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. 1978 Jul;75(7):3128–3132. doi: 10.1073/pnas.75.7.3128

Use of computerized multidimensional scaling to compare immunoelectron microscopy data with protein near-neighbor information: application to the 30S ribosome from Escherichia coli.

P T Gaffney, G Craven
PMCID: PMC392727  PMID: 80010

Abstract

A three-dimensional model of the protein arrangement in the Escherichia coli 30S ribosome was constructed by using computerized multidimensional scaling of immunoelectron microscope data. This enabled data comparison between the new electron microscope technique and other methods such as crosslinking, chemical protection, affinity labeling, energy transfer, and assembly interactions. The immunoelectron microscopy data are reasonably consistent with those from other sources. Reasons for some inconsistent data are discussed and our calculation of the dimensions of the proteins, both globular and elongated, are summarized.

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Selected References

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  1. Bollen A., Cedergren R. J., Sankoff D., Lapalme G. Spatial configuration of ribosomal proteins: a computer-generated model of the 30S subunit. Biochem Biophys Res Commun. 1974 Aug 5;59(3):1069–1078. doi: 10.1016/s0006-291x(74)80088-4. [DOI] [PubMed] [Google Scholar]
  2. Changchien L. M., Craven G. R. Proximity relationships among the 30 S ribosomal proteins during assembly in vitro. J Mol Biol. 1977 Jun 15;113(1):103–122. doi: 10.1016/0022-2836(77)90043-2. [DOI] [PubMed] [Google Scholar]
  3. Engelman D. M., Moore P. B., Schoenborn B. P. Neutron scattering measurements of separation and shape of proteins in 30S ribosomal subunit of Escherichia coli: S2-S5, S5-S8, S3-S7. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3888–3892. doi: 10.1073/pnas.72.10.3888. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fiser I., Scheit K. H., Stöffler G., Kuechler E. Proteins at the mRNA binding site of the Escherichia coli ribosome. FEBS Lett. 1975 Aug 15;56(2):226–229. doi: 10.1016/0014-5793(75)81097-0. [DOI] [PubMed] [Google Scholar]
  5. Funatsu G., Yaguchi M., Wittmann-Liebold B. Primary stucture of protein S12 from the small Escherichia coli ribosomal subunit. FEBS Lett. 1977 Jan 15;73(1):12–17. doi: 10.1016/0014-5793(77)80004-5. [DOI] [PubMed] [Google Scholar]
  6. Held W. A., Ballou B., Mizushima S., Nomura M. Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem. 1974 May 25;249(10):3103–3111. [PubMed] [Google Scholar]
  7. Hill W. E., Thompson J. D., Anderegg J. W. X-ray scattering study of ribosomes from Escherichia coli. J Mol Biol. 1969 Aug 28;44(1):89–102. doi: 10.1016/0022-2836(69)90406-9. [DOI] [PubMed] [Google Scholar]
  8. Huang K. H., Cantor C. R. Studies of 30 S Escherichia coli ribosome reassembly using individual proteins labeled with an environmentally sensitive fluorescent prode. J Mol Biol. 1975 Oct 5;97(4):423–441. doi: 10.1016/s0022-2836(75)80052-0. [DOI] [PubMed] [Google Scholar]
  9. Huang K. H., Fairclough R. H., Cantor C. R. Singlet energy transfer studies of the arrangement of proteins in the 30 S Escherichia coli ribosome. J Mol Biol. 1975 Oct 5;97(4):443–470. doi: 10.1016/s0022-2836(75)80053-2. [DOI] [PubMed] [Google Scholar]
  10. Kuntz I. D., Jr, Kauzmann W. Hydration of proteins and polypeptides. Adv Protein Chem. 1974;28:239–345. doi: 10.1016/s0065-3233(08)60232-6. [DOI] [PubMed] [Google Scholar]
  11. Lake J. A., Kahan L. Ribosomal proteins S5, S11, S13 and S19 localized by electron microscopy of antibody-labeled subunits. J Mol Biol. 1975 Dec 25;99(4):631–644. doi: 10.1016/s0022-2836(75)80177-x. [DOI] [PubMed] [Google Scholar]
  12. Lake J. A., Pendergast M., Kahan L., Nomura M. Localization of Escherichia coli ribosomal proteins S4 and S14 by electron microscopy of antibody-labeled subunits. Proc Natl Acad Sci U S A. 1974 Dec;71(12):4688–4692. doi: 10.1073/pnas.71.12.4688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lake J. A. Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes. J Mol Biol. 1976 Jul 25;105(1):131–139. doi: 10.1016/0022-2836(76)90200-x. [DOI] [PubMed] [Google Scholar]
  14. Lindemann H., Wittmann-Liebold B. Primary structure of protein S13 from the small ribosomal subunit of Escherichia coli. FEBS Lett. 1976 Dec 1;71(2):251–255. doi: 10.1016/0014-5793(76)80944-1. [DOI] [PubMed] [Google Scholar]
  15. Lutter L. C., Kurland C. G., Stöffler G. Protein neighborhoods in the 30S ribosomal subunit of Escherichia coli. FEBS Lett. 1975 Jun 15;54(2):144–150. doi: 10.1016/0014-5793(75)80062-7. [DOI] [PubMed] [Google Scholar]
  16. Mizushima S., Nomura M. Assembly mapping of 30S ribosomal proteins from E. coli. Nature. 1970 Jun 27;226(5252):1214–1214. doi: 10.1038/2261214a0. [DOI] [PubMed] [Google Scholar]
  17. Morgan J., Brimacombe R. A preliminary three-dimensional arrangement of the proteins in the Escherichia coli 30-S ribosomal sub-particle. Eur J Biochem. 1973 Sep 3;37(3):472–480. doi: 10.1111/j.1432-1033.1973.tb03008.x. [DOI] [PubMed] [Google Scholar]
  18. Pongs O., Rossner E. Comparison of the reactions of chemically reactive analogs of U-G-A and of A-U-G with ribosomes of Escherichia coli. Nucleic Acids Res. 1976 Jul;3(7):1625–1633. doi: 10.1093/nar/3.7.1625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pongs O., Stöffler G., Bald R. W. Location of protein S1 of Escherichia coli ribosomes at the 'A'-site of the codon binding site. Affinity labeling studies with a 3'-modified A-U-G analog. Nucleic Acids Res. 1976 Jul;3(7):1635–1646. doi: 10.1093/nar/3.7.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Pongs O., Stöffler G., Lanka E. The codon binding site of the Escherichia coli ribosome as studied with a chemically reactive A-U-G analog. J Mol Biol. 1975 Dec 5;99(2):301–315. doi: 10.1016/s0022-2836(75)80148-3. [DOI] [PubMed] [Google Scholar]
  21. Schreiner G., Nierhaus K. H. Protein involved in the binding of dihydrostreptomycin to ribosomes of Escherichia coli. J Mol Biol. 1973 Nov 25;81(1):71–82. doi: 10.1016/0022-2836(73)90248-9. [DOI] [PubMed] [Google Scholar]
  22. Sommer A., Traut R. R. Identification of neighboring protein pairs in the Escherichia coli 30 S ribosomal subunit by crosslinking with methyl-4-mercaptobutyrimidate. J Mol Biol. 1976 Oct 5;106(4):995–1015. doi: 10.1016/0022-2836(76)90348-x. [DOI] [PubMed] [Google Scholar]
  23. Tischendorf G. W., Zeichhardt H., Stöffler G. Architecture of the Escherichia coli ribosome as determined by immune electron microscopy. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4820–4824. doi: 10.1073/pnas.72.12.4820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tischendorf G. W., Zeichhardt H., Stöffler G. Determination of the location of proteins L14, L17, L18, L19, L22, L23 on the surface of the 5oS ribosomal subunit of Escherichia coli by immune electron microscopy. Mol Gen Genet. 1974;134(3):187–208. doi: 10.1007/BF00267715. [DOI] [PubMed] [Google Scholar]
  25. Vandekerckhove J., Rombauts W., Wittman Liebold B. The primary structure of protein S16 from Escherichia coli ribosomes. FEBS Lett. 1977 Jan 15;73(1):18–21. doi: 10.1016/0014-5793(77)80005-7. [DOI] [PubMed] [Google Scholar]
  26. Wabl M. R. Electron microscopic localization of two proteins on the surface of the 50 S ribosomal subunit of Escherichia coli using specific antibody markers. J Mol Biol. 1974 Apr 5;84(2):241–247. doi: 10.1016/0022-2836(74)90582-8. [DOI] [PubMed] [Google Scholar]

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