The behavior of annealed branched polymers near adsorbing surfaces plays a fundamental role in many biological and industrial processes. Most importantly single stranded RNA in solution tends to fold ...up and self-bind to form a highly branched structure. Using a mean field theory, we both perturbatively and numerically examine the adsorption of branched polymers on surfaces of several different geometries in a good solvent. Independent of the geometry of the wall, we observe that as branching density increases, surface tension decreases. However, we find a coupling between the branching density and curvature in that a further lowering of surface tension occurs when the wall curves towards the polymer, but the amount of lowering of surface tension decreases when the wall curves away from the polymer. We find that for branched polymers confined into spherical cavities, most of branch-points are located in the vicinity of the interior wall and the surface tension is minimized for a critical cavity radius. For branch polymers next to sinusoidal surfaces, we find that branch-points accumulate at the valleys while end-points on the peaks.
We study the ground states of crystals on spherical surfaces. These ground states consist of positive disclination defects in structures spanning from flat and weakly curved caps to closed shells. ...Comparing two continuum theories and one discrete-lattice simulation, we first investigate the transition between defect-free caps to single-disclination ground states and show it to be continuous and symmetry breaking. Further, we show that ground states adopt icosahedral subgroup symmetries across the full range of curvatures, even far from the closure of complete shells. While superficially similar to other models of 2D "jellium" (e.g., superconducting disks and 2D Wigner crystals), the interplay between the free edge of caps and the non-Euclidean geometry of its embedding leads to nontrivial ground state behavior that is without counterpart in planar jellium models.
By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the ...energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.
On virus growth and form Zandi, Roya; Dragnea, Bogdan; Travesset, Alex ...
Physics reports,
01/2020, Letnik:
847
Journal Article
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Here, we review approaches aimed at deciphering the physical mechanisms responsible for viral structure and assembly. We discuss the basic principles of condensed matter physics, macroscopic ...electrostatics and elastomechanics as they apply to nanosized two-dimensional biomolecular shells with spherical topology and icosahedral symmetry, as well as their proper extension to nonspherical structures pertinent to retroviruses. We examine the relation between the virus structure, the physical interactions that are driving their (self)assembly and the thermodynamics of transition from an isotropic protein solution to the assembled shell state, and discuss the driving forces for large-scale structural reorganizations characterizing maturation processes in the already assembled nano-shells. We furthermore review physical models corresponding to the condensed states of confined genome-carrying biopolymers in viral nano-shells during virus self-assembly and host-cell infection processes, and show how the combination of discrete and continuum coarse grained mechanics, commonly used in the fundamental physical description of viruses, together with the pertinent description of generic long-range electrostatic and specific short-range interactions give insight into the details of structural order and mechanical properties of viruses and elucidates their role in nano-container and nano-machine functions.
Size Regulation of ss-RNA Viruses Zandi, Roya; van der Schoot, Paul
Biophysical journal,
01/2009, Letnik:
96, Številka:
1
Journal Article
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While a monodisperse size distribution is common within one kind of spherical virus, the size of viral shells varies from one type of virus to another. In this article, we investigate the physical ...mechanisms underlying the size selection among spherical viruses. In particular, we study the effect of genome length and genome and protein concentrations on the size of spherical viral capsids in the absence of spontaneous curvature and bending energy. We find that the coat proteins could well adjust the size of the shell to the size of their genome, which in turn depends on the number of charges on it. Furthermore, we find that different stoichiometric mixtures of proteins and genome can produce virus particles of various sizes, consistent with in vitro experiments.
A virus binding to a surface causes stress of the virus cage near the contact area. Here, we investigate the potential role of substrate-induced structural perturbation in the mechanical response of ...virus particles to adsorption. This is particularly relevant to the broad category of viruses stabilized by weak noncovalent interactions. We utilize atomic force microscopy to measure height distributions of the brome mosaic virus upon adsorption from solution on atomically flat substrates and present a continuum model that captures our observations and provides estimates of elastic properties and of the interfacial energy of the virus, without recourse to indentation.
A nearly 3-year-old boy on nightly dialysis presented emergently with sudden loss of vision. On examination, his visual acuity was light perception in the right eye and no light perception in the ...left eye. There was bilateral optic disk edema, diffuse pallor of posterior poles, and a cherry red spot in the left fundus. The patient was subsequently found to be hemodynamically unstable and admitted to the pediatric intensive care unit with presumed septic shock. Optical coherence tomography revealed paracentral acute middle maculopathy lesions in the right eye and diffusely thick retina in the left eye. Magnetic resonance imaging and magnetic resonance angiography of the brain and vessels did not reveal any acute findings. The patient’s presentation was most consistent with bilateral nonarteritic ischemic optic neuropathy and unilateral central retinal artery occlusion. On repeat evaluation 9 months later, vision was largely unchanged.
Virus Mechanics under Molecular Crowding Zeng, Cheng; Scott, Liam; Malyutin, Andrey ...
The journal of physical chemistry. B,
02/2021, Letnik:
125, Številka:
7
Journal Article
Recenzirano
Viruses avoid exposure of the viral genome to harmful agents with the help of a protective protein shell known as the capsid. A secondary effect of this protective barrier is that macromolecules that ...may be in high concentration on the outside cannot freely diffuse across it. Therefore, inside the cell and possibly even outside, the intact virus is generally under a state of osmotic stress. Viruses deal with this type of stress in various ways. In some cases, they might harness it for infection. However, the magnitude and influence of osmotic stress on virus physical properties remains virtually unexplored for single-stranded RNA virusesthe most abundant class of viruses. Here, we report on how a model system for the positive-sense RNA icosahedral viruses, brome mosaic virus (BMV), responds to osmotic pressure. Specifically, we study the mechanical properties and structural stability of BMV under controlled molecular crowding conditions. We show that BMV is mechanically reinforced under a small external osmotic pressure but starts to yield after a threshold pressure is reached. We explain this mechanochemical behavior as an effect of the molecular crowding on the entropy of the “breathing” fluctuation modes of the virus shell. The experimental results are consistent with the viral RNA imposing a small negative internal osmotic pressure that prestresses the capsid. Our findings add a new line of inquiry to be considered when addressing the mechanisms of viral disassembly inside the crowded environment of the cell.
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 an 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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