RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses

Erdemci-Tandogan, Gonca; Orland, Henri; Zandi, Roya

doi:10.1103/physrevlett.119.188102

Cited by 15 publications

(13 citation statements)

References 53 publications

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“…The simulations and analytical studies performed in Refs. [32][33][34][35]56] are consistent with these results: the viral RNA with a larger degree of branching has a competitive edge over the other viral RNAs or non-viral randomly branched RNAs, keeping all other chain quantities equal. Indeed, all mean-field theories, numerical calculations and simulations up to now have indicated that the encapsidation free energy of both annealed and quenched branched polymers is significantly lower than that of linear polymers.…”

Section: Discussionsupporting

confidence: 76%

“…While previous theoretical studies have focused on the scaling behavior of linear and branched flexible polymers [32,34,35,48,[56][57][58], in this paper we study the impact of the stiffness or Kuhn length on the encapsidation of RNA by capsid proteins. In general the duplexed segments of viral RNA contain on average about five to six base-pairs [11].…”

Section: Discussionmentioning

confidence: 99%

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The effect of RNA stiffness on the self-assembly of virus particles

Erdemci-Tandogan

Schoot

et al. 2017

J. Phys.: Condens. Matter

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Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.

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Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

The effect of RNA stiffness on the self-assembly of virus particles

Erdemci-Tandogan

Schoot

et al. 2017

J. Phys.: Condens. Matter

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“…Since the self-assembly of virus particles involves a wide range of thermodynamics parameters, different time scales and an extraordinary number of possible pathways, the kinetics of assembly has remained elusive, linked to Levinthal's paradox for protein folding [8,[22][23][24]. The role of the genome on the assembly pathways and the structure of the capsid is even more intriguing [5,[25][26][27][28][29][30]. The kinetics of virus growth in the presence of RNA is at least 3 orders of magnitude faster than that of empty capsid assembly, indicating that the mechanism of assembly of CPs around RNA might be quite different.…”

Section: Introductionmentioning

confidence: 99%

How a Virus Circumvents Energy Barriers to Form Symmetric Shells

Panahandeh

Marichal

et al. 2020

ACS Nano

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Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly ordered structure in the host cell. Using small-angle X-ray scattering, we find out that a disorder-order transition occurs under physiological conditions upon an increase in capsid protein concentrations. Our cryo-transmission electron microscopy reveals closed spherical shells containing in vitro transcribed viral RNA even at pH 7.5, in marked contrast with the previous observations. We use Monte Carlo simulations to explain this disorder-order transition and find that, as the shell grows, the structures of disordered intermediates in which the distribution of pentamers does not belong to the icosahedral subgroups become energetically so unfavorable that the caps can easily dissociate and reassemble overcoming the energy barriers for the formation of perfect icosahedral shells. In addition, we monitor the growth of capsids under the condition that the nucleation and growth is the dominant pathway and show that the key for the disorder-order transition in both en masse and nucleation and growth pathways lies in the strength of elastic energy compared to the other forces in the system including protein-protein interactions and the chemical potential of free subunits. Our findings explain, at least in part, why perfect virions with icosahedral order form under different conditions including physiological ones.

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“…An important aspect of virus assembly in the presence of genomic RNA is the need for genome compaction [ 10 ], and several groups have made important contributions to the modelling of this aspect of virus assembly [ 11 • , 12 , 13 • , 14 • ]. The impact of non-specific electrostatic interactions between genomic RNAs and CP [ 15 , 16 , 17 , 18 , 19 •• ] and of the stiffness of the RNA molecule on the assembly process [ 20 • ] have been analysed. It has also been shown that the secondary structure of the RNA molecules play an essential role in determining capsid morphology in the self-assembly of Cowpea Chlorotic Mottle Virus (CCMV)-like particles [ 21 ].…”

Section: Introductionmentioning

confidence: 99%