Intermittency of Deformation and the Elastic Limit of an Icosahedral Virus under Compression

Effect of particle stiffness and surface properties on the non-linear viscoelasticity of dense microgel suspensions

HYPOTHESIS

Particle surface chemistry and internal softness are two fundamental parameters in governing the mechanical properties of dense colloidal suspensions, dictating structure and flow, therefore of interest from materials fabrication to processing.

EXPERIMENTS

Here, we modulate softness by tuning the crosslinker content of poly(N-isopropylacrylamide) microgels, and we adjust their surface properties by co-polymerization with polyethylene glycol chains, controlling adhesion, friction and fuzziness. We investigate the distinct effects of these parameters on the entire mechanical response from restructuring to complete fluidization of jammed samples at varying packing fractions under large-amplitude oscillatory shear experiments, and we complement rheological data with colloidal-probe atomic force microscopy to unravel variations in the particles' surface properties.

FINDINGS

Our results indicate that surface properties play a fundamental role at smaller packings; decreasing adhesion and friction at contact causes the samples to yield and fluidify in a lower deformation range. Instead, increasing softness or fuzziness has a similar effect at ultra-high densities, making suspensions able to better adapt to the applied shear and reach complete fluidization over a larger deformation range. These findings shed new light on the single-particle parameters governing the mechanical response of dense suspensions subjected to deformation, offering synthetic approaches to design materials with tailored mechanical properties.

Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy

The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.

Surface characterization of alkane viral anchoring films prepared by titanate-assisted organosilanization

Studies of virus adsorption on surfaces with optimized properties have attracted a lot of interest, mainly due to the influence of the surface in the retention, orientation and stability of the viral capsids. Besides, viruses in whole or in parts can be used as cages or vectors in different areas, such as biomedicine and materials science. A key requirement for virus nanocage application is their physical properties, i.e. their mechanical response and the distribution of surface charge, which determine virus-substrate interactions and stability. In the present work we show two examples of viruses exhibiting strong surface interactions on homogeneous hydrophobic surfaces. The surfaces were prepared by titanate assisted organosilanization, a sol-gel spin coating process, followed by a mild annealing step. We show by surface and interface spectroscopies that the process allows trapping triethoxy-octylsilane (OCTS) molecules, exhibiting a hydrophobic alkane rich surface finishing. Furthermore, the surfaces remain flat and behave as more efficient sorptive surfaces for virus particles than mica or graphite (HOPG). Also, we determine by atomic force microscopy (AFM) the mechanical properties of two types of viruses (human adenovirus and reovirus) and compare the results obtained on the OCTS functionalized surfaces with those obtained on mica and HOPG. Finally, the TIPT+OCTS surfaces were validated as platforms for the morphological and mechanical characterization of virus particles by using adenovirus as initial model and using HOPG and mica as standard control surfaces. Then, the same characteristics were determined on reovirus using TIPT+OCTS and HOPG, as an original contribution to the catalogue of physical properties of viral particles.

Resolving the different bulk moduli within individual soft nanogels using small-angle neutron scattering

The bulk modulus, K, quantifies the elastic response of an object to an isotropic compression. For soft compressible colloids, knowing K is essential to accurately predict the suspension response to crowding. Most colloids have complex architectures characterized by different softness, which additionally depends on compression. Here, we determine the different values of K for the various morphological parts of individual nanogels and probe the changes of K with compression. Our method uses a partially deuterated polymer, which exerts the required isotropic stress, and small-angle neutron scattering with contrast matching to determine the form factor of the particles without any scattering contribution from the polymer. We show a clear difference in softness, compressibility, and evolution of K between the shell of the nanogel and the rest of the particle, depending on the amount of cross-linker used in their synthesis.

How Softness Matters in Soft Nanogels and Nanogel Assemblies

Softness plays a key role in determining the macroscopic properties of colloidal systems, from synthetic nanogels to biological macromolecules, from viruses to star polymers. However, we are missing a way to quantify what the term "softness" means in nanoscience. Having quantitative parameters is fundamental to compare different systems and understand what the consequences of softness on the macroscopic properties are. Here, we propose different quantities that can be measured using scattering methods and microscopy experiments. On the basis of these quantities, we review the recent literature on micro- and nanogels, i.e. cross-linked polymer networks swollen in water, a widely used model system for soft colloids. Applying our criteria, we address the question what makes a nanomaterial soft? We discuss and introduce general criteria to quantify the different definitions of softness for an individual compressible colloid. This is done in terms of the energetic cost associated with the deformation and the capability of the colloid to isotropically deswell. Then, concentrated solutions of soft colloids are considered. New definitions of softness and new parameters, which depend on the particle-to-particle interactions, are introduced in terms of faceting and interpenetration. The influence of the different synthetic routes on the softness of nanogels is discussed. Concentrated solutions of nanogels are considered and we review the recent results in the literature concerning the phase behavior and flow properties of nanogels both in three and two dimensions, in the light of the different parameters we defined. The aim of this review is to look at the results on micro- and nanogels in a more quantitative way that allow us to explain the reported properties in terms of differences in colloidal softness. Furthermore, this review can give researchers dealing with soft colloids quantitative methods to define unambiguously which softness matters in their compound.

Monitoring SARS-CoV-2 Surrogate TGEV Individual Virions Structure Survival under Harsh Physicochemical Environments

Effective airborne transmission of coronaviruses via liquid microdroplets requires a virion structure that must withstand harsh environmental conditions. Due to the demanding biosafety requirements for the study of human respiratory viruses, it is important to develop surrogate models to facilitate their investigation. Here we explore the mechanical properties and nanostructure of transmissible gastroenteritis virus (TGEV) virions in liquid milieu and their response to different chemical agents commonly used as biocides. Our data provide two-fold results on virus stability: First, while particles with larger size and lower packing fraction kept their morphology intact after successive mechanical aggressions, smaller viruses with higher packing fraction showed conspicuous evidence of structural damage and content release. Second, monitoring the structure of single TGEV particles in the presence of detergent and alcohol in real time revealed the stages of gradual degradation of the virus structure in situ. These data suggest that detergent is three orders of magnitude more efficient than alcohol in destabilizing TGEV virus particles, paving the way for optimizing hygienic protocols for viruses with similar structure, such as SARS-CoV-2.

Intranuclear HSV-1 DNA ejection induces major mechanical transformations suggesting mechanoprotection of nucleus integrity

Maintaining nuclear integrity is essential to cell survival when exposed to mechanical stress. Herpesviruses, like most DNA and some RNA viruses, put strain on the nuclear envelope as hundreds of viral DNA genomes replicate and viral capsids assemble. It remained unknown, however, how nuclear mechanics is affected at the initial stage of herpesvirus infection-immediately after viral genomes are ejected into the nuclear space-and how nucleus integrity is maintained despite an increased strain on the nuclear envelope. With an atomic force microscopy force volume mapping approach on cell-free reconstituted nuclei with docked herpes simplex type 1 (HSV-1) capsids, we explored the mechanical response of the nuclear lamina and the chromatin to intranuclear HSV-1 DNA ejection into an intact nucleus. We discovered that chromatin stiffness, measured as Young's modulus, is increased by ∼14 times, while nuclear lamina underwent softening. Those transformations could be associated with a mechanism of mechanoprotection of nucleus integrity facilitating HSV-1 viral genome replication. Indeed, stiffening of chromatin, which is tethered to the lamina meshwork, helps to maintain nuclear morphology. At the same time, increased lamina elasticity, reflected by nucleus softening, acts as a "shock absorber," dissipating the internal mechanical stress on the nuclear membrane (located on top of the lamina wall) and preventing its rupture.

Virus Mechanics under Molecular Crowding

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 viruses-the 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.

Disassembly Intermediates of the Brome Mosaic Virus Identified by Charge Detection Mass Spectrometry

Capsid disassembly and genome release are critical steps in the lifecycle of a virus. However, their mechanisms are poorly understood, both in vivo and in vitro. Here, we have identified two in vitro disassembly pathways of the brome mosaic virus (BMV) by charge detection mass spectrometry and transmission electron microscopy. When subjected to a pH jump to a basic environment at low ionic strength, protein-RNA interactions are disrupted. Under these conditions, BMV appears to disassemble mainly through a global cleavage event into two main fragments: a near complete capsid that has released the RNA and the released RNA complexed to a small number of the capsid proteins. Upon slow buffer exchange to remove divalent cations at neutral pH, capsid protein interactions are disrupted. The BMV virions swell but there is no measurable loss of the RNA. Some of the virions break into small fragments, leading to an increase in the abundance of species with masses less than 1 MDa. The peak attributed to the BMV virion shifts to a higher mass with time. The mass increase is attributed to additional capsid proteins associating with the disrupted capsid protein-RNA complex, where the RNA is presumably partially exposed. It is likely that this pathway is more closely related to how the capsid disassembles in vivo, as it offers the advantage of protecting the RNA with the capsid protein until translation begins.