Hidden symmetry of the anomalous bluetongue virus capsid and its role in the infection process.

Clear understanding of the principles that control the arrangement of proteins and their self-assembly into viral shells is very important for the development of antiviral strategies. Here we consider the structural peculiarities and hidden symmetry of the anomalous bluetongue virus (BTV) capsid. Each of its three concentric shells violates the paradigmatic geometrical model of Caspar and Klug, which is otherwise well suited to describe most of the known icosahedral viral shells. As we show, three icosahedral spherical lattices, which are commensurate with each other and possess locally hexagonal (primitive or honeycomb) order, underlie the proteinaceous shells of the BTV capsid. This interpretation of the multishelled envelope allows us to discuss the so-called "symmetry mismatch" between its layers. We also analyze the structural stability of the considered spherical lattices on the basis of the classical theory of spherical packing and relate the proximity of the outer spherical lattice to destabilization with the fact that during infection of the cell VP2 trimers are detached from the surface of the BTV capsid. An electrostatic mechanism that can assist in this detachment is discussed in detail.

Spherical structure factor and classification of hyperuniformity on the sphere.

Understanding how particles are arranged on the surface of a sphere is not only central to numerous physical, biological, soft matter, and materials systems but also finds applications in computational problems, approximation theory, and analysis of geophysical and meteorological measurements. Objects that lie on a sphere experience constraints that are not present in Euclidean (flat) space and that influence both how the particles can be arranged as well as their statistical properties. These constraints, coupled with the curved geometry, require a careful extension of quantities used for the analysis of particle distributions in Euclidean space to distributions confined to the surface of a sphere. Here, we introduce a framework designed to analyze and classify structural order and disorder in particle distributions constrained to the sphere. The classification is based on the concept of hyperuniformity, which was first introduced 15 years ago and since then studied extensively in Euclidean space, yet has only very recently been considered also for spherical surfaces. We employ a generalization of the structure factor on the sphere, related to the power spectrum of the corresponding multipole expansion of particle density distribution. The spherical structure factor is then shown to couple with cap number variance, a measure of density variations at different scales, allowing us to analytically derive different forms of the variance pertaining to different types of distributions. Based on these forms, we construct a classification of hyperuniformity for scale-free particle distributions on the sphere and show how it can be extended to include other distribution types as well. We demonstrate that hyperuniformity on the sphere can be defined either through a vanishing spherical structure factor at low multipole numbers or through a scaling of the cap number variance-in both cases extending the Euclidean definition, while at the same time pointing out crucial differences. Our work thus provides a comprehensive tool for detecting global, long-range order on spheres and for the analysis of spherical computational meshes, biological and synthetic spherical assemblies, and ordering phase transitions in spherically distributed particles.

Role of metallic core for the stability of virus-like particles in strongly coupled electrostatics.

Electrostatic interactions play important roles in the formation and stability of viruses and virus-like particles (VLPs) through processes that often involve added, or naturally occurring, multivalent ions. Here, we investigate the electrostatic or osmotic pressure acting on the proteinaceous shell of a generic model of VLPs, comprising a charged outer shell and a metallic nanoparticle core, coated by a charged layer and bathed in an aqueous electrolyte solution. Motivated by the recent studies accentuating the role of multivalent ions for the stability of VLPs, we focus on the effects of multivalent cations and anions in an otherwise monovalent ionic solution. We perform extensive Monte-Carlo simulations based on appropriate Coulombic interactions that consistently take into account the effects of salt screening, the dielectric polarization of the metallic core, and the strong-coupling electrostatics due to multivalent ions. We specifically study the intricate roles these factors play in the electrostatic stability of the model VLPs. It is shown that while the insertion of a metallic nanoparticle by itself can produce negative, inward-directed, pressure on the outer shell, addition of only a small amount of multivalent counterions can robustly engender negative pressures, enhancing the VLP stability across a wide range of values for the system parameters.

Anomalous multipole expansion: Charge regulation of patchy inhomogeneously charged spherical particles.

Charge regulation is an important aspect of electrostatics in biological and colloidal systems, where the charges are generally not fixed but depend on the environmental variables. Here, we analyze the charge regulation mechanism in patchy inhomogeneously charged spherical particles, such as globular proteins, colloids, or viruses. Together with the multipole expansion of inhomogeneously charged spherical surfaces, the charge regulation mechanism on the level of linear approximation is shown to lead to a mixing between different multipole moments depending on their capacitance-the response function of the charge distribution with respect to the electrostatic potential. This presents an additional anomalous feature of molecular electrostatics in the presence of ionic screening. We demonstrate the influence of charge regulation on several examples of inhomogeneously charged spherical particles, showing that it leads to significant changes in their multipole moments.

Electrostatics-Driven Inflation of Elastic Icosahedral Shells as a Model for Swelling of Viruses.

We develop a clear theoretical description of radial swelling in virus-like particles that delineates the importance of electrostatic contributions to swelling in the absence of any conformational changes. The model couples the elastic parameters of the capsid-represented as a continuous elastic shell-to the electrostatic pressure acting on it. We show that different modifications of the electrostatic interactions brought about by, for instance, changes in pH or solution ionic strength are often sufficient to achieve the experimentally observed swelling (∼10% of the capsid radius). Additionally, we derive analytical expressions for the electrostatics-driven radial swelling of virus-like particles that enable one to quickly estimate the magnitudes of physical quantities involved.

Compactness of viral genomes: effect of disperse and localized random mutations.

Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic virus in order to understand the observed sensitivity of the global compactness of their folds. We find that mutating local stretches of their genomes' sequence or structure is less disruptive to their compactness compared to inducing randomly-distributed mutations. Our findings are indicative of a mechanism for the conservation of compactness acting on a global scale of the genomes, and have several implications for understanding the interplay between local and global architecture of viral RNA genomes.

From discrete to continuous description of spherical surface charge distributions.

The importance of electrostatic interactions in soft matter and biological systems can often be traced to non-uniform charge effects, which are commonly described using a multipole expansion of the corresponding charge distribution. The standard approach when extracting the charge distribution of a given system is to treat the constituent charges as points. This can, however, lead to an overestimation of multipole moments of high order, such as dipole, quadrupole, and higher moments. Focusing on distributions of charges located on a spherical surface - characteristic of numerous biological macromolecules, such as globular proteins and viral capsids, as well as of inverse patchy colloids - we develop a novel way of representing spherical surface charge distributions based on the von Mises-Fisher distribution. This approach takes into account the finite spatial extension of individual charges, and leads to a simple yet powerful way of describing surface charge distributions and their multipole expansions. In this manner, we analyze charge distributions and the derived multipole moments of a number of different spherical configurations of identical charges with various degrees of symmetry. We show how the number of charges, their size, and the geometry of their configuration influence the behavior and relative importance of multipole magnitudes of different order. Importantly, we clearly demonstrate how neglecting the effect of charge size leads to an overestimation of high-order multipoles. The results of our work can be applied to construct analytical models of electrostatic interactions and multipole expansion of charged particles in diverse soft matter and biological systems.

Varieties of charge distributions in coat proteins of ssRNA+ viruses.

A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+ viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that-in contrast to the charge on the CPs-the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.

pH Dependence of Charge Multipole Moments in Proteins.

Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the changes in the environment-most notably, the pH of the surrounding solution. We study the effects of pH on the charge of four globular proteins by expanding their surface charge distributions in terms of multipoles. The detailed representation of the charges on the proteins is in this way replaced by the magnitudes and orientations of the multipole moments of varying order. Focusing on the three lowest-order multipoles-the total charge, dipole, and quadrupole moment-we show that the value of pH influences not only their magnitudes, but more notably and importantly also the spatial orientation of their principal axes. Our findings imply important consequences for the study of protein-protein interactions and the assembly of both proteinaceous shells and patchy colloids with dissociable charge groups.

Multivalent ion effects on electrostatic stability of virus-like nano-shells.

Electrostatic properties and stability of charged virus-like nano-shells are examined in ionic solutions with monovalent and multivalent ions. A theoretical model based on a thin charged spherical shell and multivalent ions within the "dressed multivalent ion" approximation, yielding their distribution across the shell and the corresponding electrostatic (osmotic) pressure acting on the shell, is compared with extensive implicit Monte-Carlo simulations. It is found to be accurate for positive or low negative surface charge densities of the shell and for sufficiently high (low) monovalent (multivalent) salt concentrations. Phase diagrams involving electrostatic pressure exhibit positive and negative values, corresponding to an outward and an inward facing force on the shell, respectively. This provides an explanation for the high sensitivity of viral shell stability and self-assembly of viral capsid shells on the ionic environment.

Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties.

From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the fairly conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and an interpolating set of shapes in between, all of them obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we found similarities between the capsid elastic properties of even very different viruses. As we explain in the paper, there are both structural and functional reasons for the convergence of protein sizes and capsid elastic properties. Our work presents a specific quantitative scheme to estimate relatedness between different proteins based on the details of the (quaternary) shape they form (capsid). As such, it may provide an information complementary to the one obtained from the studies of other types of protein similarity, such as the overall composition of structural elements, topology of the folded protein backbone, and sequence similarity.

Symmetry effects in electrostatic interactions between two arbitrarily charged spherical shells in the Debye-Hückel approximation.

Inhomogeneous charge distributions have important repercussions on electrostatic interactions in systems of charged particles but are often difficult to examine theoretically. We investigate how electrostatic interactions are influenced by patchy charge distributions exhibiting certain point group symmetries. We derive a general form of the electrostatic interaction energy of two permeable, arbitrarily charged spherical shells in the Debye-Hückel approximation and apply it to the case of particles with icosahedral, octahedral, and tetrahedral inhomogeneous charge distributions. We analyze in detail how charge distribution symmetry modifies the interaction energy and find that local charge inhomogeneities reduce the repulsion of two overall equally charged particles, while sufficient orientational variation in the charge distribution can turn the minimum interaction energy into an attraction. Additionally, we show that larger patches and thus lower symmetries and wave numbers result in bigger attraction given the same variation.

How simple can a model of an empty viral capsid be? Charge distributions in viral capsids.

We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding a detailed description of spatial distribution for positive and negative charges across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities, as well as dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.