Role of Genome in the Formation of Conical Retroviral Shells

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

doi:10.1021/acs.jpcb.6b02712

Cited by 8 publications

(11 citation statements)

References 44 publications

(146 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…= D[ψ(r)]e − 1 2 υ drψ 2 (r) e −iυ N 0 ds ψ(r(s)) , (19) with ψ the auxiliary field representing the monomer density field. Plugging Eqs.…”

Section: Discussion and Summarymentioning

confidence: 99%

“…Indeed, it appears that the compactness of the ssRNA wild-type viral genomes is one of the principal characteristics of their nucleotide sequence, setting them distinctly apart from randomized sequences [11,19], and that the physical compactness of the viral genome can be regarded as a primary factor among evolutionary constraints [20].…”

Section: Introductionmentioning

confidence: 99%

“…Viral RNAs are found to be compact and highly branched [18] due to the base-pairing between the nucleotides, engendering compactification and folding of the molecule. Indeed, it appears that the compactness of the ssRNA wild-type viral genomes is one of the principal characteristics of their nucleotide sequence, setting them distinctly apart from randomized sequences [11,19], and that the physical compactness of the viral genome can be regarded as a primary factor among evolutionary constraints [20].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effects of RNA branching on the electrostatic stabilization of viruses

et al. 2016

Self Cite

View full text Add to dashboard Cite

Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular the sequence will determine the possible secondary structures that the ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

show abstract

“…= D[ψ(r)]e − 1 2 υ drψ 2 (r) e −iυ N 0 ds ψ(r(s)) , (19) with ψ the auxiliary field representing the monomer density field. Plugging Eqs.…”

Section: Discussion and Summarymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Effects of RNA branching on the electrostatic stabilization of viruses

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Protein-protein interactions between CA domains are the driving force for Gag assembly in the immature hexagonal lattice 4,5 as well as for CA assembly in the mature capsid [6][7][8] . Previous computer simulations and theoretical studies have revealed key features of CA self-assembly into conical mature HIV-1 capsids [8][9][10][11][12][13][14] .…”

Section: Introductionmentioning

confidence: 99%

In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

et al. 2016

Self Cite

View full text Add to dashboard Cite

HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

show abstract

“…Experiments on synthetic polyions and nanoparticles find Q is between 0.6 and 9, depending on the molecular weight, topology of the polyanion and so on [ 30 , 55 , 56 ]. Recently, we argued that the value of Q should depend on the level of (annealed) branching, the linear charge density and the quality of the solvent of the polyanion [ 8 , 32 , 49 , 50 , 52 ]. In the next section, we make it plausible that in addition Q may well depend on the concentration of the polyanion too.…”

Section: Cargo Length and Encapsulation Efficiencymentioning

confidence: 99%

The different faces of mass action in virus assembly

et al. 2018

Self Cite

View full text Add to dashboard Cite

The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation. By invoking mass action-type arguments and a simple model describing electrostatic interactions, we show how these forms of entropy might settle the competition between negatively charged polymers of different molecular weights for co-assembly with the coat proteins. In direct competition, mass action turns out to strongly work against the encapsulation of RNAs that are significantly shorter, which is typically the case for non-viral (host) RNAs. We also find that coat proteins favor forming virus particles over nonspecific binding to other proteins in the cytosol even if these are present in vast excess. Our results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.

show abstract

Role of Genome in the Formation of Conical Retroviral Shells

Cited by 8 publications

References 44 publications

Effects of RNA branching on the electrostatic stabilization of viruses

Effects of RNA branching on the electrostatic stabilization of viruses

In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

The different faces of mass action in virus assembly

Contact Info

Product

Resources

About