Modular, Bioorthogonal Strategy for the Controlled Loading of Cargo into a Protein Nanocage

Virus capsids, i.e., viruses devoid of their genetic material, are suitable nanocarriers for biomedical applications such as drug delivery and diagnostic imaging. For this purpose, the reliable encapsulation of cargo in such a protein nanocage is crucial, which can be accomplished by the covalent attachment of the compounds of interest to the protein domains positioned at the interior of the cage. This approach is particularly valid for the capsid proteins of the cowpea chlorotic mottle virus (CCMV), which have their N-termini located at the inside of the capsid structure. Here, we examined several site-selective modification methods for covalent attachment and encapsulation of cargo at the N-terminus of the CCMV protein. Initially, we explored approaches to introduce an N-terminal azide functionality, which would allow the subsequent bioorthogonal modification with a strained alkyne to attach the desired cargo. As these methods showed compatibility issues with the CCMV capsid proteins, a strategy based on 2-pyridinecarboxaldehydes for site-specific N-terminal protein modification was employed. This method allowed the successful modification of the proteins, and was applied for the introduction of a bioorthogonal vinylboronic acid moiety. In a subsequent reaction, the proteins could be modified further with a fluorophore using the tetrazine ligation. The application of capsid assembly conditions on the functionalized proteins led to successful particle formation, showing the potential of this covalent encapsulation strategy.

Using the dendritic polymer PAMAM to form gold nanoparticles in the protein cage thermosome

The chaperonin thermosome (THS) is a protein cage that lacks binding sites for metal ions and inorganic nanoparticles. However, when poly(amidoamine) (PAMAM) is encapsulated into THS, gold nanoparticles (AuNP) can be prepared in the THS. The polymer binds HAuCl4. Subsequent reduction yields nanoparticles with narrow size distribution in the protein-polymer conjugate.

CCMV-Based Enzymatic Nanoreactors

Protein-based nanoreactors are generated by encapsulating an enzyme inside the capsid of the cowpea chlorotic mottle virus (CCMV). Here, three different noncovalent methods are described to efficiently incorporate enzymes inside the capsid of these viral protein cages. The methods are based on pH, leucine zippers, and electrostatic interactions respectively, as a driving force for encapsulation. The methods are exclusively described for the enzymes horseradish peroxidase, glucose oxidase, and Pseudozyma antarctica lipase B, but they are also applicable for other enzymes.

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.

Enzyme Encapsulation in an Engineered Lumazine Synthase Protein Cage

The packaging of active enzymes in protein cages is a powerful strategy to control catalytic activity. Using a positively supercharged variant of green fluorescent protein, GFP(+36), as a genetically programmable tag, enzymes can be rapidly and quantitatively loaded into an engineered variant of the Aquifex aeolicus cage-forming protein lumazine synthase (AaLS-13) that possesses a negatively charged lumen. The cargo is spontaneously localized within AaLS-13 cages by simply mixing the components in aqueous solution. This chapter describes a detailed protocol for the preparation of AaLS-13 cages and GFP(+36)-enzyme fusions, as well as characterization of the inclusion complexes. Suitable conditions for encapsulation and enzyme kinetic assays are also discussed.

Encapsulation of Active Enzymes within Bacteriophage P22 Virus-Like Particles

Virus-like particles (VLPs) are nonpathogenic protein cage structures derived from viral coat proteins that have found utility in the area of biomaterials and nanotechnology. VLPs have been exploited as containers for the sequestration and encapsulation of a wide range of guest molecules in their hollow interiors. The robust nature of VLPs lend them as versatile scaffolds that can be exploited to provide protection to encapsulated guest molecules, such as enzymes which are often susceptible to inactivation and degradation, and for organization and construction of new nanomaterials incorporating the chemical properties of the guest molecules. In this chapter a background and methodology for the encapsulation of enzymes on the interior of the bacteriophage P22 derived VLP is described.

Icosahedral plant viral nanoparticles - bioinspired synthesis of nanomaterials/nanostructures

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

Modular interior loading and exterior decoration of a virus-like particle

Virus-like particles (VLPs) derived from the bacteriophage P22 offer an interesting and malleable platform for encapsulation and multivalent presentation of cargo molecules. The packaging of cargo in P22 VLP is typically achieved through genetically enabled directed in vivo encapsulation. However, this approach does not allow control over the packing density and composition of the encapsulated cargos. Here, we have adopted an in vitro assembly approach to gain control over cargo packaging in P22. The packaging was controlled by closely regulating the stoichiometric ratio of cargo-fused-scaffold protein and wild-type scaffold protein during the in vitro assembly. In a "one-pot assembly reaction" coat protein subunits were incubated with varied ratios of wild-type scaffold protein and cargo-fused-scaffold protein, which resulted in the encapsulation of both components in a co-assembled capsid. These experiments demonstrate that an input stoichiometry can be used to achieve controlled packaging of multiple cargos within the VLP. The porous nature of P22 allows the escape and re-entry of wild-type scaffold protein from the assembled capsid but scaffold protein fused to a protein-cargo cannot traverse the capsid shell due to the size of the cargo. This has allowed us to control and alter the packing density by selectively releasing wild-type scaffold protein from the co-assembled capsids. We have demonstrated these concepts in the P22 system using an encapsulated streptavidin protein and have shown its highly selective interaction with biotin or biotin derivatives. Additionally, this system can be used to encapsulate small molecules coupled to biotin, or display large proteins, that cannot enter the capsid and thus remain available for the multivalent display on the exterior of the capsid when attached to a flexible biotinylated linker. Thus, we have developed a P22 system with controlled protein cargo composition and packing density, to which both small and large molecules can be attached at high copy number on the interior or exterior of the capsid.

Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity

The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.

Engineering Recombinant Virus-like Nanoparticles from Plants for Cellular Delivery

Understanding capsid assembly following recombinant expression of viral structural proteins is critical to the design and modification of virus-like nanoparticles for biomedical and nanotechnology applications. Here, we use plant-based transient expression of the Bluetongue virus (BTV) structural proteins, VP3 and VP7, to obtain high yields of empty and green fluorescent protein (GFP)-encapsidating core-like particles (CLPs) from leaves. Single-particle cryo-electron microscopy of both types of particles revealed considerable differences in CLP structure compared to the crystal structure of infection-derived CLPs; in contrast, the two recombinant CLPs have an identical external structure. Using this insight, we exploited the unencumbered pore at the 5-fold axis of symmetry and the absence of encapsidated RNA to label the interior of empty CLPs with a fluorescent bioconjugate. CLPs containing 120 GFP molecules and those containing approximately 150 dye molecules were both shown to bind human integrin via a naturally occurring Arg-Gly-Asp motif found on an exposed loop of the VP7 trimeric spike. Furthermore, fluorescently labeled CLPs were shown to interact with a cell line overexpressing the surface receptor. Thus, BTV CLPs present themselves as a useful tool in targeted cargo delivery. These results highlight the importance of detailed structural analysis of VNPs in validating their molecular organization and the value of such analyses in aiding their design and further modification.

Scaffolding of Enzymes on Virus Nanoarrays: Effects of Confinement and Virus Organization on Biocatalysis

Organizing active enzyme molecules on nanometer-sized scaffolds is a promising strategy for designing highly efficient supported catalytic systems for biosynthetic and sensing applications. This is achieved by designing model nanoscale enzymatic platforms followed by thorough analysis of the catalytic activity. Herein, the virus fd bacteriophage is considered as an enzyme nanocarrier to study the scaffolding effects on enzymatic activity. Nanoarrays of randomly oriented, or directionally patterned, fd bacteriophage virus are functionalized with the enzyme glucose oxidase (GOx), using an immunological assembly strategy, directly on a gold electrode support. The scaffolding process on the virus capsid is monitored in situ by AFM (atomic force microscopy) imaging, while cyclic voltammetry is used to interrogate the catalytic activity of the resulting functional GOx-fd nanoarrays. Kinetic analysis reveals the ability to modulate the activity of GOx via nanocarrier patterning. The results evidence, for the first time, enhancement of the enzymatic activity due to scaffolding on a filamentous viral particle.

Assembling Enzymatic Cascade Pathways inside Virus-Based Nanocages Using Dual-Tasking Nucleic Acid Tags

The packaging of proteins into discrete compartments is an essential feature for cellular efficiency. Inspired by Nature, we harness virus-like assemblies as artificial nanocompartments for enzyme-catalyzed cascade reactions. Using the negative charges of nucleic acid tags, we develop a versatile strategy to promote an efficient noncovalent co-encapsulation of enzymes within a single protein cage of cowpea chlorotic mottle virus (CCMV) at neutral pH. The encapsulation results in stable 21-22 nm sized CCMV-like particles, which is characteristic of an icosahedral T = 1 symmetry. Cryo-EM reconstruction was used to demonstrate the structure of T = 1 assemblies templated by biological soft materials as well as the extra-swelling capacity of these T = 1 capsids. Furthermore, the specific sequence of the DNA tag is capable of operating as a secondary biocatalyst as well as bridging two enzymes for co-encapsulation in a single capsid while maintaining their enzymatic activity. Using CCMV-like particles to mimic nanocompartments can provide valuable insight on the role of biological compartments in enhancing metabolic efficiency.

Virus-like particles: Next-generation nanoparticles for targeted therapeutic delivery

Most drug therapies distribute the agents throughout the entire body, even though the drugs are typically only needed at specific tissues. This often limits dosage and causes discomfort and harmful side‐effects. Significant research has examined nanoparticles (NPs) for use as targeted delivery vehicles for therapeutic cargo, however, major clinical success has been limited. Current work focuses mainly on liposomal and polymer‐based NPs, but emerging research is exploring the engineering of viral capsids as noninfectious protein‐based NPs—termed virus‐like particles (VLPs). This review covers the research that has been performed thus far and outlines the potential for these VLPs to become highly effective delivery vehicles that overcome the many challenges encountered for targeted delivery of therapeutic cargo.

Symmetry-Directed Design of Protein Cages and Protein Lattices and Their Applications

The assembly of individual protein subunits into large-scale structures is important in many biological contexts. Proteins may assemble into geometrical cages or extended lattices that are characterized by a high degree of symmetry; examples include viral capsids and bacterial S-layers. The precisely defined higher order structure exhibited by these assemblies has inspired efforts to design such structures de novo by applying the principles of symmetry evident in natural protein assemblies. Here we discuss progress towards this goal and also examples of natural protein cages and lattices that have been engineered to repurpose them towards a diverse range of applications in materials science and nano-medicine.

Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology

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

Protein Nanoparticles as Multifunctional Biocatalysts and Health Assessment Sensors

The use of protein nanoparticles for biosensing, biocatalysis and drug delivery has exploded in the last few years. The ability of protein nanoparticles to self-assemble into predictable, monodisperse structures is of tremendous value. The unique properties of protein nanoparticles such as high stability, and biocompatibility, along with the potential to modify them led to development of novel bioengineering tools. Together, the ability to control the interior loading and external functionalities of protein nanoparticles makes them intriguing nanodevices. This review will focus on a number of recent examples of protein nanoparticles that have been engineered towards imparting the particles with biocatalytic or biosensing functionality.

Highly efficient enzyme encapsulation in a protein nanocage: towards enzyme catalysis in a cellular nanocompartment mimic

The study of enzyme behavior in small nanocompartments is crucial for the understanding of biocatalytic processes in the cellular environment. We have developed an enzymatic conjugation strategy to attach a model enzyme to the interior of a cowpea chlorotic mottle virus capsid. It is shown that with this methodology high encapsulation efficiencies can be achieved. Additionally, we demonstrate that the encapsulation does not affect the enzyme performance in terms of a decreased activity or a hampered substrate diffusion. Finally, it is shown that the encapsulated enzymes are protected against proteases. We believe that our strategy can be used to study enzyme kinetics in an environment that approaches physiological conditions.

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

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

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.

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

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

Compartmentalization Approaches in Soft Matter Science: From Nanoreactor Development to Organelle Mimics

Compartmentalization is an essential feature found in living cells to ensure that biological processes occur without being affected by undesired external influences. Over the years many scientists have designed self-assembled soft matter structures that mimic these natural catalytic compartments. The rationale behind this research is threefold. First of all, compartmentalization leads to the creation of a secluded environment for the catalytic species, which solves compatibility issues and which can improve catalyst efficiency and selectivity. Secondly, nano- and micro-compartments are constructed with the aim to obtain microenvironments that more closely mimic the cellular architecture. These biomimetic platforms are used to attain a better understanding of how cellular processes are executed. Thirdly, natural design rules are applied to create biomolecular assemblies with unusual functionality, which for example are used as artificial organelles. Here, recent developments will be discussed regarding these compartmentalized catalytic systems, with a selected number of illustrative examples to demonstrate which strategies have been followed, and to show to what extent the ambitious goals of this field of science have been reached. The focus here is on the field of soft matter science, covering the wide spectrum from polymeric assemblies to protein nanocages.

Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartments

Two different organometallic complexes were immobilized into a single ferritin protein cage which was crystallized to determine each binding sites.

Methods for production of uniform small-sized polymersome with rigid membrane

We report a facile methodology for the formation of uniform small-sized poly(ethylene glycol)-block-polystyrene (PEG-b-PS) polymersomes, via extrusion and sonication methods by using organic solvent as plasticizing agent.

Modified TMV Particles as Beneficial Scaffolds to Present Sensor Enzymes

Tobacco mosaic virus (TMV) is a robust nanotubular nucleoprotein scaffold increasingly employed for the high density presentation of functional molecules such as peptides, fluorescent dyes, and antibodies. We report on its use as advantageous carrier for sensor enzymes. A TMV mutant with a cysteine residue exposed on every coat protein (CP) subunit (TMVCys) enabled the coupling of bifunctional maleimide-polyethylene glycol (PEG)-biotin linkers (TMVCys/Bio). Its surface was equipped with two streptavidin [SA]-conjugated enzymes: glucose oxidase ([SA]-GOx) and horseradish peroxidase ([SA]-HRP). At least 50% of the CPs were decorated with a linker molecule, and all thereof with active enzymes. Upon use as adapter scaffolds in conventional "high-binding" microtiter plates, TMV sticks allowed the immobilization of up to 45-fold higher catalytic activities than control samples with the same input of enzymes. Moreover, they increased storage stability and reusability in relation to enzymes applied directly to microtiter plate wells. The functionalized TMV adsorbed to solid supports showed a homogeneous distribution of the conjugated enzymes and structural integrity of the nanorods upon transmission electron and atomic force microscopy. The high surface-increase and steric accessibility of the viral scaffolds in combination with the biochemical environment provided by the plant viral coat may explain the beneficial effects. TMV can, thus, serve as a favorable multivalent nanoscale platform for the ordered presentation of bioactive proteins.

Design of Enzyme-Encapsulated Protein Containers by In Vivo Crystal Engineering

Crystalline protein assemblies of polyhedra crystal (PhC) can be utilized as solid enzyme containers for long-term storage of enzymes with retention of their enzymatic activity. The enzymes can be released from the crystals at the optimum pH for the enzymatic activity by dissolution of the crystals using in vivo crystal engineering.

Design of a VLP-nanovehicle for CYP450 enzymatic activity delivery

BACKGROUND

The intracellular delivery of enzymes for therapeutic use has a promising future for the treatment of several diseases such as genetic disorders and cancer. Virus-like particles offer an interesting platform for enzymatic delivery to targeted cells because of their great cargo capacity and the enhancement of the biocatalyst stability towards several factors important in the practical application of these nanoparticles.

RESULTS

We have designed a nano-bioreactor based on the encapsulation of a cytochrome P450 (CYP) inside the capsid derived from the bacteriophage P22. An enhanced peroxigenase, CYPBM3, was selected as a model enzyme because of its potential in enzyme prodrug therapy. A total of 109 enzymes per capsid were encapsulated with a 70 % retention of activity for cytochromes with the correct incorporation of the heme cofactor. Upon encapsulation, the stability of the enzyme towards protease degradation and acidic pH was increased. Cytochrome P450 activity was delivered into Human cervix carcinoma cells via transfecting P22-CYP nanoparticles with lipofectamine.

CONCLUSION

This work provides a clear demonstration of the potential of biocatalytic virus-like particles as medical relevant enzymatic delivery vehicles for clinical applications.

Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor

Nature uses protein compartmentalization to great effect for control over enzymatic pathways, and the strategy has great promise for synthetic biology. In particular, encapsulation in nanometer-sized containers to create nanoreactors has the potential to elicit interesting, unexplored effects resulting from deviations from well-understood bulk processes. Self-assembled protein shells for encapsulation are especially desirable for their uniform structures and ease of perturbation through genetic mutation. Here, we use the MS2 capsid, a well-defined porous 27 nm protein shell, as an enzymatic nanoreactor to explore pore-structure effects on substrate and product flux during the catalyzed reaction. Our results suggest that the shell can influence the enzymatic reaction based on charge repulsion between small molecules and point mutations around the pore structure. These findings also lend support to the hypothesis that protein compartments modulate the transport of small molecules and thus influence metabolic reactions and catalysis in vitro.

Biomolecular engineering of virus-like particles aided by computational chemistry methods

Multi-scale investigation of VLP self-assembly aided by computational methods is facilitating the design, redesign, and modification of functionalized VLPs.

Positional assembly of hemin and gold nanoparticles in graphene-mesoporous silica nanohybrids for tandem catalysis

A hybrid catalyst in which two different types of enzyme mimics are positioned in spatially separate domains within a graphene–mesoporous silica support is presented.

Here, for the first time, a hybrid catalyst in which hemin and gold nanoparticles are positioned in spatially separate domains within a graphene–mesoporous silica support is presented. Specifically, monomeric hemin can be anchored on the inner exposed graphene surface of a graphene–mesoporous silica hybrid (GS) via π–π stacking interactions. After the assembly, such nanocomposites can function as a peroxidase mimic. Next, gold nanoparticles, which act as artificial glucose oxidase, can be conjugated to the functional NH₂ groups present on the outer coated silica surface. As a result, the integrated catalysts containing multiple catalytic sites can be used to catalyze sequential reactions, without the aid of true enzymes. This work is an important step forward in positional assembly of biomimetic catalysts for artificially mimicking natural organelles or important chemical transformations in the future.

Constructing catalytic antimicrobial nanoparticles by encapsulation of hydrogen peroxide producing enzyme inside the P22 VLP

Here we examine a self-assembling virus like particle to construct catalytically active nanoparticles that can inhibit bacterial growth. The results suggest that encapsulation of enzymes inside VLPs can be exploited to develop new bionanomaterials with useful functionalities.

Production and applications of engineered viral capsids

As biological agents, viruses come in an astounding range of sizes, with varied shapes and surface morphologies. The structures of viral capsids are generally assemblies of hundreds of copies of one or a few proteins which can be harnessed for use in a wide variety of applications in biotechnology, nanotechnology, and medicine. Despite their complexity, many capsid types form as homogenous populations of precise geometrical assemblies. This is important in both medicine, where well-defined therapeutics are critical for drug performance and federal approval, and nanotechnology, where precise placement affects the properties of the desired material. Here we review the production of viruses and virus-like particles with methods for selecting and manipulating the size, surface chemistry, assembly state, and interior cargo of capsid. We then discuss many of the applications used in research today and the potential commercial and therapeutic products from engineered viral capsids.

Chemotherapy pro-drug activation by biocatalytic virus-like nanoparticles containing cytochrome P450

This work shows, for the first time, the encapsulation of a highly relevant protein in the biomedical field into virus-like particles (VLPs). A bacterial CYP variant was effectively encapsulated in VLPs constituted of coat protein from cowpea chlorotic mottle virus (CCMV). The catalytic VLPs are able to transform the chemotherapeutic pro-drug, tamoxifen, and the emerging pro-drug resveratrol. The chemical nature of the products was identified, confirming similar active products than those obtained with human CYP. The enzymatic VLPs remain stable after the catalytic reaction. The potential use of these biocatalytic nanoparticles as targeted CYP carriers for the activation of chemotherapy drugs is discussed.

Encapsulation of an enzyme cascade within the bacteriophage P22 virus-like particle

Developing methods for investigating coupled enzyme systems under conditions that mimic the cellular environment remains a significant challenge. Here we describe a biomimetic approach for constructing densely packed and confined multienzyme systems through the co-encapsulation of 2 and 3 enzymes within a virus-like particle (VLP) that perform a coupled cascade of reactions, creating a synthetic metabolon. Enzymes are efficiently encapsulated in vivo with known stoichiometries, and the kinetic parameters of the individual and coupled activities are characterized. From the results we develop and validate a mathematical model for predicting the expected kinetics for coupled reactions under co-localized conditions.

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.

INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES

The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins.

[Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41

Biomolecular scaffolds for enhanced signaling and catalytic efficiency

Proteins inherently are not designed to be standalone entities. Whether it is a multi-step biochemical reaction or a signaling event that triggers several other cascading events, proteins are naturally designed to function cohesively. Several natural systems have been developed through evolution to co-localize the functional proteins of the same pathway in order to ensure efficient communication of signals or intermediates. This review focuses on some selected examples of where synthetic scaffolds inspired by nature have been used to enhance the overall biological pathway performance. Applications encompass both in vivo and in vitro systems that address two key biological events in cell signaling and biosynthesis will be discussed.

Supramolecular catalysis. Part 2: artificial enzyme mimics

The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.

Cascade reactions in nanoreactors

In an attempt to mimic the biosynthetic efficiencies of nature and in a search for greener, more sustainable alternatives to nowadays ways of producing chemicals, one-pot cascade reactions have attracted a lot of attention in the past decade. Since most catalysts are not compatible with each other, compartmentalization techniques have often been applied to prevent catalyst inactivation. A various array of nanoreactors have been developed to meet the demand of having a site-isolated catalyst system, while maintaining the catalyst activity. Both multienzyme nanoreactors as well as enzyme/metal catalyst or organocatalyst systems have shown great potential in one-pot cascade reactions and hold promise for future developments in this field.

Hepatitis virus capsid polymorph stability depends on encapsulated cargo size

Protein cages providing a controlled environment to encapsulated cargo are a ubiquitous presence in any biological system. Well-known examples are capsids, the regular protein shells of viruses, which protect and deliver the viral genome. Since some virus capsids can be loaded with nongenomic cargoes, they are interesting for a variety of applications ranging from biomedical delivery to energy harvesting. A question of vital importance for such applications is how does capsid stability depend on the size of the cargo? A nanoparticle-templated assembly approach was employed here to determine how different polymorphs of the Hepatitis B virus icosahedral capsid respond to a gradual change in the encapsulated cargo size. It was found that assembly into complete virus-like particles occurs cooperatively around a variety of core diameters, albeit the degree of cooperativity varies. Among these virus-like particles, it was found that those of an outer diameter corresponding to an icosahedral array of 240 proteins (T = 4) are able to accommodate the widest range of cargo sizes.

Geometric curvature controls the chemical patchiness and self-assembly of nanoparticles

When organic molecules are tethered onto non-spherical nanoparticles, their chemical properties depend on the particles' local curvature and shape. Based on this observation, we show here that it is possible to engineer chemical patchiness across the surface of a non-spherical nanoparticle using a single chemical species. In particular, when acidic ligands are used, regions of the particle surface with different curvature become charged at different pH values of the surrounding solution. This interplay between particle shape and local electrostatics allows for fine control over nanoscale self-assembly leading to structures with varying degrees of complexity. These structures range from particle cross-stacks to open-lattice crystals, the latter with pore sizes on the order of tens of nanometres, that is, at the lower synthetic limits of metallic mesoporous materials.