Protein scaffolds: A tool for multi-enzyme assembly

Exploiting SpyTag/SpyCatcher Technology to Design New Artificial Catalytic Copper Proteins

Designing artificial metal binding sites within a protein is challenging since amino acid residues need to be placed in desired positions in the final construct and the use of non-natural amino acids is difficult. The alternative approach of directing the insertion of artificial metal coordination systems presents the difficulty of grafting such site in a single desired position. Spy protein is composed of a protein component (SpyCatcher) which binds spontaneously an oligopeptide (SpyTag) with formation of an isopeptide bond. A SpyTag peptide equipped with an ATCUN (amino terminal copper and nickel) binding site is designed to bind copper(II) with high femtomolar affinity both in the absence of SpyCatcher and in the reconstituted Spy construct. The Cu2+ ATCUN site in the reconstituted Spy protein presents a catalytic activity in reactive oxygen species production, higher than that of the SpyTag peptide alone. This method offers a novel approach for constructing artificial metalloproteins by incorporating functional metal binding sites into a peptide, which can then be clicked onto its protein counterpart. The small size and modularity of this construct make it versatile for integration into other protein systems, eventually moving the complexity from a protein to a peptide and highlighting its potential for protein design.

Virus-like particle encapsulation of functional proteins: advances and applications

Proteins face several challenges in biomedicine, including issues with antibody production, degradation by proteases, rapid clearance by the kidneys, and short half-lives. To address these problems, various nano delivery systems have been developed, with virus-like particles (VLPs) emerging as a leading solution. VLPs, which are self-assembled protein complexes, offer effective encapsulation and transport of proteins. They provide enhanced stability, extended circulation time, preserved biological activity, improved targeting for therapies or imaging, and reduced side effects due to minimized systemic exposure. This review explores various methods for encapsulating proteins within VLPs. It assesses the benefits and limitations of each method and their applications in imaging, therapeutic enzyme delivery, vaccines, immunotherapy, nanoreactors, and biosensors. Future advancements in VLPs will depend on improving packaging methods, controlling protein loading, optimizing assembly techniques, and enhancing capsid design. The review also discusses current challenges and proposes solutions to advance the use of VLPs in various applications.

Porous protein crystals: synthesis and applications

Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.

Engineering bio-brick protein scaffolds for organizing enzyme assemblies

Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi-enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6-fold compared to free enzymes, with the covalent stapling outperforming the metal-driven assembly. This enhancement likely stems from higher-order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial-organizing tools, for more efficient enzymatic cascade reactions.

Hybrid Impedimetric Biosensors for Express Protein Markers Detection

Impedimetric biosensors represent a powerful and promising tool for studying and monitoring biological processes associated with proteins and can contribute to the development of new approaches in the diagnosis and treatment of diseases. The basic principles, analytical methods, and applications of hybrid impedimetric biosensors for express protein detection in biological fluids are described. The advantages of this type of biosensors, such as simplicity and speed of operation, sensitivity and selectivity of analysis, cost-effectiveness, and an ability to be integrated into hybrid microfluidic systems, are demonstrated. Current challenges and development prospects in this area are analyzed. They include (a) the selection of materials for electrodes and formation of nanostructures on their surface; (b) the development of efficient methods for biorecognition elements' deposition on the electrodes' surface, providing the specificity and sensitivity of biosensing; (c) the reducing of nonspecific binding and interference, which could affect specificity; (d) adapting biosensors to real samples and conditions of operation; (e) expanding the range of detected proteins; and, finally, (f) the development of biosensor integration into large microanalytical system technologies. This review could be useful for researchers working in the field of impedimetric biosensors for protein detection, as well as for those interested in the application of this type of biosensor in biomedical diagnostics.

Application of artificial scaffold systems in microbial metabolic engineering

In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.

Engineering of CYP82Y1, a cytochrome P450 monooxygenase: a key enzyme in noscapine biosynthesis in opium poppy

Protein engineering provides a powerful base for the circumvention of challenges tied with characteristics accountable for enzyme functions. CYP82Y1 introduces a hydroxyl group (-OH) into C1 of N-methylcanadine as the substrate to yield 1-hydroxy-N-methylcanadine. This chemical process has been found to be the gateway to noscapine biosynthesis. Owning to the importance of CYP82Y1 in this biosynthetic pathway, it has been selected as a target for enzyme engineering. The insertion of tags to the N- and C-terminal of CYP82Y1 was assessed for their efficiencies for improvement of the physiological performances of CYP82Y1. Although these attempts achieved some positive results, further strategies are required to dramatically enhance the CYP82Y1 activity. Here methods that have been adopted to achieve a functionally improved CYP82Y1 will be reviewed. In addition, the possibility of recruitment of other techniques having not yet been implemented in CYP82Y1 engineering, including the substitution of the residues located in the substrate recognition site, formation of the synthetic fusion proteins, and construction of the artificial lipid-based scaffold will be discussed. Given the fact that the pace of noscapine synthesis is constrained by the CYP82Y1-catalyzing step, the methods proposed here are capable of accelerating the rate of reaction performed by CYP82Y1 through improving its properties, resulting in the enhancement of noscapine accumulation.

Non-Immunoglobulin Synthetic Binding Proteins for Oncology

Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.

The increased efficiency of porphyran hydrolysis by constructing a multifunctional enzyme complex from marine microorganisms

Porphyran, a polysaccharide composed of red algae, is a source of a multifunctional oligosaccharide material and raw biomass with various physiological activities. The glycolysis of porphyrans into oligosaccharides through various porphyranases is an approach for obtaining high-quality and promising alternative resources. In this study, porphyran was extracted from Porphyra yezoensis and used as a research substrate. We also established an efficient hydrolysis method using an enzymatic complex obtained through cohesin-dockerin interactions that degrade natural polysaccharides. The cohesion-dockerin interaction is designed to genetically bind the dockerin module to the end of an existing enzyme and then attach the cohesin module to obtain a protein complex. The designed protein complex has been shown to further increase the activity on the substrate, which can be considered a useful method to obtain efficient oligosaccharides or monosaccharides through hydrolysis of red algae for bioresources.

Assembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding

Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.

Synthetic Multienzyme Assemblies for Natural Product Biosynthesis

In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.

A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates

BACKGROUND

Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps.

RESULTS

We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures.

CONCLUSIONS

We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.

Synthesis of Novel Polymer-Assisted Organic-Inorganic Hybrid Nanoflowers and Their Application in Cascade Biocatalysis

This study reports on the synthesis of novel bienzyme polymer-assisted nanoflower complexes (PANF), their morphological and structural characterization, and their effectiveness as cascade biocatalysts. First, highly porous polyamide 6 microparticles (PA6 MP) are synthesized by activated anionic polymerization in solution. Second, the PA6 MP are used as carriers for hybrid bienzyme assemblies comprising glucose oxidase (GOx) and horseradish peroxidase (HRP). Thus, four PANF complexes with different co-localization and compartmentalization of the two enzymes are prepared. In samples NF GH/PA and NF GH@PA, both enzymes are localized within the same hybrid flowerlike organic-inorganic nanostructures (NF), the difference being in the way the PA6 MP are assembled with NF. In samples NF G/PAiH and NF G@PAiH, only GOx is located in the NF, while HRP is preliminary immobilized on PA6 MP. The morphology and the structure of the four PANF complexes have been studied by microscopy, spectroscopy, and synchrotron X-ray techniques. The catalytic activity of the four PANF was assessed by a two-step cascade reaction of glucose oxidation. The PANF complexes are up to 2-3 times more active than the free GOx/HRP dyad. They also display enhanced kinetic parameters, superior thermal stability in the 40-60 °C range, optimum performance at pH 4-6, and excellent storage stability. All PANF complexes are active for up to 6 consecutive operational cycles.

The optimal docking strength for reversibly tethered kinases

Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.

Programming an Orthogonal Self-Assembling Protein Cascade Based on Reactive Peptide-Protein Pairs for In Vitro Enzymatic Trehalose Production

Trehalose is an important rare sugar that protects biomolecules against environmental stress. We herein introduce a dual enzyme cascade strategy that regulates the proportion of cargos and scaffolds, to maximize the benefits of enzyme immobilization. Based upon the self-assembling properties of the shell protein (EutM) from the ethanolamine utilization (Eut) bacterial microcompartment, we implemented the catalytic synthesis of trehalose from soluble starch with the coimmobilization of α-amylase and trehalose synthase. This strategy improved enzymatic cascade activity and operational stability. The cascade system enabled the efficient production of trehalose with a yield of ∼3.44 g/(L U), 1.5 times that of the free system. Moreover, its activity was maintained over 12 h, while the free system was almost completely inactivated after 4 h, demonstrating significantly enhanced thermostability. In conclusion, an attractive self-assembly coimmobilization platform was developed, which provides an effective biological process for the enzymatic synthesis of trehalose in vitro.

Protein engineering approach to enhance activity assays of mono-ADP-ribosyltransferases through proximity

Human mono-ADP-ribosylating PARP enzymes have been linked to several clinically relevant processes and many of these PARPs have been suggested as potential drug targets. Despite recent advances in the field, efforts to discover inhibitors have been hindered by the lack of tools to rapidly screen for high potency compounds and profile them against the different enzymes. We engineered mono-ART catalytic fragments to be incorporated into a cellulosome-based octavalent scaffold. Compared to the free enzymes, the scaffold-based system results in an improved activity for the tested PARPs due to improved solubility, stability and the proximity of the catalytic domains, altogether boosting their activity beyond 10-fold in the case of PARP12. This allows us to measure their activity using a homogeneous NAD+ conversion assay, facilitating its automation to lower the assay volume and costs. The approach will enable the discovery of more potent compounds due to increased assay sensitivity.