A chaperonin as protein nanoreactor for atom-transfer radical polymerization

Virus-like Particles Armored by an Endoskeleton

Many virus-like particles (VLPs) have good chemical, thermal, and mechanical stabilities compared to those of other biologics. However, their stability needs to be improved for the commercialization and use in translation of VLP-based materials. We developed an endoskeleton-armored strategy for enhancing VLP stability. Specifically, the VLPs of physalis mottle virus (PhMV) and Qβ were used to demonstrate this concept. We built an internal polymer "backbone" using a maleimide-PEG15-maleimide cross-linker to covalently interlink viral coat proteins inside the capsid cavity, while the native VLPs are held together by only noncovalent bonding between subunits. Endoskeleton-armored VLPs exhibited significantly improved thermal stability (95 °C for 15 min), increased resistance to denaturants (i.e., surfactants, pHs, chemical denaturants, and organic solvents), and enhanced mechanical performance. Single-molecule force spectroscopy demonstrated a 6-fold increase in rupture distance and a 1.9-fold increase in rupture force of endoskeleton-armored PhMV. Overall, this endoskeleton-armored strategy provides more opportunities for the development and applications of materials.

A Co(TAML)-based artificial metalloenzyme for asymmetric radical-type oxygen atom transfer catalysis

We show that the incorporation of a biotinylated Co(TAML) cofactor within streptavidin enables asymmetric radical-type oxygen atom transfer catalysis with improved activity and enantioselectivity.

Virus-like particles nanoreactors: from catalysis towards bio-applications

Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Artificial Organelles: Towards Adding or Restoring Intracellular Activity

Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.

Chaperonins: Nanocarriers with Biotechnological Applications

Chaperonins are molecular chaperones found in all kingdoms of life, and as such they assist in the folding of other proteins. Structurally, chaperonins are cylinders composed of two back-to-back rings, each of which is an oligomer of ~60-kDa proteins. Chaperonins are found in two main conformations, one in which the cavity is open and ready to recognise and trap unfolded client proteins, and a "closed" form in which folding takes place. The conspicuous properties of this structure (a cylinder containing a cavity that allows confinement) and the potential to control its closure and aperture have inspired a number of nanotechnological applications that will be described in this review.

Protein Nanobarrel for Integrating Chlorophyll a Molecules and Its Photochemical Performance

Taking inspiration from biology's effectiveness in nanoscale organization of chlorophylls for photosynthesis, we describe here a design for chlorophyll-protein conjugates that exploits the central hydrophobic cavity of GroEL protein nanobarrel as a binding pocket for chlorophyll. We found water-soluble conjugates of chlorophyll with GroEL could be easily generated via detergent dialysis. The number of chlorophyll units bound to GroEL is tunable by varying the equilibrium concentration of chlorophyll during dialysis. Meanwhile, it is shown that an increase in the entrapped chlorophyll amount leads to an improvement of chlorophyll-GroEL photostability. Using methyl viologen as an electron acceptor, we demonstrate that chlorophyll-GroEL has photoreduction activity, which is also switchable in on/off illumination mode. Finally, it is shown that chlorophyll-GroEL-sensitized solar cells have good photoelectric properties, yielding a high photoelectric conversion efficiency of ∼0.9%. The current strategy may be adopted for integrating other photosensitizing dyes or for other photocatalytic reactions.

Bioinspired Assembly of Double Honeycomb-Like Hierarchical Capsule Confined Encapsulation with Functional Micro/Nanocrystals

Inspired by "micro/nanoreactor" effect of cellular organelle on specific biochemical reactions, a double honeycomb-like hierarchical capsule confined encapsulation with functional micro/nanocrystals is designed. The bioinspired hierarchical capsules derived from polymeric composite microspheres are successfully fabricated through a combination of selective chemical etching and pyrolysis. In situ introduction of functional guests (including organometallic molecules, tetraethoxysilane, or metal-organic frameworks (MOFs)) into internal cellular structure of microspheres is first put forward by phase inversion method. The development of selective etching creates honeycomb-like structure on the outside surface of capsule and allows sulfur to homogeneously distribute into matrix. With the novel approach, the hierarchical channels (micro-meso-macropore) of composite capsule enhance transportation of reactants and dispersion of active sites, and thus exhibit superior photocatalytic oxidation and electromagnetic absorbing. The promising strategy will be applied more generally to encapsulate different species into hierarchical capsule with tailored properties and functionalities.

Nanoscale integration of porphyrin in GroEL protein cage: Photophysical and photochemical investigation

In this paper, we introduce a new type of functional, supramolecular porphyrin conjugate created using the bacterial GroEL protein cage based on non-specific hydrophobic interaction. The synthesis, structure and property of the porphyrin conjugate were characterized by dynamic light scattering, UV-vis spectroscopy and fluorescence spectroscopy. We observed that the model zinc-tetraphenylporphyrin (Zn-TPP) with high hydrophobicity can be well-dispersed in aqueous solutions with the aid of GroEL open chamber, which is known to be a favorable nanocompartment for aggregation-prone molecules. The maximal encapsulation efficiency of Zn-TPP in GroEL was determined to be ~98%. It is further seen that the constructed double Zn-TPP-GroEL complex exhibited good photocatalytic activity in the model reactions of the production of singlet oxygen and the reduction of methyl viologen under illumination with visible light. Moreover, we found that GroEL can significantly improve the photostability of Zn-TPP molecules as a result of nanoscale assembly within its hydrophobic chamber. Hence enhanced water solubility and photostability of Zn-TPP, which are considered as the first two hurdles for the wide usage of porphyrins, were achieved simultaneously by the development of GroEL cage as a building block. Supramolecular nanostructures formed from porphyrins (or related molecules) and GroEL for photocatalysis would greatly simplify applications of such structures.

Supramolecular Catalysis of m-Xylene Isomerization by Cucurbiturils: Transition State Stabilization, Vibrational Coupling, and Dynamic Binding Equilibrium

The ability of cucurbit[6]uril (CB6) and cucurbit[7]uril (CB7) to catalyze the thermally activated 1,2-methyl shift isomerization pathway of m-xylene in vacuum is investigated using infrequent metadynamics. CB6 is predicted to effectively and selectively catalyze the meta-to-para isomerization through stabilization of the transition state (TS) by van der Waals push (packing coefficient ≈74%), while inhibiting the meta-to-ortho pathway by molding effects of the cavity. Interestingly, despite the snug binding, a very low rate of host-guest vibrational energy transfer is revealed using a novel approach of host-guest partition of the mode-specific anharmonic relaxation rates and ab initio molecular dynamics. The weak vibrational coupling suggests that CB can act as a thermal buffer, possibly shielding encapsulated guests from outside vibrational perturbations such as solvent effects. This dynamic effect could provide an additional boost to the reaction rate by blocking the occurrence of reaction barrier recrossing caused by the friction with surrounding molecules. Finally, mean residence times of xylene into the hosts' cavity were estimated for a range of host-guest complexes, revealing a highly dynamic equilibrium allowing very high guest turnover rates that could minimize catalyst inhibition effects commonly suffered by other supramolecular catalysts.

Supramolecular Construction of Biohybrid Nanozymes Based on the Molecular Chaperone GroEL as a Promiscuous Scaffold

The study of enzymatic reactions in a confined space can provide valuable insight into the natural selection of nanocompartments for biocatalytic processes. Design of nanozyme capsules with the barrel-shaped protein cage of GroEL has been proposed as a promising means to constrain chemical reactions in a spatiotemporally controllable manner. Herein, we further demonstrate with hemin that the open GroEL cavity can provide a favorable microenvironment for shielding hydrophobic catalytically active species. Meanwhile, it is shown that the GroEL-caged hemin nanozyme not only has a significantly higher catalytic activity than merely dispersed hemin but also exhibits substrate specificity in the model oxidation reactions, which is a merit lacking in natural hemoproteins. To understand the underlying mechanism behind this supramolecular assembly, molecular docking and molecular dynamics simulations were performed to study the detailed interactions of hemin with the protein cage. This revealed the most likely binding mode and preferred binding residues in the paired hydrophobic α-helices lining the GroEL cavity which are genetically encoded for substrate capture. Finally, we demonstrate that the hemin-GroEL nanozyme has great potential in label-free fluorometric molecular detection when combined with suitable substrates such as homovanillic acid. We believe that our strategy is an advantageous tool for studying confined biocatalytic kinetics as simple mimics of protein-based organelles found in nature and for designing diverse nanozymes or bio-nanoreactors with the promiscuous GroEL binding cavity.

Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes

We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.

Functionalization of GroEL nanocages with hemin for label-free colorimetric assays

The design of functionalized protein nanocages as enzyme mimics is a relatively new and promising field as these biogenic nanocapsules are inherently monodisperse with precise architectures, unattainable by purely synthetic processes. This work explored the catalytic properties of the bacterial GroEL-nanocaged hemin and its performance in label-free colorimetric assays. It is demonstrated that the hemin-GroEL biohybrid has peroxidase-like activity and follows the typical Michaelis-Menten kinetics and ping-pong mechanism in the model sensing processes. The open nature and nanoreactor effect of the GroEL cage and the addition of ATP are shown to significantly influence the catalytic activity. For glucose detection with the hemin-GroEL complex, the linearity between the analyte concentration and UV-vis absorption was determined to range from 0 to 200 μM with a limit of detection (LOD) of ~ 12 μM under the defined conditions. In addition, the colorimetric detection of catechol led to a linear dynamic range of 0-120 μM with a LOD of ~ 17 μM. This indicates that the same assay could be used as a sensing platform for the detection or even oxidative removal of phenolic contaminants in the presence of H₂O₂. Thus, GroEL cage is a valuable tool for the development of nanozymes and practical applications such as clinical analysis and environmental monitoring.

Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis

The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.

Biocompatible Choline Iodide Catalysts for Green Living Radical Polymerization of Functional Polymers

Herein, nontoxic and metabolizable choline iodide analogues, including choline iodide, acetylcholine iodide, and butyrylcholine iodide, were successfully utilized as novel catalysts for "green" living radical polymerization (LRP). Through the combination of several green solvents (ethyl lactate, ethanol, and water), this green LRP process yielded low-polydispersity hydrophobic, hydrophilic, zwitterionic, and water-soluble biocompatible polymethacrylates and polyacrylates with high monomer conversions. Well-defined hydrophobic-hydrophilic and hydrophilic-hydrophilic block copolymers were also synthesized. The accessibility to a range of polymer designs is an attractive feature of this polymerization. The use of nontoxic choline iodide catalysts as well as green polymerization conditions can contribute to sustainable polymer chemistry.

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

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

Artificial Metalloenzymes: Reaction Scope and Optimization Strategies

The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.

Biocatalytic atom transfer radical polymerization in a protein cage nanoreactor

The ATRP-catalyzing enzyme horseradish peroxidase was encapsulated into the protein cage thermosome resulting in an all-protein nanoreactor system for controlled radical polymerizations.

Chaperonin-Dendrimer Conjugates for siRNA Delivery

The group II chaperonin thermosome (THS) is a hollow protein nanoparticle that can encapsulate macromolecular guests. Two large pores grant access to the interior of the protein cage. Poly(amidoamine) (PAMAM) is conjugated into THS to act as an anchor for small interfering RNA (siRNA), allowing to load the THS with therapeutic payload. THS-PAMAM protects siRNA from degradation by RNase A and traffics KIF11 and GAPDH siRNA into U87 cancer cells. By modification of the protein cage with the cell-penetrating peptide TAT, RNA interference is also induced in PC-3 cells. THS-PAMAM protein-polymer conjugates are therefore promising siRNA transfection reagents and greatly expand the scope of protein cages in drug delivery applications.

Combining Protein Cages and Polymers: from Understanding Self-Assembly to Functional Materials

Protein cages, such as viruses, are well-defined biological nanostructures which are highly symmetrical and monodisperse. They are found in various shapes and sizes and can encapsulate or template non-native materials. Furthermore, the proteins can be chemically or genetically modified giving them new properties. For these reasons, these protein structures have received increasing attention in the field of polymer-protein hybrid materials over the past years, however, advances are still to be made. This Viewpoint highlights the different ways polymers and protein cages or their subunits have been combined to understand self-assembly and create functional materials.

Molecular chaperones: functional mechanisms and nanotechnological applications

Molecular chaperones are a group of proteins that assist in protein homeostasis. They not only prevent protein misfolding and aggregation, but also target misfolded proteins for degradation. Despite differences in structure, all types of chaperones share a common general feature, a surface that recognizes and interacts with the misfolded protein. This and other, more specialized properties can be adapted for various nanotechnological purposes, by modification of the original biomolecules or by de novo design based on artificial structures.

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

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

Well-Defined Macromolecules Using Horseradish Peroxidase as a RAFT Initiase

Enzymatic catalysis and control over macromolecular architectures from reversible addition-fragmentation chain transfer polymerization (RAFT) are combined to give a new method of making polymers. Horseradish peroxidase (HRP) is used to catalytically generate radicals using hydrogen peroxide and acetylacetone as a mediator. RAFT is used to control the polymer structure. HRP catalyzed RAFT polymerization gives acrylate and acrylamide polymers with relatively narrow molecular weight distributions. The polymerization is rapid, typically exceeding 90% monomer conversion in 30 min. Complex macromolecular architectures including a block copolymer and a protein-polymer conjugate are synthesized using HRP to catalytically initiate RAFT polymerization.

Enzyme-mediated polymerization inside engineered protein cages

Engineered variants of the capsid-forming enzyme lumazine synthase, AaLS, were used as nanoreactors for an enzyme-mediated polymerization.

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

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

PMoA/MCM-41 catalyzed aza-Michael reaction: special effects of mesoporous nanoreactor on chemical equilibrium and reaction rate through surface energy transformation

Nanoreactors as catalysts can affect not only speed but also the chemical equilibrium of the reaction under investigation.