SPM Investigations of Viruses

Viruses have been good targets for imaging with AFM especially in the early phase of its application to biology. Bacteriophage T4 is first imaged by Kolbe et al. [1537] with a distinction of the head and tail. The result is soon improved by Ikai and his collaborators with a successful imaging of tail fibers of 2nm in diameter. Zenhausern et al. and Imai et al. image the tobacco mosaic virus as well as bacteriophages [1538-1541].

According to Ikai et al. [1538] the dimension of the T4 phage in air dried state is: the head (W=140nm, H=50-60nm); the tail (W=40nm, H=17-20 nm), the tail-fiber (W=7-8nm, H=1-2nm). Occasionally phage particles with very low head height are observed corresponding to "empty" head particles that were devoid of DNA normally packed in the head. One advantage of AFM over other microscopic methods like electron microscopy is its ability to directly give information about the height of the specimen [256].

Tobacco Mosaic Virus (TMV or Satellite TMV) is the most popular object among other numerous mosaic viruses investigated so far [953, 1045]. Colloidal solutions of TMV behave similarly to those of commonly known protein ones and can therefore be studied in the same way. TMV microcrystals fail to grow at low supersaturations. It is found that two-dimensional nuclei are the source of growth steps both at high and at rather low supersaturations. However, at higher supersaturations (typically used for TMV crystallization), three-dimensional nuclei provide the major source of growth steps [118, 545, 546]. Two other mosaic viruses studied recently are the icosahedral turnip yellow mosaic virus (TYMV) and the cucumber mosaic virus (CMV) [783]. Growth of these crystals proceeds by two-dimensional (2D) nucleation. The authors present highly resolved AFM images of the hexameric and pentameric capsomers of the T=3 capsids on the surface of the individual TYMV virions which are as small as 28 nm in diameter. According to data obtained by X-ray crystallography the capsid of TYMV is composed of 180 identical protein subunits, each of about 20kDa, organized into 12 pentameric and 20 hexameric capsomers which project about 40Å above the surface of the virion. The authors particularly emphasize that the difference between the highest and lowest points on the capsid surface mentioned above is accurately reflected by AFM. The CTM virus capsomer structure is much finer and cannot be resolved to appropriate quality as yet. Clear in situ AFM images of structural peculiarities of virus crystal surfaces obtained under various experimental conditions help to interpret X-ray crystallography data. A series of images with scan sizes of 300x300nm reveals evolution of the surface layer of the (101) face of the TYMV crystals, when exposed to equilibrium conditions. Structural defects in crystal lattice such as vacancies, individual particles, dislocations and aggregates are excellently discernible.

Fig. 1. AFM image of potato virus X subjected to phosphorylation. Scan size 2400 x 2400 nm, height 22 nm. Image cortesy of Prof. I.V. Yaminsky, MSU&ATC.

Once a living biological specimen is under the AFM tip and in a favorable environment the system can be maintained and studied for hours. Thus, biological processes can be studied in real time. Haberle et al. [1531] study the viral infection process of mammalian cells. Living monkey kidney cells are reproducibly imaged with resolution on the 10nm scale and then a solution of pox viruses is added to the medium. In the first instance the cell membrane is observed to soften for a short period as the viral infection of the cell took place. Exocytosis events are then observed as viral proteins are expelled from the cell. Finally, the emergence of the progeny viruses is witnessed when large temporary protrusions of 200-300nm cross section appear in the membrane leaving scars.

A notable paper that elegantly demonstrates how AFM's high resolution enables the relationship between structure and function to be drawn is that of Müller et al. [1530]. These researchers achiev subnanometer resolution of the f29 bacteriophage headtail connector to provide structural evidence that the connector and its movement play an important role in the packing of the viral DNA.

The promising AFM technique involving AFM tips functionalized with specific molecules can be easily extended to the sphere of virology. The prospects of this technique are outlined by R.d.S. Pereira [346]. It is proposed that the use of the enzyme reverse transcriptase from the AIDS virus to modify AFM cantilever can make it a powerful tool to test new medications capable of inhibiting this enzyme and inactivating the action of the virus [E001-E004]. In addition, immobilization of one virus particle on the AFM tip opens up the possibility of measuring the force necessary for this virus to infect a single cell [1535]. In this way, a test medication that could weaken these Van der Waals forces could be a potent anti-virus drug and could avoid virus infection.

Ohnesorge et al. [1536] report observing exocytosis of a virus from an infected cell in real time. In spite of the low spatial resolution (scan sizes of 3.6x2.0µm) time resolution is relatively high, reaching one image frame per second, so rearrangement of parts of the cytosceleton is discernible. The virus itself is also characterized with a much higher resolution of ~2-3nm, enabling the identification of substructural elements on the surface.

The binding of influenza viruses to supported lipid membrane as well as the effect of the substrate-exposed lipid monolayer on defect structures in self-assembled, fully hydrated bilayers are studied in order to develop a novel biosensor capable of recognition of specific viruses and other macromolecules [1039]. The spherical particles are of about 200nm in diameter and may be slightly elongated in the scanning direction due to partial deformation by the AFM tip. Later, extended study of influenza hemagglutinin is reported [696].

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ID	Reference list (newly come references are marked red)
118	AFM studies of the nucleation and growth mechanisms of macromolecular crystals Y.G. Kuznetsov, A.J. Malkin, A. McPherson Journal of Crystal Growth, 196 (1999), 2-4, 489-502
256	STM and AFM of bio/organic molecules and structures A. Ikai Surface Science Reports, 26 (1997), 8, 261-332
346	Atomic force microscopy as a novel pharmacological tool R.d.S. Pereira Biochemical Pharmacology, 62 (2001), 8, 975-983
352	Atomic force microscopy examination of tobacco mosaic virus and virion RNA Y.F. Drygin, M.O. Gallyamov, I.V. Yaminsky, O.A. Bordunova FEBS Letters, 425 (1998), 2, 217-221
545	In situ atomic force microscopy studies of protein and virus crystal growth mechanisms A.J. Malkin, Y.G. Kuznetsov, W. Glantz, A. McPherson Journal of Crystal Growth, 168 (1996), 1-4, 63-73
546	In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization A.J. Malkin, A. McPherson, Y.G. Kuznetsov Journal of Crystal Growth, 196 (1999), 2-4, 471-488
597	Mechanisms of protein and virus crystal growth: An atomic force microscopy study of canavalin and STMV crystallization T.A. Land, J.J. De Yoreo, A.J. Malkin, Y.G. Kutznesov, A. McPherson Journal of Crystal Growth, 166 (1996), 1-4, 893-899
696	Self-assembly of influenza hemagglutinin: studies of ectodomain aggregation by in situ atomic force microscopy R.F. Epand, C.M. Yip, L.V. Chernomordik, D.L. LeDuc, Y.-K. Shin, R.M. Epand Biochimica et Biophysica Acta (BBA)/Biomembranes, 1513 (2001), 2, 167-175
783	Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy A.J. Malkin, Y.G. Kuznetsov, A. McPherson Journal of Crystal Growth, 232 (2001), 1-4, 173-183
953	Tobacco mosaic virus adsorption on self-assembled and Langmuir-Blodgett monolayers studied by TIRF and SFM D.W. Britt, V. Hlady, J. Buijs Thin Solid Films, 327-329 (1998), 824-828
975	AFM review study on pox viruses and living cells Ohnesorge F.M., Horber J.K.H., Haberle W., Czerny C.P., Smith D.P.E., Binning G. Biophys. J. 73 (1997), 2183-2194
1039	Nanostructure of supported phospholipid monolayers and bilayers by scanning probe microscopy L.K. Tamm, C. Bohm, J. Yang, Z. Shao, J. Hwang, M. Edidin, E. Betzig Thin Solid Films, 284-285 (1996), 813-816
1045	Progress in scanning probe microscopy H.K. Wickramasinghe Acta Materialia, 48 (2000), 1, 347-358
1528	Imaging and nano-dissection of tobacco mosaic virus by atomic force microscopy Bushell G.R., Watson G.S., Holt S.A., Myhra S. J. Microscopy 180 (1995), 174-181
1529	Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces Lyubchenko Y.L., Oden P.I., Lampner D., Lindsay S.M., Dunker K.A. Nucl. Acids Res. (1993) 21: 1117-1123
1530	The bacteriophage phi 29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution Müller D.J., Engel A., Carrascosa J.L., Velez M. EMBO J. (1997) 16: 2547-2553
1531	In situ investigation of single living cells infected by viruses Haberle W, Horber J.K.H., Ohnesorge F.M., Smith D.P.E., Binnig G. Ultramicroscopy 42-44 (1992), 1161-1167
1532	Imaging surface and submembranous structures with the atomic force microscope: A study on living cancer cells, fibroblasts and macrophages Braet F, Seynaeve C, de Zanger R, Wisse E. J Microsc 190 (1998), 328-338
1533	Investigation of Virus Crystal Growth Mechanisms by In Situ Atomic Force Microscopy A.J. Malkin, T.A. Land, Yu.G. Kuznetsov, A. McPherson, J.J. De Yoreo Phys. Rev. Lett. 75 (14) (1995) 2778
1535	Kinetics and mechanics of cell adhesion Zhu C. J Biomech 33 (2000), 23-33
1536	AFM review study on pox viruses and living cells Ohnesorge F.M., Horber J.K.H., Haberle W., Czerny C.P., Smith D.P.E., Binning G. Biophys J 73 (1997), 2183-2194
1537	Atomic force microscopy imaging of T4 bacteriophages on silicon substrates W.F. Kolbe, D.F. Ogletree and M.B. Salmeron Ultramicroscopy 42-44 (1992) 1113
1538	Atomic force microscope of bacteriophage T4 and its tube-baseplate complex A. Ikai, K. Yoshimura, F. Arisaka, A. Ritani and K. Imai FEBS Lett. 326 (1993) 39
1539	Scanning tunneling microscopy/atomic force microscopy studies of bacteriophage T4 and its tail fibers A. Ikai, K. Imai, K. Yoshimura, M. Tomitori, O. Nishikawa, R. Kokawa, K. Kobayashi and M. Yamamoto J. Vac. Sci. Technol. B 12 (1994) 1478
1540	Scanning force microscopy and cryo-electron microscopy of tobacco mosaic virus as a test specimen F. Zenhausern, M. Adrian, R. Emch, M. Taborelli, M. Jobin and P. Descouts Ultramicroscopy 42-44 (1992) 1168
1541	Scanning Tunneling and Atomic Force Microscopy of T4 Bacteriophage and Tobacco Mosaic Virus K. Imai, K. Yoshimura, M. Tomitori, O. Nishikawa, R. Kokawa, K. Kobayashi, M. Yamamoto and A. Ikai Jpn. J. Appl. Phys. 32 (1993) 2962
1353	Imaging of viruses by atomic force microscopy Yu. G. Kuznetsov, A. J. Malkin, R. W. Lucas, M. Plomp and A. McPherson Journal of General Virology, 82 (2001), 2025-2034
1367	Immobilisation of Semliki forest virus for atomic force microscopy M. Moloney, L. McDonnell and H. O'Shea Ultramicroscopy, Vol. 91 (1-4) (2002) pp. 275-279
1701	Rapid visualization at high resolution of pathogens by atomic force microscopy: structural studies of herpes simplex virus-1 Marco Plomp, Marcia K. Rice, Edward K. Wagner, Alexander McPherson, and Alexander J. Malkin Am. J. Pathol., 160 (2002) 1959-1966
1717	Atomic force microscopy and electron microscopy analysis of retrovirus gag proteins assembled in vitro on lipid bilayers Guy Zuber and Eric Barklis Biophys. J., 78 (2000) 373-384
1754	Differences in the susceptibility of streptococcus pyogenes to rokitamycin and erythromycin a revealed by morphostructural atomic force microscopy Pier Carlo Braga and Davide Ricci J. Antimicrob. Chemother., 50 (2002) 457-460
1775	Atomic force microscopy analysis of bacteriophages KZ and T4 Nadezda Matsko, Dmitry Klinov, Anatoliy Manykin, Viktor Demin, and Sergey Klimenko J. Electron Microsc. (Tokyo), 50 (2001) 417-422
1776	Visualization by atomic force microscopy of tobacco mosaic virus movement protein-RNA complexes formed in vitro O. I. Kiselyova, I. V. Yaminsky, E. M. Karger, O. Yu. Frolova, Y. L. Dorokhov, and J. G. Atabekov J. Gen. Virol., 82 (2001) 1503-1508
2487	The interaction of DNA with bacteriophage phi 29 connector: a study by AFM and TEM M. Valle, J. M. Valpuesta, J. L. Carrascosa, J. Tamayo, R. Garcia J. Struct. Biol., 116 (1996) 3, 390-398
1871	AFM imaging and elasticity measurements on living rat liver macrophages C. Rotsch, F. Braet, E. Wisse, M. Radmacher Cell. Biol. Int., 21 (1997) 11, 685-696
2109	Effects of relative humidity and applied force on atomic force microscopy images of the filamentous phage fd X. Ji, J. Oh, A. K. Dunker, K. W. Hipps Ultramicroscopy, 72 (1998) 3-4, 165-176
1917	Atomic force microscopy examination of tobacco mosaic virus and virion RNA Y. F. Drygin, O. A. Bordunova, M. O. Gallyamov, I. V. Yaminsky FEBS Letters, 425 (1998) 2, 217-221
2463	Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy A. J. Malkin, Y. G. Kuznetsov, R. W. Lucas, A. McPherson J. Struct. Biol., 127 (1999) 1, 35-43
1961	Atomic force microscopy studies of icosahedral virus crystal growth Y. G. Kuznetsov, A. J. Malkin, R. W. Lucas, A. McPherson Colloids. Surf. B. Biointerfaces, 19 (2000) 4, 333-346
2394	Scanning force microscopy study on a single-stranded DNA: the genome of parvovirus B19 G. Zuccheri, A. Bergia, G. Gallinella, M. Musiani, B. Samori Chembiochem., 2 (2001) 3, 199-204
2544	Visual representation by atomic force microscopy (AFM) of tomato spotted wilt virus ribonucleoproteins J. W. Kellmann, P. Liebisch, K. P. Schmitz, B. Piechulla Biol. Chem., 382 (2001) 11, 1559-1562
1896	Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology A. J. Malkin, M. Plomp, A. McPherson Acta Crystallogr. D: Biol. Crystallogr., 58 (2002) 1, 1617-1621
E001	Perspectives of non-nucleoside reverse transcriptase inhibitors (NNTIs) in the therapy of HIV-1 infection De Clercq E. Farmaco 54 (1999), 26-45
E002	The role of non-nucleoside reverse transcriptase inhibitors (NNTIs) in the therapy of HIV-1 infection De Clercq E. Antiviral Res 38 (1998), 153-79
E003	Structural biology of HIV Turner B.G., Summers M.F. J Mol Biol 285 (1999), 1-32
E004	The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1 Rodgers D.W., Gamblin S.J., Harris B.A., Ray S., Culp J.S., Hellmig B., Woolf D.J., Debouck C., Harrison S.C. Proc Natl Acad Sci USA 92 (1995), 1222-6