Adsorption of annealed branched polymers on curved surfaces

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.

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“…A detailed derivation of Eq. 2 is given in [45]. In this model, the stem-loop or hair-pin configurations of RNA are counted as the end points.…”

Section: Modelmentioning

confidence: 99%

Effects of RNA branching on the electrostatic stabilization of viruses

et al. 2016

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“…A closer inspection of micrographs from individual particles revealed that native immature HIV‐1 particles differ from each other with respect to their local curvature, average radius, and protein coverage at budding, suggesting that each particle really possessed its own unique topology. From theoretical studies of icosahedral virus models and spherical packings of interacting isotropic subunits, it is clear that curvature plays a major role in thermodynamic stability and the geometry of the ground state . However, the relationship between the geometry of immature HIV‐1 and its stability and, subsequently, virus infectivity is unknown.…”

Section: Introductionmentioning

confidence: 99%

Virus Matryoshka: A Bacteriophage Particle—Guided Molecular Assembly Approach to a Monodisperse Model of the Immature Human Immunodeficiency Virus

Saxena

Malyutin

et al. 2016

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Immature human immunodeficiency virus type 1 (HIV-1) is approximately spherical, but is constructed from a hexagonal lattice of the Gag protein. As a hexagonal lattice is necessarily flat, the local symmetry cannot be maintained throughout the structure. This geometrical frustration presumably results in bending stress. In natural particles, the stress is relieved by incorporation of packing defects, but the magnitude of this stress and its significance for the particles is not known. In order to control this stress, we have now assembled the Gag protein on a quasi-spherical template derived from bacteriophage P22. This template is monodisperse in size and electron-transparent, enabling the use of cryo-electron microscopy in structural studies. These templated assemblies are far less polydisperse than any previously described virus-like particles (and, while constructed according to the same lattice as natural particles, contain almost no packing defects). This system gives us the ability to study the relationship between packing defects, curvature and elastic energy, and thermodynamic stability. As Gag is bound to the P22 template by single-stranded DNA, treatment of the particles with DNase enabled us to determine the intrinsic radius of curvature of a Gag lattice, unconstrained by DNA or a template. We found that this intrinsic radius is far larger than that of a virion or P22-templated particle. We conclude that Gag is under elastic strain in a particle; this has important implications for the kinetics of shell growth, the stability of the shell, and the type of defects it will assume as it grows.

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“…where and are the fugacities of the end and branched points of the annealed chain, respectively (54) and is the effective excluded volume of each monomer. It is worth mentioning that in this model, the stem-loop or hair-pin configurations of RNA are considered as end points.…”

Section: Numerical Calculationsmentioning

confidence: 99%