Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses

Šiber, Antonio; Podgornik, Rudolf

doi:10.1103/physreve.78.051915

Cited by 81 publications

(130 citation statements)

References 48 publications

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“…Thus the phenomenon of overcharging is associated with many factors other than the structure of RNA [14][15][16][17]22]. Our numerical solutions of the polyelectrolyte Poisson-Boltzmann theory, without any additional assumptions regarding the effective monomer charge, do not support a universal overcharging of the virion.…”

Section: Introductionmentioning

confidence: 68%

“…(1) describes the entropic cost for a nonuniform polymer density, and the last two lines in Eq. (1) describe the electrostatic interactions between the polyelectrolyte, the salt ions, and the charged capsid at the level of Poisson-Boltzmann theory [22]. The full derivation of the standard form of the free energy can be found in Refs.…”

Section: Theorymentioning

confidence: 99%

“…In virtually all theoretical studies published to date investigating the overcharging in viruses, the genome is modeled as a simple linear polyelectrolyte chain [15,[22][23][24]. Thus the phenomenon of overcharging is associated with many factors other than the structure of RNA [14][15][16][17]22].…”

Section: Introductionmentioning

confidence: 99%

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RNA topology remolds electrostatic stabilization of viruses

et al. 2014

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Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell: the capsid. Spontaneous coassembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively charged RNA and the positively charged inner capsid wall. Using field theoretic formulation we show that the inherently branched RNA secondary structure allows viruses to maximize the amount of encapsulated genome and make assembly more efficient, allowing viral RNAs to out-compete cellular RNAs during replication in infected host cells.

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Section: Introductionmentioning

confidence: 68%

Section: Theorymentioning

confidence: 99%

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RNA topology remolds electrostatic stabilization of viruses

et al. 2014

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“…[11][12][13][14][15][16][17][18] A molecular understanding of the dominant forces behind the organization of the genome inside virus capsids would enable development of strategies to package desired new RNA/DNA sequences with the use of required proteins or their equivalents. A fundamental understanding of how evolution has sculpted the viral assembly via interdependence between proteins and nucleic acids would thus enable biomimicry in aqueous assembly of natural and synthetic polymers with potential technological implications in applications such as safe gene delivery platforms.…”

Section: Introductionmentioning

confidence: 99%

Electrostatics of capsid-induced viral RNA organization

Forrey

Muthukumar

2009

The Journal of Chemical Physics

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We have addressed the role of electrostatics in the formation of genome structure in the Pariacoto virus, where substantial experimental data are available. We have used Langevin dynamics simulation of a coarse-grained model, based on the published crystal structure of the rigid portion of the Pariacoto capsid and including flexible N-terminal protein arms, attached to the rigid capsid at the appropriate locations. The inclusion of charged residues in our model was dictated solely by the location of charges inherent in the Pariacoto sequence itself. Although the viral genome and other exogenous RNA sequences used in experimental studies can assume secondary structures, we have intentionally used uniformly charged flexible polyelectrolyte lacking predetermined secondary structures as the substitute for the viral genome, in order to see whether the same final assembled genome structure emerges without invoking secondary RNA structures. The intent of our study was to investigate the internal environment presented by the capsid proteins of Pariacoto virus, specifically whether the topological features and electrostatic potential at the inner capsid surface can induce complexation of generic negatively charged polyelectrolyte into structures similar to those observed experimentally with packaged RNA. We find that the charge decoration on the interior of the capsid templates the assembly of the flexible polyelectrolyte, allowing hybridizationlike folding of similarly charged strands, and eventually organizing dodecahedral assembly of the polymer. Our results from a generic flexible polyelectrolyte for the assembled structure and bimodal monomer distribution are remarkably matched to that of the viral RNA found experimentally. Results of our work can be interpreted primarily as a consequence of electrostatics, as consideration of base-pairing has been omitted. We propose that our work supports the growing body of evidence that electrostatic interactions play a crucial role in RNA viral assembly and structure.

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“…[23][24][25][26][27][28][29][30][31][32][33][34][35] Since the focus of this paper is on HIV particles, we employ Edwards-de GennesLifshitz theory to calculate the free energy of a linear polymer confined in a cylindrical and conical shell. [36][37][38] In the ground-state approximation of long chains, it reads…”

Section: Modelmentioning

confidence: 99%

Role of Genome in the Formation of Conical Retroviral Shells

et al. 2016

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Human immunodeficiency virus (HIV) capsid proteins spontaneously assemble around the genome into a protective protein shell called the capsid, which can take on a variety of shapes broadly classified as conical, cylindrical and irregular. The majority of capsids seen in in vivo studies are conical in shape, while in vitro experiments have shown a preference for cylindrical capsids. The factors involved in the selection of the unique shape of HIV capsids are not well understood, and in particular the impact of RNA on the formation of the capsid is not known. In this work, we study the role of the genome and its interaction with the capsid protein by modeling the genomic RNA through a mean-field theory. Our results show that the confinement free energy for a homopolymeric model genome confined in a conical capsid is

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Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses

Cited by 81 publications

References 48 publications

RNA topology remolds electrostatic stabilization of viruses

RNA topology remolds electrostatic stabilization of viruses

Electrostatics of capsid-induced viral RNA organization

Role of Genome in the Formation of Conical Retroviral Shells

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