Nanoreactors: Strategies to encapsulate enzyme biocatalysts in virus-like particles

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.

Column-free purification of an artificial protein nanocage, TIP60

Protein nanocages, which have inner cavities and surface pores, are attractive materials for various applications, such as in catalysts and medicine. Recently, we produced an artificial protein nanocage, TIP60, and demonstrated its potential as a stimuli-responsive nanocarrier. In the present study, we report a simple purification method for TIP60 that can replace time-consuming and costly affinity chromatography purification. TIP60, which has an anionic surface charge, aggregated at mildly acidic pH and redissolved at neutral pH, maintaining its cage structure. This pH-responsive reversible precipitation allowed us to purify TIP60 from soluble fractions of the E. coli cell lysate by controlling the pH. Compared with conventional Ni-NTA column purification, the pH-responsive precipitation method provided purified TIP60 with similar purity (∼80%) and higher yield. This precipitation purification method should facilitate the large-scale investigation and practical use of TIP60 nanocages.

Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production

Hydrogenases are microbial metalloenzymes capable of catalyzing the reversible interconversion between molecular hydrogen and protons with high efficiency, and have great potential in the development of new electrocatalysts for renewable fuel production. Here, we engineered the intact proteinaceous shell of the carboxysome, a self-assembling protein organelle for CO₂ fixation in cyanobacteria and proteobacteria, and sequestered heterologously produced [NiFe]-hydrogenases into the carboxysome shell. The protein-based hybrid catalyst produced in E. coli shows substantially improved hydrogen production under both aerobic and anaerobic conditions and enhanced material and functional robustness, compared to unencapsulated [NiFe]-hydrogenases. The catalytically functional nanoreactor as well as the self-assembling and encapsulation strategies provide a framework for engineering new bioinspired electrocatalysts to improve the sustainable production of fuels and chemicals in biotechnological and chemical applications.

Indoleamine 2,3 dioxygenase 1 immobilization on magnetic nanoparticles for screening inhibitors from coffee

In this study, a ligand fishing method was developed to screen potential indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors from coffee extracts by immobilization of IDO1 enzyme on amino-modified magnetic nanoparticles combined with UHPLC-Q-TOF-MS/MS analysis. Parameters including enzyme concentration, immobilization time, the pH of glutaraldehyde and the amount of magnetic nanoparticles were optimized. The results indicated that immobilized IDO1 could be reused 5 times and was stable during storage for 7 days. Several IDO1 ligands were captured by incubating immobilized IDO1 with coffee extract, of which 10 showed an obvious difference comparing to non-conjugated bare nanoparticles. In vitro inhibitory activity was further performed by CE analysis, in which ferulic acid and chlorogenic acid had better IDO1 inhibitory activity, with IC₅₀ value of 113.7 μM and 307.5 μM. These results demonstrate that this method provides an effective platform for identifying and screening IDO1 inhibitors from natural products.

Surface decorated reporter-tagged chikungunya virus-like particles for clinical diagnostics and identification of virus entry inhibitors

The ever-evolving and versatile VLP technology is becoming an increasingly popular area of science. This study presents surface decorated reporter-tagged VLPs of CHIKV, an enveloped RNA virus of the genus alphavirus and its applications. Western blot, IFA and live-cell imaging confirm the expression of reporter-tagged CHIK-VLPs from transfected HEK293Ts. CryoEM micrographs reveal particle diameter as ∼67nm and 56-70 nm, respectively, for NLuc CHIK-VLPs and mCherry CHIK-VLPs. Our study demonstrates that by exploiting NLuc CHIK-VLPs as a detector probe, robust ratiometric luminescence signal in CHIKV-positive sera compared to healthy controls can be achieved swiftly. Moreover, the potential activity of the Suramin drug as a CHIKV entry inhibitor has been validated through the reporter-tagged CHIK-VLPs. The results reported in this study open new avenues in the eVLPs domain and offer potential for large-scale screening of clinical samples and antiviral agents targeting entry of CHIKV and other alphaviruses.

Assembly of Protein Cages for Drug Delivery

Nanoparticles (NPs) have been widely used as target delivery vehicles for therapeutic goods; however, compared with inorganic and organic nanomaterials, protein nanomaterials have better biocompatibility and can self-assemble into highly ordered cage-like structures, which are more favorable for applications in targeted drug delivery. In this review, we concentrate on the typical protein cage nanoparticles drugs encapsulation processes, such as drug fusion expression, diffusion, electrostatic contact, covalent binding, and protein cage disassembly/recombination. The usage of protein cage nanoparticles in biomedicine is also briefly discussed. These materials can be utilized to transport small molecules, peptides, siRNA, and other medications for anti-tumor, contrast, etc.

Protein cargo encapsulation by virus‐like particles: Strategies and applications

Viruses and the recombinant protein cages assembled from their structural proteins, known as virus-like particles (VLPs), have gained wide interest as tools in biotechnology and nanotechnology. Detailed structural information and their amenability to genetic and chemical modification make them attractive systems for further engineering. This review describes the range of non-enveloped viruses that have been co-opted for heterologous protein cargo encapsulation and the strategies that have been developed to drive encapsulation. Spherical capsids of a range of sizes have been used as platforms for protein cargo encapsulation. Various approaches, based on native and non-native interactions between the cargo proteins and inner surface of VLP capsids, have been devised to drive encapsulation. Here, we outline the evolution of these approaches, discussing their benefits and limitations. Like the viruses from which they are derived, VLPs are of interest in both biomedical and materials applications. The encapsulation of protein cargo inside VLPs leads to numerous uses in both fundamental and applied biocatalysis and biomedicine, some of which are discussed herein. The applied science of protein-encapsulating VLPs is emerging as a research field with great potential. Developments in loading control, higher order assembly, and capsid optimization are poised to realize this potential in the near future. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Virus-like Particles: Fundamentals and Biomedical Applications

Nanotechnology is a fast-evolving field focused on fabricating nanoscale objects for industrial, cosmetic, and therapeutic applications. Virus-like particles (VLPs) are self-assembled nanoparticles whose intrinsic properties, such as heterogeneity, and highly ordered structural organization are exploited to prepare vaccines; imaging agents; construct nanobioreactors; cancer treatment approaches; or deliver drugs, genes, and enzymes. However, depending upon the intrinsic features of the native virus from which they are produced, the therapeutic performance of VLPs can vary. This review compiles the recent scientific literature about the fundamentals of VLPs with biomedical applications. We consulted different databases to present a general scenario about viruses and how VLPs are produced in eukaryotic and prokaryotic cell lines to entrap therapeutic cargo. Moreover, the structural classification, morphology, and methods to functionalize the surface of VLPs are discussed. Finally, different characterization techniques required to examine the size, charge, aggregation, and composition of VLPs are described.

Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors

Protein cages are attractive as molecular scaffolds for the fundamental study of enzymes and metabolons and for the creation of biocatalytic nanoreactors for in vitro and in vivo use. Virus-like particles (VLPs) such as those derived from the P22 bacteriophage capsid protein make versatile self-assembling protein cages and can be used to encapsulate a broad range of protein cargos. In vivo encapsulation of enzymes within VLPs requires fusion to the coat protein or a scaffold protein. However, the expression level, stability, and activity of cargo proteins can vary upon fusion. Moreover, it has been shown that molecular crowding of enzymes inside VLPs can affect their catalytic properties. Consequently, testing of numerous parameters is required for production of the most efficient nanoreactor for a given cargo enzyme. Here, we present a set of acceptor vectors that provide a quick and efficient way to build, test, and optimize cargo loading inside P22 VLPs. We prototyped the system using a yellow fluorescent protein and then applied it to mevalonate kinases (MKs), a key enzyme class in the industrially important terpene (isoprenoid) synthesis pathway. Different MKs required considerably different approaches to deliver maximal encapsulation as well as optimal kinetic parameters, demonstrating the value of being able to rapidly access a variety of encapsulation strategies. The vector system described here provides an approach to optimize cargo enzyme behavior in bespoke P22 nanoreactors. This will facilitate industrial applications as well as basic research on nanoreactor-cargo behavior.

Protein Mediated Enzyme Immobilization

Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.

Transport of Molecular Cargo by Interaction with Virus-Like Particle RNA

Virus-like particles (VLPs) derived from Leviviridae virions contain substantial amounts of cellular and plasmid-derived RNA. This encapsidated polynucleotide serves as a reservoir for the efficient binding of the intercalating dye thiazole orange (TO). Polyethylene glycol (PEG) molecules and oligopeptides of varying length, end-functionalized with TO, were loaded into VLPs up to approximately 50 % of the mass of the capsid protein (hundreds to thousands of cargo molecules per particle, depending on size). The kinetics of TO-PEG binding included a significant entropic cost for the reptation of long chains through the capsid pores. Cargo molecules were released over periods of 20-120 hours following simple reversible first-order kinetics in most cases. These observations define a simple general method for the noncovalent packaging, and subsequent release, of functional molecules inside nucleoprotein nanocages in a manner independent of modifications to the capsid protein.

Protein scaffolds: A tool for multi-enzyme assembly

The synthesis of complex molecules using multiple enzymes simultaneously in one reaction vessel has rapidly emerged as a new frontier in the field of bioprocess technology. However, operating different enzymes together in a single vessel limits their operational performance which needs to be addressed. With this respect, scaffolding proteins play an immense role in bringing different enzymes together in a specific manner. The scaffolding improves the catalytic performance, enzyme stability and provides an optimal micro-environment for biochemical reactions. This review describes the components of protein scaffolds, different ways of constructing a protein scaffold-based multi-enzyme complex, and their effects on enzyme kinetics. Moreover, different conjugation strategies viz; dockerin-cohesin interaction, SpyTag-SpyCatcher system, peptide linker-based ligation, affibody, and sortase-mediated ligation are discussed in detail. Various analytical and characterization tools that have enabled the development of these scaffolding strategies are also reviewed. Such mega-enzyme complexes promise wider applications in the field of biotechnology and bioengineering.

The Role of Virus-Like Particles in Medical Biotechnology

Virus-like particles (VLPs) are protein-based, nanoscale, self-assembling, cage architectures, which have relevant applications in biomedicine. They can be used for the development of vaccines, imaging approaches, drug and gene therapy delivery systems, and in vitro diagnostic methods. Today, three relevant viruses are targeted using VLP-based recombinant vaccines. VLP-based drug delivery, nanoreactors for therapy, and imaging systems are approaches under development with promising outcomes. Several VLP-based vaccines are under clinical evaluation. Herein, an updated view on the VLP-based biomedical applications is provided; advanced methods for the production, functionalization, and drug loading of VLPs are described, and perspectives for the field are identified.

Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production

Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.

The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.

Plant viral nanoparticles for packaging and in vivo delivery of bioactive cargos

Nanoparticles have unique capabilities and considerable promise for many different biological uses. One capability is delivering bioactive cargos to specific cells, tissues, or organisms. Depending on the task, there are multiple variables to consider including nanoparticle selection, targeting strategies, and incorporating cargo so it can be delivered in a biologically active form. One nanoparticle option, genetically controlled plant viral nanoparticles (PVNPs), is highly uniform within a given virus but quite variable between viruses with a broad range of useful properties. PVNPs are flexible and versatile tools for incorporating and delivering a wide range of small or large molecule cargos. Furthermore, PVNPs can be modified to create nanostructures that can solve problems in medical, environmental, and basic research. This review discusses the currently available techniques for delivering bioactive cargos with PVNPs and potential cargos that can be delivered with these strategies. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Assembly and Stability of Simian Virus 40 Polymorphs

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N = 12 pentamers (T = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The N = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a T = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing via the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.

Immobilization of lipase Eversa Transform 2.0 on poly(urea-urethane) nanoparticles obtained using a biopolyol from enzymatic glycerolysis

In this work, the free lipase Eversa^® Transform 2.0 was used as a catalyst for enzymatic glycerolysis reaction in a solvent-free system. The product was evaluated by nuclear magnetic resonance (¹H NMR) and showed high conversion related to hydroxyl groups. In sequence, the product of the glycerolysis was used as stabilizer and biopolyol for the synthesis of poly(urea-urethane) nanoparticles (PUU NPs) aqueous dispersion by the miniemulsion polymerization technique, without the use of a further surfactant in the system. Reactions resulted in stable dispersions of PUU NPs with an average diameter of 190 nm. After, the formation of the PUU NPs in the presence of concentrated lipase Eversa^® Transform 2.0 was studied, aiming the lipase immobilization on the NP surface, and a stable enzymatic derivative with diameters around 231 nm was obtained. The hydrolytic enzymatic activity was determined using ρ-nitrophenyl palmitate (ρ-NPP) and the immobilization was confirmed by morphological analysis using transmission electron microscopy and fluorescence microscopy.

Bioengineered Polyhydroxyalkanoates as Immobilized Enzyme Scaffolds for Industrial Applications

Enzymes function as biocatalysts and are extensively exploited in industrial applications. Immobilization of enzymes using support materials has been shown to improve enzyme properties, including stability and functionality in extreme conditions and recyclability in biocatalytic processing. This review focuses on the recent advances utilizing the design space of in vivo self-assembled polyhydroxyalkanoate (PHA) particles as biocatalyst immobilization scaffolds. Self-assembly of biologically active enzyme-coated PHA particles is a one-step in vivo production process, which avoids the costly and laborious in vitro chemical cross-linking of purified enzymes to separately produced support materials. The homogeneous orientation of enzymes densely coating PHA particles enhances the accessibility of catalytic sites, improving enzyme function. The PHA particle technology has been developed into a remarkable scaffolding platform for the design of cost-effective designer biocatalysts amenable toward robust industrial bioprocessing. In this review, the PHA particle technology will be compared to other biological supramolecular assembly-based technologies suitable for in vivo enzyme immobilization. Recent progress in the fabrication of biological particulate scaffolds using enzymes of industrial interest will be summarized. Additionally, we outline innovative approaches to overcome limitations of in vivo assembled PHA particles to enable fine-tuned immobilization of multiple enzymes to enhance performance in multi-step cascade reactions, such as those used in continuous flow bioprocessing.

Tuning the catalytic properties of P22 nanoreactors through compositional control

Enzymes are biomacromolecular protein catalysts that are widely used in a plethora of industrial-scale applications due to their high selectivity, efficiency and ability to work under mild conditions. Many industrial processes require the immobilization of enzymes to enhance their performance and stability. Encapsulation of enzymes in protein cages provides an excellent immobilization platform to create nanoreactors with enhanced enzymatic stability and desired catalytic activities. Here we show that the catalytic activity of nanoreactors, derived from the bacteriophage P22 viral capsids, can be finely-tuned by controlling the packaging stoichiometry and packing density of encapsulated enzymes. The packaging stoichiometry of the enzyme alcohol dehydrogenase (AdhD) was controlled by co-encapsulating it with wild-type scaffold protein (wtSP) at different stoichiometric ratios using an in vitro assembly approach and the packing density was controlled by selectively removing wtSP from the assembled nanoreactors. An inverse relationship was observed between the catalytic activity (k_cat) of AdhD enzyme and the concentration of co-encapsulated wtSP. Selective removal of the wtSP resulted in the similar activity of AdhD in all nanoreactors despite the difference in the volume occupied by enzymes inside nanoreactors, indicating that the AdhD enzymes do not experience self-crowding even under high molarity of confinement (M_conf) conditions. The approach demonstrated here not only allowed us to tailor the activity of encapsulated AdhD catalysts but also the overall functional output of nanoreactors (enzyme-VLP complex). The approach also allowed us to differentiate the effects of crowding and confinement on the functional properties of enzymes encapsulated in an enclosed system, which could pave the way for designing more efficient nanoreactors.

Encapsulation of Enzymes in Porous Capsules via Particle Templating

The entrapment of enzymes in capsules is a smart strategy to concentrate them in confined spaces and control their exposure to outside environments. Enzymes can be caged in the interior of capsules during their formation (preloading) or postloaded within prefabricated and permeable hollow shells. On the other hand, enzymes can also be deposited within the shell or on the surface of the capsules. Each of these strategies has intrinsic limitations, and a common enemy is the undesired desorption of enzymes.Here, we describe the formation of enzyme-loaded polymeric capsules prepared with the Layer-by-Layer method and the template-assisted entrapment of enzymes through coprecipitation (preloading) within calcium carbonate particles, as an example of an efficient preloading strategy, and draw attention at the key parameters that influence this immobilization method.

Bio-Catalysis and Biomedical Perspectives of Magnetic Nanoparticles as Versatile Carriers

In recent years, magnetic nanoparticles (MNPs) have gained increasing attention as versatile carriers because of their unique magnetic properties, biocatalytic functionalities, and capabilities to work at the cellular and molecular level of biological interactions. Moreover, owing to their exceptional functional properties, such as large surface area, large surface-to-volume ratio, and mobility and high mass transference, MNPs have been employed in several applications in different sectors such as supporting matrices for enzymes immobilization and controlled release of drugs in biomedicine. Unlike non-magnetic carriers, MNPs can be easily separated and recovered using an external magnetic field. In addition to their biocompatible microenvironment, the application of MNPs represents a remarkable green chemistry approach. Herein, we focused on state-of-the-art two majorly studied perspectives of MNPs as versatile carriers for (1) matrices for enzymes immobilization, and (2) matrices for controlled drug delivery. Specifically, from the applied perspectives of magnetic nanoparticles, a series of different applications with suitable examples are discussed in detail. The second half is focused on different metal-based magnetic nanoparticles and their exploitation for biomedical purposes.

Three-Dimensional Protein Cage Array Capable of Active Enzyme Capture and Artificial Chaperone Activity

Development of protein cages for encapsulation of active enzyme cargoes and their subsequent arrangement into a controllable three-dimensional array is highly desirable. However, cargo capture is typically challenging because of difficulties in achieving reversible assembly/disassembly of protein cages in mild conditions. Herein we show that by using an unusual ferritin cage protein that undergoes triggerable assembly under mild conditions, we can achieve reversible filling with protein cargoes including an active enzyme. We demonstrate that these filled cages can be arrayed in three-dimensional crystal lattices and have an additional chaperone-like effect, increasing both thermostability and enzymatic activity of the encapsulated enzyme.

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.