Diffusion-Limited Cargo Loading of an Engineered Protein Container

Towards controlling activity of a peptide asparaginyl ligase (PAL) by lumazine synthetase compartmentalization

Peptide asparaginyl ligases (PALs) hold significant potential in protein bioconjugation due to their excellent kinetic properties and broad substrate compatibility. However, realizing their full potential in biocatalytic applications requires precise control of their activity. Inspired by nature, we aimed to compartmentalize a representative PAL, OaAEP1-C247A, within protein containers to create artificial organelles with substrate sorting capability. Two encapsulation approaches were explored using engineered lumazine synthases (AaLS). The initial strategy involved tagging the PAL with a super-positively charged GFP(+36) for encapsulation into the super-negatively charged AaLS-13 variant, but it resulted in undesired truncation of the enzyme. The second approach involved genetic fusion of the OaAEP1-C247A with a circularly permutated AaLS variant (cpAaLS) and its co-production with AaLS-13, which successfully enabled compartmentalization of the PAL within a patch-work protein cage. Although the caged PAL retained its activity, it was significantly reduced compared to the free enzyme (∼30-40-fold), likely caused by issues related to OaAEP1-C247A stability and folding. Nevertheless, these findings demonstrated the feasibility of the AaLS encapsulation approach and encourage further optimization in the design of peptide-ligating artificial organelles in E. coli, aiming for a more effective and stable system for protein modifications.

Advancements of the Molecular Directed Design and Structure-Activity Relationship of Ferritin Nanocage

Ferritin nanocages possess remarkable structural properties and biological functions, making them highly attractive for applications in functional materials and biomedicine. This comprehensive review presents an overview of the molecular characteristics, extraction and identification of ferritin, ferritin receptors, as well as the advancements in the directional design of high-order assemblies of ferritin and the applications based on its unique structural properties. Specifically, this Review focuses on the regulation of ferritin assembly from one to three dimensions, leveraging the symmetry of ferritin and modifications on key interfaces. Furthermore, it discusses targeted delivery of nutrition and drugs through facile loading and functional modification of ferritin. The aim of this Review is to inspire the design of micro/nano functional materials using ferritin and the development of nanodelivery vehicles for nutritional fortification and disease treatment.

Exciplex Emission and Förster Resonance Energy Transfer in Polycyclic Aromatic Hydrocarbon-Based Bischromophoric Cyclophanes and Homo[2]catenanes

Energy transfer and exciplex emission are not only crucial photophysical processes in many living organisms but also important for the development of smart photonic materials. We report, herein, the rationally designed synthesis and characterization of two highly charged bischromophoric homo[2]catenanes and one cyclophane incorporating a combination of polycyclic aromatic hydrocarbons, i.e., anthracene, pyrene, and perylene, which are intrinsically capable of supporting energy transfer and exciplex formation. The possible coconformations of the homo[2]catenanes, on account of their dynamic behavior, have been probed by Density Functional Theory calculations. The unique photophysical properties of these exotic molecules have been explored by steady-state and time-resolved absorption and fluorescence spectroscopies. The tetracationic pyrene-perylene cyclophane system exhibits emission emanating from a highly efficient Förster resonance energy transfer (FRET) mechanism which occurs in 48 ps, while the octacationic homo[2]catenane displays a weak exciplex photoluminescence following extremely fast (<0.3 ps) exciplex formation. The in-depth fundamental understanding of these photophysical processes involved in the fluorescence of bischromophoric cyclophanes and homo[2]catenanes paves the way for their use in future bioapplications and photonic devices.

Tunable In Vivo Colocalization of Enzymes within P22 Capsid-Based Nanoreactors

Virus-like particles (VLPs) derived from bacteriophage P22 have been explored as biomimetic catalytic compartments. In vivo colocalization of enzymes within P22 VLPs uses sequential fusion to the scaffold protein, resulting in equimolar concentrations of enzyme monomers. However, control over enzyme stoichiometry, which has been shown to influence pathway flux, is key to realizing the full potential of P22 VLPs as artificial metabolons. We present a tunable strategy for stoichiometric control over in vivo co-encapsulation of P22 cargo proteins, verified for fluorescent protein cargo by Förster resonance energy transfer. This was then applied to a two-enzyme reaction cascade. l-homoalanine, an unnatural amino acid and chiral precursor to several drugs, can be synthesized from the readily available l-threonine by the sequential activity of threonine dehydratase and glutamate dehydrogenase. We found that the loading density of both enzymes influences their activity, with higher activity found at lower loading density implying an impact of molecular crowding on enzyme activity. Conversely, increasing overall loading density by increasing the amount of threonine dehydratase can increase activity from the rate-limiting glutamate dehydrogenase. This work demonstrates the in vivo colocalization of multiple heterologous cargo proteins in a P22-based nanoreactor and shows that controlled stoichiometry of individual enzymes in an enzymatic cascade is required for the optimal design of nanoscale biocatalytic compartments.

Bridging the Gap between Nonliving Matter and Cellular Life

A cell, the fundamental unit of life, contains the requisite blueprint information necessary to survive and to build tissues, organs, and systems, eventually forming a fully functional living creature. A slight structural alteration can result in data misprinting, throwing the entire life process off balance. Advances in synthetic biology and cell engineering enable the predictable redesign of biological systems to perform novel functions. Individual functions and fundamental processes at the core of the biology of cells can be investigated by employing a synthetically constrained micro or nanoreactor. However, constructing a life-like structure from nonliving building blocks remains a considerable challenge. Chemical compartments, cascade signaling, energy generation, growth, replication, and adaptation within micro or nanoreactors must be comparable with their biological counterparts. Although these reactors currently lack the power and behavioral sophistication of their biological equivalents, their interface with biological systems enables the development of hybrid solutions for real-world applications, such as therapeutic agents, biosensors, innovative materials, and biochemical microreactors. This review discusses the latest advances in cell membrane-engineered micro or nanoreactors, as well as the limitations associated with high-throughput preparation methods and biological applications for the real-time modulation of complex pathological states.

Engineered Nonviral Protein Cages Modified for MR Imaging

Diagnostic medical imaging utilizes magnetic resonance (MR) to provide anatomical, functional, and molecular information in a single scan. Nanoparticles are often labeled with Gd(III) complexes to amplify the MR signal of contrast agents (CAs) with large payloads and high proton relaxation efficiencies (relaxivity, r1). This study examined the MR performance of two structurally unique cages, AaLS-13 and OP, labeled with Gd(III). The cages have characteristics relevant for the development of theranostic platforms, including (i) well-defined structure, symmetry, and size; (ii) the amenability to extensive engineering; (iii) the adjustable loading of therapeutically relevant cargo molecules; (iv) high physical stability; and (v) facile manufacturing by microbial fermentation. The resulting conjugates showed significantly enhanced proton relaxivity (r1 = 11-18 mM-1 s-1 at 1.4 T) compared to the Gd(III) complex alone (r1 = 4 mM-1 s-1). Serum phantom images revealed 107% and 57% contrast enhancements for Gd(III)-labeled AaLS-13 and OP cages, respectively. Moreover, proton nuclear magnetic relaxation dispersion (1H NMRD) profiles showed maximum relaxivity values of 50 mM-1 s-1. Best-fit analyses of the 1H NMRD profiles attributed the high relaxivity of the Gd(III)-labeled cages to the slow molecular tumbling of the conjugates and restricted local motion of the conjugated Gd(III) complex.

Post-Assembly Modification of Protein Cages by Ubc9-Mediated Lysine Acylation

Although viruses have been successfully repurposed as vaccines, antibiotics, and anticancer therapeutics, they also raise concerns regarding genome integration and immunogenicity. Virus-like particles and non-viral protein cages represent a potentially safer alternative but often lack desired functionality. Here, we investigated the utility of a new enzymatic bioconjugation method, called lysine acylation using conjugating enzymes (LACE), to chemoenzymatically modify protein cages. We equipped two structurally distinct protein capsules with a LACE-reactive peptide tag and demonstrated their modification with diverse ligands. This modular approach combines the advantages of chemical conjugation and genetic fusion and allows for site-specific modification with recombinant proteins as well as synthetic peptides with facile control of the extent of labeling. This strategy has the potential to fine-tune protein containers of different shape and size by providing them with new properties that go beyond their biologically native functions.

How Pore Architecture Regulates the Function of Nanoscale Protein Compartments

Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.

Designing Stacked Assembly of Type III Rubisco for CO2 Fixation with Higher Efficiency

The slow catalytic rate of the carboxylation enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major barrier to increasing the rate of carbon assimilation from the atmosphere into the biosphere. It is of great importance to establish a method to improve the carboxylation efficiency of Rubisco. Inspired by the assembly of Rubisco in carboxysomes, herein, we presented a rational protein engineering approach for the construction of one-dimensional (1D) protein arrays of type III Rubisco through designed π-π stacking interactions by using crystal structural information as a guide. In aqueous solutions, the dimensions of these 1D protein arrays collectively span nearly the entire nano- and micrometer scale (200 nm to 5.0 μm) by adjusting protein and NaCl concentrations. As a result, the stacked Rubisco assemblies increase by 40% in the carboxylase activity, while their turnover number (k_cat) is around twofold larger than that of wild-type III Rubisco. Notably, upon heat treatment at temperature up to 75 °C for 30 min, most of the assembled nanostructures and the enzyme activity are retained. More importantly, the initial relative activity of stacked assemblies retained 91% after 10 cycles of reuse. This work provides a simple, effective solution for the improvement of the CO₂ carboxylation efficiency of Rubisco.

Rational design of engineered H-ferritin nanoparticles with improved siRNA delivery efficacy across an in vitro model of the mouse BBB

Gene therapy holds tremendous potential for the treatment of incurable brain diseases including Alzheimer's disease (AD), stroke, glioma, and Parkinson's disease. The main challenge is the lack of effective gene delivery systems traversing the blood-brain barrier (BBB), due to the complex microvessels present in the brain which restrict substances from the circulating blood passing through. Recently, increasing efforts have been made to develop promising gene carriers for brain-related disease therapies. One such development is the self-assembled heavy chain ferritin (HFn) nanoparticles (NPs). HFn NPs have a unique hollow spherical structure that can encapsulate nucleic acid drugs (NADs) and specifically bind to cancer cells and BBB endothelial cells (BBB ECs) via interactions with the transferrin receptor 1 (TfR1) overexpressed on their surfaces, which increases uptake through the BBB. However, the gene-loading capacity of HFn is restricted by its limited interior volume and negatively charged inner surface; therefore, these drawbacks have prompted the demand for strategies to remould the structure of HFn. In this work, we analyzed the three-dimensional (3D) structure of HFn using Chimera software (v 1.14) and developed a class of internally cationic HFn variants (HFn+ NPs) through arginine mutation on the lumenal surface of HFn. These HFn+ NPs presented powerful electrostatic forces in their cavities, and exhibited higher gene encapsulation efficacy than naive HFn. The top-performing candidate, HFn2, effectively delivered siRNA to glioma cells after traversing the BBB and achieved the highest silencing efficacy among HFn+ NPs. Overall, our findings demonstrate that HFn+ NPs obtained by this genetic engineering method provide critical insights into the future development of nucleic acid delivery carriers with BBB-crossing ability.

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.

Protein Cages: From Fundamentals to Advanced Applications

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

Chemically induced protein cage assembly with programmable opening and cargo release

Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.

Triggered Reversible Disassembly of an Engineered Protein Nanocage*

Protein nanocages play crucial roles in sub-cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to disassemble and reassemble on demand under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.

Bionanomaterials based on protein self-assembly: Design and applications in biotechnology

Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.

Thermal-triggered packing of lipophilic NIR dye IR780 in hepatitis B core at critical ionic strength and cargo-host ratio for improved stability and enhanced cancer phototherapy

Virus-like particles (VLPs) holding internal cavity with diameter from tens up to one hundred nanometers are attractive platform for drug delivery. Nevertheless, the packing of drugs in the nanocage mainly relies on complicated disassembly-reassembly process. In this study, hepatitis B core protein (HBc) VLPs which can withstand temperature up to 90 °C was employed as carrier to load a lipophilic near infrared dye IR780. It was found that an attaching-dis-atching-diffusing process was involved for the entering of IR780 in the cavity of HBc. The first two steps were associated with the electrostatic interactions between oppositely charged HBc and IR780, which was critically manipulated by ionic strength and HBc/IR780 mass ratio at which they were mixed; while the diffusion of IR780 across the shell of HBc showed a temperature-dependent manner that can be triggered by thermal induced pore-opening of the HBc capsid. At optimized condition, about 1055 IR780 molecules were encapsulated in each HBc by simply mixing them for 10 min at 60 °C. Compared with free IR780, the HBc-IR780 particles showed significantly improved aqueous and photostability, as well as enhanced photothermal and photodynamic performance for cancer therapy. This study provides a novel drug loading strategy and nanomemedicine for cancer phototherapies.

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.

Cell-Specific Delivery Using an Engineered Protein Nanocage

Nanoparticle-based delivery systems have shown great promise for theranostics and bioimaging on the laboratory scale due to favorable pharmacokinetics and biodistribution. In this study, we examine the utility of a cage-forming variant of the protein lumazine synthase, which was previously designed and evolved to encapsulate biomacromolecular cargo. Linking antibody-binding domains to the exterior of the cage enabled binding of targeting immunoglobulins and cell-specific uptake of encapsulated cargo. Protein nanocages displaying antibody-binding domains appear to be less immunogenic than their unmodified counterparts, but they also recruit serum antibodies that can mask the efficacy of the targeting antibody. Our study highlights the strengths and limitations of a common targeting strategy for practical nanoparticle-based delivery applications.

Redesign of protein nanocages: the way from 0D, 1D, 2D to 3D assembly

Compartmentalization is a hallmark of living systems. Through compartmentalization, ubiquitous protein nanocages such as viral capsids, ferritin, small heat shock proteins, and DNA-binding proteins from starved cells fulfill a variety of functions, while their shell-like structures hold great promise for various applications in the field of nanomedicine and nanotechnology. However, the number and structure of natural protein nanocages are limited, and these natural protein nanocages may not be suited for a given application, which might impede their further application as nanovehicles, biotemplates or building blocks. To overcome these shortcomings, different strategies have been developed by scientists to construct artificial protein nanocages, and 1D, 2D and 3D protein arrays with protein nanocages as building blocks through genetic and chemical modification to rival the size and functionality of natural protein nanocages. This review outlines the recent advances in the field of the design and construction of artificial protein nanocages and their assemblies with higher order, summarizes the strategies for creating the assembly of protein nanocages from zero-dimension to three dimensions, and introduces their corresponding applications in the preparation of nanomaterials, electrochemistry, and drug delivery. The review will highlight the roles of both the inter-subunit/intermolecular interactions at the key interface and the protein symmetry in constructing and controlling protein nanocage assemblies with different dimensions.

Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling

Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn-Cys-Leu recognition sequence with counterparts possessing an N-terminal Gly-Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys-Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins.

Protein cages and virus-like particles: from fundamental insight to biomimetic therapeutics

Protein cages (viral and non-viral) found in nature have evolved for a variety of purposes and are found in all kingdoms of life. The main functions of these nanoscale compartments are the protection and delivery of nucleic acids e.g. virus capsids, or the enrichment and sequestration of metabolons e.g. bacterial microcompartments. This review focuses on recent developments of protein cages for use in immunotherapy and therapeutic delivery. In doing so, we highlight the unique ways in which protein cages have informed on fundamental principles governing bio-nano interactions. With the enormous existing design space among naturally occurring protein cages, there is still much to learn from studying them as biomimetic particles.

Cytoplasmic glycoengineering enables biosynthesis of nanoscale glycoprotein assemblies

Glycosylation of proteins profoundly impacts their physical and biological properties. Yet our ability to engineer novel glycoprotein structures remains limited. Established bacterial glycoengineering platforms require secretion of the acceptor protein to the periplasmic space and preassembly of the oligosaccharide substrate as a lipid-linked precursor, limiting access to protein and glycan substrates respectively. Here, we circumvent these bottlenecks by developing a facile glycoengineering platform that operates in the bacterial cytoplasm. The Glycoli platform leverages a recently discovered site-specific polypeptide glycosyltransferase together with variable glycosyltransferase modules to synthesize defined glycans, of bacterial or mammalian origin, directly onto recombinant proteins in the E. coli cytoplasm. We exploit the cytoplasmic localization of this glycoengineering platform to generate a variety of multivalent glycostructures, including self-assembling nanomaterials bearing hundreds of copies of the glycan epitope. This work establishes cytoplasmic glycoengineering as a powerful platform for producing glycoprotein structures with diverse future biomedical applications.

Established bacterial glycoengineering platforms limit access to protein and glycan substrates. Here the authors design a cytoplasmic protein glycosylation system, Glycoli, to generate a variety of multivalent glycostructures.

Virus-Inspired Function in Engineered Protein Cages

The structural and functional diversity of proteins combined with their genetic programmability has made them indispensable modern materials. Well-defined, hollow protein capsules have proven to be particularly useful due to their ability to compartmentalize macromolecules and chemical processes. To this end, viral capsids are common scaffolds and have been successfully repurposed to produce a suite of practical protein-based nanotechnologies. Recently, the recapitulation of viromimetic function in protein cages of nonviral origin has emerged as a strategy to both complement physical studies of natural viruses and produce useful scaffolds for diverse applications. In this perspective, we review recent progress toward generation of virus-like behavior in nonviral protein cages through rational engineering and directed evolution. These artificial systems can aid our understanding of the emergence of viruses from existing cellular components, as well as provide alternative approaches to tackle current problems, and open up new opportunities, in medicine and biotechnology.

Tailoring enzyme microenvironment: State-of-the-art strategy to fulfill the quest for efficient bio-catalysis

Enzymes as green industrial biocatalysts have become a powerful norm that offers several advantages over traditional catalytic agents with regard to process efficiency, reusability, sustainability, and overall cost-effective ratio. However, enzymes obtained from natural origins are often engineered/tailored since their native forms do not fulfill the acute need for the industrial application. Revolutionary developments in protein engineering provide excellent opportunities for designing and constructing novel industrial biocatalysts with improved functional properties including catalytic activity, stability, substrate specificity, and reaction product inhibition. Momentum in enzyme immobilization has enabled robustness and optimal functions in extreme industrial environments, such as high temperature or organic solvents. The emergence of multi-enzyme catalytic cascade based on a combination of biocatalysts presents multifarious opportunities in biosynthesis, biocatalysis, and biotransformation. This review focuses on the emerging and state-of-the-art enzyme engineering trends and approaches to constructing innovative nano- and microstructured biocatalysts with enhanced catalytic activity and stability features requisite for industrial exploitation. Continuous key developments in this direction together with protein engineering in unique ways might offer ever-increasing opportunities for future biocatalysis-based industrial bioprocesses.

A protein-protein host-guest complex: Thermostable ferritin encapsulating positively supercharged green fluorescent protein

We characterize the encapsulation of supercharged green fluorescent protein, GFP(+36), by thermophilic ferritin from Archaeoglobus fulgidus (AfFtn). The AfFtn-GFP(+36) assembly is rapid, nearly stoichiometric, and robust. Using a more stably assembled mutant AfFtn, we show that encapsulation can occur in the presence of mostly assembled cages, in addition to encapsulation starting from AfFtn individual subunits. Assembly and encapsulation do not occur with non-supercharged GFP or the alternately supercharged GFP(-30), highlighting the role of complementary electrostatic interactions between the cargo and AfFtn cage interior. We also present a method for verifying protein-protein encapsulation, using nickel nitrilotriacetic acid agarose resin. AfFtn-supercharged protein host-guest complexes could find applications in enzyme studies, protein separations, and in vivo protein stabilization and targeted delivery.

Rational Engineering of a Designed Protein Cage for siRNA Delivery

Oligonucleotide therapeutics have transformative potential in modern medicine but are poor drug candidates in themselves unless fitted with compensatory carrier systems. We describe a simple approach to transform a designed porous protein cage into a nucleic acid delivery vehicle. By introducing arginine mutations to the lumenal surface, a positively supercharged capsule is created, which can encapsidate oligonucleotides in vitro with high binding affinity. We demonstrate that the siRNA-loaded cage is taken up by mammalian cells and releases its cargo to induce RNAi and knockdown gene expression. These general concepts could also be applied to alternative scaffold designs, expediting the development of artificial protein cages toward delivery applications.

Engineering enzyme microenvironments for enhanced biocatalysis

Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.

Programmable In Vitro Coencapsidation of Guest Proteins for Intracellular Delivery by Virus-like Particles

Bioinspired self-sorting and self-assembling systems using engineered versions of natural protein cages are being developed for biocatalysis and therapeutic delivery. The packaging and intracellular delivery of guest proteins is of particular interest for both in vitro and in vivo cell engineering. However, there is a lack of bionanotechnology platforms that combine programmable guest protein encapsidation with efficient intracellular uptake. We report a minimal peptide anchor for in vivo self-sorting of cargo-linked capsomeres of murine polyomavirus (MPyV) that enables controlled encapsidation of guest proteins by in vitro self-assembly. Using Förster resonance energy transfer, we demonstrate the flexibility in this system to support coencapsidation of multiple proteins. Complementing these ensemble measurements with single-particle analysis by super-resolution microscopy shows that the stochastic nature of coencapsidation is an overriding principle. This has implications for the design and deployment of both native and engineered self-sorting encapsulation systems and for the assembly of infectious virions. Taking advantage of the encoded affinity for sialic acids ubiquitously displayed on the surface of mammalian cells, we demonstrate the ability of self-assembled MPyV virus-like particles to mediate efficient delivery of guest proteins to the cytosol of primary human cells. This platform for programmable coencapsidation and efficient cytosolic delivery of complementary biomolecules therefore has enormous potential in cell engineering.

Bacterial encapsulins as orthogonal compartments for mammalian cell engineering

We genetically controlled compartmentalization in eukaryotic cells by heterologous expression of bacterial encapsulin shell and cargo proteins to engineer enclosed enzymatic reactions and size-constrained metal biomineralization. The shell protein (EncA) from Myxococcus xanthus auto-assembles into nanocompartments inside mammalian cells to which sets of native (EncB,C,D) and engineered cargo proteins self-target enabling localized bimolecular fluorescence and enzyme complementation. Encapsulation of the enzyme tyrosinase leads to the confinement of toxic melanin production for robust detection via multispectral optoacoustic tomography (MSOT). Co-expression of ferritin-like native cargo (EncB,C) results in efficient iron sequestration producing substantial contrast by magnetic resonance imaging (MRI) and allowing for magnetic cell sorting. The monodisperse, spherical, and iron-loading nanoshells are also excellent genetically encoded reporters for electron microscopy (EM). In general, eukaryotically expressed encapsulins enable cellular engineering of spatially confined multicomponent processes with versatile applications in multiscale molecular imaging, as well as intriguing implications for metabolic engineering and cellular therapy.

Artificial compartments have been expressed in prokaryotes and yeast, but similar capabilities have been missing for mammalian cell engineering. Here the authors use bacterial encapsulins to engineer genetically controlled multifunctional orthogonal compartments in mammalian cells.

Design of a confined environment using protein cages and crystals for the development of biohybrid materials

There is growing interest in the design of protein assemblies for use in materials science and bionanotechnology. Protein assemblies, such as cages and crystalline protein structures, provide confined chemical environments that allow immobilization of metal complexes, nanomaterials, and proteins by metal coordination, assembly/disassembly reactions, genetic manipulation and crystallization methods. Protein assembly composites can be used to prepare hybrid materials with catalytic, magnetic and optical properties for cellular applications due to their high stability, solubility and biocompatibility. In this feature article, we focus on the recent development of ferritin as the most promising molecular template protein cage and in vivo and in vitro engineering of protein crystals as solid protein materials with functional properties.

Diversification of Protein Cage Structure Using Circularly Permuted Subunits

Self-assembling protein cages are useful as nanoscale molecular containers for diverse applications in biotechnology and medicine. To expand the utility of such systems, there is considerable interest in customizing the structures of natural cage-forming proteins and designing new ones. Here we report that a circularly permuted variant of lumazine synthase, a cage-forming enzyme from Aquifex aeolicus (AaLS) affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein, cpAaLS, self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Moreover, cpAaLS proteins integrate into wild-type and other engineered AaLS assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments. This addition to the family of AaLS cages broadens the scope of this system for further applications and highlights the utility of circular permutation as a potentially general strategy for tailoring the properties of cage-forming proteins.

Substrate Sorting by a Supercharged Nanoreactor

Compartmentalization of proteases enables spatially and temporally controlled protein degradation in cells. Here we show that an engineered lumazine synthase protein cage, which possesses a negatively supercharged lumen, can exploit electrostatic effects to sort substrates for an encapsulated protease. This proteasome-like nanoreactor preferentially cleaves positively charged polypeptides over both anionic and zwitterionic substrates, inverting the inherent substrate specificity of the guest enzyme approximately 480 fold. Our results suggest that supercharged nanochambers could provide a simple and potentially general means of conferring substrate specificity to diverse encapsulated catalysts.

Tailoring lumazine synthase assemblies for bionanotechnology

The cage-forming protein lumazine synthase is readily modified, evolved and assembled with other components.

Enzyme Encapsulation in an Engineered Lumazine Synthase Protein Cage

The packaging of active enzymes in protein cages is a powerful strategy to control catalytic activity. Using a positively supercharged variant of green fluorescent protein, GFP(+36), as a genetically programmable tag, enzymes can be rapidly and quantitatively loaded into an engineered variant of the Aquifex aeolicus cage-forming protein lumazine synthase (AaLS-13) that possesses a negatively charged lumen. The cargo is spontaneously localized within AaLS-13 cages by simply mixing the components in aqueous solution. This chapter describes a detailed protocol for the preparation of AaLS-13 cages and GFP(+36)-enzyme fusions, as well as characterization of the inclusion complexes. Suitable conditions for encapsulation and enzyme kinetic assays are also discussed.

Overcoming the Incompatibility Challenge in Chemoenzymatic and Multi-Catalytic Cascade Reactions

Multi-catalytic cascade reactions bear a great potential to minimize downstream and purification steps, leading to a drastic reduction of the produced waste. In many examples, the compatibility of chemo- and biocatalytic steps could be easily achieved. Problems associated with the incompatibility of the catalysts and their reactions, however, are very frequent. Cascade-like reactions can hardly occur in this way. One possible solution to combine, in principle, incompatible chemo- and biocatalytic reactions is the defined control of the microenvironment by compartmentalization or scaffolding. Current methods for the control of the microenvironment of biocatalysts go far beyond classical enzyme immobilization and are thus believed to be very promising tools to overcome incompatibility issues and to facilitate the synthetic application of cascade reactions. In this Minireview, we will summarize recent synthetic examples of (chemo)enzymatic cascade reactions and outline promising methods for their spatial control either by using bio-derived or synthetic systems.

Decorating Self-Assembled Peptide Cages with Proteins

An ability to organize and encapsulate multiple active proteins into defined objects and spaces at the nanoscale has potential applications in biotechnology, nanotechnology, and synthetic biology. Previously, we have described the design, assembly, and characterization of peptide-based self-assembled cages (SAGEs). These ≈100 nm particles comprise thousands of copies of de novo designed peptide-based hubs that array into a hexagonal network and close to give caged structures. Here, we show that, when fused to the designed peptides, various natural proteins can be co-assembled into SAGE particles. We call these constructs pSAGE for protein-SAGE. These particles tolerate the incorporation of multiple copies of folded proteins fused to either the N or the C termini of the hubs, which modeling indicates form the external and internal surfaces of the particles, respectively. Up to 15% of the hubs can be functionalized without compromising the integrity of the pSAGEs. This corresponds to hundreds of copies giving mM local concentrations of protein in the particles. Moreover, and illustrating the modularity of the SAGE system, we show that multiple different proteins can be assembled simultaneously into the same particle. As the peptide-protein fusions are made via recombinant expression of synthetic genes, we envisage that pSAGE systems could be developed modularly to actively encapsulate or to present a wide variety of functional proteins, allowing them to be developed as nanoreactors through the immobilization of enzyme cascades or as vehicles for presenting whole antigenic proteins as synthetic vaccine platforms.

Modular interior loading and exterior decoration of a virus-like particle

Virus-like particles (VLPs) derived from the bacteriophage P22 offer an interesting and malleable platform for encapsulation and multivalent presentation of cargo molecules. The packaging of cargo in P22 VLP is typically achieved through genetically enabled directed in vivo encapsulation. However, this approach does not allow control over the packing density and composition of the encapsulated cargos. Here, we have adopted an in vitro assembly approach to gain control over cargo packaging in P22. The packaging was controlled by closely regulating the stoichiometric ratio of cargo-fused-scaffold protein and wild-type scaffold protein during the in vitro assembly. In a "one-pot assembly reaction" coat protein subunits were incubated with varied ratios of wild-type scaffold protein and cargo-fused-scaffold protein, which resulted in the encapsulation of both components in a co-assembled capsid. These experiments demonstrate that an input stoichiometry can be used to achieve controlled packaging of multiple cargos within the VLP. The porous nature of P22 allows the escape and re-entry of wild-type scaffold protein from the assembled capsid but scaffold protein fused to a protein-cargo cannot traverse the capsid shell due to the size of the cargo. This has allowed us to control and alter the packing density by selectively releasing wild-type scaffold protein from the co-assembled capsids. We have demonstrated these concepts in the P22 system using an encapsulated streptavidin protein and have shown its highly selective interaction with biotin or biotin derivatives. Additionally, this system can be used to encapsulate small molecules coupled to biotin, or display large proteins, that cannot enter the capsid and thus remain available for the multivalent display on the exterior of the capsid when attached to a flexible biotinylated linker. Thus, we have developed a P22 system with controlled protein cargo composition and packing density, to which both small and large molecules can be attached at high copy number on the interior or exterior of the capsid.

The C-terminal peptide of Aquifex aeolicus riboflavin synthase directs encapsulation of native and foreign guests by a cage-forming lumazine synthase

Encapsulation of specific enzymes in self-assembling protein cages is a hallmark of bacterial compartments that function as counterparts to eukaryotic organelles. The cage-forming enzyme lumazine synthase (LS) from Bacillus subtilis (BsLS), for example, encapsulates riboflavin synthase (BsRS), enabling channeling of lumazine from the site of its generation to the site of its conversion to vitamin B2 Elucidating the molecular mechanisms underlying the assembly of these supramolecular complexes could help inform new approaches for metabolic engineering, nanotechnology, and drug delivery. To that end, we investigated a thermostable LS from Aquifex aeolicus (AaLS) and found that it also forms cage complexes with the cognate riboflavin synthase (AaRS) when both proteins are co-produced in the cytosol of Escherichia coli A 12-amino acid-long peptide at the C terminus of AaRS serves as a specific localization sequence responsible for targeting the guest to the protein compartment. Sequence comparisons suggested that analogous peptide segments likely direct RS complexation by LS cages in other bacterial species. Covalent fusion of this peptide tag to heterologous guest molecules led to their internalization into AaLS assemblies both in vivo and in vitro, providing a firm foundation for creating tailored biomimetic nanocompartments for medical and biotechnological applications.

Structure and assembly of scalable porous protein cages

Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a ∼1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable ∼3-MDa and ∼6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.

Protein Nanoparticles as Multifunctional Biocatalysts and Health Assessment Sensors

The use of protein nanoparticles for biosensing, biocatalysis and drug delivery has exploded in the last few years. The ability of protein nanoparticles to self-assemble into predictable, monodisperse structures is of tremendous value. The unique properties of protein nanoparticles such as high stability, and biocompatibility, along with the potential to modify them led to development of novel bioengineering tools. Together, the ability to control the interior loading and external functionalities of protein nanoparticles makes them intriguing nanodevices. This review will focus on a number of recent examples of protein nanoparticles that have been engineered towards imparting the particles with biocatalytic or biosensing functionality.