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. 1983 May;42(2):171–180. doi: 10.1016/S0006-3495(83)84383-5

DNA and protein lattice-lattice interactions in the filamentous bacteriophages.

C J Marzec, L A Day
PMCID: PMC1329220  PMID: 6860774

Abstract

The relations between the protein coats and DNAs of the four filamentous bacteriophages fd, Xf, Pf1, and Pf3 are considered. These viruses have similar morphologies, yet show a diversity of detailed structure, having different protein coat symmetries (helical and rotational), different coat protein sizes (44-50 amino acids per subunit) and sequences, different nucleotide axial translations (2.3-5.5 A), and different ratios of nucleotides per coat protein subunit (integers 1.0 and 2.0, and nonintegers approximately 2.4). These divergences are all reconciled quantitatively by means of two theoretical concepts: the pitch connection and the restricted pitch connection. The pitch connection relates protein and DNA surface lattices with arbitrary, nonintegral nucleotide/subunit ratios in a nonrandom way. The restricted pitch connection selects a preferred set of n/s values. Both relations are derived formally in a mathematical appendix. The available structural data are explained, including the fd DNA pitch indicated by x-ray diffraction photos and the similar DNA morphologies of Xf and fd. Predictions are made for the existence of nonclassical inverted DNA structures (I-DNA) in Pf1 and Pf3.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Banner D. W., Nave C., Marvin D. A. Structure of the protein and DNA in fd filamentous bacterial virus. Nature. 1981 Feb 26;289(5800):814–816. doi: 10.1038/289814a0. [DOI] [PubMed] [Google Scholar]
  2. Berkowitz S. A., Day L. A. Turbidity measurements in an analytical ultracentrifuge. Determinations of mass per length for filamentous viruses fd, Xf, and Pf3. Biochemistry. 1980 Jun 10;19(12):2696–2702. doi: 10.1021/bi00553a025. [DOI] [PubMed] [Google Scholar]
  3. Casadevall A., Day L. A. DNA packing in the filamentous viruses fd, Xf, Pf1 and Pf3. Nucleic Acids Res. 1982 Apr 10;10(7):2467–2481. doi: 10.1093/nar/10.7.2467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Caspar D. L., Makowski L. The symmetries of filamentous phage particles. J Mol Biol. 1981 Jan 25;145(3):611–617. doi: 10.1016/0022-2836(81)90549-0. [DOI] [PubMed] [Google Scholar]
  5. Chothia C., Levitt M., Richardson D. Structure of proteins: packing of alpha-helices and pleated sheets. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4130–4134. doi: 10.1073/pnas.74.10.4130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cross T. A., Tsang P., Opella S. J. Comparison of protein and deoxyribonucleic acid backbone structures in fd and Pf1 bacteriophages. Biochemistry. 1983 Feb 15;22(4):721–726. doi: 10.1021/bi00273a002. [DOI] [PubMed] [Google Scholar]
  7. Day L. A., Wiseman R. L., Marzec C. J. Structure models for DNA in filamentous viruses with phosphates near the center. Nucleic Acids Res. 1979 Nov 24;7(6):1393–1403. doi: 10.1093/nar/7.6.1393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Enea V., Zinder N. D. A delection mutant of bacteriophage f1 containing no intact cistrons. Virology. 1975 Nov;68(1):105–114. doi: 10.1016/0042-6822(75)90152-x. [DOI] [PubMed] [Google Scholar]
  9. Fritzsche H., Cross T. A., Opella S. J., Kallenbach N. R. Structure and architecture of the bacterial virus fd. An infrared linear dichroism study. Biophys Chem. 1981 Nov;14(3):283–291. doi: 10.1016/0301-4622(81)85029-6. [DOI] [PubMed] [Google Scholar]
  10. Grant R. A., Lin T. C., Konigsberg W., Webster R. E. Structure of the filamentous bacteriophage fl. Location of the A, C, and D minor coat proteins. J Biol Chem. 1981 Jan 10;256(1):539–546. [PubMed] [Google Scholar]
  11. Herrmann R., Neugebauer K., Zentgraf H., Schaller H. Transposition of a DNA sequence determining kanamycin resistance into the single-stranded genome of bacteriophage fd. Mol Gen Genet. 1978 Feb 16;159(2):171–178. doi: 10.1007/BF00270890. [DOI] [PubMed] [Google Scholar]
  12. Makowski L., Caspar D. L., Marvin D. A. Filamentous bacteriophage Pf1 structure determined at 7A resolution by refinement of models for the alpha-helical subunit. J Mol Biol. 1980 Jun 25;140(2):149–181. doi: 10.1016/0022-2836(80)90101-1. [DOI] [PubMed] [Google Scholar]
  13. Marvin D. A., Pigram W. J., Wiseman R. L., Wachtel E. J., Marvin F. J. Filamentous bacterial viruses. XIL. Molecular architecture of the class I (fd, If1, IKe) virion. J Mol Biol. 1974 Sep 25;88(3):581–598. doi: 10.1016/0022-2836(74)90409-4. [DOI] [PubMed] [Google Scholar]
  14. Marvin D. A., Wiseman R. L., Wachtel E. J. Filamentous bacterial viruses. XI. Molecular architecture of the class II (Pf1, Xf) virion. J Mol Biol. 1974 Jan 15;82(2):121–138. doi: 10.1016/0022-2836(74)90336-2. [DOI] [PubMed] [Google Scholar]
  15. Marzec C. J., Day L. A. DNA and protein packing in type I filamentous bacteriophage. Biophys J. 1980 Oct;32(1):240–242. doi: 10.1016/S0006-3495(80)84947-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nave C., Brown R. S., Fowler A. G., Ladner J. E., Marvin D. A., Provencher S. W., Tsugita A., Armstrong J., Perham R. N. Pf1 filamentous bacterial virus. X-ray fibre diffraction analysis of two heavy-atom derivatives. J Mol Biol. 1981 Jul 15;149(4):675–707. doi: 10.1016/0022-2836(81)90353-3. [DOI] [PubMed] [Google Scholar]
  17. Newman J., Day L. A., Dalack G. W., Eden D. Hydrodynamic determination of molecular weight, dimensions, and structural parameters of Pf3 virus. Biochemistry. 1982 Jul 6;21(14):3352–3358. doi: 10.1021/bi00257a016. [DOI] [PubMed] [Google Scholar]
  18. Newman J., Swinney H. L., Day L. A. Hydrodynamic properties and structure of fd virus. J Mol Biol. 1977 Nov 5;116(3):593–603. doi: 10.1016/0022-2836(77)90086-9. [DOI] [PubMed] [Google Scholar]
  19. Peterson C., Winter W. T., Dalack G. W., Day L. A. Structure of the filamentous bacteriophage, Pf3, by X-ray fiber diffraction. J Mol Biol. 1982 Dec 25;162(4):877–881. doi: 10.1016/0022-2836(82)90552-6. [DOI] [PubMed] [Google Scholar]
  20. Thomas G. J., Jr, Day L. A. Conformational transitions in Pf3 and their implications for the structure and assembly of filamentous bacterial viruses. Proc Natl Acad Sci U S A. 1981 May;78(5):2962–2966. doi: 10.1073/pnas.78.5.2962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Torbet J., Maret G. High-field magnetic birefringence study of the structure of rodlike phages Pf1 and fd in solution. Biopolymers. 1981 Dec;20(12):2657–2669. doi: 10.1002/bip.1981.360201212. [DOI] [PubMed] [Google Scholar]
  22. Webster R. E., Grant R. A., Hamilton L. A. Orientation of the DNA in the filamentous bacteriophage f1. J Mol Biol. 1981 Oct 25;152(2):357–374. doi: 10.1016/0022-2836(81)90247-3. [DOI] [PubMed] [Google Scholar]
  23. Wiseman R. L., Day L. A. Different packaging of DNA in the filamentous viruses Pf1 and Xf. J Mol Biol. 1977 Nov 5;116(3):607–611. doi: 10.1016/0022-2836(77)90088-2. [DOI] [PubMed] [Google Scholar]

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