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

Supramolecular protein polymers using mini-ferritin Dps as the building block

Production of long polymer chains with iron oxidation and storage activity, built from protein nanocages using a click chemistry approach.

The equilibrium structure of self-assembled protein nano-cages

Understanding how highly symmetric, robust, monodisperse protein nano-cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to investigate the assembly of protein subunits into the structures with different sizes and symmetries. Using Monte Carlo simulation, we obtain global minimum energy structures. Our results suggest that the physical properties including the spontaneous curvature, flexibility and bending rigidity of coat proteins are sufficient to predict the size, symmetry and shape selectivity of the assembly products. Further, on a thermodynamic basis, we discuss the polymorphism of nano-cages observed in assembly experiments.

Microstructural metrology of tobacco mosaic virus nanorods during radial compression and heating

We determined stress-induced deformations and the thermal stability of nanorod-shaped tobacco mosaic virus (TMV) capsids in coffee-ring structures by X-ray nanodiffraction. The hexagonal capsids lattice transforms under compression in the outer boundary zone of the coffee-ring into a tetragonal lattice. The helical pitch of the nanorods increases by about 2.5% across the outer boundary zone while the lateral distance between nanorods decreases continuously across the whole coffee-ring structure by about 2% due to compressive forces. The diffraction patterns show a mixture of helical scattering and Bragg peaks attributed to a lattice of nanorods interlocked by their helical grooves. Thermo-nanodiffraction reveals water loss up to about 100 °C resulting in a reduction of the helical pitch by about 6% with respect to its maximum value and a reduction of the nanorods separation by about 0.5 nm. Up to about 200 °C the pitch is increasing again by about 2%. Secondary crystallization in the bulk reaches a maximum at 150-160 °C. At higher temperatures the crystallinity is continuously decreasing up to about 220 °C. Above about 200 °C and depending on the heating history, the nanorods start disintegrating into small, randomly oriented aggregates.

Archaeal Lsm rings as stable self-assembling tectons for protein nanofabrication

We have exploited the self-assembling properties of archaeal-derived protein Lsmα to generate new supramolecular forms based on its stable ring-shaped heptamer. We show that engineered ring tectons incorporating cysteine sidechains on obverse faces of the Lsmα₇ toroid are capable of forming paired and stacked formations. A Cys-modified construct, N10C/E61C-Lsmα, appears to organize into disulfide-mediated tube formations up to 45 nm in length. We additionally report fabrication of cage-like protein clusters through conjugation of Cu²⁺ to His-tagged variants of the Lsmα₇ tecton. These 400 kDa protein capsules are seen as cube particles with visible pores, and are reversibly dissembled into their component ring tectons by EDTA. The β-rich Lsmα supramolecular assemblies described are amenable to further fusion modifications, or for surface attachment, so providing potential for future applications that exploit the RNA-binding capacity of Lsm proteins, such as sensing applications.

Synthetic plant virology for nanobiotechnology and nanomedicine

Nanotechnology is a rapidly expanding field seeking to utilize nano-scale structures for a wide range of applications. Biologically derived nanostructures, such as viruses and virus-like particles (VLPs), provide excellent platforms for functionalization due to their physical and chemical properties. Plant viruses, and VLPs derived from them, have been used extensively in biotechnology. They have been characterized in detail over several decades and have desirable properties including high yields, robustness, and ease of purification. Through modifications to viral surfaces, either interior or exterior, plant-virus-derived nanoparticles have been shown to support a range of functions of potential interest to medicine and nano-technology. In this review we highlight recent and influential achievements in the use of plant virus particles as vehicles for diverse functions: from delivery of anticancer compounds, to targeted bioimaging, vaccine production to nanowire formation. WIREs Nanomed Nanobiotechnol 2017, 9:e1447. doi: 10.1002/wnan.1447 For further resources related to this article, please visit the WIREs website.

Polymeric Tubular Structures

Nature makes use of tubular structures for the spatial separation of matter on many different length scales, ranging from the nanometer scale (selective channels based on folded proteins) up to the centimeter scale (blood vessels). Today, polymer chemists and engineers can prepare polymeric tubular structures via a variety of different methods also covering many lengthscales, from nanometers to meters. The synthetic approaches described in this chapter vary significantly from the folding of single polymer chains via the self-assembly of DNA fragments to coordinative metal-organic nanotubes to tubes engineerd from bulk polymers using a range of porous or fibrous templates. While all examples reported in this chapter form tubular structures and thereby mimic their naturally occuring counterparts, it is mainly the engineered tubes that are more straightforward to prepare that also show some bio-inspired function.

Directed assembly of defined oligomeric photosynthetic reaction centres through adaptation with programmable extra-membrane coiled-coil interfaces

A challenge associated with the utilisation of bioenergetic proteins in new, synthetic energy transducing systems is achieving efficient and predictable self-assembly of individual components, both natural and man-made, into a functioning macromolecular system. Despite progress with water-soluble proteins, the challenge of programming self-assembly of integral membrane proteins into non-native macromolecular architectures remains largely unexplored. In this work it is shown that the assembly of dimers, trimers or tetramers of the naturally monomeric purple bacterial reaction centre can be directed by augmentation with an α-helical peptide that self-associates into extra-membrane coiled-coil bundle. Despite this induced oligomerisation the assembled reaction centres displayed normal spectroscopic properties, implying preserved structural and functional integrity. Mixing of two reaction centres modified with mutually complementary α-helical peptides enabled the assembly of heterodimers in vitro, pointing to a generic strategy for assembling hetero-oligomeric complexes from diverse modified or synthetic components_. Addition of two coiled-coil peptides per reaction centre monomer was also tolerated despite the challenge presented to the pigment-protein assembly machinery of introducing multiple self-associating sequences. These findings point to a generalised approach where oligomers or longer range assemblies of multiple light harvesting and/or redox proteins can be constructed in a manner that can be genetically-encoded, enabling the construction of new, designed bioenergetic systems in vivo or in vitro.

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Reaction centre monomers are engineered to assemble as oligomers in vivo.

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A fused coiled coil bundle programs dimer, trimer and tetramer formation.

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Assembled oligomeric reaction centres are structurally and functionally intact.

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Coiled coils can be used to assemble reaction centre hetero-oligomers in vitro.

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Addition of two coiled-coil peptides per reaction centre monomer is tolerated.

Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science

Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.

A sight on protein-based nanoparticles as drug/gene delivery systems

Polymeric nanomaterials have extensively been applied for the preparation of targeted and controlled release drug/gene delivery systems. However, problems involved in the formulation of synthetic polymers such as using of the toxic solvents and surfactants have limited their desirable applications. In this regard, natural biomolecules including proteins and polysaccharide are suitable alternatives due to their safety. According to literature, protein-based nanoparticles possess many advantages for drug and gene delivery such as biocompatibility, biodegradability and ability to functionalize with targeting ligands. This review provides a general sight on the application of biodegradable protein-based nanoparticles in drug/gene delivery based on their origins. Their unique physicochemical properties that help them to be formulated as pharmaceutical carriers are also discussed.

Directed Growth of Virus Nanofilaments on a Superhydrophobic Surface

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

Metal-induced self-assembly of peroxiredoxin as a tool for sorting ultrasmall gold nanoparticles into one-dimensional clusters

Nanomanipulation of matter to create responsive, ordered materials still remains extremely challenging. Supramolecular chemistry has inspired new strategies by which such nanomaterials can be synthesized step by step by exploiting the self-recognition properties of molecules. In this work, the ring-shaped architecture of the 2-Cys peroxiredoxin I protein from Schistosoma mansoni, engineered to have metal ion-binding sites, is used as a template to build up 1D nanoscopic structures through metal-induced self-assembly. Chromatographic and microscopic analyses demonstrate the ability of the protein rings to stack directionally upon interaction with divalent metal ions and form well-defined nanotubes by exploiting the intrinsic recognition properties of the ring surfaces. Taking advantage of such behavior, the rings are then used to capture colloidal Ni(2+)-functionalized ultrasmall gold nanoparticles and arrange them into 1D arrays through stacking into peapod-like complexes. Finally, as the formation of such nano-peapods strictly depends on nanoparticle dimensions, the peroxiredoxin template is used as a colloidal cut-off device to sort by size the encapsulated nanoparticles. These results open up possibilities in developing Prx-based methods to synthesize new advanced functional materials.

A smart platform for hyperthermia application in cancer treatment: cobalt-doped ferrite nanoparticles mineralized in human ferritin cages

Magnetic nanoparticles, MNPs, mineralized within a human ferritin protein cage, HFt, can represent an appealing platform to realize smart therapeutic agents for cancer treatment by drug delivery and magnetic fluid hyperthermia, MFH. However, the constraint imposed by the inner diameter of the protein shell (ca. 8 nm) prevents its use as heat mediator in MFH when the MNPs comprise pure iron oxide. In this contribution, we demonstrate how this limitation can be overcome through the controlled doping of the core with small amount of Co(II). Highly monodisperse doped iron oxide NPs with average size of 7 nm are mineralized inside a genetically modified variant of HFt, carrying several copies of α-melanocyte-stimulating hormone peptide, which has already been demonstrated to have excellent targeting properties toward melanoma cells. HFt is also conjugated to poly(ethylene glycol) molecules to increase its in vivo stability. The investigation of hyperthermic properties of HFt-NPs shows that a Co doping of 5% is enough to strongly enhance the magnetic anisotropy and thus the hyperthermic efficiency with respect to the undoped sample. In vitro tests performed on B16 melanoma cell line demonstrate a strong reduction of the cell viability after treatment with Co doped HFt-NPs and exposure to the alternating magnetic field. Clear indications of an advanced stage of apoptotic process is also observed from immunocytochemistry analysis. The obtained data suggest this system represents a promising candidate for the development of a protein-based theranostic nanoplatform.

Supramolecular protein assemblies in the nucleus of human cells

Genetically encoded supramolecular protein assemblies (SMPAs) are induced to form in living cells by combination of distinct self-assembly properties. A single fusion construct contains genes encoding the heavy chain (H) of human ferritin and the citrine fluorescent protein, the latter exposing a weak dimerization interface, as well as a nuclear localization signal. Upon expression in HeLa cells, in vivo confocal fluorescence and differential interference contrast imaging revealed extended SMPA structures exclusively in the nuclei. Assemblies were typically round and took alveolar, shell-like, or hybrid structure. Transmission electron microscopy revealed a crystalline packing. Site-specific mutagenesis of the citrine dimerization interface clarified the mechanism of SMPA formation. The constituent proteins retained their activity in iron binding and fluorescence emission, thus suggesting a general strategy for formation of synthetic cellular bodies with specific biochemical function.

Template-free, hollow and porous platinum nanotubes derived from tobamovirus and their three-dimensional structure at the nanoscale

A tobamovirus is used as a removable template for facile production of a porous platinum nanotube with a 13 nm central channel.

Free energy of adsorption for a peptide at a liquid/solid interface via nonequilibrium molecular dynamics

Protein adsorption is of wide interest including in many technological applications such as tissue engineering, nanotechnology, biosensors, drug delivery, and vaccine production among others. Understanding the fundamentals of such technologies and their design would be greatly aided by an ability to efficiently predict the conformation of an adsorbed protein and its free energy of adsorption. In the study reported here, we show that this is possible when data obtained from nonequilibrium thermodynamic integration (NETI) combined with steered molecular dynamics (SMD) is subject to bootstrapping. For the met-enkephalin pentapeptide at a water-graphite interface, we were able to obtain accurate predictions for the location of the adsorbed peptide and its free energy of adsorption from around 50 and 80 SMD simulations, respectively. It was also shown that adsorption in this system is both energetically and entropically driven. The free energy of adsorption was also decomposed into that associated with formation of the cavity in the water near the graphite surface sufficient to accommodate the adsorbed peptide and that associated with insertion of the peptide into this cavity. This decomposition reveals that the former is modestly energetically and entropically unfavorable, whereas the latter is the opposite in both regards to a much greater extent.

Protein nanotechnology: what is it?

Protein nanotechnology is an emerging field that is still defining itself. It embraces the intersection of protein science, which exists naturally at the nanoscale, and the burgeoning field of nanotechnology. In this opening chapter, a select review is given of some of the exciting nanostructures that have already been created using proteins, and the sorts of applications that protein engineers are reaching towards in the nanotechnology space. This provides an introduction to the rest of the volume, which provides inspirational case studies, along with tips and tools to manipulate proteins into new forms and architectures, beyond Nature's original intentions.

Protein nanotubes, channels and cages

Proteins are the work-horses of life and excute the essential processes involved in the growth and repair of cells. These roles include all aspects of cell signalling, metabolism and repair that allow living things to exist. They are not only chemical catalysts and machine components, they are also structural components of the cell or organism, capable of self-organisation into strong supramolecular cages, fibres and meshes. How proteins are encoded genetically and how they are sythesised in vivo is now well understood, and for an increasing number of proteins, the relationship between structure and function is known in exquisite detail. The next challenge in bionanoscience is to adapt useful protein systems to build new functional structures. Well-defined natural structures with potential useful shapes are a good starting point. With this in mind, in this chapter we discuss the properties of natural and artificial protein channels, nanotubes and cages with regard to recent progress and potential future applications. Chemistries for attaching together different proteins to form superstructures are considered as well as the difficulties associated with designing complex protein structures ab initio.

Self-assembly of glutathione S-transferase into nanowires

This study presents the Ni-ion-directed self-assembly of a C(2)-symmetric homodimeric enzyme into nanowires. A genetically introduced His-tag arm stretches out of the central structure of a C(2)-symmetric homodimer of glutathione S-transferase, which is used as a linker to recruit a second building block through interprotein metal coordination, forming self-assembled one-dimensional nanostructures with excellent enzymatic activity.

Selective targeting of melanoma by PEG-masked protein-based multifunctional nanoparticles

Background

Nanoparticle-based systems are promising for the development of imaging and therapeutic agents. The main advantage of nanoparticles over traditional systems lies in the possibility of loading multiple functionalities onto a single molecule, which are useful for therapeutic and/or diagnostic purposes. These functionalities include targeting moieties which are able to recognize receptors overexpressed by specific cells and tissues. However, targeted delivery of nanoparticles requires an accurate system design. We present here a rationally designed, genetically engineered, and chemically modified protein-based nanoplatform for cell/tissue-specific targeting.

Methods

Our nanoparticle constructs were based on the heavy chain of the human protein ferritin (HFt), a highly symmetrical assembly of 24 subunits enclosing a hollow cavity. HFt-based nanoparticles were produced using both genetic engineering and chemical functionalization methods to impart several functionalities, ie, the α-melanocyte-stimulating hormone peptide as a melanoma-targeting moiety, stabilizing and HFt-masking polyethylene glycol molecules, rhodamine fluorophores, and magnetic resonance imaging agents. The constructs produced were extensively characterized by a number of physicochemical techniques, and assayed for selective melanoma-targeting in vitro and in vivo.

Results

Our HFt-based nanoparticle constructs functionalized with the α-melanocyte-stimulating hormone peptide moiety and polyethylene glycol molecules were specifically taken up by melanoma cells but not by other cancer cell types in vitro. Moreover, experiments in melanoma-bearing mice indicate that these constructs have an excellent tumor-targeting profile and a long circulation time in vivo.

Conclusion

By masking human HFt with polyethylene glycol and targeting it with an α-melanocyte-stimulating hormone peptide, we developed an HFt-based melanoma-targeting nanoplatform for application in melanoma diagnosis and treatment. These results could be of general interest, because the same strategy can be exploited to develop ad hoc nanoplatforms for specific delivery towards any cell/tissue type for which a suitable targeting moiety is available.

Assembly of protein building blocks using a short synthetic peptide

Combining proteins or their defined domains offers new enhanced functions. Conventionally, two proteins are either fused into a single polypeptide chain by recombinant means or chemically cross-linked. However, these strategies can have drawbacks such as poor expression (recombinant fusions) or aggregation and inactivation (chemical cross-linking), especially in the case of large multifunctional proteins. We developed a new linking method which allows site-oriented, noncovalent, yet irreversible stapling of modified proteins at neutral pH and ambient temperature. This method is based on two distinct polypeptide linkers which self-assemble in the presence of a specific peptide staple allowing on-demand and irreversible combination of protein domains. Here we show that linkers can either be expressed or be chemically conjugated to proteins of interest, depending on the source of the proteins. We also show that the peptide staple can be shortened to 24 amino acids still permitting an irreversible combination of functional proteins. The versatility of this modular technique is demonstrated by stapling a variety of proteins either in solution or to surfaces.

Silver ion incorporation and nanoparticle formation inside the cavity of Pyrococcus furiosus ferritin: structural and size-distribution analyses

Highly symmetrical protein cage architectures from three different iron storage proteins, heavy and light human ferritin chains (HuHFt and HuLFt) and ferritin from the hyperthemophilic bacterium Pyrococcus furiosus (PfFt), have been used as models for understanding the molecular basis of silver ion deposition and metal core formation inside the protein cavity. Biomineralization using protein cavities is an important issue for the fabrication of biometamaterials under mild synthetic conditions. Silver nanoparticles (AgNPs) were produced with high yields within PfFt but not within HuHFt and HuLFt. To explain the molecular basis of silver incorporation, the X-ray crystal structure of Ag-containing PfFt has been solved. This is the first structure of a silver containing ferritin reported to date, and it revealed the presence of specific binding and nucleation sites of Ag(I) that are not conserved in other ferritin templates. The AgNP encapsulated by PfFt were further characterized by the combined use of different physical-chemical techniques. These showed that the AgNPs are endowed with a narrow size distribution (2.1 +/- 0.4 nm), high stability in water solution at millimolar concentration, and high thermal stability. These properties make the AgNP obtained within PftFt exploitable for a range of applications, in fields as diverse as catalysis in water, preparation of metamaterials, and in vivo diagnosis and antibacterial or tumor therapy.

Mycobacterial stress regulation: The Dps "twin sister" defense mechanism and structure-function relationship

In this work, we have tried to emphasize the connection between mycobacterial growth and regulation of gene expression. Utilization of multiple carbon sources and diauxic growth helps bacteria to regulate gene expression at an optimum level so that the inhospitable conditions encountered during nutrient depletion can be circumvented. These aspects will be discussed with respect to mycobacterial growth in subsequent sections. Identification and characterization of genes induced under such conditions is helpful to understand the physiology of the bacterium. Although it is necessary to compare the total expression profile of proteins as they transit from vegetative growth to stationary phase, at times a lot of insights can be deciphered from the expression pattern of one or two proteins. We have compared the protein expression and sigma factor selectivity of two such proteins in M. smegmatis to understand the differential regulation of genes playing diverse function in the same species. Some newer insights on the structure and function of one of the Dps proteins are also explained.

Fabrication of aligned magnetic nanoparticles using tobamoviruses

We used genetically modified tube-shaped tobamoviruses to produce 3 nm aligned magnetic nanoparticles. Amino acid residues facing the central channel of the virus were modified to increase the number of nucleation sites. Energy dispersive X-ray spectroscopy and superconducting quantum interference device analysis suggest that the particles consisted of Co-Pt alloy. The use of tobamovirus mutants is a promising approach to making a variety of components that can be applied to fabricate nanometer-scaled electronic devices.