Research Summary

Structure and Assembly of Filamentous Bacterial Viruses
We are studying protein-nucleic acid interactions that occur in the assembly pathways and the final structures of several filamentous bacterial viruses, all of which are in the genus Inovirus. Each of these viruses has a circular single-stranded DNA in the core of a cylindrical shell made by close-packing of thousands of copies of a small helical protein, the major coat protein. At the ends of the viruses, where the DNA molecules fold back on themselves, there are a few copies each of different minor proteins. The viruses are assembled at the cell membranes of the host cells in extrusion processes that do not lyse the cells. Given the variety of different species, the genus provides many instances in which exactly the same function is carried out by molecules of diverse sequence, allowing fruitful comparative analyses.

One such instance is the way DNA is arranged in the different virions, the function being the protection of the DNA in a structure that can be efficiently assembled by the cell, yet efficiently disassembled when the virus infects a new cell. In all cases, the DNA helix in the core has two anti-parallel strands, and the part of the major protein subunit in contact with the DNA is highly basic and highly *-helical, with its local helix axis almost parallel to the axis of the DNA. Dramatic differences occur in the details. In the Pf1 virion there is exactly one nucleotide per protein subunit (n/s = 1), and the DNA and the protein shell have the same pitch of 16 A and follow the same symmetry rule. The structural unit of two subunits and two nucleotides, one from each strand, has a rise of 6 A and a rotation of 1320, values which are about two and four times those for classical B-DNA, respectively. The protein coat forces the phosphates of both strands to the center and holds the bases unstacked on the outside. In C2 virus n/s appears to be an integer, but 2 rather than 1. In C2, the DNA has a pitch near +30 A, and is quite similar to classical DNA; the bases are stacked at the center and the phosphates are outside. Integer stoichiometry in C2 would allow its protein shell and its DNA to follow exactly the same helical symmetry rule, as is true for Pf1, but whether or not they do in C2 is not yet known. Xf virus has sequence homologies to both Pf1 and C2 yet it has a non-integer n/s ratio of 2.16, and it is clear that its DNA and protein helices do not have the same helical symmetry. Finally, Ff (M13, fd, f1) also has a non-integer n/s ratio, namely 2.40, and DNA and protein shell of different symmetry. The protein shells of Ff and Xf differ significantly, but their DNA structures are closely similar. It is clear from this brief comparison that fundamental issues of the chemical natures of DNA-protein interfaces can be addressed through comparative studies of species within this genus of viruses.




Recent Articles

Blanch EW, Hecht L, Day LA, Pederson DM, Barron LD. (2001).
Tryptophan absolute stereochemistry in viral coat proteins from raman optical activity.
J Am Chem Soc 2001 May 23;123(20):4863-4
PMID: 11457308

Day, L.A., & Maniloff, J., (2000).
Inoviridae.
In: Virus Taxonomy: The Classification and Nomenclature of Viruses. The Seventh Report of the International Committee on Taxonomy of Viruses, M.H.V. van Regenmortel, et al., Editors. (Academic Press, San Diego) pp. 267-275
Full Article

Hecht, L., Barron, L. D., Blanch, E. W., Bell, A. F., & Day, L. A. (1999).
Raman optical activity instrument for studies of biopolymer structure and dynamics.
J. Raman Spectrosc. 30, 815-825.

Blanch EW, Bell AF, Hecht L, Day LA, Barron LD. (1999).
Raman optical activity of filamentous bacteriophages: hydration of alpha-helices.
J Mol Biol. 1999 Jul 2;290(1):1-7
PMID: 10388553
Abstract  |  Full Article

Barron, L.D., Blanch, E.W., Smyth, E., Bell, A.F., Day, L.A., & Hecht, L. (1999).
Raman optical activity studies of the influence of water on structure and dynamics of proteins, viruses and nucleic acids.
In: Spectroscopy of Biological Molecules: New Directions, J. Greve, G.J. Puppels and C. Otto, Editors. (Kluwer, Dordrecht) pp. 643-646.



Shin, S., & Day, L. A. (1995).
Separation and size determination of circular and linear single-stranded DNAs by alkaline agarose gel electrophoresis.
Analytical Biochem., 226:202-206

Kostrikis, L. G., Reisberg, S. A., Kim, H. Y., Shin, S., & Day, L. A. (1995).
C2, an unusual filamentous bacterial virus: coat protein sequence and conformation, DNA size and conformation, and nucleotide/subunit ratio.
Biochemistry, 34:4077-4087

Liu, D. J., & Day, L. A. (1994).
Pf1 virus structure: helical coat protein and DNA with paraxial phosphates.
Science, 265:671-674

Marzec, C. J., & Day, L. A. (1994).
An electrostatic spatial resonance model for coaxial helical structures with applications to filamentous bacteriophages.
Biophys. J., 66:2205-2222

Kostrikis, L. G., Liu, D. J., & Day, L. A. (1994).
Ultraviolet absorption and circular dichroism of Pf1 virus: nucleotide/subunit ratio of unity, hyperchromic tyrosines and DNA bases, and high helicity in the subunits.
Biochemistry, 33:1694-1703

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C.V.

Ph.D. Oberlin College, B.A., 1958; Yale University, Ph.D., 1963; Max Planck Institute, Germany, Post Doc., 1964-1968; New York University School of Medicine, Faculty, 1969-present. PHRI, 1968-present.