Impact of a nonuniform charge distribution on virus assembly

Li, Siyu; Erdemci-Tandogan, Gonca; Wagner, Jef; Schoot, Paul van der; Zandi, Roya

doi:10.1103/physreve.96.022401

Cited by 31 publications

(39 citation statements)

References 45 publications

(48 reference statements)

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“…To do this, we consider a virus capsid with a polyanionic cargo that interacts with the polycationic RNA‐binding domains on the coat proteins lining the cavity of the protein shell. Complexation of the polycationic and polyanionic species does not necessarily lead to charge neutralization . There are strong indications for overcharging, implying the total number of charges on the negatively charged species is larger than that on the positively charged species .…”

Section: Resultsmentioning

confidence: 98%

“…Complexation of the polycationic and polyanionic species does not necessarily lead to charge neutralization . There are strong indications for overcharging, implying the total number of charges on the negatively charged species is larger than that on the positively charged species . If indeed the case, this creates a Donnan potential across the protein shell that draws in mobile ionic species, in particular positively charged ones.…”

Section: Resultsmentioning

confidence: 99%

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Experimental and Theoretical Determination of the pH inside the Confinement of a Virus‐Like Particle

Maassen

Schoot

Cornelissen

2018

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In biology, a variety of highly ordered nanometer-size protein cages is found. Such structures find increasing application in, for example, vaccination, drug delivery, and catalysis. Understanding the physiochemical properties, particularly inside the confinement of a protein cage, helps to predict the behavior and properties of new materials based on such particles. Here, the relation between the bulk solution pH and the local pH inside a model protein cage, based on virus-like particles (VLPs) built from the coat proteins of the cowpea chlorotic mottle virus, is investigated. The pH is a crucial parameter in a variety of processes and is potentially significantly influenced by the high concentration of charges residing on the interior of the VLPs. The data show a systematic more acidic pH of 0.5 unit inside the VLP compared to that of the bulk solution for pH values above pH 6, which is explained using a theoretical model based on a Donnan equilibrium. The model agrees with the experimental data over almost two orders of magnitude, while below pH 6 the experimental data point to a buffering capacity of the VLP. These results are a first step in a better understanding of the physiochemical conditions inside a protein cage.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Experimental and Theoretical Determination of the pH inside the Confinement of a Virus‐Like Particle

Maassen

Schoot

Cornelissen

2018

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“…The process of formation of virus particles in which the protein subunits encapsidate genome (RNA or DNA) to form a stable, protective shell called the capsid is an essential step in the viral life cycle [1][2][3]. The capsid proteins of many small single-stranded (ss)RNA viruses spontaneously package their wild-type (wt) and other negatively charged polyelectrolytes, a process basically driven by the electrostatic interaction between positively charged protein subunits and negatively charged cargo [4][5][6][7][8][9]. Understanding the phenomena of formation of viral particles is of great interest due to their potential applications in nanomedicine and biomaterials.…”

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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“…Following these experiments a number of simulation studies, using quenched (fixed) branched polymers as a model for RNA, have shown that the optimal length of encapsidated RNA increases when accounting for its secondary structure [12,33]. Mean-field calculations using annealed (equilibrium) branched polymers as model RNAs have also shown that the length of encapsidated polymer increases as the propensity to form larger numbers of branched points increases [32,34,35]. More importantly, these calculations show that a higher level of branching considerably increases the depth of the freeenergy gain associated with the encapsulation of RNA by a positively charged shell.…”

Section: Introductionmentioning

confidence: 99%

“…Above-mentioned theoretical and experimental studies indicate that in a head-to-head competition between two different types of RNAs, the RNA with a larger number of branching junctions or branch points should have a competitive edge over others [32,34,35]. A naive physical explanation is that branching causes RNA molecules to become more compact than structureless linear polymers of similar chain length, which are then easier to accommodate in the limited space provided by the cavity of a capsid.…”

Section: Introductionmentioning

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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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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Impact of a nonuniform charge distribution on virus assembly

Cited by 31 publications

References 45 publications

Experimental and Theoretical Determination of the pH inside the Confinement of a Virus‐Like Particle

Experimental and Theoretical Determination of the pH inside the Confinement of a Virus‐Like Particle

How a Virus Circumvents Energy Barriers to Form Symmetric Shells

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

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