Visualization of Mobility by Atomic Force Microscopy

  • Toshio AndoEmail author
  • Noriyuki Kodera
Part of the Methods in Molecular Biology book series (MIMB, volume 896)


Intrinsically disordered regions (IDRs) of proteins are very thin and hence hard to be visualized by electron microscopy. Thus far, only high-speed atomic force microscopy (HS-AFM) can visualize them. The molecular movies identify the alignment of IDRs and ordered regions in an intrinsically disordered protein (IDP) and show undulation motion of the IDRs. The visualized tail-like structures contain the information of mechanical properties of the IDRs. Here, we describe methods of HS-AFM visualization of IDPs and methods of analyzing the obtained images to characterize IDRs.

Key words

High-speed atomic force microscopy AFM High-speed AFM Visualization Dynamic imaging Mobility Mechanical properties 



This work was supported by Grant-in-Aid for Basic Research (S) from JSPS, Knowledge Cluster/MEXT—Japan, and Grant-in Aid for Scientific Research on Innovative Areas (Research in a Proposed Research Area)/MEXT—Japan.


  1. 1.
    Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K et al (2008) Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy. Chem Phys Chem 9:1859–1866PubMedCrossRefGoogle Scholar
  2. 2.
    Binnig G, Quate CF, Gerber Ch (1986) Atomic force microscopy. Phys Rev Lett 56:930–933PubMedCrossRefGoogle Scholar
  3. 3.
    Romero P, Obradovic Z, Kissinger CR et al (1997) Identifying disordered proteins from amino acid sequences. Proc IEEE Int Conf Neural Networks 1:90–95Google Scholar
  4. 4.
    Ando T, Kodera N, Takai E et al (2001) A high-speed atomic force microscope for studying biological macromolecules. Proc Natl Acad Sci U S A 98:12468–12472PubMedCrossRefGoogle Scholar
  5. 5.
    Ando T, Uchihashi T, Fukuma T (2008) High-speed atomic force microscopy for nani-visualization of dynamic biomolecular processes. Prog Surf Sci 83:337–437CrossRefGoogle Scholar
  6. 6.
    Kodera N, Yamamoto D, Ishikawa R, Ando T (2010) Video imaging of walking myosin V by high-speed atomic force microscopy. Nature 468:72–76PubMedCrossRefGoogle Scholar
  7. 7.
    Shibata M, Yamashita H, Uchihashi T et al (2010) High-speed atomic force microscopy shows dynamic molecular processes in photo-activated bacteriorhodopsin. Nat Nanotechnol 5:208–212PubMedCrossRefGoogle Scholar
  8. 8.
    Yamamoto D, Uchihashi T, Kodera N, 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)PubMedCrossRefGoogle Scholar
  9. 9.
    Milhiet P-E, Yamamoto D, Berthoumieu O et al (2010) Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy. PLos One 5:e13240 (8 pp)PubMedCrossRefGoogle Scholar
  10. 10.
    Yamamoto D, Uchihashi T, Kodera N et al (2010) High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. Methods Enzymol 475(B):541–564PubMedCrossRefGoogle Scholar
  11. 11.
    Uversky VN, Dunker AK (2010) Review understanding protein non-folding. Biochim Biophys Acta 1804:1231–1264PubMedCrossRefGoogle Scholar
  12. 12.
    Strobl GR (1996) The physics of polymers. Springer, BerlinGoogle Scholar
  13. 13.
    Manning GS (2006) The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys J 91:3607–3616PubMedCrossRefGoogle Scholar
  14. 14.
    Dietz H, Rief M (2004) Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci U S A 101:16192–16197PubMedCrossRefGoogle Scholar
  15. 15.
    Müller DJ, Baumeister W, Engel A (1999) Controlled unzipping of a bacterial surface layer with atomic force microscopy. Proc Natl Acad Sci U S A 96:13170–13174PubMedCrossRefGoogle Scholar
  16. 16.
    Yamashita H, Voïtchovsky K, Uchihashi T et al (2009) Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy. J Struct Biol 167:153–158PubMedCrossRefGoogle Scholar
  17. 17.
    Ando T, Kodera N, Maruyama D et al (2002) A High-speed atomic force microscope for studying biological macromolecules in action. Jpn J Appl Phys 41:4851–4856CrossRefGoogle Scholar
  18. 18.
    Kodera N, Sakashita M, Ando T (2006) Dynamic proportional-integral-differential controller for high-speed atomic force microscopy. Rev Sci Instrum 77:083704 (7 pp)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Department of Physics and Bio-AFM Frontier Research CenterKanazawa UniversityKanazawaJapan
  2. 2.Bio-AFM Frontier Research CenterKanazawa UniversityKanazawaJapan

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