A self-assembled protein nanotube with high aspect ratio

Protein Nanotubes as Advanced Material Platforms and Delivery Systems

Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.

From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y

The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.

Artificial Protein Cages Assembled via Gold Coordination

Artificial protein cages made from multiple copies of a single protein can be produced such that they only assemble upon addition of a metal ion. Consequently, the ability to remove the metal ion triggers protein-cage disassembly. Controlling assembly and disassembly has many potential uses including cargo loading/unloading and hence drug delivery. TRAP-cage is an example of such a protein cage which assembles due to linear coordination bond formation with Au(I) which acts to bridge constituent proteins. Here we describe the method for production and purification of TRAP-cage.

Shape-Morphing of an Artificial Protein Cage with Unusual Geometry Induced by a Single Amino Acid Change

Artificial protein cages are constructed from multiple protein subunits. The interaction between the subunits, notably the angle formed between them, controls the geometry of the resulting cage. Here, using the artificial protein cage, “TRAP-cage”, we show that a simple alteration in the position of a single amino acid responsible for Au(I)-mediated subunit–subunit interactions in the constituent ring-shaped building blocks results in a more acute dihedral angle between them. In turn, this causes a dramatic shift in the structure from a 24-ring cage with an octahedral symmetry to a 20-ring cage with a C2 symmetry. This symmetry change is accompanied by a decrease in the number of Au(I)-mediated bonds between cysteines and a concomitant change in biophysical properties of the cage.

Artificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles

Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is triggered by gold nanoparticles. Using biochemical and biophysical methods we were able to determine both the mechanical properties and the gross compositional features of the cage which, combined with mathematical models and biophysical data, allowed the structure of the cage to be predicted. The accuracy of the overall geometrical prediction was confirmed by the cryo-EM structure determined to sub-5 Å resolution. This showed the cage to be nonregular but similar to a dodecahedron, being constructed from 12 11-membered rings. Surprisingly, the structure revealed that the cage also contained a single, small gold nanoparticle at each 3-fold axis meaning that each cage acts as a synthetic framework for regular arrangement of 20 gold nanoparticles in a three-dimensional lattice.

Protein Assembly by Design

Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

Artificial Protein Cage Delivers Active Protein Cargos to the Cell Interior

Artificial protein cages have potential as programmable, protective carriers of fragile macromolecules to cells. While natural cages and VLPs have been extensively exploited, the use of artificial cages to deliver active proteins to cells has not yet been shown. TRAP-cage is an artificial protein cage with an unusual geometry and extremely high stability, which can be triggered to break apart in the presence of cellular reducing agents. Here, we demonstrate that TRAP-cage can be filled with a protein cargo and decorated with a cell-penetrating peptide, allowing it to enter cells. Tracking of both the TRAP-cage and the cargo shows that the protein of interest can be successfully delivered intracellularly in the active form. These results provide a valuable proof of concept for the further development of TRAP-cage as a delivery platform.

Construction of Ultralarge Two-Dimensional Fluorescent Protein Arrays via a Reengineered Rhodamine B-Based Molecular Tool

The self-luminous property of enhanced green fluorescent protein (EGFP) makes it an extremely attractive building block for creating functional biomaterials. A practical challenge in the design of EGFP-based materials, however, stems from the structural and chemical heterogeneity of the EGFP surface. In this study, a maleimide-functionalized rhodamine B molecule (RhG₂M) was designed as a versatile molecular tool to overcome this obstacle. Site-specific modification of an EGFP variant (EGFP-4C) with RhG₂M allowed for the fabrication of a series of well-defined two-dimensional (2D) arrays that span nano- and micrometer scales. Furthermore, the resulting ultralarge 2D EGFP-4C arrays feature both structural uniformity and flexibility, together with the inherent optical properties, making them advanced materials with great potential for practical applications. In addition, this strategy can be further extended into three dimensions and applied to the modular generation of periodic functional materials with more complex structures.

Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology

Morpheeins are proteins that reversibly assemble into different oligomers, whose architectures are governed by conformational changes of the subunits. This property could be utilized in bionanotechnology where the building of nanometric and new high-ordered structures is required. By capitalizing on the adaptability of morpheeins to create patterned structures and exploiting their inborn affinity toward inorganic and living matter, “bottom-up” creation of nanostructures could be achieved using a single protein building block, which may be useful as such or as scaffolds for more complex materials. Peroxiredoxins represent the paradigm of a morpheein that can be applied to bionanotechnology. This review describes the structural and functional transitions that peroxiredoxins undergo to form high-order oligomers, e.g., rings, tubes, particles, and catenanes, and reports on the chemical and genetic engineering approaches to employ them in the generation of responsive nanostructures and nanodevices. The usefulness of the morpheeins’ behavior is emphasized, supporting their use in future applications.

Bioinspired Protein-Based Assembling: Toward Advanced Life-Like Behaviors

The ability of living organisms to perform structure, energy, and information-related processes for molecular self-assembly through compartmentalization and chemical transformation can possibly be mimicked via artificial cell models. Recent progress in the development of various types of functional microcompartmentalized ensembles that can imitate rudimentary aspects of living cells has refocused attention on the important question of how inanimate systems can transition into living matter. Hence, herein, the most recent advances in the construction of protein-bounded microcompartments (proteinosomes), which have been exploited as a versatile synthetic chassis for integrating a wide range of functional components and biochemical machineries, are critically summarized. The techniques developed for fabricating various types of proteinosomes are discussed, focusing on the significance of how chemical information, substance transportation, enzymatic-reaction-based metabolism, and self-organization can be integrated and recursively exploited in constructed ensembles. Therefore, proteinosomes capable of exhibiting gene-directed protein synthesis, modulated membrane permeability, spatially confined membrane-gated catalytic reaction, internalized cytoskeletal-like matrix assembly, on-demand compartmentalization, and predatory-like chemical communication in artificial cell communities are specially highlighted. These developments are expected to bridge the gap between materials science and life science, and offer a theoretical foundation for developing life-inspired assembled materials toward various applications.

Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design

Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.

Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry

A symmetric designer protein forms hybrid complexes with different polyoxometalates and may serve as a building block for porous frameworks.

Protein Nanotubes: From Bionanotech towards Medical Applications

Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within living organisms over millions of years. Among these are flagellin and pilin-based systems from bacteria, viral-based capsids, and eukaryotic microtubules and amyloids. While carbon nanotubes (CNTs), and protein/peptide-CNT composites, remain one of the most researched nanosystems due to their electrical and mechanical properties, there are many concerns regarding CNT toxicity and biodegradability. Therefore, proteins have emerged as useful biotemplates for nanomaterials due to their assembly under physiologically relevant conditions and ease of manipulation via protein engineering. This review aims to highlight some of the current research employing protein nanotubes (PNTs) for the development of molecular imaging biosensors, conducting wires for microelectronics, fuel cells, and drug delivery systems. The translational potential of PNTs is highlighted.

An ultra-stable gold-coordinated protein cage displaying reversible assembly

Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery¹, and have inspired synthetic biologists to create novel protein assemblies via the precise manipulation of protein-protein interfaces. Despite the impressive array of protein cages produced in the laboratory, the design of inducible assemblies remains challenging^2,3. Here we demonstrate an ultra-stable artificial protein cage, the assembly and disassembly of which can be controlled by metal coordination at the protein-protein interfaces. The addition of a gold (I)-triphenylphosphine compound to a cysteine-substituted, 11-mer protein ring triggers supramolecular self-assembly, which generates monodisperse cage structures with masses greater than 2 MDa. The geometry of these structures is based on the Archimedean snub cube and is, to our knowledge, unprecedented. Cryo-electron microscopy confirms that the assemblies are held together by 120 S-Auⁱ-S staples between the protein oligomers, and exist in two chiral forms. The cage shows extreme chemical and thermal stability, yet it readily disassembles upon exposure to reducing agents. As well as gold, mercury(II) is also found to enable formation of the protein cage. This work establishes an approach for linking protein components into robust, higher-order structures, and expands the design space available for supramolecular assemblies to include previously unexplored geometries.

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages

The self-assembly of proteins into higher order structures is ubiquitous in living systems. It is also an essential process for the bottom-up creation of novel molecular architectures and devices for synthetic biology. However, the complexity of protein–protein interaction surfaces makes it challenging to mimic natural assembly processes in artificial systems. Indeed, many successful computationally designed protein assemblies are prescreened for “designability”, limiting the choice of components. Here, we report a simple and pragmatic strategy to assemble chosen multisubunit proteins into more complex structures. A coiled-coil domain appended to one face of the pentameric cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular supra-molecular complexes. Analysis of a tubular structure determined by X-ray crystallography has revealed a hierarchical assembly process that displays features reminiscent of the polymorphic assembly of polyomavirus proteins. The approach provides a simple and straightforward method to direct the assembly of protein building blocks which present either termini on a single face of an oligomer. This scaffolding approach can be used to generate bespoke supramolecular assemblies of functional proteins. Additionally, structural resolution of the scaffolded assemblies highlight “native-state” forced protein–protein interfaces, which may prove useful as starting conformations for future computational design.

Self-assembly behavior of the keratose proteins extracted from oxidized Ovis aries wool fibers

Water soluble keratose proteins were obtained from an Ovis Aries wool using peracetic acid oxidation. The wool samples and the extracted keratose proteins were characterized by using FTIR, XRD, SEM and TGA techniques. Fractions of α-keratose (MW = 43-53 kDa) along with protein species with molecular weights between 23 kDa and 33 kDa were identified in the SDS-PAGE analysis result of the extracted protein mixture. DLS and AFM experiments indicated that self-assembled globular nanoparticles with diameters between 15 nm and 100 nm formed at 5 mg/ml keratose concentration. On the other hand, upon incubation of 10 w % keratose solutions at 37 °C and 50 °C, interconnected keratose hydrogels with respective storage modulus (G') values of 0.17 ± 0.03 kPa and 3.7 ± 0.5 kPa were obtained. It was shown that the keratose hydrogel prepared at 37 °C supported L929 mouse fibroblast cell proliferation which suggested that these keratose hydrogels could be promising candidates in soft tissue engineering applications.

Dual Functional Modification of Alkaline Amino Acids Induces the Self-Assembly of Cylinder-Like Tobacco Mosaic Virus Coat Proteins into Gear-Like Architectures

Herein, the assembly of 3D uniform gear-like architectures is demonstrated with a tobacco mosaic virus (TMV) disk as a building block. In this context, the intrinsic behavior of the TMV disk that promotes its assembly into nanotubes is altered by a synergistic effect of dual functional modifications at the 53rd arginine mutation and the introduction of lysine groups in the periphery at 1st and 158th positions of the TMV disk, which results in the formation of 3D gear-like superstructures. Therein, the 53rd arginine moiety significantly strengthens the linkage between TMV disks in the alkaline environment through hydrogen bond interactions. The charge of lysine-modified lateral surfaces is partially neutralized in the alkaline solution, which induces the TMV disk to form a gear-like architecture to maintain its structural stability by exploiting the electrostatic repulsion between neighboring TMV disks. This study not only provides explicit evidence regarding the molecular-level understanding of how the modification of site-specific amino acid affects the assembly of resultant superstructures but also encourages the fabrication of functional protein-based nanoarchitectures.

Template-Free Construction of Highly Ordered Monolayered Fluorescent Protein Nanosheets: A Bioinspired Artificial Light-Harvesting System

Using biological materials for light-harvesting applications has attracted considerable attention in recent years. Such materials provide excellent environmental compatibility and often exhibit superior properties over synthetic materials. Herein, inspired by the outstanding energy transfer performance in coelenterates, we constructed a template-free, highly ordered two-dimensional light-harvesting system by covalent-induced coassembly of EBFP2 (donor) and EGFP (acceptor), in which the fluorescent chromophores were well distributed and adopted a fixed orientation. By introducing approximate square planar binding sites on the side surface of protein, assembly pattern was pin down and self-assembly extended in orthogonal directions to achieve monolayered and tessellated protein nanoarrays. The excellent antiself-quenching property of fluorescent proteins endowed the coassembled system with attractive light-harvesting capability. Even at high local concentrations, a low resonance energy transfer self-quenching was observed and, therefore, energy can be efficiently transferred. More importantly, the distance between adjacent chromophores is continuously adjustable. By making minor changes to the length of the inducing linker, we have achieved significant control over the size of the assembly. A micron-sized light-harvesting system with satisfactory energy transfer efficiency was finally obtained. This work developed a template-free light-harvesting system completely based on fluorescent proteins (FPs), which overcame the restriction of using templates. Not limited to this work, the special core-shell structure of FPs may be expected to direct the optimization of fluorescent dyes by cladding.

Construction of supramolecular nanotubes from protein crystals

Investigations involving the design of protein assemblies for the development of biomaterials are receiving significant attention. In nature, proteins can be driven into assemblies frequently by various non-covalent interactions. Assembly of proteins into supramolecules can be conducted under limited conditions in solution. These factors force the assembly process into an equilibrium state with low stability. Here, we report a new method for preparing assemblies using protein crystals as non-equilibrium molecular scaffolds. Protein crystals provide an ideal environment with a highly ordered packing of subunits in which the supramolecular assembled structures are formed in the crystalline matrix. Based on this feature, we demonstrate the self-assembly of supramolecular nanotubes constructed from protein crystals triggered by co-oxidation with cross-linkers. The assembly of tubes is driven by the formation of disulfide bonds to retain the intermolecular interactions within each assembly in the crystalline matrix after dissolution of the crystals.

Controllable Assembly of Flexible Protein Nanotubes for Loading Multifunctional Modules

Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly of the capsid proteins (CPs) of filamentous viruses often requires the presence of DNA or RNA molecules, which has limited their applications. Here, we describe a strategy for controllable assembly of flexible bio-nanotubes consisting of Escherichia coli expressed CP of baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) in vitro. These protein-only nanotubes were studied as a new structural platform for high-density presentation of multiple active molecules on the exterior surface by direct fusion of the protein of interest to the N-terminus of HearNPV CP (HaCP). Structural characterization using cryoelectron microscopy demonstrated that the HaCP could assemble into two closely related but structurally distinct tube types, suggesting the tunable HaCP interaction network is the major contributor to the flexibility of HaCP nanotubes. Our flexible nanotubes could tolerate larger molecular modifications compared with TMV-based templates and could be used as promising candidates for versatile molecular loading applications.

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.

Assembling gold nanoparticles into flower-like structures by complementary base pairing of DNA molecules with mediation by apoferritins

Apoferritin caged gold nanoparticles (AuNPs) were assembled into flower-like structures by precise base pairing of the attached DNA molecules. The key step was to use the eight hydrophilic channels through the apoferritin to control the exact number and locations of the DNA molecules that grafted onto the caged AuNP.

Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures

Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.

Precise and Reversible Protein-Microtubule-Like Structure with Helicity Driven by Dual Supramolecular Interactions

Protein microtubule is a significant self-assembled architecture found in nature with crucial biological functions. However, mimicking protein microtubules with precise structure and controllable self-assembly behavior remains highly challenging. In this work, we demonstrate that by using dual supramolecular interactions from a series of well-designed ligands, i.e., protein-sugar interaction and π-π stacking, highly homogeneous protein microtubes were achieved from tetrameric soybean agglutinin without any chemical or biological modification. Using combined cryo-EM single-particle reconstruction and computational modeling, the accurate structure of protein microtube was determined. The helical protein microtube is consisted of three protofilaments, each of which features an array of soybean agglutinin tetramer linked by the designed ligands. Notably, the microtubes resemble the natural microtubules in their structural and dynamic features such as the shape and diameter and the controllable and reversible assembly behavior, among others. Furthermore, the protein microtubes showed an ability to enhance immune response, demonstrating its great potential for biological applications.

The construction of functional protein nanotubes by small molecule-induced self-assembly of cricoid proteins

Induced by small molecular ethylenediamine and “zero-length” covalent crosslinking, covalently crosslinked SeSP1 protein nanotubes with great GPx activity was fabricated.

Protein nanorings organized by poly(styrene-block-ethylene oxide) self-assembled thin films

This study explores the use of block copolymer self-assembly to organize Lsmα, a protein which forms stable doughnut-shaped heptameric structures. Here, we have explored the idea that 2-D crystalline arrays of protein filaments can be prepared by stacking doughnut shaped Lsmα protein into the poly(ethylene oxide) blocks of a hexagonal microphase-separated polystyrene-b-polyethylene oxide (PS-b-PEO) block copolymer. We were able to demonstrate the coordinated assembly of such a complex hierarchical nanostructure. The key to success was the choice of solvent systems and protein functionalization that achieved sufficient compatibility whilst still promoting assembly. Unambiguous characterisation of these structures is difficult; however AFM and TEM measurements confirmed that the protein was sequestered into the PEO blocks. The use of a protein that assembles into stackable doughnuts offers the possibility of assembling nanoscale optical, magnetic and electronic structures.

One ring (or two) to hold them all – on the structure and function of protein nanotubes

Understanding the structural determinants relevant to the formation of supramolecular assemblies of homo-oligomeric proteins is a traditional and central scope of structural biology. The knowledge thus gained is crucial both to infer their physiological function and to exploit their architecture for bionanomaterials design. Protein nanotubes made by one-dimensional arrays of homo-oligomers can be generated by either a commutative mechanism, yielding an 'open' structure (e.g. actin), or a noncommutative mechanism, whereby the final structure is formed by hierarchical self-assembly of intermediate 'closed' structures. Examples of the latter process are poorly described and the rules by which they assemble have not been unequivocally defined. We have collected and investigated examples of homo-oligomeric circular arrangements that form one-dimensional filaments of stacked rings by the noncommutative mechanism in vivo and in vitro. Based on their quaternary structure, circular arrangements of protein subunits can be subdivided into two groups that we term Rings of Dimers (e.g. peroxiredoxin and stable protein 1) and Dimers of Rings (e.g. thermosome/rosettasome), depending on the sub-structures that can be identified within the assembly (and, in some cases, populated in solution under selected experimental conditions). Structural analysis allowed us to identify the determinants by which ring-like molecular chaperones form filamentous-like assemblies and to formulate a novel hypothesis by which nanotube assembly, molecular chaperone activity and macromolecular crowding may be interconnected.

Probing structural dynamics of an artificial protein cage using high-speed atomic force microscopy

A cysteine-substituted mutant of the ring-shaped protein TRAP (trp-RNA binding attenuation protein) can be induced to self-assemble into large, monodisperse hollow spherical cages in the presence of 1.4 nm diameter gold nanoparticles. In this study we use high-speed atomic force microscopy (HS-AFM) to probe the dynamics of the structural changes related to TRAP interactions with the gold nanoparticle as well as the disassembly of the cage structure. The dynamic aggregation of TRAP protein in the presence of gold nanoparticles was observed, including oligomeric rearrangements, consistent with a role for gold in mediating intermolecular disulfide bond formation. We were also able to observe that the TRAP-cage is composed of multiple, closely packed TRAP rings in an apparently regular arrangement. A potential role for inter-ring disulfide bonds in forming the TRAP-cage was shown by the fact that ring-ring interactions were reversed upon the addition of reducing agent dithiothreitol. A dramatic disassembly of TRAP-cages was observed using HS-AFM after the addition of dithiothreitol. To the best of our knowledge, this is the first report to show direct high-resolution imaging of the disassembly process of a large protein complex in real time.

Controlled nanometric fibers of self-assembled designed protein scaffolds

The use of biological molecules as platforms for templating and nanofabrication is an emerging field. Here, we use designed protein building blocks based on small repetitive units (consensus tetratricopeptide repeat - CTPR) to generate fibrillar linear nanostructures by controlling the self-assembly properties of the units. We fully characterize the kinetics and thermodynamics of the assembly and describe the polymerization process by a simple model that captures the features of the structures formed under defined conditions. This work, together with previously established functionalization potential, sets up the basis for the application of these blocks in the fabrication and templating of complex hybrid nanostructures.

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.

Peptide nanotubes

The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.

Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties

The designed assembly of proteins into well-defined supramolecular architectures not only tests our understanding of protein-protein interactions, but it also provides an opportunity to tailor materials with new physical and chemical properties. Previously, we described that RIDC3, a designed variant of the monomeric electron transfer protein cytochrome cb562, could self-assemble through Zn(2+) coordination into uniform 1D nanotubes or 2D arrays with crystalline order. Here we show that these 1D and 2D RIDC3 assemblies display very high chemical stabilities owing to their metal-mediated frameworks, maintaining their structural order in ≥90% (vol/vol) of several polar organic solvents including tetrahydrofuran (THF) and isopropanol (iPrOH). In contrast, the unassembled RIDC3 monomers denature in ∼30% THF and 50% iPrOH, indicating that metal-mediated self-assembly also leads to considerable stabilization of the individual building blocks. The 1D and 2D RIDC3 assemblies are highly thermostable as well, remaining intact at up to ∼70 °C and ∼90 °C, respectively. The 1D nanotubes cleanly convert into the 2D arrays on heating above 70 °C, a rare example of a thermal crystalline-to-crystalline conversion in a biomolecular assembly. Finally, we demonstrate that the Zn-directed RIDC3 assemblies can be used to spatiotemporally control the templated growth of small Pt(0) nanocrystals. This emergent function is enabled by and absolutely dependent on both the supramolecular assembly of RIDC3 molecules (to form a periodically organized structural template) and their innate redox activities (to direct Pt(2+) reduction).

An engineered dimeric protein pore that spans adjacent lipid bilayers

The bottom-up construction of artificial tissues is an underexplored area of synthetic biology. An important challenge is communication between constituent compartments of the engineered tissue, and between the engineered tissue and additional compartments, including extracellular fluids, further engineered tissue and living cells. Here we present a dimeric transmembrane pore that can span two adjacent lipid bilayers, and thereby allow aqueous compartments to communicate. Two heptameric staphylococcal α-hemolysin pores were covalently linked in an aligned cap-to-cap orientation. The structure of the dimer, (α7)2, was confirmed by biochemical analysis, transmission electron microscopy and single-channel electrical recording. We show that one of two β-barrels of (α7)2 can insert into the lipid bilayer of a small unilamellar vesicle, while the other spans a planar lipid bilayer. The (α7)2 pores spanning two bilayers were also observed by transmission electron microscopy.

Fibril-mediated oligomerization of pilin-derived protein nanotubes

BACKGROUND

Self-assembling protein nanotubes (PNTs) are an intriguing alternative to carbon nanotubes for applications in bionanotechnology, in part due to greater inherent biocompatibility. The type IV pilus of the gram negative bacteria Pseudomonas aeruginosa is a protein-based fibre composed of a single subunit, the type IV pilin. Engineered pilin monomers from P. aeruginosa strain K122-4 (ΔK122) have been shown to oligomerize into PNTs both in solution and at surfaces. In order to fully exploit PNTs in bionanotechonological settings, an in-depth understanding of their assembly, physical characteristics and robustness, both in solution and when constrained to surfaces, is required.

RESULTS

This study details the effectiveness of multiple initiators of ΔK122-derived PNT oligomerization and characterize the formation of PNTs in solution. The optimal initiator for the oligomerization of ΔK122 in solution was observed to be 2-methyl-2,4-pentanediol (MPD). Conversely, larger PEG molecules do not trigger oligomerization. Multi-angle light scattering analysis indicates that the pilin protein exists in a monomer-dimer equilibrium in solution, and that an intermediate species forms within three hours that then coalesces over time into high molecular weight PNTs. Transmission Electron Microscopic analysis was used to observe the formation of oligomerized ΔK122 fibrils prior to assembly into full-length PNTs.

CONCLUSIONS

The oligomerization of ΔK122 pilin derived PNTs is a fibril mediated process. The optimal trigger for PNT oligomerization in solution is MPD, and the observation that PEGs do not induce oligomerization may enable the oligomerization of pilin-derived PNTs on PEG-functionalized surfaces for implantable bionanodevices.

ZnO nanowire array-templated LbL self-assembled polyelectrolyte nanotube arrays and application for charged drug delivery

Vertically oriented and robust polyelectrolyte nanotube arrays with high density, large area and high uniformity were successfully grown on substrates by a ZnO nanowire array-templated layer-by-layer (LbL) self-assembly approach for the first time, and were further used to deliver charged drugs, showing that they not only possess pH-responsive loading property, but also significantly enhance the loading capacity and sustained release time. This work could be extended to fabricate polyelectrolyte nanotube arrays with different polyelectrolyte combinations, including weak polyelectrolyte/weak polyelectrolyte, weak polyelectrolyte/strong polyelectrolyte and strong polyelectrolyte/strong polyelectrolyte. With the great versatility to use various substrates and building blocks, the polyelectrolyte nanotube arrays may have great potential for broad applications such as biosensor arrays, bioreactor arrays and optoelectronics.

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.

Pulsating tubules from noncovalent macrocycles

Despite recent advances in synthetic nanometer-scale tubular assembly, conferral of dynamic response characteristics to the tubules remains a challenge. Here, we report on supramolecular nanotubules that undergo a reversible contraction-expansion motion accompanied by an inversion of helical chirality. Bent-shaped aromatic amphiphiles self-assemble into hexameric macrocycles in aqueous solution, forming chiral tubules by spontaneous one-dimensional stacking with a mutual rotation in the same direction. The adjacent aromatic segments within the hexameric macrocycles reversibly slide along one another in response to external triggers, resulting in pulsating motions of the tubules accompanied by a chiral inversion. The aromatic interior of the self-assembled tubules encapsulates hydrophobic guests such as carbon-60 (C(60)). Using a thermal trigger, we could regulate the C(60)-C(60) interactions through the pulsating motion of the tubules.

Trp RNA-binding attenuation protein: modifying symmetry and stability of a circular oligomer

Background

Subunit number is amongst the most important structural parameters that determine size, symmetry and geometry of a circular protein oligomer. The L-tryptophan biosynthesis regulator, TRAP, present in several Bacilli, is a good model system for investigating determinants of the oligomeric state. A short segment of C-terminal residues defines whether TRAP forms an 11-mer or 12-mer assembly. To understand which oligomeric state is more stable, we examine the stability of several wild type and mutant TRAP proteins.

Methodology/Principal Findings

Among the wild type B. stearothermophilus, B. halodurans and B. subtilis TRAP, we find that the former is the most stable whilst the latter is the least. Thermal stability of all TRAP is shown to increase with L-tryptophan concentration. We also find that mutant TRAP molecules that are truncated at the C-terminus - and hence induced to form 12-mers, distinct from their 11-mer wild type counterparts - have increased melting temperatures. We show that the same effect can be achieved by a point mutation S72N at a subunit interface, which leads to exclusion of C-terminal residues from the interface. Our findings are supported by dye-based scanning fluorimetry, CD spectroscopy, and by crystal structure and mass spectrometry analysis of the B. subtilis S72N TRAP.

Conclusions/Significance

We conclude that the oligomeric state of a circular protein can be changed by introducing a point mutation at a subunit interface. Exclusion (or deletion) of the C-terminus from the subunit interface has a major impact on properties of TRAP oligomers, making them more stable, and we argue that the cause of these changes is the altered oligomeric state. The more stable TRAP oligomers could be used in potential applications of TRAP in bionanotechnology.