Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.

Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-structure motifs. Packaging signals found in certain RNA viruses are one such prominent example of functional RNA motifs. These signals are short hairpin loops that interact with coat proteins and drive viral self-assembly.

Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages.

Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution.

Results: We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic.

Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants.

The spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for target recognition, cellular entry, and endosomal escape of the virus. At the same time, it is the part of the virus that exhibits the greatest sequence variation across the many variants which have emerged during its evolution. Recent studies have indicated that with progressive lineage emergence, the positive charge on the spike protein has been increasing, with certain positively charged amino acids (AAs) improving the binding of the spike protein to cell receptors.

Scaling properties of RNA as a randomly branching polymer.

Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching-for instance, for its spatial compactness or interaction with other biological macromolecules-RNA branching topology remains largely unexplored. Here, we use the theory of randomly branching polymers to explore the scaling properties of RNAs by mapping their secondary structures onto planar tree graphs.

Packing and trimer-to-dimer protein reconstruction in icosahedral viral shells with a single type of symmetrical structural unit.

Understanding the principles of protein packing and the mechanisms driving morphological transformations in virus shells (capsids) during their maturation can be pivotal for the development of new antiviral strategies. Here, we study how these principles and mechanisms manifest themselves in icosahedral viral capsids assembled from identical symmetric structural units (capsomeres). To rationalize such shells, we model capsomers as symmetrical groups of identical particles interacting with a short-range potential typical of the classic Tammes problem.

Dense packings of geodesic hard ellipses on a sphere.

Packing problems are abundant in nature and have been researched thoroughly both experimentally and in numerical models. In particular, packings of anisotropic, elliptical particles often emerge in models of liquid crystals, colloids, and granular and jammed matter. While most theoretical studies on anisotropic particles have thus far dealt with packings in Euclidean geometry, there are many experimental systems where anisotropically-shaped particles are confined to a curved surface, such as Pickering emulsions stabilized by ellipsoidal particles or protein adsorbates on lipid vesicles.

Measure of overlap between two arbitrary ellipses on a sphere.

Various packing problems and simulations of hard and soft interacting particles, such as microscopic models of nematic liquid crystals, reduce to calculations of intersections and pair interactions between ellipsoids. When constrained to a spherical surface, curvature and compactness lead to non-trivial behaviour that finds uses in physics, computer science and geometry. A well-known idealized isotropic example is the Tammes problem of finding optimal non-intersecting packings of equal hard disks.

Mechanics of inactive swelling and bursting of porate pollen grains.

The structure of pollen grains, which is typically characterized by soft apertures in an otherwise stiff exine shell, guides their response to changes in the humidity of the environment. These changes can lead to desiccation of the grain and its infolding but also to excessive swelling of the grain and even its bursting. Here we use an elastic model to explore the mechanics of pollen grain swelling and the role of soft, circular apertures (pores) in this process.

RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates.

RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology.

Site Correlations, Capacitance, and Polarizability From Protein Protonation Fluctuations.

We generalize the Kirkwood-Shumaker theory of protonation fluctuation for an anisotropic distribution of dissociable charges on a globular protein. The fluctuations of the total charge and the total dipole moment, in contrast to their average values, depend on the same proton occupancy correlator, thus exhibiting a similar dependence also on the solution pH. This has important consequences for the Kirkwood-Shumaker interaction and its dependence on the bathing solution conditions.

Electrostatic interactions between the SARS-CoV-2 virus and a charged electret fibre.

While almost any kind of face mask offers some protection against particles and pathogens of different sizes, the most efficient ones make use of a layered structure where one or more layers are electrically charged. These electret layers are essential for the efficient filtration of difficult-to-capture small particles, yet the exact nature of electrostatic capture with respect to the charge on both the particles and the electret fibres as well as the effect of the immediate environment remain unclear. Here, we explore in detail the electrostatic interactions between the surface of a single charged electret fibre and a model of the SARS-CoV-2 virus.

Relative humidity in droplet and airborne transmission of disease.

A large number of infectious diseases are transmitted by respiratory droplets. How long these droplets persist in the air, how far they can travel, and how long the pathogens they might carry survive are all decisive factors for the spread of droplet-borne diseases. The subject is extremely multifaceted and its aspects range across different disciplines, yet most of them have only seldom been considered in the physics community.

Mechanical design of apertures and the infolding of pollen grain.

When pollen grains become exposed to the environment, they rapidly desiccate. To protect themselves until rehydration, the grains undergo characteristic infolding with the help of special structures in the grain wall-apertures-where the otherwise thick exine shell is absent or reduced in thickness. Recent theoretical studies have highlighted the importance of apertures for the elastic response and the folding of the grain.

Effects of long-range interactions on curvature energies of viral shells.

We formulate a theory of the effects of long-range interactions on the surface tension and spontaneous curvature of proteinaceous shells based on the general Deryaguin-Landau-Verwey-Overbeek mesoscale approach to colloid stability. We derive the full renormalization formulas for the elastic properties of the shell and consider in detail the renormalization of the spontaneous curvature as a function of the corresponding Hamaker coefficient, inner and outer capsid charges, and bathing solution properties. The renormalized spontaneous curvature is found to be a nonmonotonic function of several parameters describing the system.

The role of solution conditions in the bacteriophage PP7 capsid charge regulation.

We investigate and quantify the effects of pH and salt concentration on the charge regulation of the bacteriophage PP7 capsid. These effects are found to be extremely important and substantial, introducing qualitative changes in the charge state of the capsid such as a transition from net-positive to net-negative charge depending on the solution pH. The overall charge of the virus capsid arises as a consequence of a complicated balance with the chemical dissociation equilibrium of the amino acids and the electrostatic interaction between them, and the translational entropy of the mobile solution ions, i.

Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers.

Knowledge about the nature of pathomolecular alterations preceding onset of symptoms in amyotrophic lateral sclerosis is largely lacking. It could not only pave the way for the discovery of valuable therapeutic targets but might also govern future concepts of pre-manifest disease modifying treatments. MicroRNAs are central regulators of transcriptome plasticity and participate in pathogenic cascades and/or mirror cellular adaptation to insults.

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions.

We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion.

Electrostatic self-energy of a partially formed spherical shell in salt solution: application to stability of tethered and fluid shells as models for viruses and vesicles.

We investigate the electrostatics of a partially formed, charged spherical shell in a salt solution. We solve the problem numerically at the Poisson-Boltzmann level and analytically in the Debye-Hückel regime. From the results on energetics of partially formed shells we examine the stability of tethered (crystalline) and fluid shells toward rupture.