Skip to main content

Atomic Force Microscopy of Proteins

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2073))

Abstract

Atomic force microscopy (AFM) enables imaging of surface-deposited proteins and protein structures under physiological conditions, which is a benefit compared to ultra-high vacuum techniques such as electron microscopy. AFM also has the potential to provide more information from the phase in tapping mode or from functional AFM modes. The sample preparation, probe selection, and imaging conditions are crucial for successful imaging of proteins. Here we give a detailed account of the steps toward imaging of soft samples in both air and liquid along with the basic theory underpinning these details.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   149.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Ross FM (2015) Opportunities and challenges in liquid cell electron microscopy. Science 350(6267). https://doi.org/10.1126/science.aaa9886. ARTN aaa9886

  2. Scheuring S, Fotiadis D, Moller C, Muller SA, Engel A, Muller DJ (2001) Single proteins observed by atomic force microscopy. Single Mol 2(2):59–67

    Article  CAS  Google Scholar 

  3. Garcia R, Perez R (2002) Dynamic atomic force microscopy methods. Surf Sci Rep 47(6–8):197–301. https://doi.org/10.1016/S0167-5729(02)00077-8. Pii S0167-5729(02)00077-8

    Article  CAS  Google Scholar 

  4. Hansma HG, Kim KJ, Laney DE, Garcia RA, Argaman M, Allen MJ, Parsons SM (1997) Properties of biomolecules measured from atomic force microscope images: a review. J Struct Biol 119(2):99–108. https://doi.org/10.1006/jsbi.1997.3855

    Article  CAS  Google Scholar 

  5. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56(9):930

    Article  CAS  Google Scholar 

  6. Fang S, Haplepete S, Chen W, Helms C, Edwards H (1997) Analyzing atomic force microscopy images using spectral methods. J Appl Phys 82(12):5891–5898

    Article  CAS  Google Scholar 

  7. Sheiko S, Möller M, Reuvekamp E, Zandbergen H (1994) Evaluation of the probing profile of scanning force microscopy tips. Ultramicroscopy 53(4):371–380

    Article  CAS  Google Scholar 

  8. Allen MJ, Hud NV, Balooch M, Tench RJ, Siekhaus WJ, Balhorn R (1992) Tip-radius-induced artifacts in AFM images of protamine-complexed DNA fibers. Ultramicroscopy 42:1095–1100

    Article  Google Scholar 

  9. Westra K, Mitchell A, Thomson D (1993) Tip artifacts in atomic force microscope imaging of thin film surfaces. J Appl Phys 74(5):3608–3610

    Article  CAS  Google Scholar 

  10. Müller DJ, Amrein M, Engel A (1997) Adsorption of biological molecules to a solid support for scanning probe microscopy. J Struct Biol 119(2):172–188. https://doi.org/10.1006/jsbi.1997.3875

    Article  Google Scholar 

  11. Ruzette A-V, Leibler L (2005) Block copolymers in tomorrow’s plastics. Nat Mater 4:19. https://doi.org/10.1038/nmat1295

    Article  CAS  Google Scholar 

  12. Hall A, Karplus PA, Poole LB (2009) Typical 2-Cys peroxiredoxins – structures, mechanisms and functions. FEBS J 276(9):2469–2477. https://doi.org/10.1111/j.1742-4658.2009.06985.x

    Article  CAS  PubMed Central  Google Scholar 

  13. Wood ZA, Poole LB, Hantgan RR, Karplus PA (2002) Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins. Biochemistry 41(17):5493–5504. https://doi.org/10.1021/bi012173m

    Article  CAS  Google Scholar 

  14. Saccoccia F, Di Micco P, Boumis G, Brunori M, Koutris I, Miele Adriana E, Morea V, Sriratana P, Williams David L, Bellelli A, Angelucci F (2012) Moonlighting by different stressors: crystal structure of the chaperone species of a 2-cys peroxiredoxin. Structure 20(3):429–439. https://doi.org/10.1016/j.str.2012.01.004

    Article  CAS  PubMed Central  Google Scholar 

  15. Jayawardena N, Kaur M, Nair S, Malmstrom J, Goldstone D, Negron L, Gerrard JA, Domigan LJ (2017) Amyloid fibrils from hemoglobin. Biomol Ther 7(2):37

    Google Scholar 

  16. Jalili N, Laxminarayana K (2004) A review of atomic force microscopy imaging systems: application to molecular metrology and biological sciences. Mechatronics 14(8):907–945

    Article  Google Scholar 

  17. Bryant PJ, Miller RG, Yang R (1988) Scanning tunneling and atomic force microscopy combined. Appl Phys Lett 52(26):2233–2235. https://doi.org/10.1063/1.99541

    Article  CAS  Google Scholar 

  18. Willemsen OH, Snel MME, Cambi A, Greve J, De Grooth BG, Figdor CG (2000) Biomolecular interactions measured by atomic force microscopy. Biophys J 79(6):3267–3281. https://doi.org/10.1016/S0006-3495(00)76559-3

    Article  CAS  PubMed Central  Google Scholar 

  19. Chung KH, Kim DE (2007) Wear characteristics of diamond-coated atomic force microscope probe. Ultramicroscopy 108(1):1–10. https://doi.org/10.1016/j.ultramic.2007.01.016

    Article  CAS  Google Scholar 

  20. Xu X, Raman A (2007) Comparative dynamics of magnetically, acoustically, and Brownian motion driven microcantilevers in liquids. J Appl Phys 102(3). https://doi.org/10.1063/1.2767202. Artn 034303

  21. Haugstad G (2012) Atomic force microscopy: understanding basic modes and advanced applications. John Wiley & Sons, Hoboken, NJ

    Book  Google Scholar 

  22. Research OIA (2014) Asylum research AFM manuals

    Google Scholar 

  23. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315):1109–1112. https://doi.org/10.1126/science.276.5315.1109

    Article  CAS  Google Scholar 

  24. Li YL, Liang H, Zhao HL, Chen D, Liu B, Fuhs T, Dong MD (2016) Characterization of inter- and intramolecular interactions of amyloid fibrils by AFM-based single-molecule force spectroscopy. J Nanomater:Artn 5463201. https://doi.org/10.1155/2016/5463201

  25. Petrosyan R, Bippes CA, Walheim S, Harder D, Fotiadis D, Schimmel T, Alsteens D, Muller DJ (2015) Single-molecule force spectroscopy of membrane proteins from membranes freely spanning across nanoscopic pores. Nano Lett 15(5):3624–3633. https://doi.org/10.1021/acs.nanolett.5b01223

    Article  CAS  Google Scholar 

  26. Oberhauser AF, Badilla-Fernandez C, Carrion-Vazquez M, Fernandez JM (2002) The mechanical hierarchies of fibronectin observed with single-molecule AFM. J Mol Biol 319(2):433–447. https://doi.org/10.1016/S0022-2836(02)00306-6

    Article  CAS  Google Scholar 

  27. Merkel R, Nassoy P, Leung A, Ritchie K, Evans E (1999) Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature 397(6714):50–53. https://doi.org/10.1038/16219

    Article  CAS  Google Scholar 

  28. Butt HJ, Cappella B, Kappl M (2005) Force measurements with the atomic force microscope: technique, interpretation and applications. Surf Sci Rep 59(1–6):1–152. https://doi.org/10.1016/j.surfrep.2005.08.003

    Article  CAS  Google Scholar 

  29. Radmacher M (1997) Measuring the elastic properties of biological samples with the AFM. IEEE Eng Med Biol Mag 16(2):47–57. https://doi.org/10.1109/51.582176

    Article  CAS  Google Scholar 

  30. Capella B, Baschieri P, Frediani C, Miccoli P, Ascoli C (1997) Force-distance curves by AFM – a powerful technique for studying surface interactions. IEEE Eng Med Biol Mag 16(2):58–65

    Article  Google Scholar 

  31. Lin DC, Horkay F (2008) Nanomechanics of polymer gels and biological tissues: a critical review of analytical approaches in the Hertzian regime and beyond. Soft Matter 4(4):669–682. https://doi.org/10.1039/b714637j

    Article  CAS  Google Scholar 

  32. Liang Y, Hilal N, Langston P, Starov V (2007) Interaction forces between colloidal particles in liquid: theory and experiment. Adv Colloid Interf Sci 134:151–166

    Article  Google Scholar 

  33. Ducker WA, Senden TJ, Pashley RM (1991) Direct measurement of colloidal forces using an atomic force microscope. Nature 353(6341):239

    Article  CAS  Google Scholar 

  34. Girard P (2001) Electrostatic force microscopy: principles and some applications to semiconductors. Nanotechnology 12(4):485

    Article  Google Scholar 

  35. Nakamura M, Yamada H (2007) Electrostatic force microscopy. In: Roadmap of scanning probe microscopy. Springer, New York, NY, pp 43–51

    Chapter  Google Scholar 

  36. Grütter P, Mamin H, Rugar D (1992) Magnetic force microscopy (MFM). In: Scanning tunneling microscopy II. Springer, New York, NY, pp 151–207

    Chapter  Google Scholar 

  37. Rugar D, Mamin H, Guethner P, Lambert S, Stern J, McFadyen I, Yogi T (1990) Magnetic force microscopy: general principles and application to longitudinal recording media. J Appl Phys 68(3):1169–1183

    Article  CAS  Google Scholar 

  38. Gruverman A, Kalinin SV (2006) Piezoresponse force microscopy and recent advances in nanoscale studies of ferroelectrics. J Mater Sci 41(1):107–116

    Article  CAS  Google Scholar 

  39. Kalinin SV, Rodriguez BJ, Jesse S, Shin J, Baddorf AP, Gupta P, Jain H, Williams DB, Gruverman A (2006) Vector piezoresponse force microscopy. Microsc Microanal 12(3):206–220

    Article  CAS  Google Scholar 

  40. Malvankar NS, Yalcin SE, Tuominen MT, Lovley DR (2014) Visualization of charge propagation along individual pili proteins using ambient electrostatic force microscopy. Nat Nanotechnol 9(12):1012

    Article  CAS  Google Scholar 

  41. Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491

    Article  CAS  Google Scholar 

  42. Hsieh C-W, Zheng B, Hsieh S (2010) Ferritin protein imaging and detection by magnetic force microscopy. Chem Commun 46(10):1655–1657

    Article  CAS  Google Scholar 

  43. Cohen H, Sapir T, Borovok N, Molotsky T, Di Felice R, Kotlyar AB, Porath D (2007) Polarizability of G4-DNA observed by electrostatic force microscopy measurements. Nano Lett 7(4):981–986. https://doi.org/10.1021/nl070013b

    Article  CAS  Google Scholar 

  44. Hempstead PD, Yewdall SJ, Fernie AR, Lawson DM, Artymiuk PJ, Rice DW, Ford GC, Harrison PM (1997) Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. J Mol Biol 268(2):424–448. https://doi.org/10.1006/jmbi.1997.0970

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jenny Malmström .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

An, Y., Manuguri, S.S., Malmström, J. (2020). Atomic Force Microscopy of Proteins. In: Gerrard, J., Domigan, L. (eds) Protein Nanotechnology. Methods in Molecular Biology, vol 2073. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9869-2_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9869-2_14

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9868-5

  • Online ISBN: 978-1-4939-9869-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics