Innovation: A visual approach to proteomics

Nature Reviews Molecular Cell Biology

Volumn 7, Issue 3, 2006, Pages 225-230

  Nickell, Stephan ^a   Kofler, Christine ^a   Leis, Andrew P ^a   Baumeister, Wolfgang ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; GREEN FLUORESCENT PROTEIN; PROTEIN; PROTEOME;

CELL STRUCTURE; CONFOCAL MICROSCOPY; CYTOLOGY; CYTOPLASM; ELECTRON MICROSCOPY; EUKARYOTIC CELL; FLUORESCENCE RESONANCE ENERGY TRANSFER; MACROMOLECULE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEOMICS; REVIEW; THREE DIMENSIONAL IMAGING; TOMOGRAPHY; X RAY CRYSTALLOGRAPHY; CHEMISTRY; CRYOELECTRON MICROSCOPY; GENETICS; METHODOLOGY; RED ALGA; ULTRASTRUCTURE;

EUKARYOTA;

ALGAE, RED; CRYOELECTRON MICROSCOPY; MICROSCOPY, ELECTRON; PROTEINS; PROTEOME;

EID: 33644559406     PISSN: 14710072     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrm1861     Document Type: Review

References (52)

1. Frey-Wyssling, A. The submicroscopic structure of the cytoplasm. J. R. Microsc. Soc. 60, 128-139 (1940).
2. Frey-Wyssling, A. Submicroscopic Morphology of Protoplasm and its Derivatives (Elsevier, New York, 1948).
3. Afzelius, B. A. & Maunsbach, A. B. Biological ultrastructure research; the first 50 years. Tissue Cell 36, 83-94 (2004).
4. Ball, P. Portrait of a molecule. Nature 421, 421-422 (2003).
5. Baumeister, W. From proteomic inventory to architecture. FEBS Lett. 579, 933-937 (2005).
6. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
7. Huh, W.-K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
8. Phizicky, E., Bastiaens, P. I. H., Zhu, H., Snyder, M. & Fields, S. Protein analysis on a proteomic scale. Nature 422, 208-215 (2003).
9. Hell, S. W., Dyba, M. & Jakobs, S. Concepts for nanoscale resolution in fluorescence microscopy. Curr. Opin. Neurobiol. 14, 599-609 (2004).
10. Miyawaki, A., Sawano, A. & Kogure, T. Lighting up cells: labelling proteins with fluorophores. Nature Cell Biol. 5, S1-S7 (2003).
11. Grünewald, K., Medalia, O., Gross, A., Steven, A. C. & Baumeister, W. Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophys. Chem. 100, 577-591 (2003).
12. Koster, A. J. et al. Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120, 276-308 (1997).
13. Grimm, R. et al. Energy filtered electron tomography of ice-embedded actin and vesicles. Biophys. J. 72, 482-489 (1997).
14. Grimm, R. et al. Electron tomography of ice-embedded prokaryotic cells. Biophys. J. 74, 1031-1042 (1998).
15. Dierksen, K. et al. Three-dimensional structure of lipid vesicles embedded in vitreous ice and investigated by automated electron tomography. Biophys. J. 68, 1416-1422 (1995).
16. Wolosewick, J. J. & Porter, K. R. Stereo high-voltage electron-microscopy of whole cells of human diploid line, WI-38. Am. J. Anat. 147, 303-323 (1976).
17. Heuser, J. Whatever happened to the 'microtrabecular concept'? Biol. Cell 94, 561-596 (2003).
18. Matricardi, V. R., Moretz, R. C. & Parsons, D. F. Electron-diffraction of wet proteins - catalase. Science 177, 268-270 (1972).
19. Parsons, D. F. Structure of wet specimens in electron-microscopy. Science 186, 407-414 (1974).
20. Taylor, K. A. & Glaeser, R. M. Electron-diffraction of frozen, hydrated protein crystals. Science 186, 1036-1037 (1974).
21. Burton, E. F. & Oliver, W. F. The crystal structure of ice at low temperature. Proc. R. Soc. Lond. A 153, 166-172 (1935).
22. Mayer, E. & Brüggeller, P. Complete vitrification in pure liquid water and dilute aqueous solutions. Nature 288, 569-571 (1980).
23. Dubochet, J. & McDowall, A. W. Vitrification of pure water for electron microscopy. J. Microsc. 124, RP3-RP4 (1981).
24. Steven, A. C. & Aebi, U. The next ice age: cryo-electron tomography of intact cells. Trends Cell Biol. 13, 107-110 (2003).
25. Dubochet, J. et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129-228 (1988).
26. McIntosh, J. R., Nicastro, D. & Mastronarde, D. New views of cells in 3D: an introduction to electron tomography. Trends Cell Biol. 15, 43-51 (2005).
27. Marsh, B. J. Lessons from tomographic studies of the mammalian Golgi. Biochim. Biophys. Acta 1744, 273-292 (2005).
28. Nicastro, D., McIntosh, J. R. & Baumeister, W. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography. Proc. Natl Acad. Sci. USA 102, 15889-15894 (2005).
29. Zhang, P. et al. Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr. J. Microsc. 216, 76-83 (2004).
30. Al-Amoudi, A. et al. Cryo-electron microscopy of vitreous sections. EMBO J. 23, 3583-3588 (2004).
31. Medalia, O. et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298, 1209-1213 (2002).
32. Grunewald, K. et al. Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302, 1396-1398 (2003).
33. Beck, M. et al. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306, 1387-1390 (2004).
34. Mercogliano, C. P. & DeRosier, D. J. Gold nanocluster formation using metallothionein: mass spectrometry and electron microscopy. J. Mol. Biol. 355, 211-223 (2006).
35. Böhm, J. et al. Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. Proc. Natl Acad. Sci. USA 97, 14245-14250 (2000).
36. Frangakis, A. S. et al. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl Acad. Sci. USA 99, 14153-14158 (2002).
37. Frangakis, A. S. & Forster, F. Computational exploration of structural information from cryoelectron tomograms. Curr. Opin. Struct. Biol. 14, 325-331 (2004).
38. Sali, A., Glaeser, R., Earnest, T. & Baumeister, W. From words to literature in structural proteomics. Nature 422, 216-225 (2003).
39. Aloy, P. & Russell, R. B. Structure-based systems biology: a zoom lens for the cell. FEBS Lett. 579, 1854-1858 (2005).
40. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
41. Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41-60 (2005).
42. Glaeser, R. M. Historical background: why is it important to improve automated particle selection methods? J. Struct. Biol. 145, 15-18 (2004).
43. Radon, J. Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten. Berichte über die Verhandlungen der Königlich Sächsischen Gesellschaft der Wissenschaften zu Leipzig. Math. Phys. Klasse 69, 262-277 (1917) (in German).
44. Bracewell, R. N. & Riddle, A. C. Inversion of fan-beam scans in radio astronomy. Astrophys. J. 150, 427-434 (1967).
45. DeRosier, D. J. & Klug, A. Reconstruction of three dimensional structures from electron micrographs. Nature 217, 130-134 (1968).
46. Unwin, P. N. T. & Henderson, R. Molecular-structure determination by electron-microscopy of unstained crystalline specimens. J. Mol. Biol. 94, 425-440 (1975).
47. Henderson, R. & Unwin, P. N. T. Three-dimensional model of purple membrane obtained by electron-microscopy. Nature 257, 28-32 (1975).
48. Frank, J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31, 303-319 (2002).
49. Hart, R. G. Electron microscopy of unstained material: the polytropic montage. Science 159, 1464-1467 (1968).
50. Lǔcić, V., Foerster, F. & Baumeister, W. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biophys. Biomol. Struct. 74, 833-865 (2005).
51. Leis, A. et al. Cryo-electron tomography and fluorescence microscopy of unicellular algae in vitreous cryosections. Microsc. Microanal. 11 (Suppl. 2), 330-331 (2005).
52. Ruepp, A. et al. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508-513 (2000).