Protein Cages: From Fundamentals to Advanced Applications

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

An optimized low-cost protocol for standardized production of iron-free apoferritin nanocages with high protein recovery and suitable conformation for nanotechnological applications

Ferritin is a globular protein that consists of 24 subunits forming a hollow nanocage structure that naturally stores iron oxyhydroxides. Elimination of iron atoms to obtain the empty protein called apoferritin is the first step to use this organic shell as a nanoreactor for different nanotechnological applications. Different protocols have been reported for apoferritin formation, but some are time consuming, others are difficult to reproduce and protein recovery yields are seldom reported. Here we tested several protocols and performed a complete material characterization of the apoferritin products using size exclusion chromatography, UV-vis spectroscopy, inductively coupled plasma optical emission spectrometry and dynamic light scattering. Our best method removes more than 99% of the iron from loaded holoferritin, recovering 70-80% of the original protein as monomeric apoferritin nanocages. Our work shows that pH conditions of the reduction step and the presence and nature of chelating agents affect the efficiency of iron removal. Furthermore, process conditions also seem to have an influence on the monomer:aggregate proportion present in the product. We also demonstrate that iron contents markedly increase ferritin absorbance at 280nm. The influence of iron contents on absorbance at 280nm precludes using this simple spectrophotometric measure for protein determination in ferritin‑iron complexes. Apoferritin produced following our protocol only requires readily-available, cheap and biocompatible reagents, which makes this process standardizable, scalable and applicable to be used for in vivo applications of ferritin derivatives as well as nanotechnological and biotechnological uses.

Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures

In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered.

Floating gate memory with charge storage dots array formed by Dps protein modified with site-specific binding peptides

We report a nanodot (ND) floating gate memory (NFGM) with a high-density ND array formed by a biological nano process. We utilized two kinds of cage-shaped proteins displaying SiO2 binding peptide (minTBP-1) on their outer surfaces: ferritin and Dps, which accommodate cobalt oxide NDs in their cavities. The diameters of the cobalt NDs were regulated by the cavity sizes of the proteins. Because minTBP-1 is strongly adsorbed on the SiO2 surface, high-density cobalt oxide ND arrays were obtained by a simple spin coating process. The densities of cobalt oxide ND arrays based on ferritin and Dps were 6.8 × 10(11) dots cm(-2) and 1.2 × 10(12) dots cm(-2), respectively. After selective protein elimination and embedding in a metal-oxide-semiconductor (MOS) capacitor, the charge capacities of both ND arrays were evaluated by measuring their C-V characteristics. The MOS capacitor embedded with the Dps ND array showed a wider memory window than the device embedded with the ferritin ND array. Finally, we fabricated an NFGM with a high-density ND array based on Dps, and confirmed its competent writing/erasing characteristics and long retention time.

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.

Nonvolatile flash memory based on biologically integrated hierarchical nanostructures

The first six peptides of multifunctional titanium binding peptide-1 bestowed recombinant L-ferritin, minT1-LF, was genetically engineered and used to fabricate multilayered nanoparticle architecture. The multifunctionality of minT1-LF enables specific binding of nanoparticle-accommodated minT1-LF to the silicon substrate surface and wet biochemical fabrication of gate oxide layer by its biomineralization activity. Three-dimensional (3D) nanoparticle architecture with multilayered structure was fabricated by the biological layer-by-layer method and embedded in a metal oxide-semiconductor device structure as a charge storage node of a flash memory device. The 3D-integrated multilayered nanoparticle architecture successfully worked as a charge storage node in flash memory devices that exhibited improved charge storage capacity compared with that of a conventional monolayer structure device.

Structuration and integration of magnetic nanoparticles on surfaces and devices

Different experimental approaches used for structuration of magnetic nanoparticles on surfaces are reviewed. Nanoparticles tend to organize on surfaces through self-assembly mechanisms controlled by non-covalent interactions which are modulated by their shape, size and morphology as well as by other external parameters such as the nature of the solvent or the capping layer. Further control on the structuration can be achieved by the use of external magnetic fields or other structuring techniques, mainly lithographic or atomic force microscopy (AFM)-based techniques. Moreover, results can be improved by chemical functionalization or the use of biological templates. Chemical functionalization of the nanoparticles and/or the surface ensures a proper stability as well as control of the formation of a (sub)monolayer. On the other hand, the use of biological templates facilitates the structuration of several families of nanoparticles, which otherwise may be difficult to form, simply by establishing the experimental conditions required for the structuration of the organic capsule. All these experimental efforts are directed ultimately to the integration of magnetic nanoparticles in sensors which constitute the future generation of hybrid magnetic devices.

Reactions inside nanoscale protein cages

Chemical reactions are traditionally carried out in bulk solution, but in nature confined spaces, like cell organelles, are used to obtain control in time and space of conversion. One way of studying these reactions in confinement is the development and use of small reaction vessels dispersed in solution, such as vesicles and micelles. The utilization of protein cages as reaction vessels is a relatively new field and very promising as these capsules are inherently monodisperse, in that way providing uniform reaction conditions, and are readily accessible to both chemical and genetic modifications. In this review, we aim to give an overview of the different kinds of nanoscale protein cages that have been employed as confined reaction spaces.

Native and synthetic ferritins for nanobiomedical applications: recent advances and new perspectives

Ferritin is the protein whose function is to store iron that the cell does not require immediately for metabolic processes, thereby protecting against the toxic effects of free Fe2+. Ferritin therefore plays a crucial role in iron metabolism as well as in the development of some diseases, especially those related to the presence of free Fe2+ and toxic hydroxyl radicals. In addition, ferritin is itself a catalytic bionanoparticle. Its internal cavity can be used as a nanoreactor to produce non-native metallic nanoparticles. Moreover, its external protein shell can be chemically modified, allowing ferritin to be used as a precursor for a library of metallic nanoparticles, some which may have potential applications in biomedicine, especially as multimodal imaging probes. This article presents a brief overview of the evidence for the role of native ferritin in some diseases, as well as the potential of some synthetic ferritins – in which a non-native inorganic material has been introduced into the cavity and/or the external shell has been modified – in the field of nanobiomedicine.

Ferritin in the field of nanodevices

Biomineralization of ferritin core has been extended to the artificial synthesis of homogeneous metal complex nanoparticles (NPs) and semiconductor NPs. The inner cavity of apoferritin is an ideal spatially restricted chemical reaction chamber for NP synthesis. The obtained ferritin (biocomplexes, NP and the surrounding protein shell) has attracted great interest among researchers in the field of nanodevices. Ferritins were delivered onto specific substrate locations in a one-by-one manner or a hexagonally close-packed array through ferritin outer surface interactions. After selective elimination of protein shells from the ferritin, bare NPs were left at the positions where they were delivered. The obtained NPs were used as catalysts for carbon nanotube (CNT) growth and metal induced lateral crystallization (MILC), charge storage nodes of floating gate memory, and nanometer-scale etching masks, which could not be performed by other methods.

Nanoscale positioning of inorganic nanoparticles using biological ferritin arrays fabricated by dip-pen nanolithography

In this manuscript we demonstrate the spatially controlled immobilization of ferritin proteins by directly writing them on a wide range of substrates of technological interest. Optical and fluorescence microscopy, AFM and TOF-SIMS studies confirm the successful deposition of the protein on those surfaces. Control on nanostructure shape and size, by miniaturizing the dot-like features down to a 100 nm, demonstrates the particular capabilities of the DPN approach. Ultimately, this study gives the opportunity to design nanoparticle-based arrays regarding the growing interest in the use of nanoparticles as structural and functional elements for fabricating nanodevices. Herein, we demonstrate how the protein shell of ferritins can be removed by a simple heat-treatment process while maintaining the encapsulated inorganic nanoparticle intact on the same location of the nanoarray. As a result, this study establishes how direct-write DPN approach could give the opportunity to design not only protein-based nanoarrays but also nanoparticle-based nanoarrays with high-resolution and control.

The ferritin superfamily: Supramolecular templates for materials synthesis

Members of the ferritin superfamily are multi-subunit cage-like proteins with a hollow interior cavity. These proteins possess three distinct surfaces, i.e. interior and exterior surfaces of the cages and interface between subunits. The interior cavity provides a unique reaction environment in which the interior reaction is separated from the external environment. In biology the cavity is utilized for sequestration of irons and biomineralization as a mechanism to render Fe inert and sequester it from the external environment. Material scientists have been inspired by this system and exploited a range of ferritin superfamily proteins as supramolecular templates to encapsulate nanoparticles and/or as well-defined building blocks for fabrication of higher order assembly. Besides the interior cavity, the exterior surface of the protein cages can be modified without altering the interior characteristics. This allows us to deliver the protein cages to a targeted tissue in vivo or to achieve controlled assembly on a solid substrate to fabricate higher order structures. Furthermore, the interface between subunits is utilized for manipulating chimeric self-assembly of the protein cages and in the generation of symmetry-broken Janus particles. Utilizing these ideas, the ferritin superfamily has been exploited for development of a broad range of materials with applications from biomedicine to electronics.

Hexagonal close-packed array formed by selective adsorption onto hexagonal patterns

A patterned two-dimensional hexagonally ordered array of ferritin molecules, the outer surfaces of which had been genetically modified by titanium (Ti) specific binding peptides (minT1-LF), was realized in a self-assembling manner on a hexagonal Ti thin film island made on a silicon substrate. The optimum degree of order was realized at the pH with the maximum selectivity of minT1-LF adsorption on the Ti surface with respect to the silicon dioxide (SiO2) surface. Quartz crystal microbalance (QCM) measurement revealed that minT1-LF adsorbed onto the Ti surface strongly and irreversibly, but adsorbed onto the silicon dioxide surface weakly and reversibly. It was suggested that the concentration of minT1-LF on the Ti pattern promotes hexagonal close-packed ordering and axis aligning.

The characterization of a single discrete bionanodot for memory device applications

We investigated electronic properties of a biochemically synthesized cobalt oxide bionanodot (Co-BND) by means of scanning tunneling microscopy/spectroscopy (STM/STS) and Kelvin-probe force microscopy (KFM). Experimentally obtained I-V characteristics and numerically obtained dI/dV and (dI/dV)/(I/V) from I-V revealed the band gap energy, band position of valence and conduction band of the Co-BND. KFM observation shows that bias polarity dependent surface potential change after charge injection. The observed surface potential change indicates that the Co-BND has a charge storage capability. We demonstrated the application of Co-BNDs for electronic devices by choosing flash memory as the example device. The fabricated Co-BND embedded MOS memory showed clear memory operation due to the charge confinement in the embedded Co-BNDs.

Size-controlled one-pot synthesis of fluorescent cadmium sulfide semiconductor nanoparticles in an apoferritin cavity

A simple size-controlled synthesis of cadmium sulfide (CdS) nanoparticle (NP) cores in the cavity of apoferritin from horse spleen (HsAFr) was performed by a slow chemical reaction synthesis and a two-step synthesis protocol. We found that the CdS NP core synthesis was slow and that premature CdS NP cores were formed in the apoferritin cavity when the concentration of ammonia water was low. It was proven that the control of the ammonia water concentration can govern the CdS NP core synthesis and successfully produce size-controlled CdS NP cores with diameters from 4.7 to 7.1 nm with narrow size dispersion. X-ray powder diffraction (XRD), energy dispersive spectroscopy (EDS) analysis and high-resolution transmission electron microscopy (HR-TEM) observation characterized the CdS NP cores obtained as cubic polycrystalline NPs, which showed photoluminescence with red shifts depending on their diameters. From the research of CdS NP core synthesis in the recombinant apoferritins, the zeta potential of apoferritin is important for the biomineralization of CdS NP cores in the apoferritin cavity. These synthesized CdS NPs with different photoluminescence properties will be applicable in a wide variety of nano-applications.

Non-volatile flash memory with discrete bionanodot floating gate assembled by protein template

We demonstrated non-volatile flash memory fabrication by utilizing uniformly sized cobalt oxide (Co(3)O(4)) bionanodot (Co-BND) architecture assembled by a cage-shaped supramolecular protein template. A fabricated high-density Co-BND array was buried in a metal-oxide-semiconductor field-effect-transistor (MOSFET) structure to use as the charge storage node of a floating nanodot gate memory. We observed a clockwise hysteresis in the drain current-gate voltage characteristics of fabricated BND-embedded MOSFETs. Observed hysteresis obviously indicates a memory operation of Co-BND-embedded MOSFETs due to the charge confinement in the embedded BND and successful functioning of embedded BNDs as the charge storage nodes of the non-volatile flash memory. Fabricated Co-BND-embedded MOSFETs showed good memory properties such as wide memory windows, long charge retention and high tolerance to repeated write/erase operations. A new pathway for device fabrication by utilizing the versatile functionality of biomolecules is presented.

Bioprospecting in high temperature environments; application of thermostable protein cages

The first researchers to discover life in high temperature environments could not have anticipated the impact of their findings on the biotechnology industry. Today biotech companies benefit from multimillion dollar sales of enzymes originating from microorganisms that thrive in diverse high temperature environments. In this review we highlight significant advances made towards the development of self-assembling oligomeric protein cages from hyperthermophilic organisms as amenable platforms for diverse applications in biotechnology, electronics and medicine.

Realizing a two-dimensional ordered array of ferritin molecules directly on a solid surface utilizing carbonaceous material affinity peptides

A two-dimensional hexagonally close-packed (2D-HCP) array of ferritin molecules with a nanoparticle core was fabricated directly on a carbonaceous solid substrate by genetically modifying the outer surface of the ferritin with carbonaceous materials-specific binding peptides. The displayed peptides endowed ferritins with a specific protein-substrate interaction and masked the strong nonspecific interaction. The specific interaction was weak enough to allow ferritins to be rearranged as well as an attractive protein-protein interaction that could be adjusted by selecting the buffer conditions. This method not only produced 2D-HCP arrays of ferritin but also 2D-ordered arrays of independent inorganic nanoparticles after protein elimination that can be applied to floating gate memories.

Targeting of Cancer Cells with Ferrimagnetic Ferritin Cage Nanoparticles

Protein cage architectures such as virus capsids and ferritins are versatile nanoscale platforms amenable to both genetic and chemical modification. Incorporation of multiple functionalities within these nanometer-sized protein architectures demonstrate their potential to serve as functional nanomaterials with applications in medical imaging and therapy. In the present study, we synthesized an iron oxide (magnetite) nanoparticle within the interior cavity of a genetically engineered human H-chain ferritin (HFn). A cell-specific targeting peptide, RGD-4C which binds alphavbeta3 integrins upregulated on tumor vasculature, was genetically incorporated on the exterior surface of HFn. Both magnetite-containing and fluorescently labeled RGD4C-Fn cages bound C32 melanoma cells in vitro. Together these results demonstrate the capability of a genetically modified protein cage architecture to serve as a multifunctional nanoscale container for simultaneous iron oxide loading and cell-specific targeting.

Utilization of the Pleiotropy of a Peptidic Aptamer To Fabricate Heterogeneous Nanodot-Containing Multilayer Nanostructures

Peptide aptamers (=binders) against inorganic materials often show a capacity for mineralization of their target atoms; thus they are able to function both as binding molecules and as mediators for mineralization. Although the mechanisms underlying these two properties of peptide aptamers are not yet fully understood, they have been used separately to fabricate various nanostructures. Here, we present a novel method of nanofabrication, in which binding and mineralization by a peptide aptamer are alternately utilized to assemble multilayered nanostructures comprised of metal loaded cage proteins ornamented with Ti-binding peptides.