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Atomic Force Microscopy in Biomedical Research pp 171–195Cite as

Atomic Force Microscopy Investigation of Viruses

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 736))

Abstract

Atomic force microscopy (AFM) has proven to be a valuable approach to delineate the architectures and detailed structural features of a wide variety of viruses. These have ranged from small plant satellite viruses of only 17 nm to the giant mimivirus of 750 nm diameter, and they have included diverse morphologies such as those represented by HIV, icosahedral particles, vaccinia, and bacteriophages. Because it is a surface technique, it provides images and information that are distinct from those obtained by electron microscopy, and in some cases, at even higher resolution. By enzymatic and chemical dissection of virions, internal structures can be revealed, as well as DNA and RNA. The method is relatively rapid and can be carried out on both fixed and unfixed samples in either air or fluids, including culture media. It is nondestructive and even non-perturbing. It can be applied to individual isolated virus, as well as to infected cells. AFM is still in its early development and holds great promise for further investigation of biological systems at the nanometer scale.

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References

  1. Binning, G., and Quate, C.F. (1986). Atomic force microscope. Phys. Rev. Lett. 56: 930–933.

    Google Scholar 

  2. Bustamante, C., and Keller, D. (1995). Scanning force microscopy in biology. Phys. Today 48: 32–38.

    Google Scholar 

  3. Allen, S., Davies, M.C., Roberts, C.J., Tendler, S.J.B., and Williams, P.M. (1997). Atomic force microscopy in analytical biotechnology. Trends in Biotech. 15: 101–105.

    Google Scholar 

  4. Hansma, P.K. (1994). Tapping mode atomic force microscopy in liquids. Appl. Phys. Lett. 64: 1738–1740.

    Google Scholar 

  5. Kuznetsov, Y.G., Ulbrich, P., Haubova, S., Ruml, T., and McPherson, A. (2007). Atomic force microscopy investigation of Mason-Pfizer monkey virus and human immunodeficiency virus type 1 reassembled particles. Virology 360: 434–446.

    Google Scholar 

  6. Baker, T.S., Olson, N.H., and Fuller, S.D. (1999). Adding the third dimension to virus life cycles: Three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiology and Molecular Biology Reviews 63: 862–922.

    Google Scholar 

  7. Kuznetsov, Y.G., and McPherson, A. (2006). Atomic force microscopy investigation of Turnip Yellow Mosaic Virus capsid disruption and RNA extrusion. Virology 352: 329–337.

    Google Scholar 

  8. Kuznetsov, Y.G., Gurnon, J.R., Van Etten, J.L., and McPherson, A. (2005). Atomic force microscopy investigation of a chlorella virus, PBCV-1. J Struct Biol 149: 256–263.

    Google Scholar 

  9. Xiao, C., Kuznetsov, Y.G., Sun, S., Hafenstein, S.L., Kostyuchenko, V.A., Chipman, P.R., Suzan-Monti, M., Raoult, D., McPherson, A., and Rossmann, M.G. (2009). Structural studies of the giant mimivirus. PLoS Biology 7: 958–966.

    Google Scholar 

  10. Malkin, A.J., Land, T.A., Kuznetsov, Y.G., McPherson, A., and DeYoreo, J.J. (1995). Investigation of virus crystal growth mechanisms by in situ atomic force microscopy. Physical Review Letters 75: 2778–2781.

    Google Scholar 

  11. Land, T.A., Malkin, A.J., Kuznetsov, Y.G., McPherson, A., and DeYoreo, J.J. (1996). Mechanisms of protein and virus crystal growth: An atomic force microscopy study of Canavalin and STMV crystallization. J. Cryst. Growth 166: 893–899.

    Google Scholar 

  12. Malkin, A.J., Kuznetsov, Y.G., Lucas, R.W., and McPherson, A. (1999). Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy. J Struct Biol 127: 35–43.

    Google Scholar 

  13. Malkin, A.J., Kuznetsov, Y.G., and McPherson, A. (2001). Viral Capsomere Structure, Surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy. J. Cryst. Growth 232: 173–183.

    Google Scholar 

  14. Malkin, A.J., Plomp, M., and McPherson, A. (2002). Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology. Acta crystallographica 58: 1617–1621.

    Google Scholar 

  15. Kuznetsov, Y.G., Malkin, A.J., Lucas, R.W., Plomp, M., and McPherson, A. (2001). Imaging of viruses by atomic force microscopy. The Journal of general virology 82: 2025–2034.

    Google Scholar 

  16. McPherson, A., Malkin, A.J., Kuznetsov, Y.G., and Plomp, M. (2001). Atomic force microscopy applications in macromolecular crystallography. Acta Cryst. D57: 1053–1060.

    Google Scholar 

  17. McPherson, A., Kuznetsov, Y.G., Malkin, A.J., and Plomp, M. (2004). Macromolecular crystal growth investigations using atomic force microscopy. Journal of synchrotron radiation 11: 21–23.

    Google Scholar 

  18. Makino, D.L., Larson, S.B., and McPherson, A. (2005). Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy. Acta crystallographica 61: 173–179.

    Google Scholar 

  19. Kuznetsov, Y.G., Daijogo, S., Zhou, J., Semler, B.L., and McPherson, A. (2005b). Atomic force microscopy analysis of icosahedral virus RNA. J Mol Biol 347: 41–52.

    Google Scholar 

  20. Kuznetsov, Y.G., Datta, S., Kothari, N.H., Greenwood, A., Fan, H., and McPherson, A. (2002). Atomic force microscopy investigation of fibroblasts infected with wild-type and mutant murine leukemia virus (MuLV). Biophys J 83: 3665–3674.

    Google Scholar 

  21. Kuznetsov, Y.G., Victoria, J.G., Robinson, W.E., Jr., and McPherson, A. (2003). Atomic force microscopy investigation of human immunodeficiency virus (HIV) and HIV-infected lymphocytes. J Virol 77: 11896–11909.

    Google Scholar 

  22. Kuznetsov, Y.G., Low, A., Fan, H., and McPherson, A. (2004). Atomic force microscopy investigation of wild-type Moloney murine leukemia virus particles and virus particles lacking the envelope protein. Virology 323: 189–196.

    Google Scholar 

  23. Malkin, A.J., Plomp, M., Leighton, T.J., McPherson, A., and Wheeler, K.E. (2006). Unraveling the Architecture and Structural Dynamics of Pathogens by High Resolution In vitro Atomic Force Microscopy. In Microscopy and Microanalysis, pp. 32–85. Cambridge Univ. Press, Cambridge.

    Google Scholar 

  24. Plomp, M., Rice, M.K., Wagner, E.K., McPherson, A., and Malkin, A.J. (2002). Rapid visualization at high resolution of pathogens by atomic force microscopy: structural studies of herpes simplex virus-1. Am J Pathol 160: 1959–1966.

    Google Scholar 

  25. Malkin, A.J., McPherson, A., and Gershon, P.D. (2003). Structure of intracellular mature vaccinia virus visualized by in situ AFM. J. Viol. 77: 6332–6340.

    Google Scholar 

  26. Kuznetsov, Y., Gershon, P.D., and McPherson, A. (2008). Atomic Force Microscopy Investigation of Vaccinia Virus Structure. Journal of Virology 85: 7551–7566.

    Google Scholar 

  27. Kaper, J.M. (1975). The Chemical Basis of Virus Structure, Dissociation and Reas-sembly. In The Frontiers of Biology Series. (eds. A. Neuberger, and E.L. Tatum). North-Holland, Amsterdam.

    Google Scholar 

  28. Horne, R.W., and Wildy, P. (1961). Symmetry in virus architecture. Virology 15: 348–373.

    Google Scholar 

  29. Caspar, D.L.D., and Klug, A. (1962). Physical principles in the construction of regular viruses. In Cold Spring Harbor Symposium on Quant. Biol., pp. 1–24.

    Google Scholar 

  30. Lucas, R.W., Kuznetsov, Y.G., Larson, S.B., and McPherson, A. (2001). Crystallization of Brome Mosaic Virus (BMV) and T  =  1 Brome Mosaic Virus Particles following a structural transition. Virology 286: 290–303

    Google Scholar 

  31. Reddy, V.S., Natarajan, P., Okerberg, B., Li, K., Damodaran, K.V., Morton, R.T., Brooks, C.L.I., and Johnson, J.E. (2001). Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses. J. Virol. 75: 11943–11947.

    Google Scholar 

  32. Ganser, B.K., Li, S., Klishko, V.Y., Finch, J.T., and Sundquist, W.I. (1999). Assembly and analysis of conical models for the HIV-1 core. Science 283: 80–82.

    Google Scholar 

  33. Kuznetsov, Y.G., Malkin, A.J., and McPherson, A. (1997). Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis. J Struct Biol 120: 180–191.

    Google Scholar 

  34. Low, A., Datta, S., Kuznetsov, Y., Jahid, S., Kothari, N., McPherson, A., and Fan, H. (2007). Mutation in the glycosylated gag protein of murine leukemia virus results in reduced in vivo infectivity and a novel defect in viral budding or release. J Virol 81: 3685–3692.

    Google Scholar 

  35. Rossmann, M.G. (2000). Fitting atomic models into electron-microscopy maps. Acta crystallographica 56: 1341–1349.

    Google Scholar 

  36. Rossmann, M.G., Bernal, R., and Pletnev, S.V. (2001). Combining electron microscopic with x-ray crystallographic structures. J Struct Biol 136: 190–200.

    Google Scholar 

  37. Adrian, M., Dubochet, J., Lepault, J., and McDowall, A.W. (1984). Cryoelectron microscopy of viruses. Nature (London) 308: 32–36.

    Google Scholar 

  38. Carragher, B., Potter, C.S., and Sigworth, F.J. (2007). Software tools for macromolecular microscopy. J. Struct. Biol. 157: 1–288.

    Google Scholar 

  39. Wikoff, W.R., Liljas, L., Duda, R.L., Tsuruta, H., Hendrix, R.W., and Johnson, J.E. (2000). Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289: 2129–2133.

    Google Scholar 

  40. McPherson, A. (2005). Micelle formation and crystallization as paradigms for virus assembly. Bioessays 27: 447–458.

    Google Scholar 

  41. Kuznetsov, Y.G., Zhang, M., Menees, T.M., McPherson, A., and Sandmeyer, S. (2005c). Investigation by atomic force microscopy of the structure of Ty3 retrotransposon particles. J Virol 79: 8032–8045.

    Google Scholar 

  42. Kuznetsov, Y.G., and McPherson, A. (2006b). Identification of DNA and RNA from retroviruses using ribonuclease A. Scanning 28: 278–281.

    Google Scholar 

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Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA

    Alexander McPherson

Authors
  1. Alexander McPherson
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  2. Yurii G. Kuznetsov
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Correspondence to Alexander McPherson .

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Editors and Affiliations

  1. School of Medicine, Department of Pharmacology, University of Milan, Via Vanvitelli 32, Milano, 20129, Italy

    Pier Carlo Braga

  2. , Robotics, Brain & Cognitive Sciences, Italian Institute of Technology, Via Morego 30, Genova, 16163, Italy

    Davide Ricci

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McPherson, A., Kuznetsov, Y.G. (2011). Atomic Force Microscopy Investigation of Viruses. In: Braga, P., Ricci, D. (eds) Atomic Force Microscopy in Biomedical Research. Methods in Molecular Biology, vol 736. Humana Press. https://doi.org/10.1007/978-1-61779-105-5_12

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  • DOI: https://doi.org/10.1007/978-1-61779-105-5_12

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-104-8

  • Online ISBN: 978-1-61779-105-5

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