Protein Self-Assembly: Strategies and Applications
As intriguing biomacromolecules with a vast array of biodiversity and functions, proteins are well-known essential building blocks of organisms and participate in every process of cells such as metabolism, gene transcription and expression, stimuli response, and molecule transportation. However, virtually, organisms could systematically execute most important biological functions in the form of complex hierarchical complex hierarchical structures and collective properties of protein assembly. Therefore, the protein assemblies are compelling for scientists to not only understand the sophisticated, synergistic, and highly functional process of natural life but also provide a fascinating access to prepare advanced biomaterials. In decades, deep cognition of natural protein assemblies and complex has been made, which offers people a glimpse of the altruistic behaviors happen in nature and human bodies. In the meantime, there have been undergoing unexpected and rapid developments in protein assembly field using supramolecular interaction as driven forces, and various innovative design and strategies have been emerging to construct intriguing biomaterials. This chapter proposes to lead the reader to appreciate the splendid natural protein architecture, introduce the recent advances in the research field of protein assembly, and highlight several innovative design strategies for precise manipulation of proteins into extended, periodic arrays with desired morphologies and applications.
Proteins, the ubiquitous biomacromolecules in nature, constitute great numbers and most of biological composition or soft materials. Typical protein assemblies such as cellular cytoskeleton and muscles are built in a mild way via controlled assembling processes. Meanwhile, many protein-inorganic compounds, such as the hull and skeleton of animals, also demonstrate their fascinating architectures benefiting from the spontaneous organization: The assmbling process provide a structural scaffold while the mineral substrance combine with the ordered architecture, endowing the hybrid with high mechanical strength. Beside it can function well alone (enzyme, antibody, or serum albumin); proteins can also self-assemble into exquisite superstructures and undergo important cellular functions. Therefore, the protein assembling and resulting biomaterials attract more and more attention because of their unique defined structures and interesting functions. In biologic system, the assembling processes are usually driven by the multiple, weak noncovalent interactions, providing the protein-based biomaterials with dynamically reversible regulation for high performance and environmental adaptation. Based on the inspiration of the natural bottom-up strategies, people tempt to produce artificial protein assemblies with defined structures or interesting functions via designed noncovalent interactions.
The development of supramolecular chemistry is rapid and provides a great opportunity for scientists to construct novel supramolecular assemblies as functional biomaterials. Supramolecular assemblies based on small organic molecules have been designed and achieved with a wide variety of nanostructures and functions. The abundant driven supramolecular interactions usually endow the materials with promising properties such as processability, self-healing, recyclability, and stimuli responsiveness. Therefore, designing and utilizing supramolecular interactions seem as a powerful method to induce molecular aggregation. Although scientists have begun to fabricate protein assemblies via supramolecular interaction in decades, precise manipulation of protein self-assemblies is still a challenge. Compared with assemblies through the specific small-molecule recognition, the interactions and assembling mechanism of protein assemblies are more complicated due to the structural complexity, heterogeneity, and instability of protein molecules which may cause undesirable cross binding and confusion. Therefore, precisely controlling binding sites, orientation, and specificity of the complex proteins during assembling process is the key of constructing protein assemblies via supramolecular interactions.
The purpose of this chapter is to briefly introduce the field of protein self-assembly. The assembling mechanism, structures, function, and application of typical natural protein assemblies are first described to have an initial understanding of protein-based natural assembling. Then, several supramolecular strategies for precisely constructing protein assemblies with highly ordered hierarchical structures are reviewed. The mechanism of each supramolecular interaction is described, and some typical examples are represented from the aspects of design, modification, assembling process, and application. Finally, we summarize and prospect the further development of protein assembly. We hope this chapter could let the reader to appreciate the charm of protein self-assembly and the reviewed details could provide more inspiration for future design of protein assemblies as functional biomaterials.
Natural Protein Assemblies
Beside the virus, the protein assemblies are also found in the broad fields in the living systems, such as actin filaments, amyloid fibrils, protein cages (ferritin), and protein complex (molecular chaperones, antigen-antibody composite) (Fig. 1), which are indispensable in biological functions. In other words, exploring the interaction and principles of thesis protein assembly is an access to understanding the miracles of life and providing the inspiration for designing advanced biomaterials. Here, in this section, we introduce three representative natural protein assemblies in species: actin filaments, amyloid fibrils, and ferritin. These three protein assemblies have close relationship with the consist of muscles, neurodegenerative associated diseases, and storage/release of irons, respectively.
As units of actin filaments, the actin is ubiquitous and abundant in eukaryotic cells. Generally, the globular monomer (G-actin) would self-assemble into microfilaments (F-actin) which are important architecture blocks for construction of cytoskeleton and muscle cells. The growth of actin filaments provided the physical force and used to stabilize cellular structure and drive the transportation and motility process of cells. Besides, many cellular-associated proteins that regulate the poly-/depolymerization, nucleation, and cross-linking bind to actin and thereby execute their functions, revealing its vital role in species . The actin filament is a helical ribbon with two parallel strands that self-assembled from actin monomers, whose growth is regulated by the adenosine triphosphate (ATP) and adenosine diphosphate (ADP). The helical ribbon demonstrated about 8 nm width with a thickness of about 5 nm. The actin units were grown along the filament orientation and formed helical pitch of 36 nm . To our knowledge, there is no artificial helical protein assembly with two or single strands since now, so the assembling of actin filament is inspired for the construction of a helical biomaterial with low strands and high mechanical strength.
Based on the fascinating properties, people pay more attention on the potential applications and practical utilization of filaments. The high-protein assembly seems a perfect template for recruiting other proteins/functional components to prepare biomaterials. Willner and co-workers reported a methodology to synthesis conductive gold nanowires using the in vitro reproduced self-assembling filaments as template . Gold nanoparticles were first decorated on the filaments and subsequently disassociated via dialyzing off ATP to obtain Au NPs modified G-actin monomers. By controlling the reassembling order of modified/unmodified G-actin, the actin-based Au nanowire could locate in the middle or at the end of filaments. More compelling, when the actin-based Au nanowires were deposited on a surface coated with myosin (an ATP-triggered actin-binding motor protein can “walk” along the filaments), the nanowires could be mobilized on surface with addition of ATP, revealing their potential use as nanomotors/switches. Andreev and co-workers also report using the actin filaments as template to fabricate semiconductor nanowires. Based on the actin-myosin ATP-dependent nanomotors, the in vitro assembled filaments were also used for many applications. People have used it to transport single cells and prepared oriental nanomachine with heavy meromyosin (HMM)-modified silicon nanowires as support . There were other reports that the filaments, a fascinating candidate for construction of vesicles, demonstrated robust structure due to the mechanical stability of actin and were utilized as a drug delivery system.
Amyloid fibrils are also ubiquitous in nature and associated with some diseases. The amyloids often mean aggregates of proteins or peptides folded (always misfolded) into fibrils with many copies sticking together. It has been found that some of neurodegenerative diseases such as Parkinson’s, Alzheimer’s, Huntington’s, and Creutzfeldt-Jakob disease were caused by the assembling of amyloid proteins, which lose their intrinsic functions, form fibrous deposits, and thereby disrupt the healthy function of tissues and organs . However, recent research demonstrated that amyloid fibrils also play vital roles in many biological systems such as bacteria curli fibrils, yeast prions, and spider silks, revealing its meaningful function and universal proteinaceous materials for practical application .
The assembling of amyloid fibrils underwent a nucleation-growth mechanism. In detail, because of nonspecific oligomerization of peptides or misfolded proteins, the pre-fibrillar aggregates were transiently formed as a nucleation. Subsequently, it would “recruit” soluble proteins and peptides at the ends of fibril result in the elongation of amyloids. As a self-assembly, long amyloid fibrils can be completely generated from minutes to several weeks depending on the block sequence and incubation conditions. Although amyloids can be assembled reversibly in theory, however, within the general temperature, pH, and concentration range, formation of amyloids was mostly irreversible because of the high kinetic barriers and/or large thermodynamic driving forces during the self-polymerization process. Actually, some amyloids were unusually stable in morphology and architecture under the wide range ionic strength, temperature, pH, and mechanical stress and were even tolerant with proteolysis . Besides its stability, the amyloid fibrils explored remarkable mechanical traits. Due to the robust structure and multiple hydrogen bonds along fibrils, amyloids displayed highly mechanical strength with Young’s moduli from 0.1 up to 20 GPa. Meanwhile, the interaction between acid side chains of peptides and fibers thereby influences their bending rigidity . The excellent mechanical properties reveal the amyloid fibrils as promising biomaterials.
Recently, the aspects such as synthesis artificial amyloid fibrils and functionalization of amyloid fibrils were fast growing; the amyloid-based materials were attractive because not only of its fascinating stability and mechanical properties but also its biocompatibility and highly ordered structure. Inspired by its assembling mechanism, people have reported various artificial fibrils and hydrogels, which were wildly applied in biocompatible materials for cell adhesion/culture, drug release, and gene transfer. The amyloid fibrils were also compelling templates for construction of metal and semiconductor nanostructures. What is more, with certain electrical conductivity and bio-microenvironments, it demonstrated an excellent scaffold for high-density load of luminescence molecules or metalloporphyrins to produce biocompatible photonic antennae or catalytic nanozyme. The examples above suggested great promise for developing in broad application such as biocompatible materials, energy generation, gas capture, electronic devices, sensor, and artificial enzyme . Another important aim for researching amyloid fibrils is to understand the mechanism of neurodegenerative diseases caused by misfolding protein-based amyloid and how to relieve or avoid them. Based on the formation of amyloid fibrils in Alzheimer’s disease, Qu and co-workers synthesize a polyoxometalate (POM) for inhibiting Aβ aggregation of amyloid peptides . They also found that the transition metal-doped POM demonstrated better specific recognition for Aβ aggregation and repressed the oxidase ability of Aβ-hemin complex, exhibiting a better therapeutic effect. Better understanding of amyloid fibrils would provide people more idea for neurodegenerative diseases treatments.
As ubiquitous iron storage protein cages existed in many species, ferritin consists of conserved 24 protein subunits with 4 long ɑ-helices (helices A, B, C, and D) and 1 short ɑ-helix (helix E). The subunits are assembled into a spherical structure with 4-3-2 symmetry. The assembled ferritin demonstrated 12 nm spherical cage in diameter with an 8 nm hollow capacity and 2 nm thickness shell. In eukaryotes, ferritin is self-assembled with two or three kinds of subunits. The highly homologous subunits (L, M, and H) were named by their molecular weight: “Light” 20 kDa, “Middle” 21 kDa, and “Heavy” 22.8 kDa. In different species, the various homologous subunits underwent different functions; in eukaryotic cells, only H and M subunits could catalyze the oxidization of Fe(II), while in bacteria, each subunit of ferritin has the catalytic ability . It has been found that the ability of Fe(III) stored in the cavity of ferritin could decline oxidative stress and diseases such as Parkinson’s/Alzheimer’s disease and acquired immunodeficiency syndrome (AIDS). People have also found that the H-type ferritin demonstrated better association with cancer cells through TfR1-mediated binding, revealing further application such as tumor imaging or target delivery .
Notably, free Fe (II) would transfer an electron to molecular oxygen, resulting the reactive oxygen species (ROS) and Fe (III). Extra ROS usually damage cellular components, and Fe (III) may be precipitated as Fe (III) oxide species under physiological conditions (solubility 10–10 M), both of which were harmful for cells. Therefore, the most important effect of ferritin in cell is storage and release of redox iron to precisely control intracellular concentration of free Fe (II) and Fe (III), providing suitable oxygenic environment which organisms required for undergoing their function well . During the iron storage, Fe (II) were first oxidized at the ferroxidase sites in ferritin and the Fe (III) stored in the inner core. Three metal ion binding sites participate this process: two sites in the middle formed the dinuclear-metallic ferroxidase center, while the third metal ion binding site which is located close to the inner surface and ferroxidase center acted as a gateway for the ferroxidase center. The oxidation of Fe (II) is mediated by the pH value because the pH affects the Fe (II) binding with ferroxidase center significantly. Taking HuFn as example, when pH was 6.5, affinity between Fe (II) and ferroxidase center of HuFn is diminished . This pH-effected Fe (II) binding is possibly due to the coordination environment of histidine at ferroxidase center sites (Fig. 4b).
The easy preparation, outstanding stability, and immunized properties applied the ferritin a promising material such as drug delivery and biocatalysis. Inspired by its uniform protein cavity, the ferritin was used to synthesize nanoparticles with narrow distribution. The result hybrid demonstrated higher cellular uptaking efficiency and lower toxicity in the blood. Notably, nanoparticles were synthesized via two main methods, reduction of metal iron in its inner cavity or directly reassembling ferritin subunits around the nanoparticles or molecules for encapsulation. People have reported some works preparing Pd nanoparticles and Au/Pd nanoparticles by reduction of metal iron in the ferritin, which were used for oxidation of alcohols and hydrogenation of olefins, respectively. Other catalytic metal nanoparticles such as Ag and Au NPs were also synthesized via this strategy . Small molecules such as doxorubicin and gadolinium chelates could be encapsulated inside ferritin through another method, the pH-mediated ferritin disassociation and resembling. In this process the ferritin cage would be disassociated when pH is below 2 and reassembling via increasing pH back to 7 . The doxorubicin- and gadolinium chelate-loaded ferritin was used for killing tumor and NMR imaging. Meanwhile, modification of residues in-/outside of ferritin or fusing protein components suggests some novel technological applications. Recent study reported an enhanced vaccine with multivalent effect by fusing virus surface glycoprotein antigen to the N terminus of ferritin. Compared with traditional virus vaccine, the multivalent vaccine demonstrated more potent immune response . This strategy was also used to obtain nanozyme with high density of enzyme, thus improving the catalytic activity dramatically. Moreover, the study of construction of functional materials based on assembling of polymer-modified ferritin or changed ferritin cages has also been growing in decades; we would introduce some works in later chapters.
Strategies of Artificial Protein Assemblies
The natural protein assemblies seem a gigantic database of species on earth; the compelling structure and fascinating functions come from the natural process of evolution. The natural assembly-based materials have been applicable in many aspects such as electronic devices, sensors, medicine, and bio-functioned surfaces. The behavioral, structural, and functional properties of natural assemblies could own to the prepared materials with excellent abilities. Moreover, genetic and synthetic modifications to natural assemblies also demonstrated attractiveness because the artificial changes could improve the properties of the natural backbone on purpose. Therefore, understanding of natural protein assemblies and combination with modification and synthetic alterations provide highly interesting strategy for construction of novel material. In another approach, people have been trying to construct the artificial protein assemblies and materials by using “supramolecular interactions” as driven force. The structural and functional design could be realized in this bottom-up strategy which can meet the specific requirement of materials better.
The rapid growing of artificial protein assembly profited from the development of supramolecular chemistry since the 1990s. People could design and prepare functional materials according to the deeper understanding in the supramolecular chemistry and assembling principles of natural protein assemblies. At present, artificial protein assemblies with various dimensions and shapes such as cages, spheres, tubes, fibers, ribbons, and larger crystal arrays have been successfully realized through mediation of supramolecular interactions . Lots of supramolecular forces, such as hydrophobic interaction, Coulomb force, metal ion coordination, hydrogen bonding, pi-pi stacking, and van der Waals force, have been exploited and utilized to design and construct supramolecular assemblies. The obtained supramolecular assemblies demonstrated different properties and functions according to their individual-driven forces and different media. Meanwhile, on the amount of that, supramolecular interactions are usually reversible and adjustable; the resulting assemblies thereby exhibited some excellent traits such as facile fabrication, reversibility, reusability, self-healing, stimulus responsiveness, and self-adaptation . In decades, a large number of materials with regular morphology, self-repair, and biomimetic simulation properties have been emerging based on supramolecular interactions, highlighting the supramolecular assembly as a broad platform to fabricate functional materials and exhibiting a promising prospect. In this section, we would briefly introduce the several popular supramolecular chemical strategies for construction of artificial protein assemblies, e.g., illustrate the mechanism and properties of supramolecular interactions, and show some protein assemblies and materials with charming morphologies or functions in each field for readers.
With the rapid development of computer technology, people have made a great progress in designing protein-protein interaction-driven assembly. In the aid of computer technology and based on the protein assembly database, people begun to study and master the similar sequence and structure information of family proteins and polypeptides. Through computer docking and simulation, scientists can de novo design and screen amino acid sequences with shape complementarity and suitable surface interactions to construct simple and multidimensional assembly of biological macromolecules. Utilizing this principle, Professor Baker’s team designed and obtained large-scale two-dimensional protein superlattices in 2015 using symmetrical Rosette molecular docking technology . At the beginning, the cyclic protein oligomers are stacked in the layer by correcting the shared symmetry axis. Then the amino acid sequences between the oligomer contact surfaces are calculated to make sure the shape complementary and the lowest surface energy. Finally, Baker et al. selected three soluble sequences, P321, P4212, and P6, which did not produce a large number of inclusion bodies during expression and could assemble in vivo or in vitro. Experiments showed that all three designed proteins can form large-scale two-dimensional protein arrays via the designed protein-protein interactions and shape complementary. This indicates that computer simulation and surface design can be used to prepare two-dimensional protein lattices, and a feasible strategy for computer simulation and design of other advanced structures is proposed.
Peptide-Specific Binding-Mediated Assembly
As a shorter amino acid polymer than protein, peptides are abundant in nature and classified or categorized according to their sources and function. Peptides were interesting to scientist because of several reasons in molecular biology. (1) Peptides have certain immunogenicity; the respect peptide could allow people to create peptide antibodies without purifying interested protein. (2) The synthesis, identification, and sequencing are facile via instrumental equipment such as peptide synthesizer or mass spectrometry. (3) Peptides show as regulator in clinical research and treatment. Some peptides have been provided to inhibit cancer proteins and other diseases by binding to cell receptor. (4) As structural and functional segments/tags of protein, peptides have recently been used in the study of protein structure and function. Scientists utilize the peptides as probe to research and disassociate protein complexes. The polypeptide is more simple and stable than protein; some peptides have their own second structures (e.g., alpha helix, beta folding), functions, and specific binding ability; and sequence and secondary structure of peptides have important effects on the stability and geometric structure of the assembly. In decades, many peptide assemblies, for example, fibers, nanocages, lamellae, and so on, have been successively reported , which inspired people that the polypeptide-specific binding can be used to produce protein assemblies.
Many peptides/tags (coiled coil, amyloid peptides, spy tag, etc.) have been reported to mediate the assembling of proteins. In this section, we would briefly introduce some examples driven by the well-studied peptide motif, coiled coil. Coiled coil is a kind of important peptide accessory. It is a supercoil consisting of several seven-repeat polypeptides, sequenced as HPPHCPC, in which H means hydrophobic amino acid, P is polar amino acid, and C stands for point amino acid. The seven-repeat polypeptide is also named “abcdefg” according to its location . Several units of the hepta-peptides form a single strand of coiled coil. Because of the embedding hydrophobic amino acids at “a” and “d” sites and attracting amino acids at “e” and “g” sites, multiple strands of coiled coils twisted into superhelical oligomers in the complementary way of “knobs-in-holes.”
Besides for preparing polypeptide fibers, coiled coil can also be used to construct more fine structures such as nanocages, 2D layer, large nanocages, and vesicles through precise sequence design. For example, the Jerala group reported the tetrahedron cages  based on coiled-coil assembling. They synthesized a series of polypeptide containing 12 coiled-coil segments, between which were linked by a flexible Ser-Gly-Pro-Gly polypeptide. By matching different coiled-coil sequences and combining direction and arrangement, the polypeptide can be self-assembled into tetrahedral nanocages through specific match of the coiled-coil pairs. At the same time, Jerala et al. found that when designing the sequence of coiled-coil sequences, uniform curvature arrangement is conducive to a good pairing of polypeptides and a tight and stable structure. Woolfson and co-workers used coiled coil to prepare hollow nanocage . Two types of coiled coils, a triple symmetric CC-Tri and a double symmetric CC-Di, were covalently linked together through cysteine. The linked polypeptides were first assembled into oligomers via CC-Tri, and then the oligomers were subsequently assembled into cages through CC-Di interaction with a size of about 100 nm. By fusing the CC-Tri to N- or C-terminals of proteins, such as GFP protein or functional groups, protein can be assembled in the external surface or cavity of nanocage via CC-Tri and CC-Di twisting, producing nanocage with functional groups or immune response enhanced vaccine because of multivalent effect. This proved that nanocage can be used for modular encapsulation or external attachment of proteins with various functions, providing an approach in synthesizing nanoreactors or external antigen proteins to synthesize vaccines (Fig. 7b) by immobilizing cascade enzymes. It shows its rich prospects in biomedicine.
In addition to the rich nanostructures formed by coiled coil itself, coiled coil has also been applied in various aspects, such as assistant protein recognition or oligomer formation, protein or macromolecule immobilization, polymer gelation, vesicle fusion, etc. At first, people used natural coiled coil to make heterologous dimerization of different functional proteins. With the gradual understanding of coiled coil, people began to design coiled coil from scratch to meet the requirements. Brodsky et al. designed a trimeric coiled-coil sequence, which can be linked to the C- or N-terminal to effectively facilitate the assembly and rapid folding of recombinant bacterial collagen . Coiled coil could also be modified onto PEG chain, and gel was prepared by coiled-coil interaction.
Ghosh et al. reported using coiled coil as a linker. They attached the self-suppressed coiled-coil A–B with cleavage sites and the coiled coil B alone to the N and C parts of the luciferase (FLuc), respectively. Because of the splitting of the FLuc enzyme into two parts, it did not have enzymatic activity at this time. When the protease sheared the tobacco etch virus (TEV)-protease cleavage site of NFLuc coiled coil A–TEV-B, the formed NFLuc coiled coil A could recruit the CFLuc coiled coil B, enabling two parts to combine and perform luciferase catalytic capacity . This work demonstrates the application of coiled coil in the formation of functional complexes, and the formation of vesicles has application prospects in drug transport and release.
Coulomb Force Assembly
Coulomb force often refers to the interaction between changed substances, which is usually very strong and closely related to the polarity of the medium. As a medium for most protein assemblies, water is highly polar and can directly interact with changed groups, shielding the static electricity of changed moieties and remarkably weakening the attraction between charged substances. Besides medium, other conditions such as salt concentration also effected the stability of Coulomb interaction. Therefore, in order to obtain protein assembly mediated via Coulomb interaction in aqueous solutions, constructing of multivalent charges in substances or molecules for enhancing interaction and arranging charged groups in hydrophobic microenvironments to prevent the shielding effect of water molecules seem good strategies . Various protein assemblies and functional material have been reported in decades, revealing that Coulomb interaction is a powerful method of construction protein assembly.
The facile protein assemblies seem a good platform for construction of protein functional materials. Based on the efficient electrostatic force-mediated assembling strategy of prior work, replacing positive quantum dots with dendrimers modified with SOD functional groups and using Se-modified SP1 as the building blocks, Professor Liu’s team successfully obtained protein nanowires which have the synergistic antioxidant function of double enzymes . As the fifth-generation dendrimer of polyamide ammonia (PD5), the multiple amino groups on surface ensure PD5, a strong positively charged sphere with uniform size. Liu et al. covalently modified manganese porphyrins on PD5 (MnPD5), endowing MnPD5 the catalytic ability of SOD. Se-substituted SP1 (SeSP1) have been reported demonstrating natural GPx activity. Meanwhile, the diameter of MnPD5 is about 5.3 nm, which matches the size of SeSP1 (10 nm). The research shows that the obtained MnPD5-SeSPS1 nanowires have both activities of SOD and GPx. The two enzymes can synergistically and effectively reduce the damage such as mitochondrial swelling and lipid peroxidation caused by free radicals (Fig. 8b). At the same time, the protein assembly has almost no cytotoxicity, which provides a new idea for the preparation of biocompatible anti-free radical oxidation materials.
Metal Ion Coordination Assembly
The metal ion coordination was defined as metal complex consisting of metallic coordination center and surrounding bound molecules named as ligands or complexing agents. The ligands bonded to the center atom (metal ion) via coordinate covalent bond which the ligand atom donates lone electron pair electrons to the empty orbital of metal ions. Thus the metal ion coordination is a stable interaction. The metal ions can bond with ligands with different coordination number according to self-regulation of size, charge, and electron distribution of the metal ions and the ligands. Meanwhile, most metal-ligand complex forms ordered geometric structures followed the points-on-a-sphere pattern; in this principle, the geometries were regulated through orbital overlap and ligand-ligand repulsions. There were several spatial arrangements of coordination geometries, which were summarized as linear for two-coordination, trigonal planar for three-coordination, tetrahedral/square planar for four-coordination, trigonal bipyramidal/square pyramidal for five-coordination, octahedral (orthogonal) for six-coordination, pentagonal bipyramidal/capped octahedral/capped trigonal prismatic for seven-coordination, square antiprismatic/odecahedral/bicapped trigonal prismatic for eight-coordination, and tricapped trigonal prismatic/capped square antiprismatic for nine-coordination. The various geometries provided the multiforms of assemblies driven by this interaction. The metal coordination could be reversibly destroyed by chelating agents. It was also worth noting that, depending on the conditions, different dynamic, cis-trans, facial-meridional, and optical isomers could formed based on this reversible interaction and demonstrate quite distinct properties . According to the above traits, in decades, scientists have used the metal ion coordination to produce supramolecular assemblies, in which the protein assemblies occupy a certain proportion.
People begin to demonstrate attention to metal coordination for protein assembly because metal ion complexes are very common in biological systems. Many enzymes are activated by catalytic metals. In nature, the metal complexes also play an important role in stabilizing protein subunits and protein structures and participate in protein recognition, signal transduction, neurological diseases, and cell apoptosis . Recent studies found that the metal coordination could induce aggregation of Aβ peptides, which were stable and caused neurodegenerative diseases such as Alzheimer’s disease. Therefore, the metal ion coordination is an excellent driving force for inducing supramolecular assemblies. At present, small molecular oligomers, metal-organic frameworks, and even highly ordered protein assemblies driven by metal ions have been continuously explored and developed. What is more, corresponding assemblies have also been reported in applications such as catalytic production, gas adsorption, separation and storage, new energy sources and biomedicine, etc. revealing the metal coordination a powerful tool for construction of fine structures and functional materials.
Due to its strong force, reversibility, and special spatial structure, metal ion coordination has been proved not only to construct compelling assemblies based on small molecules but also a flexible strategy to induce high-order nanostructures of biological macromolecules, such as proteins. In natural protein system, amino acids such as histidine (His), cysteine (Cys), aspartic acid (Asp), and glutamic acid (Glu) demonstrated good affinity to cooperate with metal ions, so they are often used as bonding sites for metal ion-specific coordination. Tezcan et al. first reported a stable oligomer formed by mutant cytochrome c upon zinc ion coordination. Cytochrome cb562 (cyt cb562) is a C2-symmetric stable protein consisting of four-stranded helix, which is stable and suitable for site-directed mutation design without disrupting original structure. The mutant MBPC-1 was obtained by introducing two histidine chelating sites (His59/His63, His73/His77) by site-directed mutagenesis and used for self-assembling with metal coordination. The latter crystallographic data suggested that MBPC-1 protein can split joint with other MBPC-1 in the aid of Zn ion coordination, subsequently forming a stable quadruple dimer .
After using metal ions as driving force to obtain stable two-dimensional nanomaterials in vitro, people explored how to use this assembly strategy to achieve in situ assemblies in vivo. In 2014, Tezcan et al. reported the in situ assembly of Zn ions in vivo. By designing the surface interactions and coordination sites on cyt cb562 protein, Tezcan et al. obtained AB3 mutant protein through site-directed mutagenesis. The AB3 was proved to form stable tetramers in vitro with addition of Zn ion as designed. Then, AB3 protein was further tried in vivo system; when expressed in bacteria and added with zinc ions, AB3 protein self-assembled in vivo and formed a tetramer with hydrolase activity . During the assembling process, four zinc saturated complexes help to stabilize the structure of the oligomers, while the other four zinc unsaturated complexes serve as catalytic sites for hydrolytic enzymes. The obtained Zn8:(A104/G57 AB3)4 could catalyze the hydrolysis of ampicillin and endowed ampicillin resistance. This work revealed metal coordination-mediated assembling seems an interesting strategy for the construction of protein functional materials in vivo.
The concept of host-guest (HG) system begins with the discovery of acupoint ethers and crown ethers by Lehn, Cram, and Pedersen et al. and developed to a branch of supramolecular chemistry. Nowadays, host-guest was defined as complexes that consist of two or more molecules/ions that are aggregated together via molecular recognition and noncovalent interactions such as hydrogen bonds, ionic bonds, van der Waals forces, and hydrophobic interactions. The affinity between guest and host is always highly specific because of the specific noncovalent interactions, for instance, hydrogen bonds, thereby leading to molecular recognition, which demonstrates a promising strategy for construction of precisely assemblies. In the last two decades, macrocyclic molecules, such as crown ethers, cyclodextrins, and cucurbit[n]urils, have been synthesized in succession and investigated as host to drive or regular supramolecular assembling. Based on the specific recognition and inspiration of ordered supramolecular assemblies, host-guest interactions attracted much attentions of scientists and were investigated to construct synergistic and highly ordered protein assemblies. Among the macrocyclic molecules, cone-shaped cyclodextrins and pumpkin-shaped cucurbit[n]urils demonstrate great advantages when applied in water and biological system because of their aqueous solubility and high specificity, which seems a fascinating platform for guiding protein assembling . In this section, we would briefly introduce several examples of protein assemblies induced by host-guest interactions.
Brunsveld and co-workers first reported a work for dimerization of fluorescence protein via β-cyclodextrin (β-CD) and lithocholic acids (LAs). With cooperation of strong host-guest interaction and innate noncovalent interactions between dCFP and dYFP, stable heterodimers could have been formed by β-CD and LA interactions and protein interaction with high affinity (Kd = 4×10−7 M). Meanwhile, due to the dimerization and overlap between excitation and emission of dCFP and dYFP, the heterodimer demonstrated a good efficiency of FRET. This work inspired a development of biosensors through host-guest interaction with enhanced sensitivity via stabilizing the heterodimer . As a new-generation host molecule, cucurbit[n]urils have drawn lot of interests and been applied in assembling and functionalization once synthesized. By changing the numbers of glycoluril units, cucurbit[n]urils could specifically recognize guest molecular with various sizes through geometrical fitting and hydrophobic and ion-dipole interactions. Based on this idea, cucurbiturils (CB), as a versatile molecular recognition host which can drive aggregation of ternary complexes with guest molecules in aqueous solution, demonstrated an alternative strategy to mediate protein self-assembly and specific visualization of the protein dimerization. CB can specifically capsule various guest pairs such as methyl viologen (MV)-naphthalene (Np) and methyl viologen (MV)-trans-azobenzene (trans-azo). Among thesis guest pairs, motifs consisting of two tripeptide phenylalanine-glycine-glycine (FGG) were suitable for application in protein system because of its high affinity (K = 1.5 × 1011 M−2) and facile modification on protein N-termini through molecular biology technology. Brunsveld and co-workers thus investigated the dimerization of FGG-mCFP and FGG-mYFP guided by CB . With the titration of CB into a FGG-mYFP solution, a decline in fluorescence intensity suggested the occurrence of homo-FRET caused by typical supramolecular recognition process between CB and FGG-mYFP. Size-exclusion chromatography (SEC) measurements demonstrated the high stability of formed protein dimer, which can endure high dilution. Heterodimerization between FGG-mCFP and FGG-mYFP can also be formed via high selective binding between CB and FGG motifs, which was monitored by fluorescence analysis showing an increase of the peak ratio at 527/475 nm from 0.46 to 2.73. It is worth noting that despite the high stability of the binding pair, the heterodimerization of FGG-mCFP and FGG-mYFP can reversibly disassociate via adding competing guest methyl viologen molecules. The reversible heterodimerization and FRET suggested a great bioorthogonal approach for further biosensor of methyl viologen molecules. Meanwhile, a tetrameric complex of FGG-dYFPs and FGG-dCFPs was also formed via stable CB-FGG-based host-guest interactions and designed intrinsic interactions between FGG-dYFPs and FGG-dCFPs.
Beyond genetical fusion, Liu’s team investigated modification of the biocompatible FGG tripeptides onto the design location of protein via click chemistry of mercapto-maleimide, which is used to construct more controllable protein assembly . The maleimide-functionalized FGG was first synthesized, and GST variants were designed through point mutation, where amino acids of the location for maleimide-functionalized FGG were mutated into cysteine. The orientation of two cysteines was designed in a V shape to form an angel during the growth. The modified GST variant (sjGST-2FGG) assembled into nanorings mediated by the CB-FGG host-guest interactions. This work also found that, as a supramolecular chemistry, the morphologies of protein assemblies altered when changing their dynamic equilibrium via dialysis or addition of sjGST-2FGG monomers, which renders the equilibrium between nanorings and “gapped nanorings.” This process were investigated and monitored by AFM and TEM measurements; the CB/FGG complex could undergo a dynamic equilibrium between association and dissociation. The nanorings could cleave and associate with more free monomers, resulting in extending of nanoring from the cleaved tail (Fig. 12b). This work provided a more versatile strategy for construction of protein assembly using host-guest interaction; the modification demonstrated more maneuverable than genetically fusion, suggesting a possible direction for the construction of precisely controlled protein assembly system.
Much like the specific host-guest recognitions in artificial synthesis chemistry, there were lots of proteins that could stereospecifically and reversibly recognize their selective ligands through noncovalent interactions hydrogen bonds, van der Waals forces, hydrophobic interactions, etc. This protein-ligand interaction demonstrates high specificity, reversibility, and high affinity, which reveals to be precise, smart, and stable when this fascinating interaction was utilized to guide protein assembling. In decades, inspired by the compelling natural protein-ligand interactions, people applied strategies, for example, surface modification of ligands, synthesis of various functionalized ligands, and engineer of protein with different receptor domains, to construct protein assemblies which suggested controlled architecture or functional biomaterials. In this section, we introduce some works which utilized typical protein-ligand interaction to induce protein assemblies, exhibiting that it is a promising tool for producing fine nanostructures and functional materials.
Beyond modification of ligand molecules onto the surface of proteins, synthesis of artificial linker with multiple ligands molecules and engineer receptor protein were also promising strategy to construct protein assemblies. Using strong host-guest recognition between tetrahydrofolate reductase and methotrexate, Professor Wagner’s team reported a work that an engineered dimeric tetrahydrofolate reductase (DHFR) and synthesized bicephalic methotrexate (bis-MTX) self-assembled into protein nanostructures . The dimeric protein building block, ecDHFR2, was obtained through fusion of two dihydrofolate reductase molecules with a flexible peptide linker, and artificial ligand (bis-MTX-C9) was synthesized by addition of inhibitor molecules at two ends of linker with 9 C length. Toroid protein assembly was observed from TEM when bis-MTX was mixed with ecDHFR2. Moreover, the diameter of the nanorings could be tuned via adjusting the length of peptide linkers which affects flexibility between two intertetrahydrofolate reductase domains (Fig. 13a). The size alteration of nanorings was probably due to the distinct subtle balance between entropy and conformational dynamics when using different flexible ecDHFR2 as monomers. Wagner and co-workers also found that the catalytic efficiency of the protein nanorings was size-dependent, which reveals a way to regulate catalytic activity through precisely conformational operation.
Given the receptor-ligand interaction is highly specific, cooperation of receptor-ligand interactions and other supramolecular interactions in protein assembly system would demonstrate appeal advantages than direct protein self-assembly. The designed linker for the cooperation system was synthesized with two functional sections, one fraction containing the ligand molecules recognized with protein receptor while another part undergoing a specific combination according to supramolecular interaction. The cooperation induced protein-protein associations and realized achievement of highly selective and directional assemblies without any chemical or biological modification to protein building blocks. This novel strategy provides a convenient way to construct fine nanostructures through integration of orthogonal protein-ligand interaction and additional supramolecular interactions. Through combination of receptor-ligand interactions and metal coordination, Ward and co-workers obtained a hierarchical protein self-assembly. A divalent linker (Biot2-terpy) with two biotins and a metal coordination group, terpyridine was designed and synthesized. This Biot2-terpy linker and ferrous ions formed a coordination complex ([Fe(Biot2-terpy)2]2+) with ratio of 2:1. When adding streptavidin to the coordination complex solution, streptavidin recognized and bind the biotin tails of complex, thereby forming one-dimensional protein assemblies .
Though the origin is not fully understood, hydrophobic interactions in aqueous solution are mainly due to dominant nature of the hydrogen-bonding network that accommodates hydrophobic molecules. The hydrophobic and nonpolar molecules tend to aggregate and exhaust water molecules in aqueous, which process is traditionally considered to be entropy-driven. There exists large amount of dynamic hydrogen bonds between the liquid water molecules, forming a hydrogen-bonding network. When nonpolar region or molecules are introduced, water molecules fail to form hydrogen bonds with these nonpolar substrates. The surface of nonpolar substrates without polar water shield will disrupt the original hydrogen-bonding network between water molecules. For minimizing the disrupted hydrogen-bonding network, hydrogen binds are regulated on this surface, resulting in a water “cage” around the nonpolar substrates. However, the formation of static “cage” leads to the restricted mobility of water molecules and causes dramatic decline in translational and rotational entropy of water molecules, which process is unfavorable in entropy and Gibbs free energy. Therefore, to increase the disrupted entropy and proceed with the thermodynamic system in a more favorite way, hydrophobic and nonpolar molecules would reduce their exposed surface to minimize their disruptive effect via aggregating together and driving the self-assembling/aggregation of hydrophobic and nonpolar molecules in aqueous solution . When large hydrophobic molecular is introduced, the enthalpy reorientation plays more important role in driving aggregation as well as entropy. Therefore, hydrophobic effects are complexly depended on molecular surface area, shape, and solvent polarity. The large nonpolar surfaces always demonstrate strong hydrophobic interactions and form robust assemblies in aqueous solution. As an effective driving force in water, hydrophobic assembly strategy has also been well applied in protein-related assembly.
Besides artificial polymers like PNIPAM, natural hydrophobic fragments with stimuli response also attract people’s attention to produce protein assemblies. Elastin-like polypeptide (ELP) is a polypeptide which can switch its hydrophobicity from extended hydrophilic state to a crouched hydrophobic state with increasing temperature. Due to it is a natural polypeptide, ELP could be facilely added onto protein via genetic engineer. The resulting ELP-protein conjugates demonstrated innate biocompatibility and performed as “smart” building blocks for construction of protein assemblies via hydrophobic interactions, endowing them with wider potential for in vivo applications. Cornelissen and co-workers reported a stimuli-switched protein self-assembly system in which two distinguish assembling forms were governed by pH and temperature, respectively . First, ELP was fused to the capsid protein (CP) of cowpea chlorotic mottle viruses (CCMVs) to obtain a ELP-CP fusion protein. The resulting fused ELP-CPs can self-assemble into two kinds of well-defined nanostructures via assembling mechanisms of individual fractions: when ELP was soluble in water, the CP fraction of ELP-CPs can proceed and induced a reversible pH-dependent assembling of ELP-CPs as CCMV assembling. After generating dimers from CP, the dimeric aggregations (ELP-CP2) further assemble into relatively large virus-like particles (28 nm) at low pH (5.0) and can dissociate back into ELP-CP dimers when pH above 7.5. Meanwhile, when ELP section becomes insoluble at high temperature, ELP-CPs can also self-assemble into 18 nm nanocapsules by hydrophobic ELP moiety-mediated aggregation. According to the stimulus, the designed ELP-CPs can self-assemble into pH-induced 28 nm virus-like particles or ELP-mediated 18 nm nanocapsules (Fig. 15b), providing this platform a promising “smart” material for further in vivo application.
Schiller’s team designed a gene-encoded amphiphilic block fusion protein, which could assemble into a closed organelle-like capsule in vivo through hydrophobic-mediated assembling in E. coli cells . The genetic-engineered fusion proteins could modify with functional molecules through the incorporation of nonnatural amino acids. In detail, the sequences of hydrophilic block elements (E) and hydrophobic block elements (F) Schiller used are VPGEG and VPGFG, respectively. By arranging E20 block, F20 block, and single molecule green fluorescent protein (mEGFP), different assemblies were formed. Schiller and co-workers further discussed the effect of sequence on assemblies. MEGFP-E20-F20 can be well assembled into a closed cystic morphology similar to the organelle. Other arrangements of E20, F20, and mEGFP can also form thylakoids, indicating that their arrangement has little effect on assembly. Finally, the chemical functions of these organelles can be introduced by site-specific incorporation of azido-L-phenylalanine (pAzF) nonnatural amino acids. This makes it possible for the organelle-like organelles formed by polypeptide block protein units to be developed into intracellular nanoreactors.
Conclusion and Outlook
In this chapter, we aim to introduce natural and artificial protein assemblies to the readers. Typical natural protein assemblies and several supramolecular assembling strategies for constructing artificial protein nanostructure were reviewed and demonstrated their attractive function. In the first section, the self-assembling mechanisms of natural protein polymers with various morphologies and functions were described. Because of their facile preparation and repeatability, natural protein assemblies were fascinating scaffolds to functionalization and produced materials such as cellular adhesive materials, sensors, vesicles, bioimaging, and drug deliver. Afterward, based on understanding of natural protein assemblies and supramolecular chemistry, we briefly narrated main strategies for construction of artificial protein assemblies and functional materials. In summary, protein-protein interaction, peptide-specific binding, Coulomb force, metal ion coordination, host-guest interactions, protein-ligand interaction, and hydrophobic effects were described, and several examples were taken. By combining rational design, modification of protein, and external noncovalent supramolecular strategies, people have achieved protein assemblies from simple oligomers to the large-scaled protein polymers with highly ordered nanostructures such as 0D nanocages, 1D fibers and nanotubes, 2D layers or lattices, and 3D micellar morphologies and crystals. Compared with other assembling system, protein assembly demonstrated several fascinating advantages in materials and health-care aspects. Besides the incomparable biocompatibility, the abundant source of natural proteins with rich symmetries or functions could be utilized as building blocks to drive the programmable protein assemblies, revealing its limitless possibility in preparing biomaterials with various defined nanostructures and practical applicative functions. Meanwhile, benefiting from further understanding national protein assembling process, the mechanism has provided us a sight to fabricate and design novel proteins and superstructures in de novo on purpose based on computer simulation and protein-associated database and inspired us novel idea for treatments of diseases such as protein aggregation-related disorders in health-care field.
Despite having been developed in recent years, in our opinion, the protein assembling still needs more efforts in several main aspects: First, although extended strategies for design and construction of protein assemblies have been discovered and reported as we described above, exploration of mechanism and novel methodologies of different protein assemblies is an important research faction in this field yet. The discovery of mechanism and novel methodologies would broadly open new rules and theories for better understanding of natural protein assemblies and preparing novel protein assemblies. In addition, the next-generation protein assemblies tend to cooperate two or more biological and chemical strategies, endowing assemblies more properties and ultimately producing compelling novel biomaterials on purpose rather than mimicry. Second, the institutionalization of protein assemblies has become more and more attractive to scientists. To fabricate the functional materials, using supramolecular-induced protein assemblies is the final goal for practical applications. In decades, utilizing proteins with intrinsic properties as building blocks, modifying chemical functional groups on protein scaffolds, and creating sophisticated structural traits during the protein assembling process are the main optimal design strategies to obtain functionalized protein assemblies; catalytic, dynamic, stable, photoelectric, smart biomaterials, etc. have been explored. The further functionalization would be focus on more biological associated aspects. For example, the protein biomaterials perform communication with biologic systems, mimicking, participating in, and regulating original execution of life based on the statements of biologic systems on purpose. This would provide scientists more fascinating application for understanding life or treatments in health care. Third, in vivo assembling seems the best choice to directly execute the cellular functions. However, compared with assemblies in vitro, in vivo assembling demonstrates more challenges due to complicated cellular environments and its matters such as stability, reparative ability, pharmacokinetics, adverse host reactions, toxic effects, and biodegradation. Several works have demonstrated the enchantment of in vivo protein assembling which endow the novel properties for cell and attract the attentions of scientist. The goal of generating highly ordered protein assemblies with advanced functions and wide-ranging applications in a reliable, controlled, and reproducible way will constitute an important future challenge, which requires an intimate collaboration between scientists in various disciplines such as nanoscience, materials science, and chemical biology as well as structural and synthetic biology to support the rapid development of this highly interdisciplinary research field.
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