Scanning transmission electron microscopy of nuclear structures

Methods in Cell Biology

Volumn , Issue 53, 1998, Pages 139-164

  Wall, Joseph S ^a   Hainfeld, James F ^a   Simon, Martha N ^a  

^a BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CELL NUCLEUS; HUMAN; IMAGE PROCESSING; METHODOLOGY; REVIEW; SCANNING TRANSMISSION ELECTRON MICROSCOPY; STAINING; ULTRASTRUCTURE;

ANIMALS; CELL NUCLEUS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON, SCANNING TRANSMISSION; NEGATIVE STAINING;

EID: 0031972530     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (68)

1. Alivisatos, A. P., Johnsson, K. P., Ping, X., Wilson, T. E., Loweth, C. J., Bruchez, M. P., Jr., and Schultz, P. G. (1996). Organization of 'nanocrystal molecules' using DNA. Nature (London) 382,609-611.
2. Beavis, R. C., and Chait, B. T. (1996). Matrix-assisted laser desorption/ionization mass spectrometry of proteins. In "Methods in Enzymology" (B. L. Karger, and W. S. Handcock, eds), 270, Chapter 22. Academic Press, San Diego, CA.
3. Blackwell, L. J., Borowiec, J. A., and Mastrangelo, I. A. (1996). Single-stranded binding alters human replication protein A structure and facilitates interaction with DNA-dependent protein kinase. Mol. Cell Biol. 16, 4798-4807.
4. Braig, K., Simon, M., Furuya, F., Hainfeld, J. F., and Horwich, A. L. (1993). A polypeptide bound by the chaperonin groEL is localized within a central cavity. Proc. Natl. Acad. Sei. USA 90,3978-3982.
5. CaJacob, C. A., Frey, P. A., Hainfeld, J. F., Wall, J. S., and Yang, H. (1985). Escherichia coli pyruvate dehydrogenase complex. Particle masses of the complex and component enzymes measured by scanning transmission electron microscopy. Biochemistry 24, 2425-2431.
6. Cerritelli, M. E., Wall, J. S., Simon, M. N., Conway, J. F., and Steven, A. C. (1996). Stoichiometry and domainal organization of the long tail-fiber of bacteriophage T4: A hinged viral adhesion. J. Mol. Biol. 260, 767-780.
7. Citovsky, V., Guralnick, B., Simon, M. N., and Wall, J. S. (1997). The molecular structure of Agrobacteriiim VirE2-single stranded DNA complexes involved in nuclear import. J. Mol. Biol. (in press).
8. Crevel, G., Huikeshove, H., Cotterill, S., Simon, M., Wall, J., Philpott, A., Laskey, R. A., McConnell, M., Fisher, P. A., and Berrios, M. (1997). Molecular and cellular characterization of CRP1, a Drosophila chromatin decondensation protein. J. Struct. Biol. 118, 9-22.
9. Crewe, A. V., and Wall, J. S. (1970). A scanning microscopy with 5 Å resolution. J. Mol. Biol. 48,375.
10. Crewe, A. V., Wall, J. S., and Langmore, J. (1970). Visibility of single atoms. Science 168, 1338.
11. Engel, A., and Colliex, C. (1993). Application of scanning transmission electron microscopy to the study of biological structure. Curr. Opin. Biolechnol. 4, 403-411.
12. Flanagan, J. M., Wall, J. S., Capel, M. S., Schneider, D. K., and Shanklin, J. (1995). Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore. Biochemistry 34,10910-10917.
13. Gerchman, S. E., and Ramakrishnan, V. (1987). Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl. Acad. Sei USA 84,7802-7806.
14. Gregori, L., Hainfeld, J. F., Simon, M. N., and Goldhaber, D. (1997). Binding of amyloid beta protein to the 20 S proteasome. J. Biol. Chem. 272, 58-62.
15. Hainfeld, J., and Wall, J. (1978). A walking platinum complex. Proc. Int. Congr. Electron Microsc., 9th, Toronto, 1987, Vol. 1, 248-249.
16. Hainfeld, J. F., and Furuya, F. R. (1992). A 1.4-nm gold cluster covalently attached to antibodies improves immunolabeling. J. Histochem. Cytochem 40,177-84.
17. Hainfeld, J. F., and Furuya, F. R. (1995). Silver-enhancement of nanogold and undecagold. In "Immunogold-Silver Staining: Principles, Methods, and Applications" (M. A. Hayat, éd.), pp. 71-96. CRC Press, Boca Raton, FL.
18. Hainfeld, J. F., Sprinzl, M., Mandiyan, V., Tumminia, S. J., and Boublik, M. (1991). Localization of a specific nucleotide in yeast tRNA by electron microscopy using undecagold cluster. J. Struct. Biol. 107, 1-5.
19. Hainfeld, J. F., Safer, D., Wall, J. S., Simon, M., Lin, B., and Powell, R. D. (1994). Methylamine vanadate (nanovan) negative stain. In "52nd Ann. Microscopy Society of America" (G. W. Bailey, ed.), pp. 132-133. San Francisco Press, New Orleans, LA.
20. Hamilton, M. G., Herskovits, T. H., Furcinitti, P. S., and Wall, J. S. (1989). Scanning transmission electron microscopic study of molluscan hemocyanins in various aggregation states. Comparison with light scattering molecular weights. J. Ultrastruct. Mol. Struct. Res. 102, 221-228.
21. Hastie, A. T., Marchese-Ragona, S. P., Johnson, K. A., and Wall, J. S. (1988). The structure and mass of mammalian respiratory ciliary outer arm 19S dynein. Cell Motil. Cytoskel. 11, 157-166.
22. Hough, P. V. C, Mastrangelo, I. A., Wall, J. S., Hainfeld, J. F., Simon, M. N., and Manley, J. L. (1982). DNA-protein complexes spread on N2-discharged carbon film and characterized by molecular weight and its projected distribution. Nucleosome formation in an in vitro transcription system. J. Mol. Biol. 160, 375-386.
23. Hough, P. V. C, Mastrangelo, I. A., Wall, J. S., Hainfeld, J. F., Sawadogo, M., and Roeder, R. G. (1987). The gene-specific initiation factor USF (upstream stimulatory factor) bound at the adenovirus type 2 major later promoter: Mass and three-dimensional structure. Proc. Natl. Acad. Sei. USA 84, 4826-4830.
24. Johnson, K. A., and Wall, J. S. (1983). Structure and molecular weight of the dynein ATPase. J. Cell Biol. 96, 669-678.
25. Lamy, J. N., Green, B. N., Toulmond, A., Wall, J. S., Weber, R. E., and Vinogradov, S. N. (1996). Giant hexagonal bilayer hemoglobins. Chemical Reviews 96, 3113-3124.
26. Liu, D. J., and Day, L. A. (1994). Pf 1 virus structure: Helical coat protein and DNA with paraxial phosphates. Science 265, 671-674.
27. Mandiyan, V., Tumminia, S., Wall, J. S., Hainfeld, J. F., and Boublik, M. (1991). Assembly of the Escherichia coli 30S ribosomal subunit reveals protein dependent folding of the 16S rRNA domains. Proc. Natl. Acad. Sei. USA 88, 8174-8178.
28. Marchese-Ragona, S., Wall, J. S., and Johnson, K. (1988). Structure and mass analysis of 14S dynein obtained from Tetrahymena cilia. J. Cell Biol. 106,127-132.
29. Martin, P. D., Kuchomov, A. R., Green, B. N., Oliver, R. W. A., Braswell, E. H., Wall, J. S., and Vinogradov, S. N. (1996). Mass spectrometric composition and molecular mass of Lumbriciis terrestris hemoglobin: A refined model of its quaternary structure. J. Mol. Biol. 255,154-169.
30. Marzec, C. J., and Day, L. A. (1994). An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages. Biophys. J. 67, 2205-2222.
31. Mastrangelo, I. A., Hough, P. V. C, Wall, J. S., Dodson, M., Dean, F. B., and Hunvitz, J. (1989). ATP-dependent assembly of double hexamers of SV40 T antigen at the viral origin of DNA replication. Nature (London) 338, 658-662.
32. Mastrangelo, I. A., Courey, A. J., Wall, J. S., Jackson, S. P., and Hough, P. V. C. (1991). DNA looping and Spl multimer links: A mechanism for transcriptional synergism and enhancement. Proc. Natl. Acad. Sei. USA 88, 5670-5674.
33. Mosesson, M. W., Hainfeld, J., Haschemeyer, R. H., and Wall, J. S. (1981). Identification and mass analysis of human fibrinogen molecules and their domains by scanning transmission electron microscopy (STEM). J. Mol. Biol. 153, 695-718.
34. Mosesson, M. W., Nesheim, M. E., DiOrio, J., Hainfeld, J. F., Wall, J. S., and Mann, K. G. (1985). Studies on the structure of bovine factor V by scanning transmission electron microscopy (STEM). Blood 65, 1158-1162.
35. Mosesson, M. W., Church, W. R., DiOrio, J. P., Krishnaswamy, S., Mann, K. G., Hainfeld, J. F., and Wall, J. S. (1990a). Structural model of factors V and Va based on scanning transmission electron microscope (STEM) images and STEM mass analysis. J. Biol. Client. 265, 8863-8868.
36. Mosesson, M. W., Pass, D. N., Lollar, P., DiOrio, J. P., Knutson, G. J., Hainfeld, J. F., and Wall, J. S. (1990b). Structural model of porcine factors VIII and Villa based on scanning transmission electron microscope (STEM) images and STEM mass analysis. J. Clin. Invest. 85, 1983-1990.
37. Mosesson, M. W., DiOrio, J. P., Siebenlist, K. R., Wall, J. S., and Hainfeld, J. F. (1993). Evidence for a second type of fibril branch point in fibrin polymer networks, the trimolecular branch junction. Blood 82, 1517-1521.
38. Newcomb, W. W., Trus, B. L., Booy, F. P., Steven, A. C, Wall, J. S., and Brown, J. C. (1993). Structure of herpes simplex virus capsid: Molecular composition of the pentons and the triplexes. J. Mol. Biol. 232,499-511.
39. Paredes, A. M., Simon, M. N., and Brown, D. T. (1992). The mass of the sindbis virus nucleocapsid suggests it has t = 4 icosahedral symmetry. Virology 187, 329-332.
40. Parsell, D. A., Kowal, A. S., and Lindquist, S. (1994). The S. cerevisiae Hsp 104 protein: Purification and characterization of ATP-induced structural changes. J. Biol. Chem. 269, 4480-4487.
41. Safer, D., Hainfeld, J. F., Wall, J. S., and Riordan, J. (1982). Biospecific labeling with undecagold: Visualization of the biotin binding sites on avidin. Science 218, 290-291.
42. Skripkin, E., Yusupova, G., Yusupov, M., Kessler, P., Ehresmann, C., and Ehresmann, B. (1993). Synthesis and ribosome binding properties of model mRNAs modified with undecagold cluster. Bioconjitgate Chem. 4, 549-553.
43. Stasiak, A., Tsaneva, I. R., West, S. C, Benson, C. J. B., Yu, X., and Egelman, E. H. (1994). The Escherichia coli RuvB branch migration protein forms double hexameric rings around DNA. Proc. Natl. Acad. Sei. USA 91, 7618-7622.
44. Steinen, P. M., Steven, A. C, and Roop, D. R. (1985). The molecular biology of intermediate filaments. Cell (Cambridge, Mass.) 42, 411-419.
45. Stenger, J. E., Tegtmeyer, P., Mayr, G. A., Reed, M., Wang, Y., Wang, P., Hough, P. V. C, and Mastrangelo, I. A. (1994). p53 oligomerization and DNA looping are linked with transcriptional activation. EMBO J. 13(24), 6011-6020.
46. Steven, A. C, Wall, J., Hainfeld, J., and Steinert, P. M. (1982). The structure of fibroblastic intermediate filaments: Analysis by scanning transmission electron microscopy. Proc. Natl. Acad. Sei. USA 79, 3101-3105.
47. Steven, A. C, Hainfeld, J. F., Trus, B. L., Wall, J. S., and Steinert, P. M. (1983a). The distribution of mass in heteropolymer intermediate filaments assembled in vitro: STEM analysis of vimentin/desmin and bovine epidermal keratin. J. Biol. Chem. 258, 8323-8329.
48. Steven, A. C, Hainfeld, J. F., Trus, B. L., Wall, J. S., and Steinert, P. M. (1983b). Epidermal keratin filaments assembled in vitro have masses-per-unit-length that scale according to average subunit mass: Structural basis for homologous packing of subunits in intermediate filaments. J. Cell Biol. 97, 1939-1944.
49. Steven, A. C, Hainfeld, J. F., Trus, B. L., Steinert, P. M., and Wall, J. S. (1984). Radial distributions of density within macromolecular complexes determined from dark-field electron micrographs. Proc. Natl. Acad. Sei. USA 81, 6363-6367.
50. Steven, A. C, Trus, B. L., Hainfeld, J. F., Wall, J. S., and Steinen, P. M. (1985). Conformity and diversity in the structures of intermediate filaments. Ann. N.Y. Acad. Sei. 455, 371-380.
51. Thomas, D., Schultz, P., Steven, A. C., and Wall, J. S. (1994). Mass analysis of biological macromolecular complexes by STEM. BioL Cell. 80, 181-192.
52. Trent, J. D., Nimmesgern, E., Wall, J. S., Hartl, F.-U., and Honvich, A. L. (1991). A molecular chaperone from a thermophilic archaebacterium is related to a eukaryotic protein t complex polypeptide-1. Nature (London) 354, 490-493.
53. Tumminia, S. J., Hellmann, W., Wall, J. S., and Boublik, M. (1994). Visualization of the proteinnucleic acid interactions involved in the in vitro assembly of the Escherichia coli 50S ribosomal subunit. J. Mol. Biol. 235, 1239-1250.
54. Turnquist, S., Simon, M., Egelman, E., and Anderson, D. (1992). Supercoiled DNA wraps around the bacteriophage Phi-29 head-tail connector. Proc. Natl. Acad. Sei. USA 89,10479-10483.
55. Wall, J. S. (1971). A high resolution scanning microscope for the study of single biological molecules. Ph.D. Thesis, University of Chicago, Chicago.
56. Wall, J. S. (1978). Limits on visibility of single heavy atoms in the scanning transmission electron microscopy-an experimental study. Chem. Scrip. 14, 271-278.
57. Wall, J. S., and Hainfeld, J. F. (1986). Mass mapping with the scanning transmission electron microscope. Anna. Rev. Biophys. Biopliys. Chem. 15, 355-376.
58. Wall, J. S., and Hainfeld, J. F. (1986). Mass mapping with the scanning transmission electron microscope. Annti. Rev. Biophys. Biophys. Chem. 15, 355-376.
59. Wall, J., Hainfeld, J., and Bittner, J. (1978). Preliminary measurements of uranium atom motion on carbon films at low temperatures. Ultramicroscopy 3, 81-86.
60. Wall, J. S., Hainfeld, J. F., Bartlett, P. A., and Singer, S. J. (1982). Observation of an undecagold cluster compound in the scanning transmission electron microscope. Ultramicroscopy 8,397-402.
61. Witman, G. B., Johnson, K. A., Pfister, K. K., and Wall, J. S. (1983). Fine structure and molecular weight of the outer arm dyneins of Chlamydomonas. J. Siibmicrosc. Cytol. 15, 193-197.
62. Woodcock, C. L. F., and Frank, J. (1984). Nucleosome mass distribution using image averaging. J. Ultrastruct. Res. 89, 295-305.
63. Woodcock, C. L. F., Frado, L.-L. Y., and Wall, J. S. (1979). Direct molecular weight determination of chromatin particles by STEM. J. Cell Biot. 83, 156a.
64. Woodcock, C. L. F., Frado, L.-L. Y., and Wall, J. S. (1980). Composition of native and reconstituted chromatin particles: Direct mass determination by scanning transmission electron microscopy. Proc. Natl. Acad. Sei. USA 77, 4818-4822.
65. Woodcock, C. L. F., Frado, L.-L. Y., and Rattner, J. B. (1984). The higher order structure of chromatin: Evidence for a helical ribbon arrangement. J. Cell Biol. 99,42-52.
66. Yang, Y.-S-, Datta, A., Hainfeld, J. F., Furuya, F. R., Wall, J. S., and Frey, P. A. (1994). Mapping the lipoyl groups of the pyruvate dehydrogenase complex by use of gold cluster-labels and scanning transmission electron microscopy. Biochemistry 33, 9428-9437.
67. Yu, X., and Egelman, E. H. (1992). Structural data suggest that the active and inactive forms of Rec A filament are not simply interconvertible. J. Mol. Biol. 227, 334-346.
68. Yu, X., and Egelman, E. H. (1993). The LexA represser binds within the deep helical groove of the activated RecA filament. J. Mol. Biol. 231, 29-40.