Role of Dimension and Spatial Arrangement on the Activity of Biocatalytic Cascade Reactions on Scaffolds

Nucleic Acid-based Enzyme Cascades-Current Trends and Future Perspectives

The natural micro- and nanoscale organization of biomacromolecules is a remarkable principle within living cells, allowing for the control of cellular functions by compartmentalization, dimensional diffusion and substrate channeling. In order to explore these biological mechanisms and harness their potential for applications such as sensing and catalysis, molecular scaffolding has emerged as a promising approach. In the case of synthetic enzyme cascades, developments in DNA nanotechnology have produced particularly powerful scaffolds whose addressability can be programmed with nanometer precision. In this minireview, we summarize recent developments in the field of biomimetic multicatalytic cascade reactions organized on DNA nanostructures. We emphasize the impact of the underlying design principles like DNA origami, efficient strategies for enzyme immobilization, as well as the importance of experimental design parameters and theoretical modeling. We show how DNA nanostructures have enabled a better understanding of diffusion and compartmentalization effects at the nanometer length scale, and discuss the challenges and future potential for commercial applications.

Engineered repeat proteins as scaffolds to assemble multi-enzyme systems for efficient cell-free biosynthesis

Multi-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.

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.

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.

Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold

DNA nanotechnology has increasingly been used as a platform to scaffold enzymes based on its unmatched ability to structure enzymes in a desired format. The capability to organize enzymes has taken many forms from more traditional 2D pairings on individual scaffolds to recent works introducing enzyme organizations in 3D lattices. As the ability to define nanoscale structure has grown, it is critical to fully deconstruct the impact of enzyme organization at the single-scaffold level. Here, we present an open, three-dimensional (3D) DNA wireframe octahedron which is used to create a library of spatially arranged organizations of glucose oxidase and horseradish peroxidase. We explore the contribution of enzyme spacing, arrangement, and location on the 3D scaffold to cascade activity. The experiments provide insight into enzyme scaffold design, including the insignificance of scaffold sequence makeup on activity, an increase in activity at small enzyme spacings of <10 nm, and activity changes that arise from discontinuities in scaffold architecture. Most notably, the experiments allow us to determine that enzyme colocalization itself on the DNA scaffold dominates over any specific enzyme arrangement.

Amplified electrochemical biosensing based on bienzymatic cascade catalysis confined in a functional DNA structure

Herein, an amplified and renewable electrochemical biosensor was developed via bienzymatic cascade catalysis of glucose oxidase (GOx) and horseradish peroxidase (HRP), which were confined in a functional Y-shaped DNA nanostructure oriented by a dual-thiol-ended hairpin probe (dSH-HP) with a paired stem as a rigid scaffold and unpaired loop as enclosed binding platform. For proof-of-concept assay of sequence-specific biomarker DNA related to Alzheimer's disease (aDNA), GOx and redox ferrocene-modified HRP (Fc@HRP) were chemically conjugated in two enzyme strands (GOx-ES1 and Fc@HRP-ES2), respectively. The repeated recycling of aDNA was powered by the displacement of GOx-ES1 by aDNA and exonuclease III (ExoIII)-assisted cleavage reaction for amplified output of numerous GOx-ES1 as dependent transducers, together with Fc@HRP-ES2 which was simultaneously hybridized with dSH-HP to assemble this DNA structure. Rationally, the bienzymatic cascade catalysis was motivated through GOx-catalyzed glucose oxidization to in situ generate hydrogen peroxide (H₂O₂) and overlapped HRP-catalyzed H₂O₂ decomposition to promote the electron transfer, producing significantly enhanced electrochemical signal of Fc with an ultrahigh sensitivity down to 0.22 fM of aDNA. Benefited from the unique design of dSH-HP-oriented bienzymatic cascades, this one-step strategy without non-specific blockers passivation was simple and renewable, and would pave a promising avenue for sensitive electrochemical assay of biomolecules.

Nature Inspired Multienzyme Immobilization: Strategies and Concepts

In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.

High-Throughput Multiobjective Optimization of Patterned Multifunctional Surfaces

The realization and optimization of multifunctional materials is difficult, especially when the functionalities are directly incompatible. For example, it is challenging to make surfaces both enzymatically active and water repellent, as these two properties are directly competitive because of the hydrophilic nature of the enzyme-laden surfaces. Patterning discrete domains of distinct functionalities can represent a path to multifunctionality, but the innumerable possible domain permutations present a major barrier to optimizing performance. Here, we develop a high-throughput approach for exploring patterned multifunctional surfaces that is inspired by the microtiter plate architecture. As a model system, patterned surfaces are realized with horseradish peroxidase-decorated domains amidst a background of hydrophobic fluorinated self-assembled monolayers. In experiments exploring effects of pattern geometry, the measured enzyme activity is dependent only on the surface coverage. In contrast, roll-off behavior strongly depends on the parameters of the pattern geometry. Importantly, this finding enables the precise tailoring of distinct wetting behavior of the surfaces in a manner that is independent of their enzymatic activity. The high-throughput nature of the platform facilitates multiobjective optimization of surface functionalities in a general and flexible manner.

DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions

Cellular functions rely on a series of organized and regulated multienzyme cascade reactions. The catalytic efficiencies of these cascades depend on the precise spatial organization of the constituent enzymes, which is optimized to facilitate substrate transport and regulate activities. Mimicry of this organization in a non-living, artificial system would be very useful in a broad range of applications—with impacts on both the scientific community and society at large. Self-assembled DNA nanostructures are promising applications to organize biomolecular components into prescribed, multidimensional patterns. In this review, we focus on recent progress in the field of DNA-scaffolded assembly and confinement of multienzyme reactions. DNA self-assembly is exploited to build spatially organized multienzyme cascades with control over their relative distance, substrate diffusion paths, compartmentalization and activity actuation. The combination of addressable DNA assembly and multienzyme cascades can deliver breakthroughs toward the engineering of novel synthetic and biomimetic reactors.

Lattice-Like DNA Tetrahedron Nanostructure as Scaffold to Locate GOx and HRP Enzymes for Highly Efficient Enzyme Cascade Reaction

In this work, the array arrangement of cascade enzymes was implemented by alternately and equidistantly anchoring two model enzymes glucose oxidase (GOx) and horseradish peroxidase (HRP) to the vertexes of rigid DNA tetrahedron units in lattice-like nucleic acid scaffold, in which the distance between any adjacent cascade enzymes had been regulated to the optimum for obtaining high enzyme cascade catalytic efficiency. Compared to the enzyme cascade system with no-array arrangement of cascade enzymes, the proposed enzyme cascade system allowed the intermediate H₂O₂ produced by GOx catalyzing substrate glucose to concurrently and equidistantly diffuse toward the four adjacent HRP enzyme surfaces. In this case, the invalid diffusion effect of intermediate H₂O₂ between cascade enzymes could be effectively avoided, thereby promoting the enzyme cascade reaction with high catalytic efficiency. The specific catalytic efficiency (k_cat/K_m) of the cascade enzyme system with array arrangement had been evaluated, which exhibited catalytic efficiency about 3.6 times higher than that of the randomly arranged cascade enzyme system. As a result, this strategy provided a new avenue for constructing a highly efficient enzyme cascade system with ultimate applications in biosynthesis, bioanalysis, and biodiagnostics.

Investigating the origin of high efficiency in confined multienzyme catalysis

Biomimetic strategies have successfully been applied to confine multiple enzymes on scaffolds to obtain higher catalytic efficiency of enzyme cascades than freely distributed enzymes. However, the origin of high efficiency is poorly understood. We developed a coarse-grained, particle-based model to understand the origin of high efficiency. We found that a reaction intermediate is the key in affecting reaction kinetics. In the case of unstable intermediates, the confinement of multiple enzymes in clusters enhanced the catalytic efficiency and a shorter distance between enzymes resulted in a higher reaction rate and yield. This understanding was verified by co-encapsulating multiple enzymes in metal-organic framework (MOF) nanocrystals as artificially confined multienzyme complexes. The activity enhancement of multiple enzymes in MOFs depended on the distance between enzymes, when the decay of intermediates existed. The finding of this study is useful for designing in vitro synthetic biology systems based on artificial multienzyme complexes.

Enhanced Enzyme Activity through Scaffolding on Customizable Self-Assembling Protein Filaments

Precisely organized enzyme complexes are often found in nature to support complex metabolic reactions in a highly efficient and specific manner. Scaffolding enzymes on artificial materials has thus gained attention as a promising biomimetic strategy to design biocatalytic systems with enhanced productivity. Herein, a versatile scaffolding platform that can immobilize enzymes on customizable nanofibers is reported. An ultrastable self-assembling filamentous protein, the gamma-prefoldin (γ-PFD), is genetically engineered to display an array of peptide tags, which can specifically and stably bind enzymes containing the counterpart domain through simple in vitro mixing. Successful immobilization of proteins along the filamentous template in tunable density is first verified using fluorescent proteins. Then, two different model enzymes, glucose oxidase and horseradish peroxidase, are used to demonstrate that scaffold attachment could enhance the intrinsic catalytic activity of the immobilized enzymes. Considering the previously reported ability of γ-PFD to bind and stabilize a broad range of proteins, the filament's interaction with the bound enzymes may have created a favorable microenvironment for catalysis. It is envisioned that the strategy described here may provide a generally applicable methodology for the scaffolded assembly of multienzymatic complexes for use in biocatalysis.

Electrocatalytic Volleyball: Rapid Nanoconfined Nicotinamide Cycling for Organic Synthesis in Electrode Pores

In living cells, redox chains rely on nanoconfinement using tiny enclosures, such as the mitochondrial matrix or chloroplast stroma, to concentrate enzymes and limit distances that nicotinamide cofactors and other metabolites must diffuse. In a chemical analogue exploiting this principle, nicotinamide adenine dinucleotide phosphate (NADPH) and NADP⁺ are cycled rapidly between ferredoxin–NADP⁺ reductase and a second enzyme—the pairs being juxtaposed within the 5–100 nm scale pores of an indium tin oxide electrode. The resulting electrode material, denoted (FNR+E2)@ITO/support, can drive and exploit a potentially large number of enzyme‐catalysed reactions.

Tools and strategies for constructing cell-free enzyme pathways

Single enzyme systems or engineered microbial hosts have been used for decades but the notion of assembling multiple enzymes into cell-free synthetic pathways is a relatively new development. The extensive possibilities that stem from this synthetic concept makes it a fast growing and potentially high impact field for biomanufacturing fine and platform chemicals, pharmaceuticals and biofuels. However, the translation of individual single enzymatic reactions into cell-free multi-enzyme pathways is not trivial. In reality, the kinetics of an enzyme pathway can be very inadequate and the production of multiple enzymes can impose a great burden on the economics of the process. We examine here strategies for designing synthetic pathways and draw attention to the requirements of substrates, enzymes and cofactor regeneration systems for improving the effectiveness and sustainability of cell-free biocatalysis. In addition, we comment on methods for the immobilisation of members of a multi-enzyme pathway to enhance the viability of the system. Finally, we focus on the recent development of integrative tools such as in silico pathway modelling and high throughput flux analysis with the aim of reinforcing their indispensable role in the future of cell-free biocatalytic pathways for biomanufacturing.

Efficient Electrochemical Self-Catalytic Platform Based on l-Cys-hemin/G-quadruplex and Its Application for Bioassay

Commonly, in the artificial enzyme-involved signal amplification approach, the catalytic efficiency was limited by the relatively low binding affinity between artificial enzyme and substrate. In this work, substrate l-cysteine (l-Cys) and hemin were combined into one molecule to form l-Cys-hemin/G-quadruplex as an artificial self-catalytic complex for the improvement of the binding affinity between l-Cys-hemin/G-quadruplex and l-Cys. The apparent Michaelis-Menten constant ( K_m = 2.615 μM) on l-Cys-hemin/G-quadruplex for l-Cys was further investigated to assess the affinity, which was much lower than that of hemin/G-quadruplex ( K_m = 8.640 μM), confirming l-Cys-hemin/G-quadruplex possessed better affinity to l-Cys compared with that of hemin/G-quadruplex. Meanwhile, l-Cys bilayer could be further assembled onto the surface of l-Cys-hemin/G-quadruplex based on hydrogen-bond and electrostatic interaction to concentrate l-Cys around the active center, which was beneficial to the catalytic enhancement. Through this efficient electrochemical self-catalytic platform, a sensitive thrombin aptasensor was constructed. The results exhibited good sensitivity from 0.1 pM to 80 nM and the detection limit was calculated to be 0.032 pM. This self-catalytic strategy with improved binding affinity between l-Cys-hemin/G-quadruplex and l-Cys could provide an efficient approach to improve artificial enzymatic catalytic efficiency.

PtNPs as Scaffolds to Regulate Interenzyme Distance for Construction of Efficient Enzyme Cascade Amplification for Ultrasensitive Electrochemical Detection of MMP-2

The high catalytic efficiency of enzyme cascade reaction mainly depends on optimal interenzyme distance regulated by the special scaffolds. In this work, the rigid PtNPs with different sizes were employed as scaffolds to regulate interenzyme distance for efficient enzyme cascade amplification to construct electrochemical biosensor for sensitive detection of matrix metalloproteinases-2 (MMP-2), which overcame the drawbacks of instable construction and sophisticated preparation induced by conventional scaffolds such as metal-organic frameworks (MOFs), DNA nanostructures. Here, cucurbit[7]uril functionalized PtNPs (CB[7]@PtNPs) was utilized to load ferrocene (Fc)-labeled horseradish peroxidase (HRP) and glucose oxidase (GOx) via host-guest interaction between Fc and CB[7], respectively, resulting in the formation of a stable three-dimensional netlike structure containing amounts of enzymes. Interestingly, the enzyme cascade reaction regulated by 10 nm PtNPs as scaffold showed highly catalytic efficiency. Meanwhile, the PtNPs could also serve as catalyst to accelerate the enzyme cascade reaction with further enhanced catalytic efficiency. As a result, the proposed biosensor exhibited excellent sensitivity with a wide linear range of 0.1 pg·mL^-1 to 20 ng·mL^-1 and a detection limit of 0.03 pg·mL^-1 for MMP-2. Such a strategy opened a new avenue for adopting metal nanoparticles to regulate interenzyme distance for efficient enzyme cascade amplification, thus providing a universal and easy operating method for sensitively detecting various targets such as DNA, metal ion, and protein.

Spatial organization of multi-enzyme biocatalytic cascades

Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.