Synergistic effects of mutations and nanoparticle templating in the self-assembly of cowpea chlorotic mottle virus capsids

DNA-origami-directed virus capsid polymorphism

Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.

Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer

The cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses are key steps. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of the CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. Furthermore, it was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.

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.

Cargo encapsulated hepatitis E virus-like particles for anti-HEV antibody detection

Viral capsid-nanoparticle hybrid structures incorporating quantum dots (QDs) into virus-like particles (VLPs) constitute an emerging bioinspired type of nanoarchitecture paradigm used for various applications. In the present study, we packed inorganic QDs in vitro into the hepatitis E virus-like particle (HEV-LP) and developed a fluorometric biosensor for HEV antibody detection. Firstly, for the preparation of QDs-encapsulated HEV-LPs (QDs@HEV-LP), the HEV-LPs produced by a recombinant baculovirus expression system were disassembled and reassembled in the presence of QDs using the self-assembly approach. Thus, the prepared QDs@HEV-LP exhibited excellent fluorescence properties similar to QDs. Further, in the presence of HEV antibodies in the serum samples, when mixed with QDs@HEV-LP, bind together and further bind to anti-IgG-conjugated magnetic nanoparticles (MNPs). The target-specific anti-IgG-MNPs and QDs@HEV-LP enrich the HEV antibodies by magnetic separation, and the separated QDs@HEV-LP-bound HEV antibodies are quantified by fluorescence measurement. This developed method was applied to detect the HEV antibody from sera of HEV-infected monkey from 0 to 68 days-post-infection and successfully diagnosed for HEV antibodies. The viral RNA copies number from monkey fecal samples by RT-qPCR was compared to the HEV antibody generation. This study first used QDs-encapsulated VLPs as useful fluorescence emitters for biosensing platform construction. It provides an efficient route for highly sensitive and specific antibody detection in clinical diagnosis research.

Encapsidation of Different Plasmonic Gold Nanoparticles by the CCMV CP

Different types of gold nanoparticles have been synthesized that show great potential in medical applications such as medical imaging, bio-analytical sensing and photothermal cancer therapy. However, their stability, polydispersity and biocompatibility are major issues of concern. For example, the synthesis of gold nanorods, obtained through the elongated micelle process, produce them with a high positive surface charge that is cytotoxic, while gold nanoshells are unstable and break down in a few weeks due to the Ostwald ripening process. In this work, we report the self-assembly of the capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) around spherical gold nanoparticles, gold nanorods and gold nanoshells to form virus-like particles (VLPs). All gold nanoparticles were synthesized or treated to give them a negative surface charge, so they can interact with the positive N-terminus of the CP leading to the formation of the VLPs. To induce the protein self-assembly around the negative gold nanoparticles, we use different pH and ionic strength conditions determined from a CP phase diagram. The encapsidation with the viral CP will provide the nanoparticles better biocompatibility, stability, monodispersity and a new biological substrate on which can be introduced ligands toward specific cells, broadening the possibilities for medical applications.

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.

Cargo-Compatible Encapsulation in Virus-Based Nanoparticles

Molecule encapsulation in virus-based nanoparticles (VNPs) is an emerging bioinspired way to design novel functional nanostructures and devices. Here, we report a general cargo-compatible approach to encapsulate guest materials based on the apparent critical assembly concentration (CAC_app) of VNPs. Different from the conventional buffer-exchange method, the new method drives the reassembly of VNPs to encapsulate cargoes by simply concentrating an adequately diluted mixture of VNP building blocks and cargoes to a concentration above the CAC_app. This method has been proved to work well on different types of cargoes (including inorganic nanoparticles and proteins) and VNPs. The major advantage of this method is that it can maximally preserve cargo stability and activity by providing the freedom to choose cargo-friendly buffer conditions throughout the encapsulation process. This method would benefit the realization of the potentials of VNPs and other protein nanocages as nanomaterials in diverse fields of nanotechnology.

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

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

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.

Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage

Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.

Encapsulation of Negatively Charged Cargo in MS2 Viral Capsids

Encapsulation into virus-like particles is an efficient way of loading cargo of interest for delivery applications. Here, we describe the encapsulation of proteins with tags comprising anionic amino acids or DNA and gold nanoparticles with negative surface charges inside MS2 bacteriophage capsids to obtain homogeneous nanoparticles with a diameter of 27 nm.

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.

Targeted delivery system for cancer cells consist of multiple ligands conjugated genetically modified CCMV capsid on doxorubicin GNPs complex

Targeted nano-delivery vehicles were developed from genetically modified Cowpea chlorotic mottle virus (CCMV) capsid by ligands bioconjugation for efficient drug delivery in cancer cells. RNA binding (N 1-25aa) and β-hexamer forming (N 27-41aa) domain of capsid was selectively deleted by genetic engineering to achieve the efficient in vitro assembly without natural cargo. Two variants of capsids were generated by truncating 41 and 26 amino acid from N terminus (NΔ41 and NΔ26) designated as F₁ and F₂ respectively. These capsid were optimally self-assembled in 1:2 molar ratio (F₁:F₂) to form a monodisperse nano-scaffold of size 28 nm along with chemically conjugated modalities for visualization (fluorescent dye), targeting (folic acid, FA) and anticancer drug (doxorubicin). The cavity of the nano-scaffold was packed with doxorubicin conjugated gold nanoparticles (10 nm) to enhance the stability, drug loading and sustained release of drug. The chimeric system was stable at pH range of 4–8. This chimeric nano-scaffold system showed highly specific receptor mediated internalization (targeting) and ~300% more cytotoxicity (with respect to FA⁻ delivery system) to folate receptor positive Michigan Cancer Foundation-7 (MCF7) cell lines. The present system may offer a programmable nano-scaffold based platform for developing chemotherapeutics for cancer.

Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch

Viruses are astonishing edifices in which hundreds of molecular building blocks fit into the final structure with pinpoint accuracy. We established a robust kinetic model accounting for the in vitro self-assembly of a capsid shell derived from an icosahedral plant virus by using time-resolved small-angle X-ray scattering (TR-SAXS) data at high spatiotemporal resolution. By implementing an analytical model of a spherical patch into a global fitting algorithm, we managed to identify a major intermediate species along the self-assembly pathway. With a series of data collected at different protein concentrations, we showed that free dimers self-assembled into a capsid through an intermediate resembling a half-capsid. The typical lifetime of the intermediate was a few seconds and yet the presence of so large an oligomer was not reported before. The progress in instrumental detection along with the development of powerful algorithms for data processing contribute to shedding light on nonequilibrium processes in highly complex systems such as viruses.

Application of Laser Correlation Spectroscopy for Measuring Virus Size

Dynamic light scattering method or laser correlation spectroscopy was applied to evaluation of the size of viruses. We measured correlation functions of the light scattered by human immunodeficiency viruses (HIV) and hepatitis A viruses (HAV) and found that size of HIV-1 (subtype A and B) and HAV virions were 104 nm and 28 nm, respectively. Comparison of these findings with electron microscopy data for fixed samples of the same viruses showed good agreement of the results.

Protein Cages as Containers for Gold Nanoparticles

Abundant and highly diverse, viruses offer new scaffolds in nanotechnology for the encapsulation, organization, or even synthesis of novel materials. In this work the coat protein of the cowpea chlorotic mottle virus (CCMV) is used to encapsulate gold nanoparticles with different sizes and stabilizing ligands yielding stable particles in buffered solutions at neutral pH. The sizes of the virus-like particles correspond to T = 1, 2, and 3 Caspar-Klug icosahedral triangulation numbers. We developed a simple one-step process enabling the encapsulation of commercially available gold nanoparticles without prior modification with up to 97% efficiency. The encapsulation efficiency is further increased using bis-p-(sufonatophenyl)phenyl phosphine surfactants up to 99%. Our work provides a simplified procedure for the preparation of metallic particles stabilized in CCMV protein cages. The presented results are expected to enable the preparation of a variety of similar virus-based colloids for current focus areas.

Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.

Encapsulation of nanoparticles in virus protein shells

The self-assembly of virus-like particles may lead to materials which combine the unique characteristics of viruses, such as precise size control and responsivity to environmental cues, with the properties of abiotic cargo. For a few different viruses, shell proteins are amenable to the in vitro encapsulation of non-genomic cargo in a regular protein cage. In this chapter we describe protocols of high-efficiency in vitro self-assembly around functionalized gold nanoparticles for three examples of icosahedral and non-icosahedral viral protein cages derived from a plant virus, an animal virus, and a human retrovirus. These protocols can be readily adapted with small modifications to work for a broad variety of inorganic and organic nanoparticles.

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.

Fabrication of nanoarchitectures templated by virus-based nanoparticles: strategies and applications

Biomolecular nanostructures in nature are drawing increasing interests in the field of materials sciences. As a typical group of them, virus-based nanoparticles (VNPs), which are nanocages or nanorods assembled from capsid proteins of viruses, have been widely exploited as templates to guide the fabrication of complex nanoarchitectures (NAs), because of their appropriate sizes (ca. 20-200 nm), homogeneity, addressable functionalization, facile modification via chemical and genetic routes, and convenient preparation. Foreign materials can be positioned in the inner cavity or on the outer surface of VNPs, through either direct synthesis or assembling preformed nanomaterials. Simultaneous use of the inner and outer space of VNPs facilitates integration of multiple functionalities in a single NA. This review briefly summarizes the strategies for fabrication of NAs templated by VNPs and wide applications of these NAs in fields of catalysis, energy, biomedicine, and nanophotonics, etc.

Self-assembly triggered by self-assembly: optically active, paramagnetic micelles encapsulated in protein cage nanoparticles

In this contribution, optically active and paramagnetic micelles of the ligand 1,4,7,10-tetraaza-1-(1-carboxymethylundecane)-4,7,10-triacetic acid cyclododecane (DOTAC10) have been incorporated inside capsids of the cowpea chlorotic mottle virus (CCMV) protein through a hierarchical process of self-assembly triggered by self-assembly. The DOTAC10 ligand was used to complex Gd(III), in order to form paramagnetic micelles, as well as to encapsulate an amphiphilic Zn(II) phthalocyanine (ZnPc) dye that optically confirmed the encapsulation of the micelles. The incorporation of ZnPc molecules in the paramagnetic micelles led to high capsid loading of both Gd(III) and ZnPc, as the micelles were stabilized by the amphiphilic dye encapsulation. The resulting protein cage nanoparticles (PCNs) show an improved r1 relaxivity, suggesting the possible use of these nanostructures as contrast agents (CAs) for magnetic resonance imaging (MRI). Since the encapsulated ZnPc dye also has a potential therapeutic value, the present results represent a first step towards the consecution of fully self-assembled PCNs for multimodal imaging and therapy.

Engineering a well-ordered, functional protein-gold nanoparticle assembly

The study of interactions between proteins and nanoparticles is important to advancing applications of nanoparticles in biology, medicine, and materials science. Here, we report the encapsulation of a 5-nm diameter gold nanoparticle (AuNP) by thermophilic ferritin (tF), achieved in nearly quantitative yield under mild conditions that preserved the secondary structure, ferroxidase activity, and thermal stability of the native, 4-helix bundle protein subunits. Chromatography-based assays determined that stable protein assembly around AuNPs occurred on long time scales (~48h) and was reversible. Apparent association constants were determined at 25°C for equilibrated tF-BSPP-capped AuNP samples (KA=(2.1±0.4)×10(78)M(-11)) and compared favorably to salt-assembled tF samples (KA=(2.2±0.5)×10(68)M(-11)) at the same protein concentration (0.3mg/mL). Finally, addition of gold ions and mild reducing agent to the tF-AuNP assembly produced 8-nm diameter AuNPs with surface plasmon resonance band unchanged at 520nm, indicative of templating by the protein shell.

Location of the bacteriophage P22 coat protein C-terminus provides opportunities for the design of capsid-based materials

Rational design of modifications to the interior and exterior surfaces of virus-like particles (VLPs) for future therapeutic and materials applications is based on structural information about the capsid. Existing cryo-electron microscopy-based models suggest that the C-terminus of the bacteriophage P22 coat protein (CP) extends toward the capsid exterior. Our biochemical analysis through genetic manipulations of the C-terminus supports the model where the CP C-terminus is exposed on the exterior of the P22 capsid. Capsids displaying a 6xHis tag appended to the CP C-terminus bind to a Ni affinity column, and the addition of positively or negatively charged coiled coil peptides to the capsid results in association of these capsids upon mixing. Additionally, a single cysteine appended to the CP C-terminus results in the formation of intercapsid disulfide bonds and can serve as a site for chemical modifications. Thus, the C-terminus is a powerful location for multivalent display of peptides that facilitate nanoscale assembly and capsid modification.

Norovirus capsid proteins self-assemble through biphasic kinetics via long-lived stave-like intermediates

The self-assembly kinetics for a norovirus capsid protein were probed by time-resolved small-angle X-ray scattering and then analyzed by singular value decomposition and global fitting. Only three species contribute to the total scattering intensities: dimers, intermediates comprising some 11 dimers, and icosahedral T = 3 capsids made up of 90 dimers. Three-dimensional reconstructions of the intermediate robustly show a stave-like shape consistent with an arrangement of two pentameric units connected by an interstitial dimer. Upon triggering of self-assembly, the biphasic kinetics consist of a fast step in which dimers are assembled into intermediates, followed by a slow step in which intermediates interlock into capsids. This simple kinetic model reproduces experimental data with an excellent agreement over 6 decades in time and with nanometer resolution. The extracted form factors are robust against changes in experimental conditions. These findings challenge and complement currently accepted models for the assembly of norovirus capsids.

Viral capsids as self-assembling templates for new materials

The self-assembling protein shells of viruses have provided convenient scaffolds for the construction of many new materials with well-defined nanoscale architectures. In some cases, the native amino acid functional groups have served as nucleation sites for the deposition of metals and semiconductors, leading to organic-inorganic composites with interesting electronic, magnetic, optical, and catalytic properties. Other approaches have involved the covalent modification of the protein monomers, typically with the goal of generating targeting delivery vehicles for drug and imaging cargo. Covalently modified capsid proteins have also been used to generate periodic arrays of chromophores for use in light harvesting and photocatalytic applications. All of these research areas have taken advantage of the low polydispersity, high chemical stability, and intrinsically multivalent properties that are uniquely offered by these biological building blocks.

Tunable carbon nanotube/protein core-shell nanoparticles with NIR- and enzymatic-responsive cytotoxicity

A unique procedure is developed to capture carbon nanotubes into closed virus-like protein cages with a controllable shell. The cross-linked shell varies in thickness within ≈10(0) -10(2) nm, and can be entirely removed by enzyme degradation. The cytotoxicity is entirely suppressed, but can be promoted again by enzymes and near-infrared light. These hybrids can be decorated with functional inorganic nanoparticles or processed into nanocomposites.

Controlled integration of gold nanoparticles and organic fluorophores using synthetically modified MS2 viral capsids

The placement of fluorophores in close proximity to metal nanoparticle surfaces is proposed to enhance several photophysical properties of the dyes, potentially leading to improved quantum yields and decreased photobleaching. It is difficult in practice, however, to establish and maintain the nanoscale distances that are required to maximize these effects. The type of metal, size, and shape of the nanoparticle, the physical distance separating the metal nanoparticle from the organic dye, and the spectral properties of the fluorophore itself are all proposed to influence the quantum yield and lifetime. This results in a complex behavior that can lead to either enhanced or quenched fluorescence in different contexts. In this report, we describe a well-defined system that can be used to explore these effects, while physically preventing the fluorophores from contacting the nanoparticle surfaces. The basis of this system is the spherical protein capsid of bacteriophage MS2, which was used to house gold particles within its interior volume. The exterior surface of each capsid was then modified with Alexa Fluor 488 (AF 488) labeled DNA strands. By placing AF 488 dyes at distances of 3, 12, and 24 bp from the surface of capsids containing 10 nm gold nanoparticles, fluorescence intensity enhancements of 2.2, 1.2, and 1.0 were observed, respectively. A corresponding decrease in fluorescence lifetime was observed for each distance. Because of its well-defined and modular nature, this architecture allows the rapid exploration of the many variables involved in metal-controlled fluorescence, leading to a better understanding of this phenomenon.

Designing two self-assembly mechanisms into one viral capsid protein

ELP-CP, a structural fusion protein of the thermally responsive elastin-like polypeptide (ELP) and a viral capsid protein (CP), was designed, and its assembly properties were investigated. Interestingly, this protein-based block copolymer could be self-assembled via two mechanisms into two different, well-defined nanocapsules: (1) pH-induced assembly yielded 28 nm virus-like particles, and (2) ELP-induced assembly yielded 18 nm virus-like particles. The latter were a result of the emergent properties of the fusion protein. This work shows the feasibility of creating a self-assembly system with new properties by combining two structural protein elements.

In vitro quantification of the relative packaging efficiencies of single-stranded RNA molecules by viral capsid protein

While most T=3 single-stranded RNA (ssRNA) viruses package in vivo about 3,000 nucleotides (nt), in vitro experiments have demonstrated that a broad range of RNA lengths can be packaged. Under the right solution conditions, for example, cowpea chlorotic mottle virus (CCMV) capsid protein (CP) has been shown to package RNA molecules whose lengths range from 100 to 10,000 nt. Furthermore, in each case it can package the RNA completely, as long as the mass ratio of CP to nucleic acid in the assembly mixture is 6:1 or higher. Yet the packaging efficiencies of the RNAs can differ widely, as we demonstrate by measurements in which two RNAs compete head-to-head for a limited amount of CP. We show that the relative efficiency depends nonmonotonically on the RNA length, with 3,200 nt being optimum for packaging by the T=3 capsids preferred by CCMV CP. When two RNAs of the same length-and hence the same charge-compete for CP, differences in packaging efficiency are necessarily due to differences in their secondary structures and/or three-dimensional (3D) sizes. For example, the heterologous RNA1 of brome mosaic virus (BMV) is packaged three times more efficiently by CCMV CP than is RNA1 of CCMV, even though the two RNAs have virtually identical lengths. Finally, we show that in an assembly mixture at neutral pH, CP binds reversibly to the RNA and there is a reversible equilibrium between all the various RNA/CP complexes. At acidic pH, excess protein unbinds from RNA/CP complexes and nucleocapsids form irreversibly.

Conversion of a dodecahedral protein capsid into pentamers via minimal point mutations

Protein self-assembly relies upon the formation of stabilizing noncovalent interactions across subunit interfaces. Identifying the determinants of self-assembly is crucial for understanding structure-function relationships in symmetric protein complexes and for engineering responsive nanoscale architectures for applications in medicine and biotechnology. Lumazine synthases (LS's) comprise a protein family that forms diverse quaternary structures, including pentamers and 60-subunit dodecahedral capsids. To improve our understanding of the basis for this difference in assembly, we attempted to convert the capsid-forming LS from Aquifex aeolicus (AaLS) into pentamers through a small number of rationally designed amino acid substitutions. Our mutations targeted side chains at ionic (R40), hydrogen bonding (H41), and hydrophobic (L121 and I125) interaction sites along the interfaces between pentamers. We found that substitutions at two or three of these positions could reliably generate pentameric variants of AaLS. Biophysical characterization indicates that this quaternary structure change is not accompanied by substantial changes in secondary or tertiary structure. Interestingly, previous homology-based studies of the assembly determinants in LS's had identified only one of these four positions. The ability to control assembly state in protein capsids such as AaLS could aid efforts in the development of new systems for drug delivery, biocatalysis, or materials synthesis.

Encapsulation of gold nanoparticles by simian virus 40 capsids

Viral capsid-nanoparticle hybrid structures constitute a new type of nanoarchitecture that can be used for various applications. We previously constructed a hybrid structure comprising quantum dots encapsulated by simian virus 40 (SV40) capsids for imaging viral infection pathways. Here, gold nanoparticles (AuNPs) are encapsulated into SV40 capsids and the effect of particle size and surface ligands (i.e. mPEG and DNA) on AuNP encapsulation is studied. Particle size and surface decoration play complex roles in AuNP encapsulation by SV40 capsids. AuNPs ≥15 nm (when coated with mPEG750 rather than mPEG2000), or ≥10 nm (when coated with 10T or 50T DNA) can be encapsulated. Encapsulation efficiency increased as the size of the AuNPs increased from 10 to 30 nm. In addition, the electrostatic interactions derived from negatively charged DNA ligands on the AuNP surfaces promote encapsulation when the AuNPs have a small diameter (i.e. 10 nm and 15 nm). Moreover, the SV40 capsid is able to carry mPEG750-modified 15-nm AuNPs into living Vero cells, whereas the mPEG750-modified 15-nm AuNPs alone cannot enter cells. These results will improve our understanding of the mechanisms underlying nanoparticle encapsulation in SV40 capsids and enable the construction of new functional hybrid nanostructures for cargo delivery.

Structure and stoichiometry of template-directed recombinant HIV-1 Gag particles

Size polydispersity of immature human immunodeficiency virus type 1 (HIV-1) particles represents a challenge for traditional methods of biological ultrastructural analysis. An in vitro model for immature HIV-1 particles constructed from recombinant Gag proteins lacking residues 16-99 and the p6 domain assembled around spherical nanoparticles functionalized with DNA. This template-directed assembly approach led to a significant reduction in size polydispersity and revealed previously unknown structural features of immature-like HIV-1 particles. Electron microscopy and image reconstruction of these particles suggest that the Gag shell formed from different protein regions that are connected by a "scar"-an extended defect connecting the edges of two continuous, regularly packed protein layers. Thus, instead of a holey protein array, the experimental model presented here appears to consist of a continuous array of ∼5000 proteins enveloping the core, in which regular regions are separated by extended areas of disorder.

Molecular characterization of the complete genomes of two new field isolates of Cowpea chlorotic mottle virus, and their phylogenetic analysis

Cowpea chlorotic mottle virus (CCMV, family Bromoviridae) is found worldwide and has been used as a model virus for a long time, but no data is available about the genetic diversity of field isolates. Recently, two new field isolates (Car1 and Car2) of CCMV obtained from cowpea showed distinct phenotypic symptoms when inoculated to cowpea. CCMV-Car1 induced severe mosaic and interveinal chlorosis, while CCMV-Car2 produced mild mottling and leaf rolling. Both isolates produced asymptomatic infection in Nicotiana benthamiana. The complete genome of both isolates was amplified by reverse transcription-polymerase chain reaction using specific primers against the CCMV sequences available in the GenBank database, cloned and sequenced. Both nucleotide and amino acid sequences were compared between the newly sequenced CCMV isolates and the three previously characterized CCMV strains (T, M1, and R). Phylogenetic analysis of the RNA 1 sequence showed that CCMV-Car1 was in a separate branch from the rest of the CCMV isolates while CCMV-Car2 grouped together with CCMV-R. On the basis of RNA 2 and RNA 3 sequences, two major groupings were obtained. One group included CCMV-Car1 and CCMV-Car2 isolates while the other contained CCMV-T, CCMV-M1, and CCMV-R strains. Recombination programs detected a potential recombination event in the RNA 1 sequence of CCMV-Car2 isolate but not in RNA 2 and RNA 3 sequences. The results showed that both mutations and recombination have played an important role in the genetic diversity of these two new isolates of CCMV.

Virus-based nanoparticles with inorganic cargo: what does the future hold?

An analysis of the accumulated knowledge on virus-based nanoparticles (VNPs) consisting of virus protein capsids and inorganic cargo, such as nanoparticles (NPs), nanowires, and thin layers, is presented. Virus capsids (VCs) can serve either as templates or nanoreactors when inorganic materials are formed outside or inside VCs. The third possibility is when inorganic NPs nucleate the formation of VCs. The structural and mechanistic studies of VNP formation are paving the way to a better understating of virus structure and behavior, and these facilitate promising applications of VNPs in biomedical and materials research.

Metal-ion-induced formation and stabilization of protein cages based on the cowpea chlorotic mottle virus

The cowpea chlorotic mottle virus (CCMV) is a versatile building block for the construction of nanoreactors and functional materials. Upon RNA removal, the capsid can be reversibly assembled and disassembed by adjusting the pH. At pH 5.0 the capsid is in the native assembled conformation, while at pH 7.5 it disassembles into 90 capsid protein dimers. This special property enables the encapsulation of various molecules, such as protein and enzymes, but only at low pH. It is possible to stabilize the capsid at pH 7.5 by addition of negatively charged polyelectrolytes or negatively charged particles, but these methods all fill the interior of the capsid, leaving little or no space for other cargo molecules. This pH restriction therefore severely limits the range of enzymes that can be encapsulated, and hampers the investigation of the CCMV capsid as a nanoreactor for the study of enzymes in confined spaces. Herein, the interaction of N-terminal histidine-tag-modified capsid proteins with several metal ions is reported. Depending on the conditions used, nanometer-sized protein particles or capsidlike architectures are formed that are stable at pH 7.5. This metal-mediated stabilization methodology is employed to form stable capsids containing multiple proteins at pH 7.5, thereby greatly expanding the scope of the CCMV capsid as a nanoreactor.

Viral coat proteins as flexible nano-building-blocks for nanoparticle encapsulation

Viral capsid-nanoparticle hybrid structures offer new opportunities for nanobiotechnology. We previously generated virus-based nanoparticles (VNPs) of simian virus 40 (SV40) containing quantum dots (QDs) for cellular imaging. However, as an interesting issue of nano-bio interfaces, the mechanism of nanoparticle (NP) encapsulation by viral coat proteins remains unclear. Here, four kinds of QDs with the same core/shell but different surface coatings are tested for encapsulation. All the QDs can be encapsulated efficiently and there is no correlation between the encapsulation efficiency and the surface charge of the QDs. All the SV40 VNPs encapsulating differently modified QDs show similar structures, fluorescence properties, and activity in entering living cells. These results demonstrate the flexibility of SV40 major capsid protein VP1 in NP encapsulation and provide new clues to the mechanism of NP packaging by viral shells.

Thermodynamics of nanospheres encapsulated in virus capsids

We investigate the thermodynamics of complexation of functionalized charged nanospheres with viral proteins. The physics of this problem is governed not only by electrostatic interaction between the proteins and the nanosphere cores (screened by salt ions), but also by configurational degrees of freedom of the charged protein N tails. We approach the problem by constructing an appropriate complexation free-energy functional. On the basis of both numerical and analytical studies of this functional we construct the phase diagram for the assembly which contains the information on the assembled structures that appear in the thermodynamical equilibrium, depending on the size and surface charge density of the nanosphere cores. We show that both the nanosphere core charge and its radius determine the size of the capsid that forms around the core.

Viral genomic single-stranded RNA directs the pathway toward a T=3 capsid

The molecular mechanisms controlling genome packaging by single-stranded RNA viruses are still largely unknown. It is necessary in most cases for the protein to adopt different conformations at different positions on the capsid lattice in order to form a viral capsid from multiple copies of a single protein. We showed previously that such quasi-equivalent conformers of RNA bacteriophage MS2 coat protein dimers (CP(2)) can be switched by sequence-specific interaction with a short RNA stem-loop (TR) that occurs only once in the wild-type phage genome. In principle, multiple switching events are required to generate the phage T=3 capsid. We have therefore investigated the sequence dependency of this event using two RNA aptamer sequences selected to bind the phage coat protein and an analogous packaging signal from phage Qbeta known to be discriminated against by MS2 coat protein both in vivo and in vitro. All three non-cognate stem-loops support T=3 shell formation, but none shows the kinetic-trapping effect seen when TR is mixed with equimolar CP(2). We show that this reflects the fact that they are poor ligands compared with TR, failing to saturate the coat protein under the assay conditions, ensuring that sufficient amounts of both types of dimer required for efficient assembly are present in these reactions. Increasing the non-cognate RNA concentration restores the kinetic trap, confirming this interpretation. We have also assessed the effects of extending the TR stem-loop at the 5' or 3' end with short genomic sequences. These longer RNAs all show evidence of the kinetic trap, reflecting the fact that they all contain the TR sequence and are more efficient at promoting capsid formation than TR. Mass spectrometry has shown that at least two pathways toward the T=3 shell occur in TR-induced assembly reactions: one via formation of a 3-fold axis and another that creates an extended 5-fold complex. The longer genomic RNAs suppress the 5-fold pathway, presumably as a consequence of steric clashes between multiply bound RNAs. Reversing the orientation of the extension sequences with respect to the TR stem-loop produces RNAs that are poor assembly initiators. The data support the idea that RNA-induced protein conformer switching occurs throughout assembly of the T=3 shell and show that both positional and sequence-specific effects outside the TR stem-loop can have significant impacts on the precise assembly pathway followed.

A theory for viral capsid assembly around electrostatic cores

We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus capsids assemble around nanoparticles functionalized with polyelectrolyte. We model interactions between capsid proteins and nanoparticle surfaces as the interaction of polyelectrolyte brushes with opposite charge using the nonlinear Poisson Boltzmann equation. The models predict that there is a threshold density of functionalized charge, above which capsids efficiently assemble around nanoparticles, and that light scatter intensity increases rapidly at early times without the lag phase characteristic of empty capsid assembly. These predictions are consistent with and enable interpretation of preliminary experimental data. However, the models predict a stronger dependence of nanoparticle incorporation efficiency on functionalized charge density than measured in experiments and do not completely capture a logarithmic growth phase seen in experimental light scatter. These discrepancies may suggest the presence of metastable disordered states in the experimental system. In addition to discussing future experiments for nanoparticle-capsid systems, we discuss broader implications for understanding assembly around charged cores such as nucleic acids.