovsky K, Uchihashi T, Antoranz Contera S, Ryan J F, and Ando T (2009) Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy. J. Struct. Biol. 167: 153-158.
43. Miyagi A, Ando T, and Lyubchenko Y L (2011) Dynamics of nucleosomes assessed with time-lapse high speed atomic force microscopy. Biochemistry 50: 7901-7908.
44. Suzuki Y, Higuchi Y, Hizume K, Yokokawa M, Yoshimura S H, Yoshikawa K, and Takeyasu K (2010) Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy. Ultramicroscopy 110: 682-688.
45. Yamashita H, Taoka A, Uchihashi T, Asano T, Ando T, and Fukumori Y (2012) Single molecule imaging on living bacterial cell surface by high-speed AFM. J. Mol. Biol. 422: 300-309.
46. Yamamoto D, Uchihashi T, Kodera N, and Ando T (2008) Anisotropic diffusion of point defects in two-dimensional crystal of streptavidin observed by high-speed atomic force microscopy. Nanotechnology 19: 384009 (9 pp).
47. Sanchez H, Suzuki Y, Yokokawa M, Takeyasu K, and Wyman C (2011) Protein-DNA interactions in high speed AFM: single molecule diffusion analysis of human RAD54. Integr. Biol. 3: 1127-1134.
48. Igarashi K, Koivula A, Wada M, Kimura S, Penttilä M, and Samejima M (2009) High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose. J. Biol. Chem. 284: 36186-36190.
49. Gilmore J L, Suzuki Y, Tamulaitis G, Siksnys V, Takeyasu K, and Lyubchenko Y L (2009) Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy. Biochemistry 48: 10492-10498.
50. Suzuki Y, Gilmore J L, Yoshimura S H, Henderson R M, Lyubchenko Y L, and Takeyasu K (2011) Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region. Biophys. J. 101: 2992-2998.
51. Endo M, Hidaka K, and Sugiyama H (2011) Direct AFM observation of an opening event of a DNA cuboid constructed via a prism structure. Org. Biomol. Chem. 9: 2075-2077.
52. Endo M, Katsuda Y, Hidaka K, and Sugiyama H (2010) Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132: 1592-1597.
53. Sannohe Y, Endo M, Katsuda Y, Hidaka K, and Sugiyama H (2010) Visualization of dynamic conformational switching of the G-quadruplex in a DNA nanostructure. J. Am. Chem. Soc. 132: 16311-16313.
54. Tanaka F, Mochizuki T, Liang X, Asanuma H, Tanaka S, Suzuki K, Kitamura S, Nishikawa A, Ui-Tei K, and Hagiya M (2010) Robust and photocontrollable DNA capsules using azobenzenes. Nano Lett. 10: 3560-3565.
55. Wickham F J S, Endo M, Katsuda Y, Hidaka K, Bath J, Sugiyama H, and Turberfield A J (2011) Direct observation of stepwise movement of a synthetic molecular transporter. Nat. Nanotechnol. 6: 166-169.
56. Shinohara K, Kodera N, and Oohashi T (2010) Single-molecule imaging of photodegradation reaction in a chiral helical π-conjugated polymer chain. J. Polym. Sci. A 48: 4103-4107.
57. Inoue S, Uchihashi T, Yamamoto D, and Ando T (2011) Direct observation of surfactant aggregate behavior on a mica surface using highspeed atomic force microscopy. Chem. Commun. 47: 4974-4976.
58. Itani T and Santillan J J (2010) In situ characterization of photoresist dissolution. Appl. Phys. Exp. 3: 061601 (3 pp).
59. Gresser M J, Myers J A, and Boyer P D (1982) Catalytic site cooperativity of beef heart mitochondrial F1 adenosine triphosphatase. Correlations of initial velocity, bound intermediate, and oxygen exchange measurements with an alternating three-site model. J. Biol. Chem. 257: 12030-12038.
60. 1-ATPase. Nature 386: 299-302.
61. 1-ATPase is a highly efficient molecular motor that rotates with discrete 120° steps. Cell 93: 1117-1124.
62. 1-ATPase from bovine heart mitochondria. Nature 370: 621-628.
63. 1 motor of ATP synthase. Nature 396: 279-282.
64. 1-ATPase. Nature 427: 465-458.
65. Rondelez Y, Tresset G, Nakashima T, Kato-Yamada Y, Fujita H, Takeuchi S, and Noji H (2005) Highly coupled ATP synthesis by F1-ATPase single molecules. Nature 433: 773-777.
66. 1-ATPase by forcible forward rotation. FEBS Lett. 583: 3187-3191.
67. Furuike S, Hossain M D, Maki Y, Adachi K, Suzuki T, Kohori A, Itoh H, Yoshida M, and Kinoshita K, Jr (2008) Axle-less F1-ATPase rotates in the correct direction. Science 319: 955-958.
68. Shirakihara Y, Leslie A G, Abrahams J P, Walker J E, Ueda T, Sekimoto Y, Kambara M, Kagawa Y, and Yoshida M (1997) The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer. Structure 5: 825-836.
69. Haupts U, Tittor J, and Oesterhelt D (1999) Closing in on bacteriorhodopsin: Progress in understanding the molecule. Annu. Rev. Biophys. Biomol. Struct. 28: 367-399.
70. Lanyi J K (2004) Bacteriorhodopsin. Annu. Rev. Physiol. 66: 665-688.
71. Kimura Y, Vassylyev D G, Miyazawa A, Kidera A, Matsushima M, Mitsuoka K, Murata K, Hirai T, and Fujiyoshi Y (1997) Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 389: 206-211.
72. Luecke H, Schobert B, Richter H T, Cartailler J P, and Lanyi J K (1999) Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291: 899-911.
73. Luecke H, Schobert B, Lanyi J K, Spudich E N, and Spudich J L (2001) Crystal structure of sensory rhodopsin II at 2.4 Angstroms: Insights into color tuning and transducer interaction. Science 293: 1499-1503.
74. Sass H J, Büldt G, Gessenich R, Hehn D, Neff D, Schlesinger R, Berendzen J, and Ormos P (2000) Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin. Nature 406: 649-653.
75. Subramaniam S and Henderson R (2000) Molecular mechanism of vectorial proton translocation by bacteriorhodopsin. Nature 406: 653-657.
76. Otto H, Marti T, Holz M, Mogi T, Lindau M, Khorana H G, and Heyn M P (1989) Aspartic acid-96 is the internal proton donor in the reprotonation of the Schiff base of bacteriorhodopsin. Proc. Natl. Acad. Sci. USA 86: 9228-9232.
77. Komrakov A Y and Kaulen A D (1995) M-decay in the bacteriorhodopsin photocycle: effect of cooperativity and pH. Biophys. Chem. 56: 113-119.
78. Tokaji Z (1997) Dimeric-like kinetic cooperativity of the bacteriorhodopsin molecules in purple membranes. Biophys. J. 65: 1130-1134.
79. Yamamoto D, Nagura N, Omote S, Taniguchi M, and Ando T (2009) Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy. Biophys. J. 97: 2358-2367.
80. Yamamoto D, Uchihashi T, Kodera N, Yamashita H, Nishikori S, Ogura T, Shibata M, and Ando T (2010) High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. Methods Enzymol. 475: 541-564.
81. Pittenger B, Erina N, and Su C (2010) Quantitative mechanical property mapping at the nanoscale with Peak Force QNM. Veeco Appl. Note 128: 1-12.
82. Novak P, Li C, Shevchuk A I, Stepanyan R, Caldwell M, Hughes S, Smart T G, Gorelik J, Ostanin V P, Lab M J, Moss G W J, Frolenkov G I, Klenerman D, and Korchev Y E (2009) Nanoscale live-cell imaging using hopping probe ion conductance microscopy. Nat. Methods 6: 279-281.
83. Pastré D, Iwamoto H, Liu J, Szabo G, and Shao Z (2001) Characterization of AC mode scanning ion-conductance microscopy. Ultramicroscopy 90: 13-19.
84. Happel P, Hoffmann G, Mann S A, and Dietzel I D (2003) Monitoring cell movements and volume changes with pulse-mode scanning ion conductance microscopy. J. Microsc. 212: 144-151.
85. Mann S A, Hoffmann G, Hengstenberg A, Schuhmann W, and Dietzel I D (2002) Pulse-mode scanning ion conductance microscopy - a method to investigate cultured hippocampal cells. J. Neurosci. Methods 116: 113-117.