Skip to main content
SpringerLink
Log in

High-Resolution Imaging of 2D Outer Membrane Protein F Crystals by Atomic Force Microscopy

  • Protocol
  • First Online:
Electron Crystallography of Soluble and Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 955))

Abstract

In this chapter the methodological bases are provided to achieve subnanometer resolution on two-dimensional (2D) membrane protein crystals by atomic force microscopy (AFM). This is outlined in detail with the example of AFM studies of the outer membrane protein F (OmpF) from the bacterium Escherichia coli (E. coli). We describe in detail the high-resolution imaging of 2D OmpF crystals in aqueous solution and under near-physiological conditions. The topographs of OmpF, and stylus effects and artifacts encountered when imaging by AFM are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933

    Article  PubMed  Google Scholar 

  2. Gerber C, Lang HP (2007) How the doors to the nanoworld were opened. Nat Nanotec 1:3–5

    Article  Google Scholar 

  3. Dufrêne YF (2008) Towards nanomicrobiology using atomic force microscopy. Nat Rev Microbiol 6:674–680

    Article  PubMed  Google Scholar 

  4. Engel A, Gaub HE (2008) Structure and mechanics of membrane proteins. Annu Rev Biochem 77:127–148

    Article  PubMed  CAS  Google Scholar 

  5. Frederix PLTM, Akiyama T, Staufer U, Gerber C, Fotiadis D, Müller DJ et al (2003) Atomic force bio-analytics. Curr Opin Chem Biol 7:641–647

    Article  PubMed  CAS  Google Scholar 

  6. Müller DJ, Dufrêne YF (2008) Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology. Nat Nano­technol 3:261–269

    Article  PubMed  Google Scholar 

  7. Müller DJ, Helenius J, Alsteens D, Dufrêne YF (2009) Force probing surfaces of living cells to molecular resolution. Nat Chem Biol 5:383–390

    Article  PubMed  Google Scholar 

  8. Puchner EM, Gaub HE (2009) Force and function: probing proteins with AFM-based force spectroscopy. Curr Opin Struct Biol 19:605–614

    Article  PubMed  CAS  Google Scholar 

  9. Engel A, Lyubchenko Y, Müller DJ (1999) Atomic force microscopy: a powerful tool to observe biomolecules at work. Trends Cell Biol 9:77–80

    Article  PubMed  CAS  Google Scholar 

  10. Engel A, Müller DJ (2000) Observing single biomolecules at work with the atomic force microscope. Nat Struct Biol 7:715–718

    Article  PubMed  CAS  Google Scholar 

  11. Müller DJ, Engel A (2007) Atomic force microscopy and spectroscopy of native membrane proteins. Nat Protoc 2:2191–2197

    Article  PubMed  Google Scholar 

  12. Müller DJ, Wu N, Palczewski K (2008) Vertebrate membrane proteins: structure, function, and insights from biophysical approaches. Pharmacol Rev 60:43–78

    Article  PubMed  Google Scholar 

  13. Müller DJ (2008) AFM: a nanotool in membrane biology. Biochemistry 47:7986–7998

    Article  PubMed  Google Scholar 

  14. Han WH, Lindsay SM, Dlakic M, Harrington RE (1997) Kinked DNA. Nature 386:563

    Article  PubMed  CAS  Google Scholar 

  15. Han WH, Lindsay SM, Jing TW (1996) A magnetically driven oscillating probe microscope for operation in liquids. Appl Phys Lett 69:4111–4113

    Article  CAS  Google Scholar 

  16. Hansma PK, Cleveland JP, Radmacher M, Walters DA, Hillner PE, Bezanilla M et al (1994) Tapping mode atomic force microscopy in liquids. Appl Phys Lett 64:1738–1740

    Article  CAS  Google Scholar 

  17. Putman CAJ, Vanderwerf KO, de Grooth BG, Vanhulst NF, Greve J (1994) Tapping mode atomic-force microscopy in liquid. Appl Phys Lett 64:2454–2456

    Article  CAS  Google Scholar 

  18. Zhong Q, Inniss D, Kjoller K, Elings VB (1993) Fractured polymer/silica fiber surface studied by tapping mode atomic force microscopy. Surf Sci Lett 290:L688–L692

    Article  CAS  Google Scholar 

  19. Fukuma T (2008) Instrumentation and biological applications of high-resolution frequency modulation atomic force microscopy in liquid. J Nano Res 4:1–10

    Article  CAS  Google Scholar 

  20. Fukuma T, Jarvis SP (2006) Development of liquid environment frequency modulation atomic force microscope with low noise deflection sensor for cantilevers of various dimensions. Rev Sci Inst 77:043701

    Article  Google Scholar 

  21. Hoogenboom BW, Hug HJ, Pellmont Y, Martin S, Frederix PLTM, Fotiadis D et al (2006) Quantitative dynamic-mode scanning force microscopy in liquid. Appl Phys Letters 88:193109

    Article  Google Scholar 

  22. Hoogenboom BW, Suda K, Engel A, Fotiadis D (2007) The supramolecular assemblies of voltage-dependent anion channels in the native membrane. J Mol Biol 370:246–255

    Article  PubMed  CAS  Google Scholar 

  23. Hansma PK, Schitter G, Fantner GE, Prater C (2006) Applied physics. High-speed atomic force microscopy. Science 314:601–602

    Article  PubMed  CAS  Google Scholar 

  24. Yokokawa M, Wada C, Ando T, Sakai N, Yagi A, Yoshimura SH et al (2006) Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL. EMBO J 25:4567–4576

    Article  PubMed  CAS  Google Scholar 

  25. Müller DJ, Fotiadis D, Scheuring S, Müller SA, Engel A (1999) Electrostatically balanced subnanometer imaging of biological specimens by atomic force microscope. Biophys J 76:1101–1111

    Article  PubMed  Google Scholar 

  26. Fotiadis D, Scheuring S, Müller SA, Engel A, Müller DJ (2002) Imaging and manipulation of biological structures with the AFM. Micron 33:385–397

    Article  PubMed  CAS  Google Scholar 

  27. Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA et al (1992) Crystal structures explain functional properties of two E. coli porins. Nature 358:727–733

    Article  PubMed  CAS  Google Scholar 

  28. Dorset DL, Engel A, Häner M, Massalski A, Rosenbusch JP (1983) Two-dimensional crystal packing of matrix porin. A channel forming protein in Escherichia coli outer membranes. J Mol Biol 165:701–710

    Article  PubMed  CAS  Google Scholar 

  29. Hoenger A, Gross H, Aebi U, Engel A (1990) Localization of the lipopolysaccharides in metal-shadowed reconstituted lipid-porin membranes. J Struct Biol 103:185–195

    Article  CAS  Google Scholar 

  30. Hoenger A, Pages JM, Fourel D, Engel A (1993) The orientation of porin OmpF in the outer membrane of Escherichia coli. J Mol Biol 233:400–413

    Article  PubMed  CAS  Google Scholar 

  31. Müller DJ, Engel A (1999) Voltage and pH-induced channel closure of porin OmpF visualized by atomic force microscopy. J Mol Biol 285:1347–1351

    Article  PubMed  Google Scholar 

  32. Schabert FA, Engel A (1994) Reproducible acquisition of Escherichia coli porin surface topographs by atomic force microscopy. Biophys J 67:2394–2403

    Article  PubMed  CAS  Google Scholar 

  33. Schabert FA, Henn C, Engel A (1995) Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy. Science 268:92–94

    Article  PubMed  CAS  Google Scholar 

  34. Engel A, Massalski A, Schindler H, Dorset DL, Rosenbusch JP (1985) Porin channel triplets merge into single outlets in Escherichia coli outer membranes. Nature 317:643–645

    Article  PubMed  CAS  Google Scholar 

  35. Tanaka M, Sackmann E (2005) Polymer-supported membranes as models of the cell surface. Nature 437:656–663

    Article  PubMed  CAS  Google Scholar 

  36. Müller DJ, Amrein M, Engel A (1997) Adsorption of biological molecules to a solid support for scanning probe microscopy. J Struct Biol 119:172–188

    Article  PubMed  Google Scholar 

  37. Müller DJ, Engel A (2008) Strategies to prepare and characterize native membrane proteins and protein membranes by AFM. Curr Opin Coll Int Sci 13:338–350

    Article  Google Scholar 

  38. Müller DJ, Sass H-J, Müller S, Büldt G, Engel A (1999) Surface structures of native bacteriorhodopsin depend on the molecular packing arrangement in the membrane. J Mol Biol 285:1903–1909

    Article  PubMed  Google Scholar 

  39. Müller DJ, Engel A (1997) The height of biomolecules measured with the atomic force microscope depends on electrostatic interactions. Biophys J 73:1633–1644

    Article  PubMed  Google Scholar 

  40. Misell DL, Brown EB (1987) Electron diffraction: an introduction for biologists. In: Glauert AM (ed) Practical methods in electron microscopy, vol 2. Elsevier Science Publishers B.V., The Netherlands

    Google Scholar 

  41. Schwarz UD, Haefke H, Reimann P, Güntherodt H-J (1994) Tip artefacts in scanning force microscopy. J Microsc 173:183–197

    Article  CAS  Google Scholar 

  42. Xu S, Arnsdorf MF (1994) Calibration of the scanning (atomic) force microscope with gold particles. J Microsc 173:199–210

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to Andreas Engel for his continous support. This work was supported by the Swiss National Foundation for Scientific Research (Grant 31003A_125150 to D.F.), the National Center of Competence in Research (NCCR) TransCure, and the European Science Foundation (Grant 09-EuroSYNBIO-FP-012 NANOCELL to D.F. and D.J.M.).

Author information

Authors and Affiliations

  1. Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland

    Dimitrios Fotiadis

  2. ETH Zürich, Biosystems Science and Engineering (BSSE), Basel, Switzerland

    Daniel J. Müller

Authors
  1. Dimitrios Fotiadis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel J. Müller
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel J. Müller .

Editor information

Editors and Affiliations

  1. School of Biology, Georgia Institute of Technology, Ferst Dr. 310, Atlanta, 30332, Georgia, USA

    Ingeborg Schmidt-Krey

  2. , Dept. Biochemistry & Biophysics, University of California, San Francisco, 16th St. 600, San Francisco, 94158, California, USA

    Yifan Cheng

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Fotiadis, D., Müller, D.J. (2013). High-Resolution Imaging of 2D Outer Membrane Protein F Crystals by Atomic Force Microscopy. In: Schmidt-Krey, I., Cheng, Y. (eds) Electron Crystallography of Soluble and Membrane Proteins. Methods in Molecular Biology, vol 955. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-176-9_24

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-176-9_24

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-175-2

  • Online ISBN: 978-1-62703-176-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation