Skip to main content

Atomic Force Microscopy of Protein Shells: Virus Capsids and Beyond

  • Protocol
  • First Online:
Single Molecule Analysis

Abstract

In Atomic Force Microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person uses a white cane. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization a variety physicochemical properties able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties.

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

Access this chapter

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 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA (2008) Bacterial microcompartments: their properties and paradoxes. BioEssays 30(11–12):1084–1095. doi:10.1002/bies.20830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Querol-Audí J, Casañas A, Usón I, Luque D, Castón JR, Fita I, Verdaguer N (2009) The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP. EMBO J 28(21):3450

    Article  PubMed  PubMed Central  Google Scholar 

  3. Wimmer E, Mueller S, Tumpey TM, Taubenberger JK (2009) Synthetic viruses: a new opportunity to understand and prevent viral disease. Nat Biotechnol 27(12):1163. doi:10.1038/nbt.1593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Wörsdörfer B, Woycechowsky KJ, Hilvert D (2011) Directed evolution of a protein container. Science 331(6017):589

    Article  PubMed  Google Scholar 

  5. Lai Y-T, Reading E, Hura GL, Tsai K-L, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO (2014) Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem 6(12):1065–1071. doi:10.1038/nchem.2107. http://www.nature.com/nchem/journal/v6/n12/abs/nchem.2107.html#supplementary-information

  6. Flint SJ, Enquist LW, Racaniello VR, Skalka AM (2004) Principles of virology. ASM Press, Washington, DC

    Google Scholar 

  7. Douglas T, Young M (1998) Host-guest encapsulation of materials by assembled virus protein cages. Nature 393(6681):152–155

    Article  CAS  Google Scholar 

  8. Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276(14):10577–10580. doi:10.1074/jbc.R100005200

    Article  CAS  PubMed  Google Scholar 

  9. Agirre J, Aloria K, Arizmendi JM, Iloro I, Elortza F, Sánchez-Eugenia R, Marti GA, Neumann E, Rey FA, Guérin DMA (2011) Capsid protein identification and analysis of mature Triatoma virus (TrV) virions and naturally occurring empty particles. Virology 409(1):91–101. doi:10.1016/j.virol.2010.09.034

    Article  CAS  PubMed  Google Scholar 

  10. Cordova A, Deserno M, Gelbart WM, Ben-Shaul A (2003) Osmotic shock and the strength of viral capsids. Biophys J 85(1):70–74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Baker TS, Olson NH, Fuller SD (1999) Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 63(4):862–922

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Hinterdorfer P, Van Oijen A (2009) Handbook of single-molecule biophysics. Springer, Dordrecht

    Book  Google Scholar 

  13. Muller 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

    Article  CAS  PubMed  Google Scholar 

  14. Armanious A, Aeppli M, Jacak R, Refardt D, Sigstam T, Kohn T, Sander M (2016) Viruses at solid-water interfaces: a systematic assessment of interactions driving adsorption. Environ Sci Technol 50(2):732–743. doi:10.1021/acs.est.5b04644

    Article  CAS  PubMed  Google Scholar 

  15. Llauró A, Guerra P, Irigoyen N, Rodríguez José F, Verdaguer N, de Pablo Pedro J (2014) Mechanical stability and reversible fracture of vault particles. Biophys J 106(3):687–695

    Article  PubMed  PubMed Central  Google Scholar 

  16. Ivanovska IL, Pablo PJC, Ibarra B, Sgalari G, MacKintosh FC, Carrascosa JL, Schmidt CF, Wuite GJL (2004) Bacteriophage capsids: tough nanoshells with complex elastic properties. Proc Natl Acad Sci U S A 101(20):7600–7605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Llauro A, Luque D, Edwards E, Trus BL, Avera J, Reguera D, Douglas T, Pablo PJ, Caston JR (2016) Cargo-shell and cargo-cargo couplings govern the mechanics of artificially loaded virus-derived cages. Nanoscale 8(17):9328–9336. doi:10.1039/c6nr01007e

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Carpick RW, Ogletree DF, Salmeron M (1997) Lateral stiffness: a new nanomechanical measurement for the determination of shear strengths with friction force microscopy. Appl Phys Lett 70(12):1548–1550

    Article  CAS  Google Scholar 

  19. Xiao C, Kuznetsov YG, Sun SY, Hafenstein SL, Kostyuchenko VA, Chipman PR, Suzan-Monti M, Raoult D, McPherson A, Rossmann MG (2009) Structural studies of the giant mimivirus. PLoS Biol 7(4):958–966. doi:10.1371/journal.pbio.1000092. ARTN e1000092

    Article  CAS  Google Scholar 

  20. Vinckier A, Heyvaert I, Dhoore A, Mckittrick T, Vanhaesendonck C, Engelborghs Y, Hellemans L (1995) Immobilizing and imaging microtubules by atomic-force microscopy. Ultramicroscopy 57(4):337–343

    Article  CAS  PubMed  Google Scholar 

  21. Carrasco C, Luque A, Hernando-Perez M, Miranda R, Carrascosa JL, Serena PA, de Ridder M, Raman A, Gomez-Herrero J, Schaap IAT, Reguera D, de Pablo PJ (2011) Built-in mechanical stress in viral shells. Biophys J 100(4):1100–1108. doi:10.1016/j.bpj.2011.01.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Roos WH, Bruinsma R, Wuite GJL (2010) Physical virology. Nat Phys 6(10):733–743. doi:10.1038/Nphys1797

    Article  CAS  Google Scholar 

  23. Miyatani T, Horii M, Rosa A, Fujihira M, Marti O (1997) Mapping of electrical double-layer force between tip and sample surfaces in water with pulsed-force-mode atomic force microscopy. Appl Phys Lett 71(18):2632–2634

    Article  CAS  Google Scholar 

  24. de Pablo PJ, Colchero J, Gomez-Herrero J, Baro AM (1998) Jumping mode scanning force microscopy. Appl Phys Lett 73(22):3300–3302

    Article  Google Scholar 

  25. Ortega-Esteban A, Horcas I, Hernando-Perez M, Ares P, Perez-Berna AJ, San Martin C, Carrascosa JL, de Pablo PJ, Gomez-Herrero J (2012) Minimizing tip-sample forces in jumping mode atomic force microscopy in liquid. Ultramicroscopy 114(0):56–61

    Article  CAS  PubMed  Google Scholar 

  26. Legleiter J, Park M, Cusick B, Kowalewski T (2006) Scanning probe acceleration microscopy (SPAM) in fluids: mapping mechanical properties of surfaces at the nanoscale. Proc Natl Acad Sci U S A 103(13):4813–4818

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Villarrubia JS (1997) Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation. J Res Natl Inst Stand Technol 102(4):425–454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. doi:10.1002/jcc.20084

    Article  CAS  PubMed  Google Scholar 

  29. Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W (2011) Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci U S A 108(4):1355–1360. doi:10.1073/pnas.1015739108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zink M, Grubmuller H (2009) Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J 96(4):1350–1363. doi:10.1016/j.bpj.2008.11.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Landau LD, Lifshizt E (1986) Theory of elasticity, 3rd edn. Pergamon, London

    Google Scholar 

  32. Zlotnick A (2003) Are weak protein-protein interactions the general rule in capsid assembly? Virology 315(2):269–274. doi:10.1016/S0042-6822(03)00586-5

    Article  CAS  PubMed  Google Scholar 

  33. Ortega-Esteban A, Condezo GN, Perez-Berna AJ, Chillon M, Flint SJ, Reguera D, San Martin C, de Pablo PJ (2015) Mechanics of viral chromatin reveals the pressurization of human adenovirus. ACS Nano 9(11):10826–10833. doi:10.1021/acsnano.5b03417

    Article  CAS  PubMed  Google Scholar 

  34. Zhou HX, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37:375–397. doi:10.1146/annurev.biophys.37.032807.125817

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Hernando-Pérez M, Lambert S, Nakatani-Webster E, Catalano CE, de Pablo PJ (2014) Cementing proteins provide extra mechanical stabilization to viral cages. Nat Commun 5:4520. doi:10.1038/ncomms5520

    Article  PubMed  Google Scholar 

  36. Ortega-Esteban A, Pérez-Berná AJ, Menéndez-Conejero R, Flint SJ, San Martín C, de Pablo PJ (2013) Monitoring dynamics of human adenovirus disassembly induced by mechanical fatigue. Sci Rep 3:1434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Medina E, Nakatani E, Kruse S, Catalano CE (2012) Thermodynamic characterization of viral procapsid expansion into a functional capsid shell. J Mol Biol 418(3–4):167–180. doi:10.1016/j.jmb.2012.02.020

    Article  CAS  PubMed  Google Scholar 

  38. Ortega-Esteban A, Bodensiek K, San Martin C, Suomalainen M, Greber UF, de Pablo PJ, Schaap IA (2015) Fluorescence tracking of genome release during mechanical unpacking of single viruses. ACS Nano 9(11):10571–10579. doi:10.1021/acsnano.5b03020

    Article  CAS  PubMed  Google Scholar 

  39. Gaiduk A, Kuhnemuth R, Antonik M, Seidel CA (2005) Optical characteristics of atomic force microscopy tips for single-molecule fluorescence applications. ChemPhysChem 6(5):976–983. doi:10.1002/cphc.200400485

    Article  CAS  PubMed  Google Scholar 

  40. Zhang S, Aslan H, Besenbacher F, Dong MD (2014) Quantitative biomolecular imaging by dynamic nanomechanical mapping. Chem Soc Rev 43(21):7412–7429

    Article  CAS  PubMed  Google Scholar 

  41. Cartagena A, Hernando-Perez M, Carrascosa JL, de Pablo PJ, Raman A (2013) Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy. Nanoscale 5(11):4729–4736. doi:10.1039/c3nr34088k

    Article  CAS  PubMed  Google Scholar 

  42. Israelachvili J (2002) Intermolecular and surface forces. Academic, London

    Google Scholar 

  43. Hernando-Perez M, Cartagena-Rivera AX, Losdorfer Bozic A, Carrillo PJ, San Martin C, Mateu MG, Raman A, Podgornik R, de Pablo PJ (2015) Quantitative nanoscale electrostatics of viruses. Nanoscale 7(41):17289–17298. doi:10.1039/c5nr04274g

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We acknowledge to our collaborators and projects FIS2014-59562-R, FIS2015-71108-REDT, Fundación BBVA and “María de Maeztu” Program for Units of Excellence in R&D (MDM-2014-0377).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Pedro J. de Pablo .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Martín-González, N., Ortega-Esteban, A., Moreno-Madrid, F., Llauró, A., Hernando-Pérez, M., de Pablo, P.J. (2018). Atomic Force Microscopy of Protein Shells: Virus Capsids and Beyond. In: Peterman, E. (eds) Single Molecule Analysis. Methods in Molecular Biology, vol 1665. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7271-5_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7271-5_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7270-8

  • Online ISBN: 978-1-4939-7271-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics