Abstract
Single-particle nanoindentation by atomic force microscopy (AFM) is an emergent technique to characterize the material properties of nano-sized proteinaceous systems. AFM uses a very small tip attached to a cantilever to scan the surface of the substrate. As a result of the sensitive feedback loop of AFM, the force applied by the tip on the substrate during scanning can be controlled and monitored. By accurately controlling this scanning force, topographical maps of fragile substrates can be acquired to study the morphology of the substrate. In addition, mechanical properties of the substrate like stiffness and breaking point can be determined by using the force spectroscopy capability of AFM. Here we discuss basics of AFM operation and how this technique is used to determine the structure and mechanical properties of protein nanocages, in particular viral particles. Knowledge of morphology as well as mechanical properties is essential for understanding viral life cycles, including genome packaging, capsid maturation, and uncoating, but also contributes to the development of diagnostics, vaccines, imaging modalities, and targeted therapeutic devices based on viruslike particles.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933
Colton RJ, Baselt DR, Dufrene YF et al (1997) Scanning probe microscopy. Curr Opin Chem Biol 1:370–377
Walters DA, Cleveland JP, Thomson NH et al (1996) Short cantilevers for atomic force microscopy. Rev Sci Instrum 67:3583–3590
Santos NC, Castanho MA (2004) An overview of the biophysical applications of atomic force microscopy. Biophys Chem 107:133–149
Hafner JH, Cheung CL, Woolley AT et al (2001) Structural and functional imaging with carbon nanotube AFM probes. Prog Biophys Mol Biol 77:73–110
Wong SS, Harper JD, Lansbury PT et al (1998) Carbon nanotube tips: high-resolution probes for imaging biological systems. J Am Chem Soc 120:603–604
Churnside AB, Sullan RM, Nguyen DM et al (2012) Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. Nano Lett 12:3557–3561
Cleveland JP, Manne S, Bocek D et al (1993) A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy. Rev Sci Instrum 64:403–405
Sader JE, Chon JWM, Mulvaney P (1999) Calibration of rectangular atomic force microscope cantilevers. Rev Sci Instrum 70:3967–3969
Sader JE (1998) Frequency response of cantilever beams immersed in viscous fluids with applications to the atomic force microscope. J Appl Phys 84:64–76
Hutter JL, Bechhoefer J (1993) Calibration of atomic-force microscope tips. Rev Sci Instrum 64:1868–1873
García R (2010) Amplitude modulation AFM in liquid. Amplitude modulation atomic force microscopy. Wiley, Weinheim, pp 77–90
García R (2010) Amplitude modulation atomic force microscopy. Wiley, Weinheim
de Pablo PJ, Colchero J, Gomez-Herrero J et al (1998) Jumping mode scanning force microscopy. Appl Phys Lett 73:3300–3302
Berquand A (2011) Quantitative imaging of living biological samples by peakforce QNM atomic force microscopy. Bruker Application Note #135
Baclayon M, Roos WH, Wuite GJL (2010) Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 9:1678–1688
Florin E, Moy V, Gaub H (1994) Adhesion forces between individual ligand-receptor pairs. Science 264:415–417
Fotiadis D, Scheuring S, Muller SA et al (2002) Imaging and manipulation of biological structures with the AFM. Micron 33:385–397
Lee YJ, Yi H, Kim WJ et al (2009) Fabricating genetically engineered high-power lithium-ion batteries using multiple virus genes. Science 324:1051–1055
Nam KT, Kim DW, Yoo PJ et al (2006) Virus-enabled synthesis and assembly of nanowires for lithium ion battery electrodes. Science 312:885–888
Nam KT, Wartena R, Yoo PJ et al (2008) Stamped microbattery electrodes based on self-assembled M13 viruses. Proc Natl Acad Sci U S A 105:17227–17231
Grasso S, Santi L (2010) Viral nanoparticles as macromolecular devices for new therapeutic and pharmaceutical approaches. Int J Physiol Pathophysiol Pharmacol 2:161–178
Hooker JM, Kovacs EW, Francis MB (2004) Interior surface modification of bacteriophage MS2. J Am Chem Soc 126:3718–3719
Huang Z, Santi L, LePore K et al (2006) Rapid, high-level production of hepatitis B core antigen in plant leaf and its immunogenicity in mice. Vaccine 24:2506–2513
Schmidt U, Gunther C, Rudolph R et al (2001) Protein and peptide delivery via engineered polyomavirus-like particles. FASEB J 15:1646–1648
Storni T, Ruedl C, Schwarz K et al (2004) Nonmethylated CG motifs packaged into virus-like particles induce protective cytotoxic T cell responses in the absence of systemic side effects. J Immunol 172:1777–1785
Tanaka T, Shimura H, Sasaki T et al (2004) Gallbladder cancer treatment using adenovirus expressing the HGF/NK4 gene in a peritoneal implantation model. Cancer Gene Ther 11:431–440
Yamada T, Iwasaki Y, Tada H et al (2003) Nanoparticles for the delivery of genes and drugs to human hepatocytes. Nat Biotechnol 21:885–890
Knez M, Sumser MP, Bittner AM et al (2004) Binding the tobacco mosaic virus to inorganic surfaces. Langmuir 20:441–447
Kuznetsov YG, Low A, Fan H et al (2005) Atomic force microscopy investigation of isolated virions of murine leukemia virus. J Virol 79:1970–1974
Lyubchenko YL, Oden PI, Lampner D et al (1993) Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. Nucleic Acids Res 21:1117–1123
Kienberger F, Zhu R, Moser R et al (2004) Dynamic force microscopy for imaging of viruses under physiological conditions. Biol Proced Online 6:120–128
Muller DJ, Amrein M, Engel A (1997) Adsorption of biological molecules to a solid support for scanning probe microscopy. J Struct Biol 119:172–188
Snijder J, Reddy VS, May ER et al (2013) Integrin and defensin modulate the mechanical properties of adenovirus. J Virol 87:2756–2766
Roos WH (2011) How to perform a nanoindentation experiment on a virus. Methods Mol Biol 783:251–264
Dutt S, Tanha J, Evoy S et al (2013) Immobilization of P22 bacteriophage Tailspike protein on Si surface for optimized salmonella capture. J Anal Bioanal Tech 7:2
Gray JJ (2004) The interaction of proteins with solid surfaces. Curr Opin Struct Biol 14:110–115
Zlotnick A, Aldrich R, Johnson JM et al (2000) Mechanism of capsid assembly for an icosahedral plant virus. Virology 277:450–456
Carrasco C, Carreira A, Schaap IA et al (2006) DNA-mediated anisotropic mechanical reinforcement of a virus. Proc Natl Acad Sci U S A 103:13706–13711
Roos WH, Radtke K, Kniesmeijer E et al (2009) Scaffold expulsion and genome packaging trigger stabilization of herpes simplex virus capsids. Proc Natl Acad Sci U S A 106:9673–9678
Roos WH, Gibbons MM, Arkhipov A et al (2010) Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophys J 99:1175–1181
Klug WS, Bruinsma RF, Michel JP et al (2006) Failure of viral shells. Phys Rev Lett 97:228101
Milling A, Mulvaney P, Larson I (1996) Direct measurement of repulsive van der Waals interactions using an atomic force microscope. J Colloid Interface Sci 180:460–465
Cappella B, Dietler G (1999) Force-distance curves by atomic force microscopy. Surf Sci Rep 34:1–104
Gibbons MM, Klug WS (2007) Nonlinear finite-element analysis of nanoindentation of viral capsids. Phys Rev E Stat Nonlin Soft Matter Phys 75:031901
Ivanovska IL, de Pablo PJ, Ibarra B et al (2004) Bacteriophage capsids: tough nanoshells with complex elastic properties. Proc Natl Acad Sci U S A 101:7600–7605
Michel JP, Ivanovska IL, Gibbons MM et al (2006) Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. Proc Natl Acad Sci U S A 103:6184–6189
Snijder J, Ivanovska IL, Baclayon M et al (2012) Probing the impact of loading rate on the mechanical properties of viral nanoparticles. Micron 43:1343–1350
Roos WH, Bruinsma R, Wuite GJL (2010) Physical virology. Nat Phys 6:733–743
Mateu MG (2012) Mechanical properties of viruses analyzed by atomic force microscopy: a virological perspective. Virus Res 168:1–22
Roos WH, Ivanovska IL, Evilevitch A et al (2007) Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci 64:1484–1497
Carrasco C, Castellanos M, de Pablo PJ et al (2008) Manipulation of the mechanical properties of a virus by protein engineering. Proc Natl Acad Sci U S A 105:4150–4155
Castellanos M, Perez R, Carrasco C et al (2012) Mechanical elasticity as a physical signature of conformational dynamics in a virus particle. Proc Natl Acad Sci U S A 109:12028–12033
Snijder J, Uetrecht C, Rose RJ et al (2013) Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 5:502–509
Hernando-Perez M, Miranda R, Aznar M et al (2012) Direct measurement of phage phi29 stiffness provides evidence of internal pressure. Small 8:2366–2370
Evilevitch A, Roos WH, Ivanovska IL et al (2011) Effects of salts on internal DNA pressure and mechanical properties of phage capsids. J Mol Biol 405:18–23
Klug WS, Roos WH, Wuite GJ (2012) Unlocking internal prestress from protein nanoshells. Phys Rev Lett 109:168104
Lidmar J, Mirny L, Nelson DR (2003) Virus shapes and buckling transitions in spherical shells. Phys Rev E 68:051910
Carrasco C, Luque A, Hernando-Pérez M et al (2011) Built-in mechanical stress in viral shells. Biophys J 100:1100–1108
Baclayon M, Shoemaker GK, Uetrecht C et al (2011) Prestress strengthens the shell of Norwalk virus nanoparticles. Nano Lett 11:4865–4869
Roos WH, Gertsman I, May ER et al (2012) Mechanics of bacteriophage maturation. Proc Natl Acad Sci U S A 109:2342–2347
Ortega-Esteban A, Perez-Berna AJ, Menendez-Conejero R et al (2013) Monitoring dynamics of human adenovirus disassembly induced by mechanical fatigue. Sci Rep 3:1434
Schaap IAT, Eghiaian F, des Georges A et al (2012) Effect of envelope proteins on the mechanical properties of influenza virus. J Biol Chem 287:41078–41088
Heinhorst S, Cannon GC (2008) A new, leaner and meaner bacterial organelle. Nat Struct Mol Biol 15:897–898
Carvalho FA, Carneiro FA, Martins IC et al (2012) Dengue virus capsid protein binding to hepatic lipid droplets (LD) is potassium ion dependent and is mediated by LD surface proteins. J Virol 86:2096–2108
Ebner A, Wildling L, Kamruzzahan AS et al (2007) A new, simple method for linking of antibodies to atomic force microscopy tips. Bioconjug Chem 18:1176–1184
Acknowledgments
We thank Prof. G. Nemerow (Scripps, La Jolla) for kindly providing us with the adenoviral particles. WHR is supported by a VIDI grant from the Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO). GJLW is supported by a Fundamenteel Onderzoek der Materie Projectruimte grant.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
van Rosmalen, M.G.M., Roos, W.H., Wuite, G.J.L. (2015). Material Properties of Viral Nanocages Explored by Atomic Force Microscopy. In: Orner, B. (eds) Protein Cages. Methods in Molecular Biology, vol 1252. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2131-7_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2131-7_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2130-0
Online ISBN: 978-1-4939-2131-7
eBook Packages: Springer Protocols