Self-assembled virus-like particles with magnetic cores

Design strategies for the self-assembly of polyhedral shells

The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous aggregates. Here, we investigate in detail the problem of the self-assembly of the three Archimedean shells with five contact points per vertex, i.e., the icosahedron, the snub cube, and the snub dodecahedron. We use patchy particles with five interaction sites (or patches) as model for the building blocks and recast the assembly problem as a Boolean satisfiability problem (SAT) for the patch-patch interactions. This allows us to find effective designs for all targets and to selectively suppress unwanted structures. By tuning the geometrical arrangement and the specific interactions of the patches, we demonstrate that lowering the symmetry of the building blocks reduces the number of competing structures, which in turn can considerably increase the yield of the target structure. These results cement SAT-assembly as an invaluable tool to solve inverse design problems.

Molecular dynamics simulation on surface modification of quantum scaled CuO nano-clusters to support their experimental studies

Interest in nanoparticle modification using functional chemicals has increased rapidly, as it allows more freedom of physiochemical tuning of the nanoparticle's surface into biomedically oriented and designated properties. However, the observation and detection of the thin molecular layers on the nanoparticle surface are very challenging under current analytical facilities. The focus of this research is to demonstrate fundamental interactions between the surface treated nanoparticles and their host liquid media using lab-based experimentation and simulation. In this research, investigation has been carried out on analyzing the surface compatibility and the diffusivity of modified CuO nanoparticles (CuONPs) with short-chain carboxylate-terminated molecules in biofluids. Moreover, during the current Covid-19 pandemic, the Cu/CuONPs have proved effective in killing SARS-CoV1/2 and other airborne viruses. This research was conducted at the molecular level with joint consideration of experimental and simulation studies for characterization of variables. Experimental tests conducted using Fourier Transform Infrared (FTIR) spectroscopy demonstrated several spectral ranges of interest, specifically, detection of three major carboxylate attachments (i.e., 1667-1609 cm-1, 1668-1557 cm-1, etc.) were found. From simulation, similar attachment styles were observed by the LAMMPS simulation package that mimicked similar agglomerations with a predicted diffusion coefficient as recorded to be 2.28E-9 m2/s. Viscosities of modified nanofluids were also compared with unmodified nanofluids for defining aggregation kinetics.

Protein Cages: From Fundamentals to Advanced Applications

Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.

Polyelectrolyte Encapsulation and Confinement within Protein Cage-Inspired Nanocompartments

Protein cages are nanocompartments with a well-defined structure and monodisperse size. They are composed of several individual subunits and can be categorized as viral and non-viral protein cages. Native viral cages often exhibit a cationic interior, which binds the anionic nucleic acid genome through electrostatic interactions leading to efficient encapsulation. Non-viral cages can carry various cargo, ranging from small molecules to inorganic nanoparticles. Both cage types can be functionalized at targeted locations through genetic engineering or chemical modification to entrap materials through interactions that are inaccessible to wild-type cages. Moreover, the limited number of constitutional subunits ease the modification efforts, because a single modification on the subunit can lead to multiple functional sites on the cage surface. Increasing efforts have also been dedicated to the assembly of protein cage-mimicking structures or templated protein coatings. This review focuses on native and modified protein cages that have been used to encapsulate and package polyelectrolyte cargos and on the electrostatic interactions that are the driving force for the assembly of such structures. Selective encapsulation can protect the payload from the surroundings, shield the potential toxicity or even enhance the intended performance of the payload, which is appealing in drug or gene delivery and imaging.

Virus-Like Particle: Evolving Meanings in Different Disciplines

Virus-like particle (VLP) is a term that has been in use for about 80 years. Usually, VLP has meant a particle that is like a virus, generally by appearance, but without either proven or actual virus functionality. Initially VLP referred to particles seen in electron microscope images of tissues. More recently, VLP has come to mean other things to other researchers. A key divergence has been use of VLP in association with vaccine and biotechnology applications versus use of VLP in enumeration of viruses in environmental samples. To these viral ecologists, a VLP is a particle that is virus sized, has nucleic acid, and could be a functional virus. But to vaccine developers and biotechnology researchers a VLP instead is a viral structure that intentionally lacks a viral genome. In this study, we look at the history of use of VLP, following changes in meaning as the technology to study VLPs changed.

Inorganic-organic Nanomaterials for Therapeutics and Molecular Imaging Applications

Background::

Surface modification of nanoparticles with targeting moieties can be achieved through bioconjugation chemistries to impart new Functionalities. Various polymeric nanoparticles have been used for the formulation of nanoparticles such as naturally-occurring protein cages, virus-like particles, polymeric saccharides, and liposomes. These polymers have been proven to be biocompatible, side effects free and degradable with no toxicity.

Objectives::

This paper reviews available literature on the nanoparticles pharmaceutical and medical applications. The review highlights and updates the customized solutions for selective drug delivery systems that allow high-affinity binding between nanoparticles and the target receptors.

Methods::

Bibliographic databases and web-search engines were used to retrieve studies that assessed the usability of nanoparticles in the pharmaceutical and medical fields. Data were extracted on each system in vivo and in vitro applications, its advantages and disadvantages, and its ability to be chemically and genetically modified to impart new functionalities. Finally, a comparison between naturally occurring and their synthetic counterparts was carried out.

Results::

The results showed that nanoparticles-based systems could have promising applications in diagnostics, cell labeling, contrast agents (Magnetic Resonance Imaging and Computed Tomography), antimicrobial agents, and as drug delivery systems. However, precautions should be taken to avoid or minimize toxic effect or incompatibility of nanoparticles-based systems with the biological systems in case of pharmaceutical or medical applications.

Conclusion::

This review presented a summary of recent developments in the field of pharmaceutical nanotechnology and highlighted the challenges and the merits that some of the nanoparticles- based systems both in vivo and in vitro systems.

From infection to healing: The use of plant viruses in bioactive hydrogels

Plant viruses show great diversity in shape and size, but each species forms unique nucleoprotein particles that are symmetrical and monodisperse. The genetically programed structure of plant viruses allows them to be modified by genetic engineering, bioconjugation, or encapsulation to form virus nanoparticles (VNPs) that are suitable for a broad range of applications. Plant VNPs can be used to present foreign proteins or epitopes, to construct inorganic hybrid materials, or to carry molecular cargos, allowing their utilization as imaging reagents, immunomodulators, therapeutics, nanoreactors, and biosensors. The medical applications of plant viruses benefit from their inability to infect and replicate in human cells. The structural properties of plant viruses also make them useful as components of hydrogels for tissue engineering. Hydrogels are three-dimensional networks composed of hydrophilic polymers that can absorb large amounts of water. They are used as supports for tissue regeneration, as reservoirs for controlled drug release, and are found in contact lenses, many wound healing materials, and hygiene products. They are also useful in ecological applications such as wastewater treatment. Hydrogel-based matrices are structurally similar to the native extracellular matrix (ECM) and provide a scaffold for the attachment of cells. To fully replicate the functions of the ECM it is necessary to augment hydrogels with biological cues that regulate cellular interactions. This can be achieved by incorporating functionalized VNPs displaying ligands that influence the mechanical characteristics of hydrogels and their biological properties, promoting the survival, proliferation, migration, and differentiation of embedded cells. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement.

Design and biosynthesis of functional protein nanostructures

Proteins are one of the major classes of biomolecules that execute biological functions for maintenance of life. Various kinds of nanostructures self-assembled from proteins have been created in nature over millions of years of evolution, including protein nanowires, layers and nanocages. These protein nanostructures can be reconstructed and equipped with desired new functions. Learning from and manipulating the self-assembly of protein nanostructures not only help to deepen our understanding of the nature of life but also offer new routes to fabricate novel nanomaterials for diverse applications. This review summarizes the recent research progress in this field, focusing on the characteristics, functionalization strategies, and applications of protein nanostructures.

Elucidating the Thermodynamic Driving Forces of Polyanion-Templated Virus-like Particle Assembly

A virus in its most simple form is comprised of a protein capsid that surrounds and protects the viral genome. The self-assembly of such structures, however, is a highly complex, multiprotein, multiinteraction process and has been a topic of study for a number of years. This self-assembly process is driven by the (mainly electrostatic) interaction between the capsid proteins (CPs) and the genome as well as by the protein-protein interactions, which primarily rely on hydrophobic interactions. Insight in the thermodynamics that is involved in virus and virus-like particle (VLP) formation is crucial in the detailed understanding of this complex assembly process. Therefore, we studied the assembly of CPs of the cowpea chlorotic mottle virus (CCMV) templated by polyanionic species (cargo), that is, single-stranded DNA (ssDNA), and polystyrene sulfonate (PSS) using isothermal titration calorimetry. By separating the electrostatic CP-cargo interaction from the full assembly interaction, we conclude that CP-CP interactions cause an enthalpy change of -3 to -4 kcal mol-1 CP. Furthermore, we quantify that upon reducing the CP-CP interaction, in the case of CCMV by increasing the pH to 7, the CP-cargo starts to dominate VLP formation. This is highlighted by the three times higher affinity between CP and PSS compared to CP and ssDNA, resulting in the disassembly of CCMV at neutral pH in the presence of PSS to yield PSS-filled VLPs.

Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics

Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.

Assembly and Characterization of HBc Derived Virus-like Particles with Magnetic Core

Core-virus like particles (VLPs) assembly is a kinetically complex cascade of interactions between viral proteins, nanoparticle's surface and an ionic environment. Despite many in silico simulations regarding this process, there is still a lack of experimental data. The main goal of this study was to investigate the capsid protein of hepatitis B virus (HBc) assembly into virus-like particles with superparamagnetic iron oxide nanoparticles (SPIONs) as a magnetic core in relation to their characteristics. The native form of HBc was obtained via agroinfection of Nicotiana benthamiana with pEAQ-HBc plasmid. SPIONs of diameter of 15 nm were synthesized and functionalized with two ligands, providing variety in ζ-potential and hydrodynamic diameter. The antigenic potential of the assembled core-VLPs was assessed with enzyme-linked immunosorbent assay (ELISA). Morphology of SPIONs and core-VLPs was evaluated via transmission electron microscopy (TEM). The most successful core-VLPs assembly was obtained for SPIONs functionalized with dihexadecyl phosphate (DHP) at SPIONs/HBc ratio of 0.2/0.05 mg/mL. ELISA results indicate significant decrease of antigenicity concomitant with core-VLPs assembly. In summary, this study provides an experimental assessment of the crucial parameters guiding SPION-HBc VLPs assembly and evaluates the antigenicity of the obtained structures.

Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte

The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7k_BT₀, with k_B the Boltzmann constant and T₀ = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20k_BT₀). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape.

The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements.

Size-Controlled Iron Oxide Nanoplatforms with Lipidoid-Stabilized Shells for Efficient Magnetic Resonance Imaging-Trackable Lymph Node Targeting and High-Capacity Biomolecule Display

Nanoplatforms for biomolecule delivery to the lymph nodes have attracted considerable interest as vectors for immunotherapy. Core-shell iron oxide nanoparticles are particularly appealing because of their potential as theranostic magnetic resonance imaging (MRI)-trackable vehicles for biomolecule delivery. The key challenge for utilizing iron oxide nanoparticles in this capacity is control of their coating shells to produce particles with predictable size. Size determines both the carrier capacity for biomolecule display and the carrier ability to target the lymph nodes. In this study, we develop a novel coating method to produce core-shell iron oxide nanoparticles with controlled size. We utilize lipidlike molecules to stabilize self-assembled lipid shells on the surface of iron oxide nanocrystals, allowing the formation of consistent coatings on nanocrystals of varying size (10-40 nm). We further demonstrate the feasibility of leveraging the ensuing control of nanocarrier size for optimizing the carrier functionalities. Coated nanoparticles with 10 and 30 nm cores supported biomolecule display at 10-fold and 200-fold higher capacities than previously reported iron oxide nanoparticles, while preserving monodisperse sub-100 nm size populations. In addition, accumulation of the coated nanoparticles in the lymph nodes could be tracked by MRI and at 1 h post injection demonstrated significantly enhanced lymph node targeting. Notably, lymph node targeting was 9-40 folds higher than that for previously reported nanocarriers, likely due to the ability of these nanoparticles to robustly maintain their sub-100 nm size in vivo. This approach can be broadly applicable for rational design of theranostic nanoplatforms for image-monitored immunotherapy.

Protein cage assembly across multiple length scales

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.

Compartmentalized supramolecular hydrogels based on viral nanocages towards sophisticated cargo administration

Introduction of compartments with defined spaces inside a hydrogel network brings unique features, such as cargo quantification, stabilization and diminishment of burst release, which are all desired for biomedical applications. As a proof of concept, guest-modified cowpea chlorotic mottle virus (CCMV) particles and complementary guest-modified hydroxylpropyl cellulose (HPC) were non-covalently cross-linked through the formation of ternary host-guest complexes with cucurbit[8]uril (CB[8]). Furthermore, CCMV based virus-like particles (VLPs) loaded with tetrasulfonated zinc phthalocyanine (ZnPc) were prepared, with a loading efficiency up to 99%, which are subsequently successfully integrated inside the supramolecular hydrogel network. It was shown that compartments provided by protein cages not only help to quantify the loaded ZnPc cargo, but also improve the water solubility of ZnPc to avoid undesired aggregation. Moreover, the VLPs together with ZnPc cargo can be released in a controlled way without an initial burst release. The photodynamic effect of ZnPc molecules was retained after encapsulation of capsid protein and release from the hydrogel. This line of research suggests a new approach for sophisticated drug administration in supramolecular hydrogels.

Self-assembled artificial viral capsids bearing coiled-coils at the surface

In order to construct artificial viral capsids bearing complementary dimeric coiled-coils on the surface, a β-annulus peptide bearing a coiled-coil forming sequence at the C-terminus (β-annulus-coiled-coil-B) was synthesized by a native chemical ligation of a β-annulus-SBn peptide with a Cys-containing coiled-coil-B peptide. Dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) images revealed that the β-annulus-coiled-coil-B peptide self-assembled into spherical structures of about 50 nm in 10 mM Tris-HCl buffer. Circular dichroism (CD) spectra indicated the formation of the complementary coiled-coil structure on the spherical assemblies. Addition of 0.25 equivalent of the complementary coiled-coil-A peptide to the β-annulus-coiled-coil-B peptide showed the formation of spherical assemblies of 46 ± 14 nm with grains of 5 nm at the surface, whereas addition of 1 equivalent of the complementary coiled-coil-A peptide generated fibrous assemblies.

Hybrid Assembly toward Enhanced Thermal Stability of Virus-like Particles and Antibacterial Activity of Polyoxometalates

In an effort to improve both the stability of virus-like particles (VLPs) and the medical activity of polyoxometalates (POMs), a new hybrid assembly system between human papillomavirus (HPV) capsid protein L1 and a europium-containing POM (EuW₁₀) has been constructed, for the first time, via the electrostatic interactions between them. The co-assembly of EuW₁₀ and HPV 16 L1-pentamer (L1-p) in buffer solution resulted in the encapsulation of POMs in the cavity of VLPs, which was further confirmed by cesium chloride (CsCl) gradient ultracentrifugation, SDS-PAGE, dynamic light scattering, and transmission electron microscopy, whereas the post-assembly of EuW₁₀ with the as-prepared VLPs leads to the adsorption of POMs only on the external surface of particles, and both cases improved the thermal and storage stabilities of VLPs obviously. Particularly, the encapsulation of POMs in VLPs largely improved the antibacterial activity of EuW₁₀, and thereby, the present study will be significant for both the stability improvement of protein vaccines and the development of POM medicine.

Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome

In this article, we elaborate the application of thermal decomposition based synthesis of Fe₃O₄ superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation. Further, SPMNP that are distinctly localized in subcellular compartments can be used as technology for subcellular fractionation that can complement existing tools for cell biology research. As a future perspective, isolated magnetic organelles can be extended to protein/protein complex purification for biochemical and structural biology studies.

In Vitro Assembly of Virus-Derived Designer Shells Around Inorganic Nanoparticles

Nanoparticle-templated assembly of virus shells provides a promising approach to the production of hybrid nanomaterials and a potential avenue toward new mechanistic insights in virus phenomena originating in many-body effects, which cannot be understood from examining the properties of molecular subunits alone. This approach complements the successful molecular biology perspective traditionally used in virology, and promises a deeper understanding of viruses and virus-like particles through an expanded methodological toolbox. Here we present protocols for forming a virus coat protein shell around functionalized inorganic nanoparticles.

Background-Free Imaging of a Viral Capsid Proteins Coated Anisotropic Nanoparticle on a Living Cell Membrane with Dark-Field Optical Microscopy

Exploring the diffusion dynamics of a viral capsid proteins (VCP)-functionalized nanocarrier on a living cell membrane could provide much kinetic information for the better understanding of their biological functionality. Gold nanoparticles are an excellent core material of nanocarriers because of the good biocompatibility as well as versatile surface chemistry. However, due to the strong scattering background from subcellular organelles, it is a grand challenge to selectively image an individual nanocarrier on a living cell membrane. In this work, we demonstrated a convenient strategy to effectively screen the scattering background from living cells for single-particle imaging with a polarization-resolved dual-channel imaging module. By taking advantage of the polarization of anisotropic gold nanoparticles (gold nanorods, GNRs), the signals from cell components could be counteracted after subtracting the sequential images one by one, while those transiently rotating GNRs on the cell membrane still exist in the processed image. In contrast to the previously reported methods, this method does not require a complicated optical setup alignment and sophisticated digital image analysis process. According to the single-particle imaging results, the majority of VCP-GNRs were anchoring on the cell membrane with confined diffusion. Interestingly, on further inspection of the diffusion trajectories, the particles displayed anomalous confined diffusion with randomly distributed large walking steps during the whole track. Non-Gaussian step distribution was noted, indicating heterogeneous binding and desorption processes on the cell membrane. As a consequence of the robust background screening capability, this approach would find broad applications for single-particle imaging under a noisy environment, e.g., living cells.

Biophysical analysis of BMV virions purified using a novel method

Brome mosaic virus (BMV) has been successfully loaded with different types of nanoparticles. However, studies concerning its application as a nanoparticle carrier demand high-purity virions in large amounts. Existing BMV purification protocols rely on multiple differential ultracentrifugation runs of the initially purified viral preparation. Herein, we describe an alternative method for BMV purification based on ion-exchange chromatography and size-exclusion chromatography (SEC) yielding 0.2mg of virus from 1g of plant tissue. Our method is of similar efficiency to previously described protocols and can easily be scaled up. The method results in high-quality BMV preparations as confirmed by biophysical analyses, including cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), static light scattering (SLS), and circular dichroism (CD) measurements and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) spectroscopy. Our results revealed that purified BMV capsids are stable and monodisperse and can be used for further downstream applications. In this work, we also characterize secondary structure and size fluctuations of the BMV virion at different pH values.

Icosahedral plant viral nanoparticles - bioinspired synthesis of nanomaterials/nanostructures

Viral nanotechnology utilizes virus nanoparticles (VNPs) and virus-like nanoparticles (VLPs) of plant viruses as highly versatile platforms for materials synthesis and molecular entrapment that can be used in the nanotechnological fields, such as in next-generation nanoelectronics, nanocatalysis, biosensing and optics, and biomedical applications, such as for targeting, therapeutic delivery, and non-invasive in vivo imaging with high specificity and selectivity. In particular, plant virus capsids provide biotemplates for the production of novel nanostructured materials with organic/inorganic moieties incorporated in a very precise and controlled manner. Interestingly, capsid proteins of spherical plant viruses can self-assemble into well-organized icosahedral three-dimensional (3D) nanoscale multivalent architectures with high monodispersity and structural symmetry. Using viral genetic and protein engineering of icosahedral viruses with a variety of sizes, the interior, exterior and the interfaces between coat protein (CP) subunits can be manipulated to fabricate materials with a wide range of desirable properties allowing for biomineralization, encapsulation, infusion, controlled self-assembly, and multivalent ligand display of nanoparticles or molecules for varied applications. In this review, we discuss the various functional nanomaterials/nanostructures developed using the VNPs and VLPs of different icosahedral plant viruses and their nano(bio)technological and nanomedical applications.

Encapsulation of Inorganic Nanomaterials inside Virus-Based Nanoparticles for Bioimaging

Virus-based nanoparticles (VNPs) can serve as containers for inorganic nanomaterials with excellent physical and chemical properties. Incorporation of nanomaterials inside the inner cavity of VNPs has opened up lots of possibilities for imaging applications in the field of biology and medicine. Encapsulation of inorganic nanoparticles (NPs) in VNPs can achieve the labeling of VNPs with nanoprobes and maintain the original outer surface features of VNPs at the same time. In return, VNPs enhance the stability and biocompatibility of the inorganic cargoes. This review briefly summarizes the current typical strategies to encapsulate inorganic nanomaterials in VNPs, i.e. mineralization and self-assembly, as well as the applications of these hybrid nanostructures in the field of bioimaging, including in vitro and in vivo fluorescence imaging, magnetic resonance imaging, and theranostics. Nanophotonic studies based on the VNP platform are also discussed. We anticipate that this field will continue to flourish, with new exciting opportunities stemming from advancements in the rational design of VNPs, the development of excellent inorganic nanomaterials, the integration of multiple functionalities, and the regulation of nano-bio interfacial interactions.

Beyond icosahedral symmetry in packings of proteins in spherical shells

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

Optical Characteristics and Tumor Imaging Capabilities of Near Infrared Dyes in Free and Nano-Encapsulated Formulations Comprised of Viral Capsids

Near infrared (NIR) fluorescent molecules and nanosized structures can serve as potential optical probes for image-guided removal of small tumor nodules (≲ 1 mm diameter). Although indocyanine green (ICG) remains as the only FDA-approved NIR dye, other organic dyes are under extensive development for enhanced imaging capabilities. One such dye is BrCy106-NHS where bromine is substituted for aromatic structures in cyanine dyes. Herein, we investigate the absorption and fluorescence characteristics of ICG and BrCy106-NHS, and quantitatively assess their tumor imaging capabilities in free (non-encapsulated) and a nano-encapsulated form that utilizes the capsid protein (CP) from genome-depleted plant-infecting brome mosaic virus as the encapsulating shell. We refer to these nanoconstructs as optical viral ghosts (OVGs). For example, when fabricated at CP to dye concentration ratio of 200, value of the spectrally integrated fluorescence emission for BrCy106-NHS-doped OVGs is ∼60 times higher than that of ICG-doped OVGs. Our analysis of homogenized mice intraperitoneal tumors indicate that the averaged total fluorescence emission associated with the use of BrCy106-NHS-doped can be at least about 44 times greater than that of ICG-doped OVGs. Our results suggest that OVGs containing BrCy106-NHS may potentially serve as effective optical probes for tumor imaging.

Glycosaminoglycans-Specific Cell Targeting and Imaging Using Fluorescent Nanodiamonds Coated with Viral Envelope Proteins

Understanding virus-host interactions is crucial for vaccine development. This study investigates such interactions using fluorescent nanodiamonds (FNDs) coated with vaccinia envelope proteins as the model system. To achieve this goal, we noncovalently conjugated 100 nm FNDs with rA27(aa 21-84), a recombinant envelope protein of vaccinia virus, for glycosaminoglycans (GAGs)-specific targeting and imaging of living cells. Another recombinant protein rDA27(aa 33-84) that removes the GAGs-binding sequences was also used for comparison. Three types of A27-coated FNDs were generated, including rA27(aa 21-84)-FND, rDA27(aa 33-84)-FND, and hybrid rA27(aa 21-84)/rDA27(aa 33-84)-FND. The specificity of these viral protein-FND conjugates toward GAGs binding was examined by flow cytometry, fluorescence microscopy, and gel electrophoresis. Results obtained for normal and GAGs-deficient cells showed that the recombinant proteins maintain their GAG-targeting activities even after immobilization on the FND surface. Our studies provide a new nanoparticle-based platform not only to target specific cell types but also to track the fates of these immobilized viral proteins in targeted cells as well as to isolate and enrich GAGs-associated proteins on cell membrane.

A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency

Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.

Quantum dot encapsulation in virus-like particles with tuneable structural properties and low toxicity

Quantum dot encapsulation within cowpea chlorotic mottle virus-based capsid proteins to obtain size-tuneable, non-toxic, luminescent imaging probes is presented.

Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology

Within biology, molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nanosystems that exist at the interface of living organisms and nonliving biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. Composed of self-assembling protein subunits, VLPs provide both a model for studying materials' assembly at the nanoscale and useful building blocks for materials design. The robustness and degree of understanding of many VLP structures allow for the ready use of these systems as versatile nanoparticle platforms for the conjugation of active molecules or as scaffolds for the structural organization of chemical processes. Lastly the prevalence of viruses in all domains of life has led to unique activities of VLPs in biological systems most notably the immune system. Here we discuss recent efforts to apply VLPs in a wide variety of applications with the aim of highlighting how the common structural elements of VLPs have led to their emergence as paradigms for the understanding and design of biological nanomaterials.

Design of virus-based nanomaterials for medicine, biotechnology, and energy

This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.

Viruses, Artificial Viruses and Virus-Based Structures for Biomedical Applications

Nanobiomaterials such as virus particles and artificial virus particles offer tremendous opportunities to develop new biomedical applications such as drug- or gene-delivery, imaging and sensing but also improve understanding of biological mechanisms. Recent advances within the field of virus-based systems give insights in how to mimic viral structures and virus assembly processes as well as understanding biodistribution, cell/tissue targeting, controlled and triggered disassembly or release and circulation times. All these factors are of high importance for virus-based functional systems. This review illustrates advances in mimicking and enhancing or controlling these aspects to a high degree toward delivery and imaging applications.

Intracellular cargo delivery by virus capsid protein-based vehicles: From nano to micro

Cellular delivery is an important concern for the efficiency of medicines and sensors for disease diagnoses and therapy. However, this task is quite challenging. Self-assembly virus capsid proteins might be developed as building blocks for multifunctional cellular delivery vehicles. In this work, we found that SV40 VP1 (Simian virus 40 major capsid protein) could function as a new cell-penetrating protein. The VP1 protein could carry foreign proteins into cells in a pentameric structure. A double color structure, with red QDs (Quantum dots) encapsulated by viral capsids fused with EGFP, was created for imaging cargo delivery and release from viral capsids. The viral capsids encapsulating QDs were further used for cellular delivery of micron-sized iron oxide particles (MPIOs). MPIOs were efficiently delivered into live cells and controlled by a magnetic field. Therefore, our study built virus-based cellular delivery systems for different sizes of cargos: protein molecules, nanoparticles, and micron-sized particles.

FROM THE CLINICAL EDITOR

Much research is being done to investigate methods for efficient and specific cellular delivery of drugs, proteins or genetic material. In this article, the authors describe their approach in using self-assembly virus capsid proteins SV40 VP1 (Simian virus 40 major capsid protein). The cell-penetrating behavior provided excellent cellular delivery and should give a new method for biomedical applications.

Virus-Based Nanoparticles as Versatile Nanomachines

Nanoscale engineering is revolutionizing the way we prevent, detect, and treat diseases. Viruses have played a special role in these developments because they can function as prefabricated nanoscaffolds that have unique properties and are easily modified. The interiors of virus particles can encapsulate and protect sensitive compounds, while the exteriors can be altered to display large and small molecules in precisely defined arrays. These properties of viruses, along with their innate biocompatibility, have led to their development as actively targeted drug delivery systems that expand on and improve current pharmaceutical options. Viruses are naturally immunogenic, and antigens displayed on their surface have been used to create vaccines against pathogens and to break self-tolerance to initiate an immune response to dysfunctional proteins. Densely and specifically aligned imaging agents on viruses have allowed for high-resolution and noninvasive visualization tools to detect and treat diseases earlier than previously possible. These and future applications of viruses have created an exciting new field within the disciplines of both nanotechnology and medicine.

Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles

Here we explore the formation of virus-like nanoparticles (VNPs) utilizing 22-24 nm iron oxide nanoparticles (NPs) as cores and proteins derived from viral capsids of brome mosaic virus (BMV) or hepatitis B virus (HBV) as shells. To accomplish that, hydrophobic FeO/Fe3O4 NPs prepared by thermal decomposition of iron oleate were coated with poly(maleic acid-alt-octadecene) modified with poly(ethylene glycol) (PEG) tails of different lengths and grafting densities. MRI studies show high r2/r1 relaxivity ratios of these NPs that are practically independent of the polymer coating type. The versatility and flexibility of the viral capsid protein are on display as they readily form shells that exceed their native size. The location of the long PEG tails upon shell formation was investigated by electron microscopy and small-angle X-ray scattering. PEG tails were located differently in the BMV and HBV VNPs, with the BMV VNPs preferentially entrapping the tails in the interior and the HBV VNPs allowing the tails to extend through the capsid, which highlights the differences between intersubunit interactions in these two icosahedral viruses. The robustness of the assembly reaction and the protruding PEG tails, potentially useful in modulating the immune response, make the systems introduced here a promising platform for biomedical applications.

Direct imaging of the magnetic polarity and reversal mechanism in individual Fe(3-x)O4 nanoparticles

This work reports on the experimental characterization of the magnetic domain configurations in cubic, isolated Fe3-xO4 nanoparticles with a lateral size of 25-30 nm. The magnetic polarity at remanence of single domain ferrimagnetic Fe3-xO4 nanoparticles deposited onto a carbon-silicon wafer is observed by magnetic force microscopy. The orientations of these domains provide a direct observation of the magneto-crystalline easy axes in each individual nanoparticle. Furthermore, the change in the domain orientation with an external magnetic field gives evidence of particle magnetization reversal mediated by a coherent rotation process that is also theoretically predicted by micromagnetic calculations.

Modeling Viral Capsid Assembly

I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.

Study on nanocomposite construction based on the multi-functional biotemplate self-assembled by the recombinant TMGMV coat protein for potential biomedical applications

Nowadays there is a growing interest in bio-scaffolded nanoarchitectures. Rapid progress in nanobiotechnology and molecular biology has allowed the engineering of inorganic-binding peptides termed as genetically engineered polypeptides for inorganics (GEPIs) into self-assembling biological structures to facilitate the design of novel biomedical or bioimaging devices. Here we introduce a novel nanocomposite comprising a self-assembled protein scaffold based on a recombinant tobacco mild green mosaic tobamovirus (TMGMV) coat protein (CP) and the photocatalytic TiO2 nanoparticles attached to it, which may provide a generic method for materials engineering. A template containing a modified TMGMV CP (mCP) gene, with the first six C-terminal amino acid residues deleted to accommodate more foreign peptides and expressing a site-directed mutation of A123C for bioconjugation utility, and two genetically engineered mutants, Escherichia coli-based P-mCP-Ti7 containing a C-terminal TiO2 GEPI sequence of seven peptides (Ti7) and Hi5 insect cells-derived E-CP-Ti7-His6 C-terminally fused with Ti7+His6 tag were created. Expression vectors and protocols for enriching of the two CP variants were established and the resultant proteins were identified by western blot analysis. Their RNA-free self-assembling structures were analyzed by transmission electron microscopy (TEM) and immuno-gold labeling TEM analysis. Adherence of nanoparticles to the P-mCP-Ti7 induced protein scaffold was visualized by TEM analysis. Also discussed is the Cysteine thiol reactivity in bioconjugation reactions with the maleimide-functionalized porphyrin photosensitizers which can function as clinical photodynamic therapy agents. This study introduced a novel approach to producing an assembly-competent recombinant TMGMV CP, examined its ability to serve as a novel platform for the multivalent display of surface ligands and demonstrated an alternative method for nanodevice synthesis for nanobiotechnological applications by combining GEPIs-mediated immobilization with the controllability of self-assembling recombinant TMGMV CP.

Ferritin encapsulation and templated synthesis of inorganic nanoparticles

Understanding how inorganic nanoparticles interact with proteins is paramount to their safe and effective use in vivo. Ordered protein-inorganic nanomaterial assemblies will also enable the creation of patterned structures with useful physical properties. Thermophilic ferritin (tF) from Archaeoglobus fulgidus has unique structural features and self-assembly properties that facilitate stable but also reversible interaction with gold nanoparticles (AuNPs). In this chapter we describe how to express and purify tF and induce its assembly around AuNPs. We also describe methods for characterizing the tF-AuNP complex as well as templating NP growth within the protein cavity.

Structural insights into magnetic clusters grown inside virus capsids

Magnetic nanoparticles have multiple applications in materials science. In particular, virus capsids have been suggested as promising templates for building up nanometric-sized magnetic clusters by taking advantage of their inner cavity as a nanoreactor. In this study we investigate the magnetization of individual cobalt-filled cowpea mosaic virus empty virus-like particles using atomic force microscopy. We also combine the analysis of the effects of dehydration on the structure of virus particles with a comparison of their magnetic signal to that provided by commercially available magnetic nanoparticles of similar size. These two approaches allow the evaluation of the structure of the metallic cluster grown inside the virus capsid. We conclude that, rather than forming solid clusters, cobalt inside viruses forms a discontinuous structure that does not completely fill the virus cavity and reaches about 10% of its volume.

Synthetic virology: engineering viruses for gene delivery

The success of gene therapy relies heavily on the performance of vectors that can effectively deliver transgenes to desired cell populations. As viruses have evolved to deliver genetic material into cells, a prolific area of research has emerged over the last several decades to leverage the innate properties of viruses as well as to engineer new features into them. Specifically, the field of synthetic virology aims to capitalize on knowledge accrued from fundamental virology research in order to design functionally enhanced gene delivery vectors. The enhanced viral vectors, or 'bionic' viruses, feature engineered components, or 'parts', that are natural (intrinsic to viruses or from other organisms) and synthetic (such as man-made polymers or inorganic nanoparticles). Various design strategies--rational, combinatorial, and pseudo-rational--have been pursued to create the hybrid viruses. The gene delivery vectors of the future will likely criss-cross the boundaries between natural and synthetic domains to harness the unique strengths afforded by the various functional parts that can be grafted onto virus capsids. Such research endeavors will further expand and enable enhanced control over the functional capacity of these nanoscale devices for biomedicine.