The effects of various polyanions on shell formation of some spherical viruses

Bancroft, J.B.; Hiebert, E.; Bracker, Charles E.

doi:10.1016/0042-6822(69)90029-4

Cited by 101 publications

(103 citation statements)

References 8 publications

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“…Finally, when truncated or incomplete RNAs are encapsidated, the product is frequently a T 1 virus having the properties of the satellite viruses. 8,16 While these observations are only suggestive, it is not unreasonable to speculate that the satellite virus RNAs may have been derived from RNA4 species of multipartite viruses. Of course the converse might also be considered, but because of the involvement of RNA3, this would necessarily be a more intricate and less probable process.…”

Section: Rna4 and The Evolution Of Satellite Virusesmentioning

confidence: 93%

The crystallographic structure of brome mosaic virus

Lucas

Larson

McPherson

2002

Journal of Molecular Biology

136

181

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The structure of brome mosaic virus (BMV), the type member of the bromoviridae family, has been determined from a single rhombohedral crystal by X-ray diffraction, and re®ned to an R value of 0.237 for data in the range 3.4-40.0 A Ê . The structure, which represents the native, compact form at pH 5.2 in the presence of 0.1 M Mg 2 , was solved by molecular replacement using the model of cowpea chlorotic mottle virus (CCMV), which BMV closely resembles. The BMV model contains amino acid residues 41-189 for the pentameric capsid A subunits, and residues 25-189 and 1-189 for the B and C subunits, respectively, which compose the hexameric capsomeres. In the model there are two Mg ions and one molecule of polyethylene glycol (PEG). The ®rst 25 amino acid residues of the C subunit are modeled as polyalanine. The coat protein has the canonical``jellyroll'' b-barrel topology with extended amino-terminal polypeptides as seen in other icosahedral plant viruses. Mass spectrometry shows that in native BMV virions, a signi®cant fraction of the amino-terminal peptides are apparently cleaved. No recognizable nucleic acid residue is visible in the electron density maps except at low resolution where it appears to exhibit a layered arrangement in the virion interior. It is juxtaposed closely with the interior surface of the capsid but does not interpenetrate. The protein subunits forming hexameric capsomeres, and particularly dimers, appear to interact extensively, but the subunits otherwise contact one another sparsely about the 5-fold and quasi 3-fold axes. Thus, the virion appears to be an assembly of loosely associated hexameric capsomeres, which may be the basis for the swelling and dissociation that occurs at neutral pH and elevated salt concentration. A Mg ion is observed to lie exactly on the quasi-3-fold axis and is closely coordinated by side-chains of three quasi-symmetry-related residues glutamates 84, with possible participation of side-chains from threonines 145, and asparagines 148. A presumptive Mg 2 is also present on the 5-fold axis where there is a concentration of negatively charged side-chains, but the precise coordination is unclear. In both cases these cations appear to be essential for maintenance of virion stability. Density that is contiguous with the viral interior is present on the 3-fold axis at the center of the hexameric capsomere, where there is a pore of about 6 A Ê diameter. The density cannot be attributed to cations and it was modeled as a PEG molecule.

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Section: Rna4 and The Evolution Of Satellite Virusesmentioning

confidence: 93%

The crystallographic structure of brome mosaic virus

Lucas

Larson

McPherson

2002

Journal of Molecular Biology

136

181

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“…1). In-vitro studies of solutions of capsid proteins and RNA molecules of a given virus show that under the biological pH and salinity they can spontaneously self-assemble into infectious viruses [4,5,6]. This letter focuses on the energetics of this amazing protein-RNA self-assembly.…”

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“…This letter focuses on the energetics of this amazing protein-RNA self-assembly. In addition to hydrophobic attraction between the proteins it is driven by strong Coulomb attraction between capsid proteins and RNA molecules [3,4]. Indeed, ss RNA is strongly negatively charged.…”

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Electrostatic theory of viral self-assembly

Zhang

Shklovskiǐ

2008

Physica A: Statistical Mechanics and its Applications

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Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive Nterminal tails. We explore the role played by the Coulomb interaction between the brush of positive N-terminal tails rooted at the inner surface of the capsid and the negative ss RNA molecule. We show that viruses are most stable when the total contour length of ss RNA is close to the total length of the tails. For such a structure the absolute value of the total RNA charge is approximately twice larger than the charge of the capsid. This conclusion agrees with structural data.Unlike living cells, viruses do not have any metabolic activity, which may mean that they are in the state of thermal equilibrium. This is one of the reasons why the statistical physics can be used for understanding of viruses. The structure of viruses is also dramatically simple. Inside the protein capsid each virus carries its genome, which consists of one or more DNA or RNA molecules and is used for reproduction in host cells. The focus of this letter is on viruses with single stranded RNA (ss RNA) genomes. Detailed image reconstruction of apparently spherical viruses reveals their icosahedral symmetry. This is why such a virus capsid can be viewed as a curved two-dimensional crystal closed on itself [1, 2, 3].Here we concentrate on the viruses of the so called T = 3 class, in which a capsid is made of precisely 180 identical proteins, or of 60 triangular blocks consisting of three proteins each (see Fig. 1). In-vitro studies of solutions of capsid proteins and RNA molecules of a given virus show that under the biological pH and salinity they can spontaneously self-assemble into infectious viruses [4,5,6]. This letter focuses on the energetics of this amazing protein-RNA self-assembly. In addition to hydrophobic attraction between the proteins it is driven by strong Coulomb attraction between capsid proteins and RNA molecules [3,4]. Indeed, ss RNA is strongly negatively charged. Its backbone has one negative phosphate per nucleotide or per 0.65 nm. We denote the total ss RNA charge of a virus particle as −Q r . According to Tab. I of T = 3 viruses Q r is about several thousand in units of the proton charge. On the other hand, for many viruses their capsid proteins carry substantial net positive charge q p , which can reach 17. The net positive charge of the capsid of a T = 3 virus Q c = 180q p can, therefore, reach 3000. Although, in biological conditions the protein-RNA interaction is screened by monovalent salt at the Debye-Huckel screening radius r s , attraction energy of such big charges is still very large.A dramatic feature of the group A of T = 3 viruses collected in the upper part of Tab. I is that almost all the capsid protein charge is concentrated in the N-terminal tail located inside the capsid (Fig. 1). We define such an N-terminal tail as the flexible sequence of amino acids, which starts from the N-terminus of the protein an...

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“…In a series of classic experiments, Bancroft and coworkers (1,2) demonstrated that certain viruses can encapsidate nonnative RNA and even generic polyanions. Dominance of the electrostatics as the driving force for viral assembly has led to the expectation of a simple relationship between the total capsid charge Q P and the genome charge Q R , as every nucleotide carries one unit of negative charge.…”

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Thermodynamic basis for the genome to capsid charge relationship in viral encapsidation

Ting

Wang

2011

Proc. Natl. Acad. Sci. U.S.A.

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We establish an appropriate thermodynamic framework for determining the optimal genome length in electrostatically driven viral encapsidation. Importantly, our analysis includes the electrostatic potential due to the Donnan equilibrium, which arises from the semipermeable nature of the viral capsid, i.e., permeable to small mobile ions but impermeable to charged macromolecules. Because most macromolecules in the cellular milieu are negatively charged, the Donnan potential provides an additional driving force for genome encapsidation. In contrast to previous theoretical studies, we find that the optimal genome length is the result of combined effects from the electrostatic interactions of all charged species, the excluded volume and, to a very significant degree, the Donnan potential. In particular, the Donnan potential is essential for obtaining negatively overcharged viruses. The prevalence of overcharged viruses in nature may suggest an evolutionary preference for viruses to increase the amount of genome packaged by utilizing the Donnan potential (through increases in the capsid radius), rather than high charges on the capsid, so that structural stability of the capsid is maintained.polyelectrolyte | viral assembly T he most prevalent viruses in nature are single-stranded RNA viruses with the genetic material enclosed in icosahedral-shaped capsids made up of 60 T protein units, where the T-number is a small integer index. The protein units (capsomers) often contain highly basic peptide arms that extend into the capsid interior and, under physiological conditions, are positively charged. Electrostatic attraction provides the driving force for encapsidating the negatively charged RNA, which, in turn, helps overcome the electrostatic repulsion among the capsomers during the capsid assembly.In a series of classic experiments, Bancroft and coworkers (1, 2) demonstrated that certain viruses can encapsidate nonnative RNA and even generic polyanions. Dominance of the electrostatics as the driving force for viral assembly has led to the expectation of a simple relationship between the total capsid charge Q P and the genome charge Q R , as every nucleotide carries one unit of negative charge. Belyi and Muthukumar (3) compiled data for 19 wild type viruses from several viral families and found an apparent "universal" charge ratio of Q R ∕Q P ≈ 1.6, which they explained by combining the ground-state dominance approximation for polyelectrolyte binding to an oppositely charged polymer brush with the Manning condensation theory (4). The former predicts a 1∶1 charge ratio and the latter is used as a qualitative argument for the actual charge on the RNA being less than the nominal charge. Hu, et al. (5), however, assumed that the RNA winds around individual peptide arms and found that the viruses are most stable when the total contour length of the RNA is close to the total length of the peptide arms; this roughly gives a charge ratio of 2. In other works that ignore the peptide arms completely, there is additional disagreemen...

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The effects of various polyanions on shell formation of some spherical viruses

Cited by 101 publications

References 8 publications

The crystallographic structure of brome mosaic virus

The crystallographic structure of brome mosaic virus

Electrostatic theory of viral self-assembly

Thermodynamic basis for the genome to capsid charge relationship in viral encapsidation

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