The refined crystal structure of cowpea mosaic virus at 2.8 A resolution

Nanoindentation of virus capsids in a molecular model

A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C(alpha) atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model, while a buckling transition is observed in continuum models.

Hydrazone ligation strategy to assemble multifunctional viral nanoparticles for cell imaging and tumor targeting

Multivalent nanoparticle platforms are attractive for biomedical applications because of their improved target specificity, sensitivity, and solubility. However, their controlled assembly remains a considerable challenge. An efficient hydrazone ligation chemistry was applied to the assembly of Cowpea mosaic virus (CPMV) nanoparticles with individually tunable levels of a VEGFR-1 ligand and a fluorescent PEGylated peptide. The nanoparticles recognized VEGFR-1 on endothelial cell lines and VEGFR1-expressing tumor xenografts in mice, validating targeted CPMV as a nanoparticle platform in vivo.

Steric and electrostatic complementarity in the assembly of two-dimensional virus arrays

A highly ordered assembly of biological molecules provides a powerful means to study the organizational principles of objects at the nanoscale. Two-dimensional cowpea mosaic virus arrays were assembled in an ordered manner on mica using osmotic depletion effects and a drop-and-dry method. The packing of the virus array was controlled systematically from rhombic packing to hexagonal packing by modulating the concentrations of poly(ethylene glycol) surfactant in the virus solutions. The orientation and packing symmetry of the virus arrays were found to be tuned by the concentrations of surfactants in the sample solutions. A phenomenological model for the present system is proposed to explain the assembly array morphology under the influence of the surfactant. Steric and electrostatic complementarity of neighboring virus capsids is found to be the key factors in controlling the symmetry of packing.

PEGylated viral nanoparticles for biomedicine: the impact of PEG chain length on VNP cell interactions in vitro and ex vivo

PEGylation is an effective strategy for reducing biospecific interactions for pharmaceuticals. The plant virus Cowpea mosaic virus (CPMV) has been studied for potential nanobiomedical applications by virtue of its natural interactions with mammalian endothelial cells. To investigate the degree of PEGylation required to retarget CPMV-based formulations to other destinations, two CPMV-PEG formulations, CPMV-PEG1000 (P1) and CPMV-PEG2000 (P2) were tested. Modeling suggested that the PEG chains were displayed as flattened mushrooms on the particle with an estimated surface grafting area of 0.53% for P1 and 0.83% for P2. Only the P2 formulation effectively shielded the particles from interacting with cells or tissues, suggesting that either key interacting regions on the particle surface were blocked or that a sufficient hydration shell had been generated to inhibit cellular interactions. The large CPMV surface area available after PEGylation allows further attachment of imaging and therapeutic molecules to the particle to generate multifunctionality.

Cowpea mosaic virus: the plant virus-based biotechnology workhorse

In the 50 years since it was first described, Cowpea mosaic virus (CPMV) has become one of the most intensely studied plant viruses. Research in the past 15 to 20 years has shifted from studying the underlying genetics and structure of the virus to focusing on ways in which it can be exploited in biotechnology. This work led first to the use of virus particles to present peptides, then to the creation of a variety of replicating virus vectors and finally to the development of a highly efficient protein expression system that does not require viral replication. The circle has been completed by the use of the latter system to create empty particles for peptide presentation and other novel uses. The history of CPMV in biotechnology can be likened to an Ouroborus, an ancient symbol depicting a snake or dragon swallowing its own tail, thus forming a circle.

Efficient generation of cowpea mosaic virus empty virus-like particles by the proteolytic processing of precursors in insect cells and plants

To elucidate the mechanism of formation of cowpea mosaic virus (CPMV) particles, RNA-2-encoded precursor proteins were expressed in Spodoptera frugiperda cells. Processing of the 105K and 95K polyproteins in trans to give the mature Large (L) and Small (S) coat proteins required both the 32K proteinase cofactor and the 24K proteinase itself, while processing of VP60, consisting of the fused L-S protein, required only the 24K proteinase. Release of the L and S proteins resulted in the formation of virus-like particles (VLPs), showing that VP60 can act as a precursor of virus capsids. Processing of VP60 expressed in plants also led to efficient production of VLPs. Analysis of the VLPs produced by the action of the 24K proteinase on precursors showed that they were empty (RNA-free). This has important implications for the use of CPMV VLPs in biotechnology and nanotechnology as it will permit the use of noninfectious particles.

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this representation an elastic network is used as a structural scaffold to describe and maintain the overall shape of a protein and a physics-based coarse-grained model (MARTINI-2.1) is used to describe both inter- and intramolecular interactions in the system. The results show that when used in molecular dynamics simulations ELNEDIN models can be built so that the resulting structural and dynamical properties of a protein, including its collective motions, are comparable to those obtained using atomistic protein models. We then evaluate the behavior of such models in (1) long, microsecond time-scale, simulations, (2) the modeling of very large macromolecular assemblies, a viral capsid, and (3) the study of a protein-protein association process, the reassembly of the ROP homodimer. The results for this series of tests indicate that ELNEDIN models allow microsecond time-scale molecular dynamics simulations to be carried out readily, that large biological entities such as the viral capsid of the cowpea mosaic virus can be stably modeled as assemblies of independent ELNEDIN models, and that ELNEDIN models show significant promise for modeling protein-protein association processes.

Exploitation of plant and archaeal viruses in bionanotechnology

CPMV (cowpea mosaic virus), a plant virus, is a naturally occurring sphere-like nanoparticle, and is used as a synthon and/or template in bionanoscience. The virions formed by CPMV can be regarded as programmable nanobuilding blocks with a diameter of ∼30 nm. A range of molecules have been attached to this viral nanoscaffold, yielding stable nanoparticles that display multiple copies of the desired molecule. It has been shown that, in addition to surface amine groups, surface carboxy groups are also addressable, and a procedure has been developed that enables introduction of reactive thiols at the virion surface that avoids virus aggregation. Furthermore, the virions can be functionalized to form electroactive nanoparticles. Methods for the construction of arrays and multilayers, using a layer-by-layer approach, have been established. As proof of concept, for example, CPMV particles have been immobilized on surfaces and arranged in defined layers. Engineered variants of CPMV can be used as templates for mineralization with, for example, silica to give monodisperse robust silica nanoparticles of ∼32 nm. SIRV2 (Sulfolobus islandicus rod-shaped virus 2), is a robust archaeal virus, resistant to high temperature and low pH. SIRV2 can act as a template for site-selective and spatially controlled chemical modification. Both the ends and the body of the virus, or the ends only, can be chemically addressed; SIRV2 can be regarded as a structurally unique nanobuilding block.

Measurement of monovalent and polyvalent carbohydrate-lectin binding by back-scattering interferometry

Carbohydrate-protein binding is important to many areas of biochemistry. Here, backscattering interferometry (BSI) has been shown to be a convenient and sensitive method for obtaining quantitative information about the strengths and selectivities of such interactions. The surfaces of glass microfluidic channels were covalently modified with extravidin, to which biotinylated lectins were subsequently attached by incubation and washing. The binding of unmodified carbohydrates to the resulting avidin-immobilized lectins was monitored by BSI. Dose-response curves that were generated within several minutes and were highly reproducible in multiple wash/measure cycles provided adsorption coefficients that showed mannose to bind to concanavalin A (conA) with 3.7 times greater affinity than glucose consistent with literature values. Galactose was observed to bind selectively and with similar affinity to the lectin BS-1. The avidities of polyvalent sugar-coated virus particles for immobilized conA were much higher than monovalent glycans, with increases of 60-200 fold per glycan when arrayed on the exterior surface of cowpea mosaic virus or bacteriophage Qbeta. Sugar-functionalized PAMAM dendrimers showed size-dependent adsorption, which was consistent with the expected density of lectins on the surface. The sensitivity of BSI matches or exceeds that of surface plasmon resonance and quartz crystal microbalance techniques, and is sensitive to the number of binding events, rather than changes in mass. The operational simplicity and generality of BSI, along with the near-native conditions under which the target binding proteins are immobilized, make BSI an attractive method for the quantitative characterization of the binding functions of lectins and other proteins.

Advances in High-Pressure Biophysics: Status and Prospects of Macromolecular Crystallography

A survey of the main interests of high pressure for molecular biophysics highlights the possibility of exploring the whole conformational space using pressure perturbation. A better understanding of fundamental mechanisms responsible for the effects of high pressure on biomolecules requires high-resolution molecular information. Thanks to recent instrumental and methodological progress taking advantage of the remarkable adaptation of the crystalline state to hydrostatic compression, pressure-perturbed macromolecular crystallography is now a full-fledged technique applicable to a variety of systems, including large assemblies. This versatility is illustrated by selected applications, including DNA fragments, a tetrameric protein, and a viral capsid. Binding of compressed noble gases to proteins is commonly used to solve the phase problem, but standard macromolecular crystallography would also benefit from the transfer of experimental procedures developed for high-pressure studies. Dedicated short-wavelength synchrotron radiation beamlines are unarguably required to fully exploit the various facets of high-pressure macromolecular crystallography.

Model-independent analysis of QCM data on colloidal particle adsorption

Quartz crystal microbalance (QCM) is widely used for studying soft interfaces in liquid environment. Many of these interfaces are heterogeneous in nature, in the sense that they are composed of discrete, isolated entities adsorbed at a surface. When characterizing such interfaces, one is interested in determining parameters such as surface coverage and size of the surface-adsorbed entities. The current strategy is to obtain this information by fitting QCM data--shifts in resonance frequency, DeltaF, and bandwidth, DeltaGamma--with the model derived for smooth, homogeneous films using the film acoustic thickness and shear elastic moduli as fitting parameters. Investigating adsorption of liposomes and icosahedral virus particles on inorganic surfaces of titania and gold, we demonstrate that the predictions of this model are at variance with the experimental observations. In particular, while the model predicts that the ratio between the bandwidth and frequency shifts, DeltaGamma/DeltaF (the Df ratio), should increase with both surface coverage and particle size, we observe that this ratio increases with increasing particle size but decreases with increasing surface coverage, demonstrating that QCM response in heterogeneous films, such as those composed of adsorbed colloidal particles, does not conform with the predictions of the homogeneous film model. Employing finite element method (FEM) calculations, we show that hydrodynamic effects are the cause of this discrepancy. Finally, we find that the size of the adsorbed colloidal particles can be recovered from a model-independent analysis of the plot of the DeltaGamma/DeltaF ratio versus the frequency shift on many overtones.

Endothelial targeting of cowpea mosaic virus (CPMV) via surface vimentin

Cowpea mosaic virus (CPMV) is a plant comovirus in the picornavirus superfamily, and is used for a wide variety of biomedical and material science applications. Although its replication is restricted to plants, CPMV binds to and enters mammalian cells, including endothelial cells and particularly tumor neovascular endothelium in vivo. This natural capacity has lead to the use of CPMV as a sensor for intravital imaging of vascular development. Binding of CPMV to endothelial cells occurs via interaction with a 54 kD cell-surface protein, but this protein has not previously been identified. Here we identify the CPMV binding protein as a cell-surface form of the intermediate filament vimentin. The CPMV-vimentin interaction was established using proteomic screens and confirmed by direct interaction of CPMV with purified vimentin, as well as inhibition in a vimentin-knockout cell line. Vimentin and CPMV were also co-localized in vascular endothelium of mouse and rat in vivo. Together these studies indicate that surface vimentin mediates binding and may lead to internalization of CPMV in vivo, establishing surface vimentin as an important vascular endothelial ligand for nanoparticle targeting to tumors. These results also establish vimentin as a ligand for picornaviruses in both the plant and animal kingdoms of life. Since bacterial pathogens and several other classes of viruses also bind to surface vimentin, these studies suggest a common role for surface vimentin in pathogen transmission.

Chemical modification of viruses and virus-like particles

Protein capsids derived from viruses may be modified by methods, generated, isolated, and purified on large scales with relative ease. In recent years, methods for their chemical derivatization have been employed to broaden the properties and functions accessible to investigators desiring monodisperse, atomic-resolution structures on the nanometer scale. Here we review the reactions and methods used in these endeavors, including the modification of lysine, cysteine, and tyrosine side chains, as well as the installation of unnatural amino acids, with particular attention to the special challenges imposed by the polyvalency and size of virus-based scaffolds.

Protein cages, rings and tubes: useful components of future nanodevices?

There is a great deal of interest in the possibility that complex nanoscale devices can be designed and engineered. Such devices will lead to the development of new materials, electronics and smart drugs. Producing complex nanoscale devices, however will present many challenges and the components of such devices will require a number of special features. Devices will be engineered to incorporate desired functionalities but, because of the difficulties of controlling matter precisely at the nanoscale with current technology, the nanodevice components must self-assemble. In addition, nanocomponents that are to have wide applicability in various devices must have enough flexibility to integrate into a large number of potentially very different environments. These challenges are daunting and complex, and artificial nanodevices have not yet been constructed. However, the existence of nanomachines in nature in the form of proteins (eg, enzymes) suggests that they will be possible to produce. As the material from which nature's nanomachines are made, proteins seem ideal to form the basis of engineered components of such nanodevices. Initially, engineering projects may focus on building blocks such as rings, cages and tubes, examples of which exist in nature and may act as a useful start point for modification and further development. This review focuses on the recent research and possible future development of such protein building blocks.

The capsid proteins of a large, icosahedral dsDNA virus

Chilo iridescent virus (CIV) is a large (approximately 1850 A diameter) insect virus with an icosahedral, T=147 capsid, a double-stranded DNA (dsDNA) genome, and an internal lipid membrane. The structure of CIV was determined to 13 A resolution by means of cryoelectron microscopy (cryoEM) and three-dimensional image reconstruction. A homology model of P50, the CIV major capsid protein (MCP), was built based on its amino acid sequence and the structure of the homologous Paramecium bursaria chlorella virus 1 Vp54 MCP. This model was fitted into the cryoEM density for each of the 25 trimeric CIV capsomers per icosahedral asymmetric unit. A difference map, in which the fitted CIV MCP capsomers were subtracted from the CIV cryoEM reconstruction, showed that there are at least three different types of minor capsid proteins associated with the capsomers outside the lipid membrane. "Finger" proteins are situated at many, but not all, of the spaces between three adjacent capsomers within each trisymmetron, and "zip" proteins are situated between sets of three adjacent capsomers at the boundary between neighboring trisymmetrons and pentasymmetrons. Based on the results of segmentation and density correlations, there are at least eight finger proteins and three dimeric and two monomeric zip proteins in one asymmetric unit of the CIV capsid. These minor proteins appear to stabilize the virus by acting as intercapsomer cross-links. One transmembrane "anchor" protein per icosahedral asymmetric unit, which extends from beneath one of the capsomers in the pentasymmetron to the internal leaflet of the lipid membrane, may provide additional stabilization for the capsid. These results are consistent with the observations for other large, icosahedral dsDNA viruses that also utilize minor capsid proteins for stabilization and for determining their assembly.

Insights into virus capsid assembly from non-covalent mass spectrometry

The assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self-assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti-viral therapeutics. It will also be important in bio-nanotechnology where there is a plethora of applications for such well-defined macromolecular complexes, including cell-specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non-covalently bound macromolecular complexes under near-physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007.

Chemical addressability of ultraviolet-inactivated viral nanoparticles (VNPs)

Background

Cowpea Mosaic Virus (CPMV) is increasingly being used as a nanoparticle platform for multivalent display of molecules via chemical bioconjugation to the capsid surface. A growing variety of applications have employed the CPMV multivalent display technology including nanoblock chemistry, in vivo imaging, and materials science. CPMV nanoparticles can be inexpensively produced from experimentally infected cowpea plants at high yields and are extremely stable. Although CPMV has not been shown to replicate in mammalian cells, uptake in mammalian cells does occur in vitro and in vivo. Thus, inactivation of the virus RNA genome is important for biosafety considerations, however the surface characteristics and chemical reactivity of the particles must be maintained in order to preserve chemical and structural functionality.

Methodology/Principal Findings

Short wave (254 nm) UV irradiation was used to crosslink the RNA genome within intact particles. Lower doses of UV previously reported to inactivate CPMV infectivity inhibited symptoms on inoculated leaves but did not prohibit systemic virus spread in plants, whereas higher doses caused aggregation of the particles and an increase in chemical reactivity further indicating broken particles. Intermediate doses of 2.0–2.5 J/cm² were shown to maintain particle structure and chemical reactivity, and cellular binding properties were similar to CPMV-WT.

Conclusions

These studies demonstrate that it is possible to inactivate CPMV infectivity while maintaining particle structure and function, thus paving the way for further development of CPMV nanoparticles for in vivo applications.

Capillarity-induced disassembly of virions in carbon nanotubes

Studying the transport and fate of viruses through nanochannels is of great importance. By using the nanochannel of a carbon nanotube (CNT) as an ideal model, we evaluated the possibility of capillarity-induced viral transport through a closely fitting nanochannel and explored the mechanisms involved. It is shown both experimentally and theoretically that Cowpea mosaic virus can enter CNTs by capillarity. However, when introduced into a nanotube the protein capsid may disassemble. During the initial capillary filling stage, anomalous needle-shaped high pressure exists in the centre of the nanotube's entrance. This high pressure, combining with the significant negative pressure within the nanotube, may account for the disassembly of the virions.

On-virus construction of polyvalent glycan ligands for cell-surface receptors

Glycans arrayed on the exterior of virus particles were used as substrates for glycosyltransferase reactions to build di- and trisaccharides from the virus surface. The resulting particles exhibited tight and specific associations with cognate receptors on beads and cells, in one example defeating in cis cell-surface interactions in a manner characteristic of polyvalent binding. Combined with the ability of viruses to provide structurally well-defined attachment points, the methodology provides a convenient and powerful way to prepare complex carbohydrate ligands for clustered receptors.

Long term storage of virus templated fluorescent materials for sensing applications

Wild type, mutant, and chemically modified Cowpea mosaic viruses (CPMV) were studied for long term preservation in the presence and absence of cryoprotectants. Viral complexes were reconstituted and tested via fluorescence spectroscopy and a UV/vis-based RNase assay for structural integrity. When viruses lyophilized in the absence of cryoprotectant were rehydrated and RNase treated, UV absorption increased, indicating that the capsids were damaged. The addition of trehalose during lyophilization protected capsid integrity for at least 7 weeks. Measurements of the fluorescence peak maximum of CPMV lyophilized with trehalose and reconstituted also indicate that the virus remained intact. Microarray binding assays indicated that CPMV particles chemically modified for use as a fluorescent tracer were intact and retained binding specificity after lyophilization in the presence of trehalose. Thus, we demonstrate that functionalized CPMV nanostructures can be stored for the long term, enabling their use in practical sensing applications.

Nanoscale memory characterization of virus-templated semiconducting quantum dots

We have developed a substrate-based bottom-up approach to assemble two different color emitting quantum dots (CdSe/ZnS core/shell QDs) on the surface of a novel virus mutant, CPMV-T184C. Electrical characteristics of individual hybrids were investigated by conductive atomic force microscopy for potential digital memory applications (i.e., RAM). These individual 40 nm CPMV-QD(1,2) hybrids exhibited reversible bistable electrical behavior during repeatable writing-reading-erasing processes at the nanoscale.

Folic acid-mediated targeting of cowpea mosaic virus particles to tumor cells

Cowpea mosaic virus (CPMV) is a well-characterized nanoparticle that has been used for a variety of nanobiotechnology applications. CPMV interacts with several mammalian cell lines and tissues in vivo. To overcome natural CPMV targeting and redirect CPMV particles to cells of interest, we attached a folic acid-PEG conjugate by using the copper-catalyzed azide-alkyne cycloaddition reaction. PEGylation of CPMV completely eliminated background binding of the virus to tumor cells. The PEG-folate moiety allowed CPMV-specific recognition of tumor cells bearing the folate receptor. In addition, by testing CPMV formulations with different amounts of the PEG-FA moiety displayed on the surface, we show that higher-density loading of targeting ligands on CPMV may not be necessary for efficient targeting to tumor cells. These studies help to define the requirements for efficiently targeting nanoparticles and protein cages to tumors.

Assembly of multilayer arrays of viral nanoparticles via biospecific recognition: a quartz crystal microbalance with dissipation monitoring study

The development of multilayered thin film assemblies containing (bio)molecules is driven by the need to miniaturize sensors, reactors, and biochips. Viral nanoparticles (VNPs) have become popular nanobuilding blocks for material fabrication, and our research has focused on the well-characterized plant virus Cowpea mosaic virus (CPMV). In a previous study, we have reported the construction of multilayer VNP assemblies. Here we extend these studies by providing further details on the formation and properties of arrays that are made by the alternating deposition of biotinylated CPMV particles and streptavidin molecules. Array formation was followed in real time by a quartz crystal microbalance with dissipation monitoring. Our data provide indications that multiple interactions between biotin and streptavidin not only promote the assembly of a multilayered structure but also generate cross-links within each layer of CPMV particles. The degree of intralayer and interlayer cross-linking and hence the mechanical properties and order of the array can be modulated by the grafting density and spacer length of the biotin moieties on the CPMV particles.

Cowpea mosaic virus capsid: a promising carrier for the development of carbohydrate based antitumor vaccines

Immunotherapy targeting tumor cell surface carbohydrates is a promising approach for cancer treatment. However, the low immunogenecity of carbohydrates presents a formidable challenge. We describe here the enhancement of carbohydrate immunogenicity by an ordered display on the surface of the cowpea mosaic virus (CPMV) capsid. The Tn glycan, which is overexpressed on numerous cancer cell surfaces, was selected as the model antigen for our study. Previously it has been shown that it is difficult to induce a strong T cell-dependent immune response against the monomeric form of Tn presented in several ways on different carriers. In this study, we first synthesized Tn antigens derivatized with either a maleimide or a bromoacetamide moiety that was conjugated selectively to a cysteine mutant of CPMV. The glycoconjugate was then injected into mice and pre- and post-immune antibody levels in the mice sera were measured by enzyme-linked immunosorbant assays. High total antibody titers and, more importantly, high IgG titers specific for Tn were obtained in the post-immune day 35 serum, suggesting the induction of T cell-dependent antibody isotype switching by the glycoconjugate. The antibodies generated were able to recognize Tn antigens presented in their native conformations on the surfaces of both MCF-7 breast cancer cells and the multidrug resistant breast cancer cell line NCI-ADR RES. These results suggest that the CPMV capsid can greatly enhance the immunogenicity of weak antigens such as Tn and this can provide a promising tool for the development of carbohydrate based anti-cancer vaccines.

Self-assembly of nanoparticles at interfaces

Developments in the assembly of nanoparticles at liquid-liquid interfaces are reviewed where the assemblies can be controlled by tuning the size of the nanoparticles and the chemical characteristics of the ligands. Both synthetic and biological nanoparticles are discussed. By controlling the type of ligands, uniform and Janus-type nanoparticles can be produced where, at liquid-liquid interfaces, subsequent reactions of the ligands can be used to generate crosslinked sheets of nanoparticles at the interface that have applications including novel encapsulants, filtration devices with well-defined porosities, and controlled release materials. By controlling the size and volume fraction of the nanoparticles and the chemical nature of the ligands, nanoparticle-polymer composites can be generated where either enthalpy or entropy can be used to control the spatial distribution of the nanoparticles, thereby, producing auto-responsive materials that self-heal, self-corral assemblies of nanoparticles, or self-direct morphologies. Such systems hold great promise for generating novel optical, acoustic, electronic and magnetic materials.

Chemical Introduction of Reactive Thiols Into a Viral Nanoscaffold: A Method that Avoids Virus Aggregation

The use of viral nanoparticles (VNPs) as building blocks for material fabrication has received particular attention in recent years. In earlier studies we showed the applicability of native gel electrophoresis in an agarose matrix as a useful method for the characterization of chemically modified VNPs. Here, we extend these studies and analyze the observed band pattern of intact Cowpea mosaic virus (CPMV) VNPs in agarose gels and show the applicability of native agarose gels for monitoring interparticle linkage of thiol-containing CPMV mutant particles. In addition, we report a protocol that allows the introduction of acetate-protected thiols to CPMV by means of a chemical reaction (rather than genetic modification). The advantage of this approach is that, by incorporating protected thiol groups, the formation of disulfide bonds leading to interparticle linkage is prevented. The resulting thiol-modified CPMV-SH(n) particles are stable, and following deprotection, the introduced thiols are reactive and can be labeled with thiol-selective reagents. They therefore provide a useful additional building block in the CPMV toolbox.

Bio-distribution, toxicity and pathology of cowpea mosaic virus nanoparticles in vivo

Virus-based nanoparticles (VNPs) from a variety of sources are being developed for biomedical and nanotechnology applications that include tissue targeting and drug delivery. However, the fate of most of those particles in vivo has not been investigated. Cowpea mosaic virus (CPMV), a plant comovirus, has been found to be amenable to the attachment of a variety of molecules to its coat protein, as well as to modification of the coat protein sequence by genetic means. We report here the results of studies of the bio-distribution, toxicology, and pathology of CPMV in mice. Plasma clearance and tissue biodistribution were measured using CPMV particles derivatized with lanthanide metal complexes. CPMV particles were cleared rapidly from plasma, falling to undetectable levels within 20 min. By 30 min the majority of the injected VNPs were trapped in the liver and to a lesser extent the spleen with undetectable amounts in other tissues. At doses of 1 mg, 10 mg and 100 mg per kg body weight, no toxicity was noted and the mice appeared to be normal. Hematology was essentially normal, although with the highest dose examined, the mice were somewhat leukopenic with relative decreases in both neutrophils and lymphocytes. Histological examination of the spleen showed cellular infiltration, which upon flow cytometry analyses revealed elevated B lymphocytes on the first day following virus administration that subsequently subsided. Microscopic evaluation of various other tissues revealed a lack of apparent tissue degeneration or necrosis. Overall, CPMV appears to be a safe and non-toxic platform for in vivo biomedical applications.

A Dissection of the Protein–Protein Interfaces in Icosahedral Virus Capsids

We selected 49 icosahedral virus capsids whose crystal structures are reported in the Protein Data Bank. They belong to the T=1, T=3, pseudo T=3 and other lattice types. We identified in them 779 unique interfaces between pairs of subunits, all repeated by icosahedral symmetry. We analyzed the geometric and physical chemical properties of these interfaces and compared with interfaces in protein-protein complexes and homodimeric proteins, and with crystal packing contacts. The capsids contain one to 16 subunits implicated in three to 66 unique interfaces. Each subunit loses 40-60% of its accessible surface in contacts with an average of 8.5 neighbors. Many of the interfaces are very large with a buried surface area (BSA) that can exceed 10,000 A(2), yet 39% are small with a BSA<800 A(2) comparable to crystal packing contacts. Pairwise capsid interfaces overlap, so that one-third of the residues are part of more than one interface. Those with a BSA>800 A(2) resemble homodimer interfaces in their chemical composition. Relative to the protein surface, they are non-polar, enriched in aliphatic residues and depleted of charged residues, but not of neutral polar residues. They contain one H-bond per about 200 A(2) BSA. Small capsid interfaces (BSA<800 A(2)) are only slightly more polar. They have a similar amino acid composition, but they bury fewer atoms and contain fewer H-bonds for their size. Geometric parameters that estimate the quality of the atomic packing suggest that the small capsid interfaces are loosely packed like crystal packing contacts, whereas the larger interfaces are close-packed as in protein-protein complexes and homodimers. We discuss implications of these findings on the mechanism of capsid assembly, assuming that the larger interfaces form first to yield stable oligomeric species (capsomeres), and that medium-size interfaces allow the stepwise addition of capsomeres to build larger intermediates.

Nanoporous crystals of chicken embryo lethal orphan (CELO) adenovirus major coat protein, hexon

CELO (chicken embryo lethal orphan) virus is an avian adenovirus that is being developed as a gene transfer vector. Its trimeric major coat protein (942 residues, 106,709 Da) has 42% sequence identity to human adenovirus type 2 (AdH2) hexon and 45% to AdH5 hexon. For structural studies, the growth of CELO virus has been optimized, and its hexon purified and crystallized. The hexon crystals, the first non-human example, diffract to 3.9 A resolution. Molecular replacement using the AdH5 model was used to identify the location of the CELO hexon within the unit cell. There is one hexon monomer in the asymmetric unit of the trigonal space group P321 (a=b=157.8 A, c=114.2 A, gamma=120 degrees) and the solvent content is 67.8%. The hexons pack in a hexagonal honeycomb so that large approximately 100 A diameter channels run through the entire crystal. This remarkable property of the crystals lends itself to their exploitation as a nanomaterial. Structural studies on CELO will elucidate the differences between avian and human adenoviruses and contribute to a better understanding of adenoviruses with non-human hosts.

Interaction between a 54-kilodalton mammalian cell surface protein and cowpea mosaic virus

Cowpea mosaic virus (CPMV), a plant virus that is a member of the picornavirus superfamily, is increasingly being used for nanotechnology applications, including material science, vascular imaging, vaccine development, and targeted drug delivery. For these applications, it is critical to understand the in vivo interactions of CPMV within the mammalian system. Although the bioavailability of CPMV in the mouse has been demonstrated, the specific interactions between CPMV and mammalian cells need to be characterized further. Here we demonstrate that although the host range for replication of CPMV is confined to plants, mammalian cells nevertheless bind and internalize CPMV in significant amounts. This binding is mediated by a conserved 54-kDa protein found on the plasma membranes of both human and murine cell lines. Studies using a deficient cell line, deglycosidases, and glycosylation inhibitors showed that the CPMV binding protein (CPMV-BP) is not glycosylated. A possible 47-kDa isoform of the CPMV-BP was also detected in the organelle and nuclear subcellular fraction prepared from murine fibroblasts. Further characterization of CPMV-BP is important to understand how CPMV is trafficked through the mammalian system and may shed light on how picornaviruses may have evolved between plant and animal hosts.

Utilisation of plant viruses in bionanotechnology

Bionanoscience/technology sits at the interface of chemistry, biology, physics, materials science, engineering and medicine and involves the exploitation of biomaterials, devices or methodologies on the nanoscale. One sub-field of bionanoscience/technology is concerned with the exploitation of biomaterials in the fabrication of new nano-materials and/or -devices. In this Perspective we describe examples of how plant viruses, focusing particularly on cowpea mosaic virus, a naturally occurring pre-formed sphere-like nanoparticle, are being used as templates and/or building blocks in bionanoscience and indicate their potential for future application.

Viral MRI contrast agents: coordination of Gd by native virions and attachment of Gd complexes by azide–alkyne cycloaddition

Icosahedral virus particles decorated with a Gd(DOTA) analogue by Cu-mediated azide-alkyne cycloaddition (CuAAC) and/or with Gd(3+) ions by coordination to the viral nucleoprotein show increased T(1) relaxivity relative to free Gd(DOTA) complexes in solution.

Generation and structural analysis of reactive empty particles derived from an icosahedral virus

Chemical and genetic modifications on the surface of viral protein cages confer unique properties to the virus particles with potential nano and biotechnological applications. The enclosed space in the interior of the virus particles further increases its versatility as a nanomaterial. In this paper, we report a simple method to generate a high yield of stable cowpea mosaic virus (CPMV) empty capsids from their native nucleoprotein counterparts by removing the encapsidated viral genome without compromising the integrity of the protein coat. Biochemical and structural comparison of artificially generated empty particles did not reveal any distinguishable differences from CPMV particles containing viral RNA. Preliminary results on the use of artificially produced empty CPMV capsids as a carrier capsule are described.

Plant viral capsids as nanobuilding blocks: construction of arrays on solid supports

The virions of Cowpea mosaic virus (CPMV) can be regarded as programmable nanobuilding blocks with a diameter of approximately 28 nm. The particles display a number of features that can be exploited for nanoscale material fabrication. In this study we use the virus-derived building blocks for construction of arrays on solid supports. Biotin-modified CPMV particles are used with Streptavidin as a linker molecule in order to enable self-assembly of arrays from the surface up by a layer-by-layer approach. CPMV particles with different fluorescent labels, which enable differential detection of each layer, have been immobilized on surfaces and arranged in defined layers. This approach provides novel structured arrays which have the potential for development as functional devices at the nanoscale.

Dielectrophoretic investigation of plant virus particles: Cow Pea Mosaic Virus and Tobacco Mosaic Virus

This paper reports experimental results on the dielectrophoretic (DEP) behaviour on two nonenveloped plant viruses of different geometrical shapes, namely Cow Pea Mosaic Virus (CPMV) and Tobacco Mosaic Virus (TMV). The DEP properties of carboxy-modified latex beads of the same size are also reported. The DEP properties of single particles were obtained from measurement of the frequency at which the DEP force on a particle goes to zero (the crossover frequency). The DEP behaviour of particle ensembles was also measured using image processing. The dielectric properties of the particles were evaluated from the DEP data. The surface conductance was found to be 0.3 nS for CPMV, 0.38 nS for TMV, and 0.52 nS for 27 nm diameter carboxy-latex beads. Data analysis has shown that the optimal condition for separation of TMV and CPMV is a low-conductivity suspending medium - below 1 mS/m.

Structural analysis of viral nucleocapsids by subtraction of partial projections

The nucleocapsid of flavivirus particles does not have a recognizable capsid structure when using icosahedral averaging for cryo-electron microscopy structure determinations. The apparent absence of a definitive capsid structure could be due to a lack of synchronization of the symmetry elements of the external glycoprotein layer with those of the core or because the nucleocapsid does not have the same structure within each particle. A technique has been developed to determine the structure of the capsid, and possibly also of the genome, for icosahedral viruses, such as flaviviruses, using cryo-electron microscopy. The method is applicable not only to the analyses of viral cores, but also to the missing structure of multi-component complexes due to symmetry mismatches. The density contributed by external glycoprotein and membrane layers, derived from previously determined three-dimensional icosahedrally averaged reconstructions, was subtracted from the raw images of the virus particles. The resultant difference images were then used for a three-dimensional reconstruction. After appropriate test data sets were constructed and tested, the procedure was applied to examine the nucleocapsids of flaviviruses, which showed that there is no distinct protein density surrounding the genome. Furthermore, there was no evidence of any icosahedral symmetry within the nucleocapsid core.

Viral nanoparticles as tools for intravital vascular imaging

A significant impediment to the widespread use of noninvasive in vivo vascular imaging techniques is the current lack of suitable intravital imaging probes. We describe here a new strategy to use viral nanoparticles as a platform for the multivalent display of fluorescent dyes to image tissues deep inside living organisms. The bioavailable cowpea mosaic virus (CPMV) can be fluorescently labeled to high densities with no measurable quenching, resulting in exceptionally bright particles with in vivo dispersion properties that allow high-resolution intravital imaging of vascular endothelium for periods of at least 72 h. We show that CPMV nanoparticles can be used to visualize the vasculature and blood flow in living mouse and chick embryos to a depth of up to 500 microm. Furthermore, we show that the intravital visualization of human fibrosarcoma-mediated tumor angiogenesis using fluorescent CPMV provides a means to identify arterial and venous vessels and to monitor the neovascularization of the tumor microenvironment.