ASSEMBLY AND STABILITY OF THE TOBACCO MOSAIC VIRUS PARTICLE

Terminal Tryptophan-Directed Anisotropic Self-Assembly for Precise Protein Nanostructure Regulation

A common challenge in nanotechnology is synthesizing nanomaterials with well-defined structures. In particular, it remains a major unresolved challenge to precisely regulate the structure and function of protein nanomaterials, which are structurally diverse, highly ordered, and complex and offer an innovative means that enables a high performance in various nanodevices, which is rarely achievable with other nanomaterials. Here an innovative approach is proposed to fabricating multi-dimensional (0- to 3D) protein nanostructures with functional and structural specialties via molecular-level regulation. This approach is based on a stable, consistent, anisotropic self-assembly of Tobacco mosaic virus (TMV) coat protein-derived engineered building blocks where genetically added tryptophan residues are externally tailored. The unique structural characteristics of each nanostructure above are demonstrated in detail through various analyses (electron microscopy, atomic force microscopy, dynamic light scattering, and small-angle X-ray scattering) and further investigated through molecular dynamics simulations, indicating that this control, anisotropic, and molecular assembly-based approach to regulating protein nanostructures holds great potential for customizing a variety of nanomaterials with unique functions and structures.

Modeling Viral Capsid Assembly: A Review of Computational Strategies and Applications

Viral capsid assembly is a complex and critical process, essential for understanding viral behavior, evolution, and the development of antiviral treatments, vaccines, and nanotechnology. Significant progress in studying viral capsid assembly has been achieved through various computational approaches, including molecular dynamics (MD) simulations, stochastic dynamics simulations, coarse-grained (CG) models, electrostatic analyses, lattice models, hybrid techniques, machine learning methods, and kinetic models. Each of these techniques offers unique advantages, and by integrating these diverse computational strategies, researchers can more accurately model the dynamic behaviors and structural features of viral capsids, deepening our understanding of the assembly process. This review provides a comprehensive overview of studies on viral capsid assembly, emphasizing their critical role in advancing our knowledge. It examines the contributions, strengths, and limitations of different computational methods, presents key computational works in the field, and analyzes milestone studies that have shaped current research.

3D-Printed Self-Assembling Helical Models for Exploring Viral Capsid Structures

This work presents a novel application of additive manufacturing in the design of self-assembling helical viral capsids using 3D-printed components. Expanding on prior work with 3D-printed self-assembling spherical capsids, we developed helical models that integrate geometric parameters and magnetic interactions to mimic key features of the assembly process of helical viral capsids. Using dual-helix phyllotactic patterns and simplified electrostatic simulations, these models consistently self-assemble into a cylinder, providing unique insights into the structural organization and stability of helical capsids. This accessible 3D-printed approach demonstrates the potential of additive manufacturing for research in mesoscale self-assembling models and in the education of complex biological assembly processes, promoting hands-on exploration of viral architecture and self-assembly mechanisms.

3D Puzzle at the Nanoscale-How do RNA Viruses Self-Assemble their Capsids into Perfectly Ordered Structures

The phenomenon of RNA virus self-organization, first observed in the mid-20th century in tobacco mosaic virus, is the subject of extensive research. Efforts to comprehend this process intensify due to its potential for producing vaccines or antiviral compounds as well as nanocarriers and nanotemplates. However, direct observation of the self-assembly is hindered by its prevalence within infected host cells. One of the approaches involves in vitro and in silico research using model viruses featuring a ssRNA(+) genome enclosed within a capsid made up of a single type protein. While various pathways are proposed based on these studies, their relevance in vivo remains uncertain. On the other hand, the development of advanced microscopic methods provide insights into the events within living cells, where following viral infection, specialized compartments form to facilitate the creation of nascent virions. Intriguingly, a growing body of evidence indicates that the primary function of packaging signals in viral RNA is to effectively initiate the virion self-assembly. This is in contrast to earlier opinions suggesting a role in marking RNA for encapsidation. Another noteworthy observation is that many viruses undergo self-assembly within membraneless liquid organelles, which are specifically induced by viral proteins.

Inter-coat protein loading of active ingredients into Tobacco mild green mosaic virus through partial dissociation and reassembly of the virion

Chemical pesticide delivery is a fundamental aspect of agriculture. However, the extensive use of pesticides severely endangers the ecosystem because they accumulate on crops, in soil, as well as in drinking and groundwater. New frontiers in nano-engineering have opened the door for precision agriculture. We introduced Tobacco mild green mosaic virus (TMGMV) as a viable delivery platform with a high aspect ratio and favorable soil mobility. In this work, we assess the use of TMGMV as a chemical nanocarrier for agriculturally relevant cargo. While plant viruses are usually portrayed as rigid/solid structures, these are "dynamic materials," and they "breathe" in solution in response to careful adjustment of pH or bathing media [e.g., addition of solvent such as dimethyl sulfoxide (DMSO)]. Through this process, coat proteins (CPs) partially dissociate leading to swelling of the nucleoprotein complexes-allowing for the infusion of active ingredients (AI), such as pesticides [e.g., fluopyram (FLP), clothianidin (CTD), rifampicin (RIF), and ivermectin (IVM)] into the macromolecular structure. We developed a "breathing" method that facilitates inter-coat protein cargo loading, resulting in up to  ~ 1000 AIs per virion. This is of significance since in the agricultural setting, there is a need to develop nanoparticle delivery strategies where the AI is not chemically altered, consequently avoiding the need for regulatory and registration processes of new compounds. This work highlights the potential of TMGMV as a pesticide nanocarrier in precision farming applications; the developed methods likely would be applicable to other protein-based nanoparticle systems.

Precision nanoengineering for functional self-assemblies across length scales

As nanotechnology continues to push the boundaries across disciplines, there is an increasing need for engineering nanomaterials with atomic-level precision for self-assembly across length scales, i.e., from the nanoscale to the macroscale. Although molecular self-assembly allows atomic precision, extending it beyond certain length scales presents a challenge. Therefore, the attention has turned to size and shape-controlled metal nanoparticles as building blocks for multifunctional colloidal self-assemblies. However, traditionally, metal nanoparticles suffer from polydispersity, uncontrolled aggregation, and inhomogeneous ligand distribution, resulting in heterogeneous end products. In this feature article, I will discuss how virus capsids provide clues for designing subunit-based, precise, efficient, and error-free self-assembly of colloidal molecules. The atomically precise nanoscale proteinic subunits of capsids display rigidity (conformational and structural) and patchy distribution of interacting sites. Recent experimental evidence suggests that atomically precise noble metal nanoclusters display an anisotropic distribution of ligands and patchy ligand bundles. This enables symmetry breaking, consequently offering a facile route for two-dimensional colloidal crystals, bilayers, and elastic monolayer membranes. Furthermore, inter-nanocluster interactions mediated via the ligand functional groups are versatile, offering routes for discrete supracolloidal capsids, composite cages, toroids, and macroscopic hierarchically porous frameworks. Therefore, engineered nanoparticles with atomically precise structures have the potential to overcome the limitations of molecular self-assembly and large colloidal particles. Self-assembly allows the emergence of new optical properties, mechanical strength, photothermal stability, catalytic efficiency, quantum yield, and biological properties. The self-assembled structures allow reproducible optoelectronic properties, mechanical performance, and accurate sensing. More importantly, the intrinsic properties of individual nanoclusters are retained across length scales. The atomically precise nanoparticles offer enormous potential for next-generation functional materials, optoelectronics, precision sensors, and photonic devices.

Cooperative Assembly of Self-Adjusting α-Helical Coiled Coils along the Length of an mRNA Chain to Form a Thermodynamically Stable Nanotube Carrier

Although mRNA delivery technology is very promising, problems in safety and transport arise due to the intrinsically low thermodynamic stability of the current mRNA carriers. Considering that mRNAs are filamentous and a nanotube is one of the most thermodynamically stable shapes among nanoassemblies, a nanotube is one of the most stable supramolecular structures that can be assembled with mRNA. Here, we develop a nanotube-shaped filamentous mRNA delivery platform that shows exceptionally high thermodynamic stability. The key to the development of the mRNA nanotube is the design of self-adjusting supramolecular building blocks (SABs) that have two disparate properties, i.e., dynamic property and stiffness, in a single molecule. The counterbalance of the dynamic property and stiffness in SABs enables the coating of mRNA by winding its way through the flexible and irregular mRNA chain via cooperative interactions. SAB nanotubes with targeting ligands installed show a high uptake efficiency in mammalian cells and controllable gene expression behavior. Thus, the mRNA nanotube provides an enabling technology toward the development of safe and stable mRNA vaccines and therapeutics.

Seeing Biomolecular Condensates Through the Lens of Viruses

Phase separation of viral biopolymers is a key factor in the formation of cytoplasmic viral inclusions, known as sites of virus replication and assembly. This review describes the mechanisms and factors that affect phase separation in viral replication and identifies potential areas for future research. Drawing inspiration from studies on cellular RNA-rich condensates, we compare the hierarchical coassembly of ribosomal RNAs and proteins in the nucleolus to the coordinated coassembly of viral RNAs and proteins taking place within viral factories in viruses containing segmented RNA genomes. We highlight the common characteristics of biomolecular condensates in viral replication and how this new understanding is reshaping our views of virus assembly mechanisms. Such studies have the potential to uncover unexplored antiviral strategies targeting these phase-separated states.

Relaxational dynamics of the T-number conversion of virus capsids

We extend a recently proposed kinetic theory of virus capsid assembly based on Model A kinetics and study the dynamics of the interconversion of virus capsids of different sizes triggered by a quench, that is, by sudden changes in the solution conditions. The work is inspired by in vitro experiments on functionalized coat proteins of the plant virus cowpea chlorotic mottle virus, which undergo a reversible transition between two different shell sizes (T = 1 and T = 3) upon changing the acidity and salinity of the solution. We find that the relaxation dynamics are governed by two time scales that, in almost all cases, can be identified as two distinct processes. Initially, the monomers and one of the two types of capsids respond to the quench. Subsequently, the monomer concentration remains essentially constant, and the conversion between the two capsid species completes. In the intermediate stages, a long-lived metastable steady state may present itself, where the thermodynamically less stable species predominate. We conclude that a Model A based relaxational model can reasonably describe the early and intermediate stages of the conversion experiments. However, it fails to provide a good representation of the time evolution of the state of assembly of the coat proteins in the very late stages of equilibration when one of the two species disappears from the solution. It appears that explicitly incorporating the nucleation barriers to assembly and disassembly is crucial for an accurate description of the experimental findings, at least under conditions where these barriers are sufficiently large.

Applicability of Different Methods for Quantifying Virucidal Efficacy Using MENNO Florades and Tomato Brown Rugose Fruit Virus as an Example

After entry of a quarantine/regulated pathogen, infected plants shall be destroyed, and the cultivated area (e.g., greenhouse) shall be disinfected. Therefore, the selection of an effective disinfectant plays an important role. With the availability of different methods for virus quantification, we investigated the application of quantitative ELISA (qELISA), RT-qPCR (reverse transcription-quantitative polymerase chain reaction), and bioassays for the quantification of disinfectant efficacy. Therefore, we estimated the titer reduction in tomato brown rugose fruit virus (ToBRFV), a regulated pathogen, in plant sap and on germ carriers after treatment with MENNO Florades 4% for 16 h. The virus load before and after the treatment was measured with the mentioned methods. The RT-qPCR and qELISA methods showed very low efficacy in the presence of the disinfectant. Although bioassays are time-consuming, need purified particles for establishing the quantification models, and are less sensitive than RT-qPCR, they were able to quantify the differences in virus titer in the presence/absence of disinfectant. Interestingly, the bioassays reached at least the lower limit sensitivity of a qELISA. By being less sensitive to the presence of the disinfectant, bioassays proved to be the only technique for the determination of the disinfectant efficacy against ToBRFV on different germ carriers as well as on virus-infected plant sap.

Highly stable, antiviral, antibacterial cotton textiles via molecular engineering

Cotton textiles are ubiquitous in daily life and are also one of the primary mediums for transmitting viruses and bacteria. Conventional approaches to fabricating antiviral and antibacterial textiles generally load functional additives onto the surface of the fabric and/or their microfibres. However, such modifications are susceptible to deterioration after long-term use due to leaching of the additives. Here we show a different method to impregnate copper ions into the cellulose matrix to form a copper ion-textile (Cu-IT), in which the copper ions strongly coordinate with the oxygen-containing polar functional groups (for example, hydroxyl) of the cellulose chains. The Cu-IT displays high antiviral and antibacterial performance against tobacco mosaic virus and influenza A virus, and Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa and Bacillus subtilis bacteria due to the antimicrobial properties of copper. Furthermore, the strong coordination bonding of copper ions with the hydroxyl functionalities endows the Cu-IT with excellent air/water retainability and superior mechanical stability, which can meet daily use and resist repeated washing. This method to fabricate Cu-IT is cost-effective, ecofriendly and highly scalable, and this textile appears very promising for use in household products, public facilities and medical settings.

Convenient site-selective protein coupling from bacterial raw lysates to coenzyme A-modified tobacco mosaic virus (TMV) by Bacillus subtilis Sfp phosphopantetheinyl transferase

A facile enzyme-mediated strategy enables site-specific covalent one-step coupling of genetically tagged luciferase molecules to coenzyme A-modified tobacco mosaic virus (TMV-CoA) both in solution and on solid supports. Bacillus subtilis surfactin phosphopantetheinyl transferase Sfp produced in E. coli mediated the conjugation of firefly luciferase N-terminally extended by eleven amino acids forming a 'ybbR tag' as Sfp-selective substrate, which even worked in bacterial raw lysates. The enzymes displayed on the protein coat of the TMV nanocarriers exhibited high activity. As TMV has proven a beneficial high surface-area adapter template stabilizing enzymes in different biosensing layouts in recent years, the use of TMV-CoA for fishing ybbR-tagged proteins from complex mixtures might become an advantageous concept for the versatile equipment of miniaturized devices with biologically active proteins. It comes along with new opportunities for immobilizing multiple functionalities on TMV adapter coatings, as desired, e.g., in handheld systems for point-of-care detection.

Alcohol-perturbed self-assembly of the tobacco mosaic virus coat protein

The self-assembly of the tobacco mosaic virus coat protein is significantly altered in alcohol-water mixtures. Alcohol cosolvents stabilize the disk aggregate and prevent the formation of helical rods at low pH. A high alcohol content favours stacked disk assemblies and large rafts, while a low alcohol concentration favours individual disks and short stacks. These effects appear to be caused by the hydrophobicity of the alcohol additive, with isopropyl alcohol having the strongest effect and methanol the weakest. We discuss several effects that may contribute to preventing the protein-protein interactions between disks that are necessary to form helical rods.

Aperiodic crystals in biology

Biological systems display a broad palette of hierarchically ordered designs spanning over many orders of magnitude in size. Remarkably enough, periodic order, which profusely shows up in non-living ordered compounds, plays a quite subsidiary role in most biological structures, which can be appropriately described in terms of the more general aperiodic crystal notion instead. In this topical review I shall illustrate this issue by considering several representative examples, including botanical phyllotaxis, the geometry of cell patterns in tissues, the morphology of sea urchins, or the symmetry principles underlying virus architectures. In doing so, we will realize that albeit the currently adopted quasicrystal notion is not general enough to properly account for the rich structural features one usually finds in biological arrangements of matter, several mathematical tools and fundamental notions belonging to the aperiodic crystals science toolkit can provide a useful modeling framework to this end.

Reprogramming Virus Coat Protein Carboxylate Interactions for the Patterned Assembly of Hierarchical Nanorods

The self-assembly system of the rod-shaped tobacco mosaic virus (TMV) has been studied extensively for nanoscale applications. TMV coat protein assembly is modulated by intersubunit carboxylate groups whose electrostatic repulsion limits the assembly of virus rods without incorporating genomic RNA. To engineer assembly control into this system, we reprogrammed intersubunit carboxylate interactions to produce self-assembling coat proteins in the absence of RNA and in response to unique pH and ionic environmental conditions. Specifically, engineering a charge attraction at the intersubunit E50-D77 carboxylate group through a D77K substitution stabilized the coat proteins assembly into virus-like rods. In contrast, the reciprocal E50K modification alone did not confer virus-like rod assembly. However, a combination of R46G/E50K/E97G substitutions enabled virus-like rod assembly. Interestingly, the D77K substitution displays a unique pH-dependent assembly-disassembly profile, while the R46G/E50K/E97G substitutions confer a novel salt concentration dependency for assembly control. In addition, these unique environmentally controlled coat proteins allow for the directed assembly and disassembly of chimeric virus-like rods both in solution and on substrate-attached seed rods. Combined, these findings provide a controllable means to assemble functionally discrete virus-like rods for use in nanotechnology applications.

In vivo antiviral activity and disassembly mechanism of novel 1-phenyl-5-amine-4-pyrazole thioether derivatives against Tobacco mosaic virus

A series of novel 1-phenyl-5-amine-4-pyrazole thioether derivatives containing a 1,3,4-oxadiazole moiety was designed and synthesised. In vivo antiviral bioassay results showed that most of the target compounds exhibited excellent inactivation activity against Tobacco mosaic virus (TMV). The EC₅₀ values of the inactivation activities for T₂, T₇, T₉, T₂₄, T₂₅ and T₂₇ were 15.7, 15.7, 15.5, 11.9, 12.5 and 16.5 μg/mL, respectively, which were remarkably superior over that of the commercialised antiviral agent ningnanmycin (40.3 μg/mL). Morphological study using AFM and TEM of TMV treated with T₂₄ showed that T₂₄ could significantly shorten the polymerization length of TMV particles and formed a distinct break on the rod-shaped TMV. Investigations for virus infection efficiency on tobacco leaves demonstrated that infectivity of virion had been reduced obviously upon T₂₄ treatment. Subsequently, a strong interaction between T₂₄ and TMV-CP (K_d = 3.8 μM, score 6.11) was observed through MST experiments. Molecular docking study further revealed that target compounds interact with amino acid residue Glu50 in TMV CP, causing disassembly of virion, shorting the length of the virion and reducing the infectivity of virion, and resulting in high inactivating activity of target compounds. This study provides a new insight for discovery of antiviral compounds through a new action mechanism with a new binding site.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

BACKGROUND

Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particular, tobacco, causing a production loss.

OBJECTIVES

Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon.

METHODS

Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crop samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome.

RESULTS AND DISCUSSION

PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain.

CONCLUSION

Our study is the first in Lebanon, revealing TMV infection in crop fields and highlighting the danger that may affect the future of agriculture.

Conformational behavior of coat protein in plants and association with coat protein-mediated resistance against TMV

Tobacco mosaic virus (TMV) coat protein (CP) self assembles in viral RNA deprived transgenic plants to form aggregates based on the physical conditions of the environment. Transgenic plants in which these aggregates are developed show resistance toward infection by TMV referred to as CP-MR. This phenomenon has been extensively used to protect transgenic plants against viral diseases. The mutants T42W and E50Q CP confer enhanced CP-MR as compared to the WT CP. The aggregates, when examined, show the presence of helical discs in the case of WT CP; on the other hand, mutants show the presence of highly stable non-helical long rods. These aggregates interfere with the accumulation of MP as well as with the disassembly of TMV in plant cells. Here, we explored an atomic level insight to the process of CP-MR through MD simulations. The subunit-subunit interactions were assessed with the help of MM-PBSA calculations. Moreover, classification of secondary structure elements of the protein also provided unambiguous information about the conformational changes occurring in the two chains, which indicated toward increased flexibility of the mutant protein and seconded the other results of simulations. Our finding indicates the essential structural changes caused by the mutation in CP subunits, which are critically responsible for CP-MR and provides an in silico insight into the effects of these transitions over CP-MR. These results could further be utilized to design TMV-CP-based small peptides that would be able to provide appropriate protection against TMV infection.

Precise Control Over Kinetics of Molecular Assembly: Production of Particles with Tunable Sizes and Crystalline Forms

It has been long-pursued but remains a challenge to precisely manipulate the molecular assembly process to obtain desired functional structures. Reported here is the control over the assembly of solute molecules, by a programmed recrystallization of solvent crystal grains, to form micro/nanoparticles with tunable sizes and crystalline forms. A quantitative correlation between the protocol of recrystallization temperature and the assembly kinetics results in precise control over the size of assembled particles, ranging from single-atom catalysts, pure drug nanoparticles, to sub-millimeter organic-semiconductor single crystals. The extensive regulation of the assembly rates leads to the unique and powerful capability of tuning the stacking of molecules, involving the formation of single crystals of notoriously crystallization-resistant molecules and amorphous structures of molecules with a very high propensity to crystallize, which endows it with wide-ranging applications.

Confidence maps: statistical inference of cryo-EM maps

Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.

An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete

Spirochete bacteria, including important pathogens, exhibit a distinctive means of swimming via undulations of the entire cell. Motility is powered by the rotation of supercoiled 'endoflagella' that wrap around the cell body, confined within the periplasmic space. To investigate the structural basis of flagellar supercoiling, which is critical for motility, we determined the structure of native flagellar filaments from the spirochete Leptospira by integrating high-resolution cryo-electron tomography and X-ray crystallography. We show that these filaments are coated by a highly asymmetric, multi-component sheath layer, contrasting with flagellin-only homopolymers previously observed in exoflagellated bacteria. Distinct sheath proteins localize to the filament inner and outer curvatures to define the supercoiling geometry, explaining a key functional attribute of this spirochete flagellum.

Elucidation of the viral disassembly switch of tobacco mosaic virus

Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. This process has been extensively studied using tobacco mosaic virus (TMV), and carboxylate interactions are assumed to play a critical part in this process. Here, we present two cryo‐EM structures of the helical TMV assembly at 2.0 and 1.9 Å resolution in conditions of high Ca²⁺ concentration at low pH and in water. Based on our atomic models, we identify the conformational details of the disassembly switch mechanism: In high Ca²⁺/acidic pH environment, the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca²⁺ binding site that is shared between two subunits. Upon increase in pH and lower Ca²⁺ levels, mutual repulsion of the E95/E97 pair and Ca²⁺ removal destabilize the network of interactions between adjacent subunits at lower radius and release the switch for viral disassembly.

Side chain electrostatic interactions and pH-dependent expansion of the intrinsically disordered, highly acidic carboxyl-terminus of γ-tubulin

Intramolecular electrostatic attraction and repulsion strongly influence the conformational sampling of intrinsically disordered proteins and domains (IDPs). In order to better understand this complex relationship, we have used nuclear magnetic resonance to measure side chain pK_a values and pH-dependent translational diffusion coefficients for the unstructured and highly acidic carboxyl-terminus of γ-tubulin (γ-CT), providing insight into how the net charge of an IDP relates to overall expansion or collapse of the conformational ensemble. Many of the pK_a values in the γ-CT are shifted upward by 0.3-0.4 units and exhibit negatively cooperative ionization pH profiles, likely due to the large net negative charge that accumulates on the molecule as the pH is raised. pK_a shifts of this magnitude correspond to electrostatic interaction energies between the affected residues and the rest of the charged molecule that are each on the order of 1 kcal mol^-1 . Diffusion of the γ-CT slowed with increasing net charge, indicative of an expanding hydrodynamic radius (r_H ). The degree of expansion agreed quantitatively with what has been seen from comparisons of IDPs with different charge content, yielding the general trend that every 0.1 increase in relative charge (|Q|/res) produces a roughly 5% increase in r_H . While γ-CT pH titration data followed this trend nearly perfectly, there were substantially larger deviations for the database of different IDP sequences. This suggests that other aspects of an IDP's primary amino acid sequence beyond net charge influence the sensitivity of r_H to electrostatic interactions.

Developing a Programmable, Self-Assembling Squash Leaf Curl China Virus (SLCCNV) Capsid Proteins into "Nanocargo"-like Architecture

A new era has begun in which pathogens have become useful scaffolds for nanotechnology applications. In this research/study, an attempt has been made to generate an empty cargo-like architecture from a plant pathogenic virus named Squash leaf curl China virus (SLCCNV). In this approach, SLCCNV coat protein monomers are obtained efficiently by using a yeast Pichia pastoris expression system. Further, dialysis of purified SLCCNV-CP monomers against various pH modified (5-10) disassembly and assembly buffers produced a self-assembled "Nanocargo"-like architecture, which also exhibited an ability to encapsulate magnetic nanoparticles in vitro. Bioinformatics tools were also utilized to predict the possible self-assembly kinetics and bioconjugation sites of coat protein monomers. Significantly, an in vitro biocompatibility study using SLCCNV-Nanocargo particles showed low toxicity to the cells, which eventually proved as a potential nanobiomaterial for biomedical applications.

Polymorphism in Benzene-1,3,5-tricarboxamide Supramolecular Assemblies in Water: A Subtle Trade-off between Structure and Dynamics

In biology, polymorphism is a well-known phenomenon by which a discrete biomacromolecule can adopt multiple specific conformations in response to its environment. The controlled incorporation of polymorphism into noncovalent aqueous assemblies of synthetic small molecules is an important step toward the development of bioinspired responsive materials. Herein, we report on a family of carboxylic acid functionalized water-soluble benzene-1,3,5-tricarboxamides (BTAs) that self-assemble in water to form one-dimensional fibers, membranes, and hollow nanotubes. Interestingly, one of the BTAs with the optimized position of the carboxylic group in the hydrophobic domain yields nanotubes that undergo reversible temperature-dependent dynamic reorganizations. SAXS and Cryo-TEM data show the formation of elongated, well-ordered nanotubes at elevated temperatures. At these temperatures, increased dynamics, as measured by hydrogen–deuterium exchange, provide enough flexibility to the system to form well-defined nanotube structures with apparently defect-free tube walls. Without this flexibility, the assemblies are frozen into a variety of structures that are very similar at the supramolecular level, but less defined at the mesoscopic level.

Bottom-Up Assembly of TMV-Based Nucleoprotein Architectures on Solid Supports

RNA-guided self-assembly of tobacco mosaic virus (TMV)-like nucleoprotein nanotubes is possible using 3'-terminally surface-linked scaffold RNAs containing the viral origin of assembly (OAS). In combination with TMV coat protein (CP) preparations, these scaffold RNAs can direct the growth of selectively addressable multivalent carrier particles directly at sites of interest on demand. Serving as adapter templates for the installation of functional molecules, they may promote an integration of active units into miniaturized technical devices, or enable their presentation on soft-matter nanotube systems at high surface densities advantageous for, for example, biodetection or purification applications. This chapter describes all procedures essential for the bottom-up fabrication of "nanostar" colloids with gold cores and multiple TMV-like arms, immobilized in a programmable manner by way of hybridization of the RNA scaffolds to oligodeoxynucleotides exposed on the gold beads.

Dual Functionalization of Rod-Shaped Viruses on Single Coat Protein Subunits

Plant viruses are emerging as versatile tools for nanotechnology applications since it is possible to modify their multivalent protein surfaces and thereby introduce and display new functionalities. In this chapter, we describe a tobacco mosaic virus (TMV) variant that exposes two selectively addressable amino acid moieties on each of its 2130 coat protein (CP) subunits. A lysine as well as a cysteine introduced at accessible sites of every CP can be modified with amino- and/or thiol-reactive chemistry such as N-hydroxysuccinimide esters (NHS ester) and maleimide containing reagents alone or simultaneously. This enables the pairwise immobilization of distinct molecules in close vicinity to each other on the TMV surface by simple standard conjugation protocols. We describe the generation of the mutations, the virus propagation and isolation as well as the dual functionalization of the TMV variant with two fluorescent dyes. The labeling is evaluated by SDS-PAGE and spectrophotometry and the degree of labeling (DOL) calculated.

TMV-Based Adapter Templates for Enhanced Enzyme Loading in Biosensor Applications

Nanotubular tobacco mosaic virus (TMV) particles and RNA-free lower-order coat protein (CP) aggregates have been employed as enzyme carriers in different diagnostic layouts and compared for their influence on biosensor performance. In the following, we describe a label-free electrochemical biosensor for improved glucose detection by use of TMV adapters and the enzyme glucose oxidase (GOD). A specific and efficient immobilization of streptavidin-conjugated GOD ([SA]-GOD) complexes on biotinylated TMV nanotubes or CP aggregates was achieved via bioaffinity binding. Glucose sensors with adsorptively immobilized [SA]-GOD, and with [SA]-GOD cross-linked with glutardialdehyde, respectively, were tested in parallel on the same sensor chip. Comparison of these sensors revealed that TMV adapters enhanced the amperometric glucose detection remarkably, conveying highest sensitivity, an extended linear detection range and fastest response times. These results underline a great potential of an integration of virus/biomolecule hybrids with electronic transducers for applications in biosensorics and biochips. Here, we describe the fabrication and use of amperometric sensor chips combining an array of circular Pt electrodes, their loading with GOD-modified TMV nanotubes (and other GOD immobilization methods), and the subsequent investigations of the sensor performance.

Pleiotropic Effects of Resistance-Breaking Mutations on Particle Stability Provide Insight into Life History Evolution of a Plant RNA Virus

In gene-for-gene host-virus interactions, virus evolution to infect and multiply in previously resistant host genotypes, i.e., resistance breaking, is a case of host range expansion, which is predicted to be associated with fitness penalties. Negative effects of resistance-breaking mutations on within-host virus multiplication have been documented for several plant viruses. However, understanding virus evolution requires analyses of potential trade-offs between different fitness components. Here we analyzed whether coat protein (CP) mutations in Pepper mild mottle virus that break L-gene resistance in pepper affect particle stability and, thus, survival in the environment. For this purpose, CP mutations determining the overcoming of L 3 and L 4 resistance alleles were introduced in biologically active cDNA clones. The kinetics of the in vitro disassembly of parental and mutant particles were compared under different conditions. Resistance-breaking mutations variously affected particle stability. Structural analyses identified the number and type of axial and side interactions of adjacent CP subunits in virions, which explained differences in particle stability and contribute to understanding of tobamovirus disassembly. Resistance-breaking mutations also affected virus multiplication and virulence in the susceptible host, as well as infectivity. The sense and magnitude of the effects of resistance-breaking mutations on particle stability, multiplication, virulence, or infectivity depended on the specific mutation rather than on the ability to overcome the different resistance alleles, and effects on different traits were not correlated. Thus, the results do not provide evidence of links or trade-offs between particle stability, i.e., survival, and other components of virus fitness or virulence.IMPORTANCE The effect of survival on virus evolution remains underexplored, despite the fact that life history trade-offs may constrain virus evolution. We approached this topic by analyzing whether breaking of L-gene resistance in pepper by Pepper mild mottle virus, determined by coat protein (CP) mutations, is associated with reduced particle stability and survival. Resistance-breaking mutations affected particle stability by altering the interactions between CP subunits. However, the sense and magnitude of these effects were unrelated to the capacity to overcome different resistance alleles. Thus, resistance breaking was not traded with survival. Resistance-breaking mutations also affected virus fitness within the infected host, virulence, and infectivity in a mutation-specific manner. Comparison of the effects of CP mutations on these various traits indicates that there are neither trade-offs nor positive links between survival and other life history traits. These results demonstrate that trade-offs between life history traits may not be a general constraint in virus evolution.

Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies

The rod-shaped nanoparticles of the widespread plant pathogen tobacco mosaic virus (TMV) have been a matter of intense debates and cutting-edge research for more than a hundred years. During the late 19th century, their behavior in filtration tests applied to the agent causing the 'plant mosaic disease' eventually led to the discrimination of viruses from bacteria. Thereafter, they promoted the development of biophysical cornerstone techniques such as electron microscopy and ultracentrifugation. Since the 1950s, the robust, helically arranged nucleoprotein complexes consisting of a single RNA and more than 2100 identical coat protein subunits have enabled molecular studies which have pioneered the understanding of viral replication and self-assembly, and elucidated major aspects of virus-host interplay, which can lead to agronomically relevant diseases. However, during the last decades, TMV has acquired a new reputation as a well-defined high-yield nanotemplate with multivalent protein surfaces, allowing for an ordered high-density presentation of multiple active molecules or synthetic compounds. Amino acid side chains exposed on the viral coat may be tailored genetically or biochemically to meet the demands for selective conjugation reactions, or to directly engineer novel functionality on TMV-derived nanosticks. The natural TMV size (length: 300 nm) in combination with functional ligands such as peptides, enzymes, dyes, drugs or inorganic materials is advantageous for applications ranging from biomedical imaging and therapy approaches over surface enlargement of battery electrodes to the immobilization of enzymes. TMV building blocks are also amenable to external control of in vitro assembly and re-organization into technically expedient new shapes or arrays, which bears a unique potential for the development of 'smart' functional 3D structures. Among those, materials designed for enzyme-based biodetection layouts, which are routinely applied, e.g., for monitoring blood sugar concentrations, might profit particularly from the presence of TMV rods: Their surfaces were recently shown to stabilize enzymatic activities upon repeated consecutive uses and over several weeks. This review gives the reader a ride through strikingly diverse achievements obtained with TMV-based particles, compares them to the progress with related viruses, and focuses on latest results revealing special advantages for enzyme-based biosensing formats, which might be of high interest for diagnostics employing 'systems-on-a-chip'.

Equilibrium self-assembly of small RNA viruses

We propose a description for the quasiequilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA genome molecules. We describe the assembly of such viruses as the interplay between two coupled phase-transition-like events: the formation of the protein shell (the capsid) by CPs and the condensation of a large ss viral RNA molecule. Electrostatic repulsion between the CPs competes with attractive hydrophobic interactions and attractive interaction between neutralized RNA segments mediated by the tail groups. An assembly diagram is derived in terms of the strength of attractive interactions between CPs and between CPs and the RNA molecules. It is compared with the results of recent studies of viral assembly. We demonstrate that the conventional theory of self-assembly, which does describe the assembly of empty capsids, is in general not applicable to the self-assembly of RNA-encapsidating virions.

Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy

Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report the first high-resolution structure of BSMV at 4.1 Å obtained by cryo-electron microscopy. We discovered that BSMV forms two types of virion that differ in the number of coat protein (CP) subunits per turn and interactions between the CP subunits. While BSMV and tobacco mosaic virus CP subunits have a similar fold and interact with RNA using conserved residues, the axial contacts between the CP of these two viral groups are considerably different. BSMV CP subunits lack substantial axial contacts and are held together by a previously unobserved lateral contact formed at the virion surface via an interacting loop, which protrudes from the CP hydrophobic core to the adjacent CP subunit. These data provide an insight into diversity in structural organization of helical viruses.

Directed Growth of Virus Nanofilaments on a Superhydrophobic Surface

The evaporation of single droplets of colloidal tobacco mosaic virus (TMV) nanoparticles on a superhydrophobic surface with a hexagonal pillar-pattern results in the formation of coffee-ring type residues. We imaged surface features by optical, scanning electron, and atomic force microscopies. Bulk features were probed by raster-scan X-ray nanodiffraction. At ∼100 pg/μL nanoparticle concentration, the rim of the residue connects to neighboring pillars via fibrous extensions containing flow-aligned crystalline domains. At ∼1 pg/μL nanoparticle concentration, nanofilaments of ≥80 nm diameter and ∼20 μm length are formed, extending normal to the residue-rim across a range of pillars. X-ray scattering is dominated by the nanofilament form-factor but some evidence for crystallinity has been obtained. The observation of sheets composed of stacks of self-assembled nanoparticles deposited on pillars suggests that the nanofilaments are drawn from a structured droplet interface.

Production of platinum atom nanoclusters at one end of helical plant viruses

Platinum atom clusters (Pt nanoparticles, Pt-NPs) were produced selectively at one end of helical plant viruses, tobacco mosaic virus (TMV) and potato virus X (PVX), when platinum coordinate compounds were reduced chemically by borohydrides. Size of the platinum NPs depends on conditions of the electroless deposition of platinum atoms on the virus. Results suggest that the Pt-NPs are bound concurrently to the terminal protein subunits and the 5′ end of encapsidated TMV RNA. Thus, a special structure of tobacco mosaic virus and potato X virus particles with nanoparticles of platinum, which looks like a push-pin with platinum head and virus needle, was obtained. Similar results were obtained with ultrasonically fragmented TMV particles. By contrast, the Pt-NPs fully filled the central axial hole of in vitro assembled RNA-free TMV-like particles. We believe that the results presented here will be valuable in the fundamental understanding of interaction of viral platforms with ionic metals and in a mechanism of nanoparticles formation.

Complexes assembled from TMV-derived spherical particles and entire virions of heterogeneous nature

Previously, we described some structural features of spherical particles (SPs) generated by thermal remodelling of the tobacco mosaic virus. The SPs represent a universal platform that could bind various proteins. Here, we report that entire isometric virions of heterogeneous nature bind non-specifically to the SPs. Formaldehyde (FA) was used for covalent binding of a virus to the SPs surface for stabilizing the SP-virus complexes. Transmission and high resolution scanning electron microscopy showed that the SPs surface was covered with virus particles. The architecture of SP-virion complexes was examined by immunologic methods. Mean diameters of SPs and SP-human enterovirus C and SP-cauliflower mosaic virus (CaMV) compositions were determined by nanoparticle tracking analysis (NTA) in liquid. Significantly, neither free SPs nor individual virions were detected by NTA in either FA-crosslinked or FA-untreated compositions. Entirely, all virions were bound to the SPs surface and the SP sites within the SP-CaMV complexes were inaccessible for anti-SP antibodies. Likewise, the SPs immunogenicity within the FA-treated SPs-CaMV compositions was negligible. Apparently, the SP antigenic sites were hidden and masked by virions within the compositions. Previously, we reported that the SPs exhibited adjuvant activity when foreign proteins/epitopes were mixed with or crosslinked to SPs. We found that immunogenicity of entire CaMV crosslinked to SP was rather low which could be due to the above-mentioned masking of the SPs booster. Contrastingly, immunogenicity of the FA-untreated compositions increased significantly, presumably, due to partial release of virions and unmasking of some SPs-buster sites after animals immunization.

How do filovirus filaments bend without breaking?

Viruses of the Mononegavirales have helical nucleocapsids containing a single-stranded negative-sense RNA genome complexed with the nucleoprotein and several other virus-encoded proteins. This RNA-protein complex acts as the template for replication and transcription during infection. Recent structural data has advanced our understanding of how these functions are achieved in filoviruses, which include dangerous pathogens such as Ebola virus. Polyploid filoviruses package multiple genome copies within strikingly long filamentous viral envelopes, which must be flexible to avoid breakage of the 19kb non-segmented genomic RNA. We review how the structure of filoviruses and paramyxoviruses permits this morphological flexibility in comparison to rhabdoviruses that have short, bullet-shaped virions with relatively rigid envelopes.

The development and application of new crystallization method for tobacco mosaic virus coat protein

BACKGROUND

Although tobacco mosaic virus (TMV) coat protein (CP) has been isolated from virus particles and its crystals have grown in ammonium sulfate buffers for many years, to date, no one has reported on the crystallization of recombinant TMV-CP connecting peptides expressed in E. coli.

METHODS

In the present papers genetically engineered TMV-CP was expressed, into which hexahistidine (His) tags or glutathione-S-transferase (GST) tags were incorporated. Considering that GST-tags are long peptides and His-tags are short peptides, an attempt was made to grow crystals of TMV-CP cleaved GST-tags (WT-TMV-CP32) and TMV-CP incorporated His-tags (WT-His-TMV-CP12) simultaneously in ammonium sulfate buffers and commercial crystallization reagents. It was found that the 20S disk form of WT-TMV-CP32 and WT-His-TMV-CP12 did not form high resolution crystals by using various crystallization buffers and commercial crystallization reagents. Subsequently, a new experimental method was adopted in which a range of truncated TMV-CP was constructed by removing several amino acids from the N- or the C-terminal, and high resolution crystals were grown in ammonium sulfate buffers and commercial crystallization reagents.

RESULTS

The new crystallization method was developed and 3.0 Å resolution macromolecular crystal was thereby obtained by removing four amino acids at the C-terminal of His-TMV-CP and connecting six His-tags at the N-terminal of His-TMV-CP (TR-His-TMV-CP19). The Four-layer aggregate disk structure of TR-His-TMV-CP19 was solved. This phenomenon showed that peptides at the C-terminus hindered the growth of high resolution crystals and the peptides interactions at the N-terminus were attributed to the quality of TMV-CP crystals.

CONCLUSION

A 3.0 Å resolution macromolecular crystal of TR-His-TMV-CP19 was obtained and the corresponding structure was solved by removing four amino acids at the C-terminus of TMV-CP and connecting His-tags at the N-terminus of TMV-CP. It indicated that short peptides influenced the resolution of TMV-CP crystals.

Helical viruses

Virtually all studies of structure and assembly of viral filaments have been made on plant and bacterial viruses. Structures have been determined using fiber diffraction methods at high enough resolution to construct reliable molecular models or several of the rigid plant tobamoviruses (related to tobacco mosaic virus, TMV) and the filamentous bacteriophages including Pf1 and fd. Lower-resolution structures have been determined for a number of flexible filamentous plant viruses using fiber diffraction and cryo-electron microscopy. Virions of filamentous viruses have numerous mechanical functions, including cell entry, viral disassembly, viral assembly, and cell exit. The plant viruses, which infect multicellular organisms, also use virions or virion-like assemblies for transport within the host. Plant viruses are generally self-assembling; filamentous bacteriophage assembly is combined with secretion from the host cell, using a complex molecular machine. Tobamoviruses and other plant viruses disassemble concomitantly with translation, by various mechanisms and involving various viral and host assemblies. Plant virus movement within the host also makes use of a variety of viral proteins and modified host assemblies.

Immunogenic compositions assembled from tobacco mosaic virus-generated spherical particle platforms and foreign antigens

We reported recently that RNA-free spherical particles (SPs) generated by thermal remodelling of tobacco mosaic virus (TMV) are capable of binding GFP to their surface. Here, we show that SPs represent a universal particle platform that can form compositions by binding a diversity of various foreign proteins/epitopes of viral and non-viral origin to their surface. Numerous molecules of a foreign protein linked to the SP surface were revealed by immunogold electron microscopy. Several SP-based compositions were obtained containing one of the following foreign antigens: antigenic determinant A of rubella virus E1 glycoprotein; a recombinant protein containing the M2e epitope of influenza virus A protein M2; a recombinant antigen consisting of three epitopes of influenza virus A haemagglutinin; potato virus X (PVX) coat protein (CP); BSA; and PVX CP fused with the epitope of plum pox virus CP. The ‘mixed’ compositions could be also assembled by binding two different foreign antigens to each of the SPs. Immunogenicity of foreign antigens adsorbed or linked covalently to SPs in the SP-based compositions was examined. The antigenic specificity of foreign antigens was retained, whereas their immunogenicity increased significantly. It was inferred that SPs exhibit immunopotentiating activity, in particular in the form of compositions comprising SP and foreign antigen linked covalently to their surface by formaldehyde.

Engineered Tobacco mosaic virus mutants with distinct physical characteristics in planta and enhanced metallization properties

Tobacco mosaic virus mutants were engineered to alter either the stability or surface chemistry of the virion: within the coat protein, glutamic acid was exchanged for glutamine in a buried portion to enhance the inter-subunit binding stability (E50Q), or a hexahistidine tract was fused to the surface-exposed carboxy terminus of the coat protein (6xHis). Both mutant viruses were expected to possess specific metal ion affinities. They accumulated to high titers in plants, induced distinct phenotypes, and their physical properties during purification differed from each other and from wild type (wt) virus. Whereas 6xHis and wt virions contained RNA, the majority of E50Q protein assembled essentially without RNA into rods which frequently exceeded 2 μm in length. Electroless deposition of nickel metallized the outer surface of 6xHis virions, but the central channel of E50Q rods, with significantly more nanowires of increased length in comparison to those formed in wtTMV.