A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy

Journal of Structural Biology

Volumn 116, Issue 1, 1996, Pages 120-130

  Baker, Timothy S ^a   Cheng, R Holland ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ELECTRON MICROSCOPY; FOURIER TRANSFORMATION; MOLECULAR BIOLOGY; PRIORITY JOURNAL; AUDIOVISUAL EQUIPMENT; COMPARATIVE STUDY; COMPUTER GRAPHICS; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; FOURIER ANALYSIS; FREEZING; POLYOMA VIRUS; ULTRASTRUCTURE; VIRUS CAPSID; X RAY CRYSTALLOGRAPHY;

CAPSID; COMPUTER GRAPHICS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; FOURIER ANALYSIS; FREEZING; MICROSCOPY, ELECTRON; MODELS, STRUCTURAL; MOLECULAR CONFORMATION; POLYOMAVIRUS; SOFTWARE;

EID: 0029665272     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.1996.0020     Document Type: Article

References (59)

1. Baker, T. S. (1992) Cryo-electron microscopy and three-dimensional image reconstruction of icosahedral viruses, in 10th Eur. Congr. Electron Microsc. (Granada) Vol. 3; pp. 275-279.
2. Baker, T. S., Drak, J., and Bina, M. (1988) Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core, Proc. Natl. Acad. Sci. USA 85, 422-426.
3. Baker, T. S., Drak, J., and Bina, M. (1989) The capsid of small papova viruses contains 72 pentameric capsomeres: Direct evidence from cryo-electron microscopy of simian virus 40, Biophys. J. 55, 243-253.
4. Belnap, D. M., Grochulski, W. D., Olson, N. H., and Baker, T. S. (1993) Use of radial density plots to calibrate image magnification for frozen-hydrated specimens, Ultramicroscopy 48, 347-358.
5. Cheng, R. H., Olson, N. H., Baker, T. S. (1992) Cauliflower mosaic virus, a 420 subunit (T = 7), multilayer structure, Virology 186, 655-668.
6. Cheng, R. H., Caston, J. R., Wang, G. J., Gu, F., Smith, T. J., Baker, T. S., Bozarth, R. F., Trus, B. L., Cheng, N., Wickner, R. B., and Steven, A. C. (1994a) Fungal virus capsids: Cytoplasmic compartments for the replication of double-stranded RNA formed as icosahedral shells of asymmetric Gag dimers, J. Mol. Biol. 244, 255-258.
7. Cheng, R. H., Reddy, V., Olson, N. H., Fisher, A., Baker, T. S., and Johnson, J. E. (1994b) Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography, Structure 2, 271-282.
8. Cheng, R. H., Kuhn, R. J., Olson, N. H., Rossmann, M. G., Choi, H.-K., Smith, T. J., and Baker, T. S. (1995) Three-dimensional structure of an enveloped alphavirus with T = 4 icosahedral symmetry, Cell 80, 621-630.
9. Conway, J. F., Duda, R. L., Cheng, N., Hendrix, R. W., and Steven, A. C. (1995) Proteolytic and conformational control of virus capsid maturation: The bacteriophage HK97 system, J. Mol. Biol. 253, 86-99.
10. Crowther, R. A. (1971) Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs, Philos. Trans. R. Soc. London Ser. B. 261, 221-230.
11. Crowther, R. A., Amos, L. A., Finch, J. T., DeRosier, D. J., and Klug, A. (1970) Three dimensional reconstructions of spherical viruses by Fourier synthesis from electron micrographs, Nature (London) 226, 421-425.
12. Crowther, R. A., and Amos, L. A. (1971) Harmonic analysis of electron microscope images with rotational symmetry, J. Mol. Biol. 60, 123-130.
13. Crowther, R. A., and Amos, L. A., (1972) Three-dimensional image reconstruction of some small spherical viruses, Cold Spring Harbor Symp. Quant. Biol. 36, 489-194.
14. Crowther, R. A., Kiselev, N. A., Böttcher, B., Berriman, J. A., Borisova, J. P., Ose, V., and Pumpens, P. (1994) Three-dimensional structure of hepatitis B virus core particles determined by electron cryomicroscopy, Cell 77, 943-950.
15. Dokland, T., and Murialdo, H. (1993) Structural transitions during maturation of bacteriophage lambda capsids, J. Mol. Biol. 233, 682-694.
16. Finch, J. T. (1972) The hand of the helix of tobacco mosaic virus, J. Mol. Biol. 66, 291-294.
17. Fisher, A. J., and Johnson, J. E. (1993). Ordered duplex RNA controls capsid architecture in an icosahedral animal virus, Nature (London) 361, 176-179.
18. Fuller, S. D. (1987) The T = 4 envelope of Sindbis virus is organized by interactions with a complementary T = 3 capsid, Cell 48, 923-934.
19. Fuller, S. D., Berriman, J. A., Butcher, S. J., and Gowen, B. E. (1995) Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex, Cell 81, 715-725.
20. Fuller, S. D., Butcher, S. J., Cheng, R. H., and Baker, T. S. (1996) Three-dimensional reconstruction of icosahedral particles -The uncommon line, J. Struct. Biol. 116, 48-55.
21. Griffith, J. P., Griffith, D. L., Rayment, I., Murakami, W. T. and Caspar, D. L. D. (1992) Inside polyomavirus at 25 Å resolution, Nature (London) 355, 652-654.
22. Hagensee, M., Olson, N. H., Baker, T. S., and Galloway, D. (1994) Three-dimensional structure of vaccinia virus-produced HPV-1 capsids, J. Virol. 68, 4503-1505.
23. Harauz, G., and van Heel, M. (1986) Direct 3D reconstruction from projections with initially unknown angles, in Gelsema, E. S. and Kanal L. N. (Eds.), Pattern Recognition in Practice II, pp. 279-288, Elsevier, North-Holland.
24. Ilag, L. L., Olson, N. H., Dokland, T., Music, C. L., Cheng, R. H., Bowen, Z., McKenna, R., Rossmann, M. G., Baker, T. S., and Incardona, N. L. (1995) DNA packaging intermediates of bacteriophage θX174, Structure 3, 353-363.
25. Kenney, J. M., Sjoberg, M., Garoff, H., and Fuller, S. D. (1994) Visualization of fusion activation in the Semliki Forest virus spike, Structure 2, 823-832.
26. Klug, A., and Finch, J. T. (1968) Structure of viruses of the papilloma-polyoma type. IV. Analysis of tilting experiments in the electron microscope, J. Mol. Biol. 31, 1-12.
27. Lake, J. A. (1972) Biological studies, in Lipson, H. (Ed.), Optical Transforms, pp. 153-188, Academic Press, New York.
28. Marquart, M., Deisenhofer, J., Huber, R. and Palm, W. (1980) Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Åand 1.9 Å resolution, J. Mol. Biol. 141, 369-391.
29. Martino, R. J., Johnson, C. A., Suh, E. B., Trus, B. L., and Yap, T. K. (1994). Parallel computing in biomedical research, Science 265, 902-908.
30. McKenna, R., Xi, D., Willingmann, P., Ilag, L. L., Krishnaswamy, S., Rossmann, M. G., Olson, N. H., Baker, T. S., and Incardona, N. L. (1992) The atomic structure of the single-stranded DNA bacteriophage θX174 and its functional implications, Nature (London) 355, 137-143.
31. Milligan, R. A., and Flicker, P. F. (1987) Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy, J. Cell. Biol. 105, 29-39.
32. Misell, D. L. (1978) Image analysis, enhancement and interpretation, Pract. Methods Electron Microsc. (Glauert A. M. Ed.) 7, 1-305.
33. Moody, M. F. (1990) Image analysis of electron micrographs, in Hawkes, P. W., and Valdre, U. (Eds.), Biophysical Electron Microscopy: Basic Concepts and Modern Techniques, pp. 145-287, Academic Press, New York.
34. Oliveria, M. A., Zhao, R., Lee, W. M., Kremer, M., Minor, I., Rueckert, R. R., Diana, G. D., Pevear, D. C., Dutko, F. J., McKinlay, M. A., and Rossmann, M. G. (1993) The structure of human rhinovirus 16, Structure 1, 51-68.
35. Olson, N. H., and Baker, T. S. (1989) Magnification calibration and the determination of spherical virus diameters using cryo-microscopy, Ultramicroscopy 30, 281-297.
36. Olson, N. H., Baker, T. S., Johnson, J. E., and Hendry, D. A. (1990) The three-dimensional structure of frozen-hydrated Nudaurelia capensis β, a T = 4 insect virus, J. Struct. Biol. 105, 111-122.
37. Olson, N. H., Baker, T. S., Willingmann, P., and Incardona, N. L. (1992) The three-dimensional structure of frozen-hydrated bacteriophage θX174, J. Struct. Biol. 108, 168-175.
38. Olson, N. H., Kolatkar, P. R., Oliveria, M. A., Cheng, R. H., Greve, J. M., McClelland, A., Baker, T. S., and Rossmann, M. G. (1993) Structure of a human rhinovirus complexed with its receptor molecule, Proc. Natl. Acad. Sci. USA 90, 507-511.
39. Olson, N. H., Lücken, U., Walker, S. B., Otten, M. T., and Baker, T. S. (1995) Cryoelectron microscopy and image reconstruction of spherical viruses with spot scan and FEG technologies, Proc. Microsc. Microanal. (Kansas City) 53, 1086-1087.
40. Penczek, P. A., Grassucci, R. A., and Frank, J. (1994) The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles, Ultramicroscopy 53, 251-270.
41. ab fragments by cryoelectron microscopy and X-ray crystallography, Virology 204, 777-788.
42. Radermacher, M. (1994) Three-dimensional reconstruction from random projections: Orientational alignment via Radon transforms, Ultramicroscopy 53, 121-136.
43. Rayment, I., Baker, T. S., Caspar, D. L. D., and Murakami, W. R. (1982) Polyoma virus capsid crystal structure at 22.5 Å resolution, Nature 295, 110-115.
44. Rayment, I., Baker, T. S. and Caspar, D. L. D. (1983) A description of the techniques and application of molecular replacement used to determine the structure of polyoma virus capsids at 22.5 Å resolution, Acta Crystallogr. B39, 505-516.
45. Rossmann, M. G. (1972) The Molecular Replacement Method, Gordon & Breach, New York.
46. Rossmann, M. G. (1994) Viral cell recognition and entry, Protein Sci. 3, 1712-1725.
47. Rossmann, M. G., Arnold, E., Erickson, J. W., Frankenberger, G., Griffith, J. P., Hecht, H. J., Johnson, J. E., Kamer, G., Luo, M., Mosser, A. G., Rueckert, R. R., Sherry, B., and Vriend, G. (1985) Structure of a human common cold virus and functional relationship to other picornaviruses, Nature (London) 317, 145-153.
48. Schatz, M., and van Heel, M. (1990) Invariant classification of molecular views in electron micrographs, Ultramicroscopy 32, 255-264.
49. ab fragments from a neutralizing antibody, J. Virol. 67, 1148-1158.
50. Smith, T. J., Olson, N. H., Cheng, R. H., Chase, E. S., and Baker, T. S. (1993b) Structure of a human rhinovirus-bivalently bound antibody complex: Implications for virus neutralization and antibody flexibility, Proc. Natl. Acad. Sci. USA, 90, 7015-7018.
51. Stauffacher, C. V., Usha, R., Harrington, M., Schmidt, T., Hosur, M. V., and Johnson, J. E. (1987) The structure of cowpea mosaic virus at 3.5 Å resolution, in Moras (Ed.), Crystallography in Molecular Biology, pp. 293-308, Plenum, New York.
52. Strassheim, M. L., Gruenberg, A., Veijalainen, P., Sgro, J. Y., and Parrish, C. R. (1994) Two dominant neutralizing antigenic determinants of canine parovirus are found on the threefold spike of the virus capsid, Virology 198, 175-184.
53. Tsao, J., Chapman, M. S., Agbandje, M., Keller, W., Smith, K., Wu, H., Luo, M., Smith, T. J., Rossmann, M. G., Compans, R. W., and Parrish, R. W. (1991) The three dimensional structure of canine parvovirus and its functional implications, Science 251, 1456-1464.
54. Venién-Bryan, C., and Fuller, S. D. (1994). The organization of the spike complex of Semliki Forest virus, J. Mol. Biol. 236, 572-583.
55. ab interaction site (footprint) on an icosahedral virus by cryo-electron microscopy and X-ray crystallography, Nature (London) 355, 275-278.
56. Wery, J-P., Reddy, V. S., Hosur, M. V., and Johnson, J. E. (1994) The refined three-dimensional structure of an insect virus at 2.8 Å resolution, J. Mol. Biol. 235, 565-586.
57. Wikoff, W. R., Wang, G., Parrish, C. R., Cheng, R. H., Strassheim, M. L., Baker, T. S., and Rossmann, M. G. (1994) Structures of a neutralized virus: Canine parvovirus complexed with neutralizing antibody fragments, Structure 2, 595-607.
58. Wilson, I. A., and Stanfield, R. L. (1993) Antibody-antigen interactions, Curr. Opin. Struc. Biol. 3, 113-118.
59. Zhao, X., Fox, J., Olson, N. H., Baker, T. S., and Young, M. J. (1995) In vitro assembly of cowpea chlorotic mottle virus from coat protein expressed in E. coli and in vitro transcribed viral cDNA, Virology 207, 486-494.