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Discrete Tomography in Electron Microscopy

  • J. M. Carazo
  • C. O. Sorzano
  • E. Rietzel
  • R. Schröder
  • R. Marabini
Part of the Applied and Numerical Harmonic Analysis book series (ANHA)

Abstract

Structural biology is a very fast evolving field that provides key information to understand how biological processes happen in the cell. In essence, its aim is to obtain the three-dimensional structure of biological macromolecules, and then help to establish a link between structure and function. Among the different techniques that provide this three-dimensional information, in this chapter we will concentrate on the one normally referred to as Three-dimensional Electron Microscopy (3D EM), which provides information in the resolution range of between 0.5 to about 4 nanometers of protein and of complexes of proteins and nucleic acids by a process of three-dimensional reconstruction from projections. We seek to obtain information at the highest possible resolution level, and to this end we work toward incorporating into the reconstruction process as much experimental as well as a priori information as possible. This work is an assessment of the physical considerations that lead us to believe that discrete tomography has a role to play in this field,identifying the main problems to be addressed and the range of possible applications.

Keywords

Atomic Resolution Filter Function Nuclear Magnetic Reso Cryo Electron Microscopy Discrete Tomography 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. [1]
    D. Sherwood, Crystals, X-rays and Proteins (Wiley, New York), 1976.Google Scholar
  2. [2]
    G. Wagner, S. G. Hyberts, and T. F. Havel, “NMR structure determination in solution: A critique and comparison with X-ray crystallography,” Annu. Rev. Biophys. Biomol. Struct. 21 167–198 (1992).CrossRefPubMedGoogle Scholar
  3. [3]
    D. J. De Rosier and A. Klug, “Reconstruction of three dimensional structures from electron micrographs,” Nature 217 130–134 (1968).CrossRefPubMedGoogle Scholar
  4. [4]
    W. Kiihlbrandt, D. N. Wang, and Y. Fujiyoshi, “Atomic model of plant light-harvesting complex by electron crystallography,” Nature 367 614–621 (1994).CrossRefGoogle Scholar
  5. [5]
    E. Nogales, S. G. Wolf, and K. H. Downing, “Structure of the alpha beta tubulin dimer by electron crystallography,” Nature 391 199–203 (1998).CrossRefPubMedGoogle Scholar
  6. [6]
    R. Marabini, C. San Martín, and J. M. Carazo, “Electron tomography of biological specimens,” In C. Roux and J. L. Coatrieux, Contemporary Perspectives in Three-Dimensional Biomedical Imaging Studies in Health Technology and Informatics, (IOS Press, Amsterdam), pp. 53–78,1997.Google Scholar
  7. [7]
    I. Angert, W. Jahn, K. C. Holmes, and R. R. Schröder, “A modified theory of image formation in a EFTEM,” In H. A. Calderón and M. J. Yacamán, Electron Microscopy 1998, (Institute of Physics Publishing, Philadelphia), pp. 683–684, 1998, Volume 1.Google Scholar
  8. [8]
    M. Radermacher, “The three-dimensional reconstruction of single particles from random and non random tilt series,” J. Electron Microsc. Tech. 9 359–394 (1988).CrossRefPubMedGoogle Scholar
  9. [9]
    P. Penczek, M. Radermacher, and J. Frank, “3-Dimensional reconstruction of single particles embedded in ice,” Ultramicroscopy 1 33–53 (1992).CrossRefGoogle Scholar
  10. [10]
    R. Marabini, G. T. Herman, and J. M. Carazo, “3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs),” Ultramicroscopy 72 53–65 (1998).CrossRefPubMedGoogle Scholar
  11. [11]
    U. Skoglund, L. G. Öfverstedt, R. M. Burnett, and G. Bricogne, “Maximum-entropy three-dimensional reconstruction with deconvolution of the contrast transfer function: A test application with adenovirus,” J. Struct. Biol. 117 173–188 (1996).CrossRefPubMedGoogle Scholar
  12. [12]
    R. Henderson and P. N. T. Unwin, “Three-dimensional model of purple membrane obtained by electron microscopy,” Nature 257 28–32 (1975).CrossRefPubMedGoogle Scholar
  13. [13]
    J. M. Carazo and J. L. Carrascosa, “Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections,” J. Microsc. 145 159–177 (1987).CrossRefPubMedGoogle Scholar
  14. [14]
    J. M. Carazo and J. L. Carrascosa, “Information recovery in missing angular data cases: An approach by the convex projections method in three-dimensions,” J. Microsc. 145 23–43 (1987).CrossRefGoogle Scholar
  15. [15]
    C. W. Akey and M. Radermacher, “Architecture of the Xenopus Nuclear-pore complex revealed by 3-dimensional cryoelectron microscopy,” J. Cell. Biol. 122 1–19 (1993).CrossRefPubMedGoogle Scholar
  16. [16]
    H. P. Erickson and A. Klug, “Measurement and compensation of defocusing and aberrations by Fourier processing of electron micrographs,” Phil. Trans. Roy. Soc. Lond. 261 105–118 (1971).CrossRefGoogle Scholar
  17. [17]
    F. A. Lenz, “Transfer of image information in the electron microscope,” In U. Valdré, Electron Microscopy in Material Sciences, (Academic Press, New York) pp. 540–569, 1971.Google Scholar
  18. [18]
    F. Thon, “Phase contrast electron microscopy,” In U. Valdré, Electron Microscopy in Material Sciences, (Academic Press, New York) pp. 572–625,1971.Google Scholar
  19. [19]
    J. Frank, “The envelope of electron microscopic transfer functions for partially coherent illumination,” Optik 38 519–536 (1973).Google Scholar
  20. [20]
    R. H. Wade and J. Frank, “Electron microscope transfer functions for partially coherent axial illumination and chromatic defocus spread,” Optik 49 81–92 (1977).Google Scholar
  21. [21]
    Z. H. Zhou and W. Chiu, “Prospects for using an IVEM with a FEG for imaging macromolecules toward atomic resolution,” Ultra-microscopy 49 407–416 (1993).CrossRefGoogle Scholar
  22. [22]
    K. H. Downing and D. A. Grano, “Analysis of photographic emulsions for electron microscopy of two-dimensional crystalline specimens,” Ultramicroscopy 7, 381–404 (1982).CrossRefGoogle Scholar
  23. [23]
    J. P. Langmore and M. F. Smith, “Quantitative energy-filtered electron microscopy of biological molecules in ice,” Ultramicroscopy 46 349–373 (1992).CrossRefPubMedGoogle Scholar
  24. [24]
    R. H. Wade, “A brief look at imaging and contrast transfer,” Ultra-microscopy 46 145–156 (1992).CrossRefGoogle Scholar
  25. [25]
    J. Frank, Three Dimensional Electron Microscopy of Macromolecular Assemblies (Academic Press, New York), 1996.Google Scholar
  26. [26]
    J. Zhu, P. A. Penczek, R. Schröder, and J. Frank, “Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: Procedure and application to the 70S escherichia coli ribosome,” J. Struct. Biol. 118, 197–219 (1997).CrossRefPubMedGoogle Scholar
  27. [27]
    L. D. Marks, “Wiener-filter enhancement of noisy HREM images,” Ultramicroscopy 62 43–52 (1996).CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1999

Authors and Affiliations

  • J. M. Carazo
    • 1
  • C. O. Sorzano
    • 2
  • E. Rietzel
    • 3
  • R. Schröder
    • 4
  • R. Marabini
    • 5
  1. 1.Centro Nacional de Biotecnología Campus Universidad Autónoma de MadridMadridSpain
  2. 2.Centro Nacional de Biotecnología Campus Universidad Autónoma de MadridMadridSpain
  3. 3.MPI für med. ForschungHeidelbergGermany
  4. 4.MPI für med. ForschungHeidelbergGermany
  5. 5.Department of Radiology, Medical Image Processing GroupUniversity of PennsylvaniaPhiladelphiaUSA

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