On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective

Enhancing Substrate Channeling with Multi-Enzyme Architectures in Hydrogen-Bonded Organic Frameworks

Hydrogen-bonded organic frameworks (HOF) represent an emerging category of organic structures with high crystallinity and metal-free, which are not commonly observed in alternative porous organic frameworks. These needle-like porous structure can help in stabilizing enzymes and allow transfer of molecules between enzymes participating in cascade reactions for enhanced substrate channelling. Herein, we systematically synthesized and investigated the stability of HOF at extreme conditions followed by one-pot encapsulation of single and bi-enzyme systems. Firstly, we observed HOF to be stable at pH 1 to 14 and at high temperatures (up to 115 °C). Secondly, the encapsulated glucose oxidase enzyme (GOX) showed 80 % and 90 % of its original activity at 70 °C and pH 11, respectively. Thirdly, transient time close to 0 seconds was observed for HOF encapsulated bi-enzyme cascade reaction system demonstrating a 4.25-fold improvement in catalytic activity when compared to free enzymes with enhanced substrate channelling. Our findings showcase a facile system synthesized under ambient conditions to encapsulate and stabilize enzymes at extreme conditions.

Single-Particle and Single-Molecule Characterization of Immobilized Enzymes: A Multiscale Path toward Optimizing Heterogeneous Biocatalysts

Heterogeneous biocatalysis is highly relevant in biotechnology as it offers several benefits and practical uses. To leverage the full potential of heterogeneous biocatalysts, the establishment of well-crafted protocols, and a deeper comprehension of enzyme immobilization on solid substrates are essential. These endeavors seek to optimize immobilized biocatalysts, ensuring maximal enzyme performance within confined spaces. For this aim, multidimensional characterization of heterogeneous biocatalysts is required. In this context, spectroscopic and microscopic methodologies conducted at different space and temporal scales can inform about the intraparticle enzyme kinetics, the enzyme spatial distribution, and the mass transport issues. In this Minireview, we identify enzyme immobilization, enzyme catalysis, and enzyme inactivation as the three main processes for which advanced characterization tools unveil fundamental information. Recent advances in operando characterization of immobilized enzymes at the single-particle (SP) and single-molecule (SM) levels inform about their functional properties, unlocking the full potential of heterogeneous biocatalysis toward biotechnological applications.

Tuning Chemoenzymatic Pd/Laccase Conformation Toward Optimized Heterogeneous Aerobic Oxidation

Heterogeneous chemoenzymatic catalysts differing in their spatial organization and relative orientation of their enzymatic laccase and Pd units confined into macrocellular silica foams were tested on veratryl alcohol oxidation. When operating under continuous flow, we show that the catalytic efficiency of hybrids is significantly enhanced when the Pd(II) complex is combined with a laccase exhibiting a surface located lysine next to the T1 oxidation site of the enzyme.

Modular Functionalization of Metal-Organic Frameworks for Nitrogen Recovery from Fresh Urine

Nitrogen recovery from wastewater represents a sustainable route to recycle reactive nitrogen (Nr). It can reduce the demand of producing Nr from the energy-extensive Haber-Bosch process and lower the risk of causing eutrophication simultaneously. In this aspect, source-separated fresh urine is an ideal source for nitrogen recovery given its ubiquity and high nitrogen contents. However, current techniques for nitrogen recovery from fresh urine require high energy input and are of low efficiencies because the recovery target, urea, is a challenge to separate. In this work, we developed a novel fresh urine nitrogen recovery treatment process based on modular functionalized metal-organic frameworks (MOFs). Specifically, we employed three distinct modification methods to MOF-808 and developed robust functional materials for urea hydrolysis, ammonium adsorption, and ammonia monitoring. By integrating these functional materials into our newly developed nitrogen recovery treatment process, we achieved an average of 75 % total nitrogen reduction and 45 % nitrogen recovery with a 30-minute treatment of synthetic fresh urine. The nitrogen recovery process developed in this work can serve as a sustainable and efficient nutrient management that is suitable for decentralized wastewater treatment. This work also provides a new perspective of implementing versatile advanced materials for water and wastewater treatment.

Strategies to improve the mass transfer in the CO2 capture process using immobilized carbonic anhydrase

High carbon dioxide (CO₂) concentration in the atmosphere urgently requires eco-friendly mitigation strategies. Carbonic anhydrase (CA) is a high-quality enzyme protein, available from a wide range of sources, which has an extremely high catalytic efficiency for the hydration of CO₂ compared with other catalytic CO₂ conversion systems. While free CA is costly and weakly stable, CA immobilization can significantly improve its stability and allow enzyme recycling. However, gaseous CO₂ is significantly different from traditional liquid substrates. Additionally, due to the presence of enzyme carriers, there is limited mass transfer between CO₂ and the active center of immobilized CA. Most of the available reviews provide an overview of the improvement in catalytic activity and stability of CA by different immobilization methods and substrates. However, they do not address the limited mass transfer between CO₂ and the active center of immobilized CA. Therefore, by focusing on the mass transfer process, this review presents CA immobilization strategies that are more efficient and of greater environmental tolerance by categorizing the methods of enhancing the mass transfer process at each stage of the enzymatic CO₂ capture reaction. Such improvements in this green and environmentally friendly biological carbon capture process can increase its efficiency for industrial applications.

Nano-fibrillated cellulose-based scaffolds for enzyme (co)-immobilization: Application to natural product glycosylation by Leloir glycosyltransferases

Polysaccharide-based scaffolds are promising carriers for enzyme immobilization. Here, we demonstrate a porous scaffold prepared by direct-ink-writing 3D printing of an ink consisting of nanofibrillated cellulose, carboxymethyl cellulose and citric acid for immobilization application. Negative surface charge introduced by the components made the scaffold amenable for an affinity-like immobilization via the cationic protein module Z_basic2. Z_basic2 fusions of two sugar nucleotide-dependent glycosyltransferases (C-glycosyltransferase, Z-CGT; sucrose synthase, Z-SuSy) were immobilized individually, or co-immobilized, and applied to synthesize the natural C-glycoside nothofagin. The cascade reaction involved β-C-glycosylation of phloretin (10 mM, ~90 % conversion) from UDP-glucose, provided from sucrose and catalytic amounts of UDP (1.0 mM). Enzymes were co-immobilized at ~65 mg protein/g carrier to receive activities of 9.5 U/g (Z-CGT) and 4.5 U/g (Z-SuSy) in 22-33 % yield (protein) and an effectiveness of 23 % (Z-CGT) and 13 % (Z-SuSy). The scaffold-bound enzymes were recyclable for 5 consecutive reactions.

Switch off/switch on of a cysteinyl protease as a way to preserve the active catalytic group by modification with a reversible covalent thiol modifier: Immobilization of ficin on vinyl-sulfone activated supports

The immobilization of ficin (a cysteinyl proteases) on vinyl sulfone agarose produced its almost full inactivation. It was observed that the incubation of the free and immobilized enzyme in β-mercaptoethanol produced a 20 % of enzyme activity recovery, suggesting that the inactivation due to the immobilization could be a consequence of the modification of the catalytic Cys. To prevent the enzyme inactivation during the immobilization, switching off of ficin via Cys reaction with dipyridyl-disulfide was implemented, giving a reversible disulfide bond that produced a fully inactive enzyme. The switch on of ficin activity was implemented by incubation in 1 M β-mercaptoethanol. Using this strategy to immobilize the enzyme on vinyl sulfone agarose beads, the expressed activity of the immobilized ficin could be boosted up to 80 %. The immobilized enzyme presented a thermal stabilization similar to that obtained using ficin-glyoxyl-agarose beads. This procedure may be extended to many enzymes containing critical Cys, to permit their immobilization or chemical modification.

Hydrophilic Nonwoven Nanofiber Membranes as Nanostructured Supports for Enzyme Immobilization

The high porosity, interconnected pore structure, and high surface area-to-volume ratio make the hydrophilic nonwoven nanofiber membranes (NV-NF-Ms) promising nanostructured supports for enzyme immobilization in different biotechnological applications. In this work, NV-NF-Ms with excellent mechanical and chemical properties were designed and fabricated by electrospinning in one step without using additives or complicated crosslinking processes after electrospinning. To do so, two types of ultrahigh-molecular-weight linear copolymers with very different mechanical properties were used. Methyl methacrylate-co-hydroxyethyl methacrylate (p(MMA)-co-p(HEMA)) and methyl acrylate-co-hydroxyethyl acrylate (p(MA)-co-p(HEA)) were designed and synthesized by reverse atom transfer radical polymerization (reverse-ATRP) and copper-mediated living radical polymerization (Cu0-MC-LRP), respectively. The copolymers were characterized by nuclear magnetic resonance (1H-NMR) spectroscopy and by triple detection gel permeation chromatography (GPC). The polarity, topology, and molecular weight of the copolymers were perfectly adjusted. The polymeric blend formed by (MMA)1002-co-(HEMA)1002 (M w = 230,855 ± 7418 Da; M n = 115,748 ± 35,567 Da; PDI = 2.00) and (MA)11709-co-(HEA)7806 (M w = 1.972 × 106 ± 33,729 Da; M n = 1.395 × 106 ± 35,019 Da; PDI = 1.41) was used to manufacture (without additives or chemical crosslinking processes) hydroxylated nonwoven nanofiber membranes (NV-NF-Ms-OH; 300 nm in fiber diameter) with excellent mechanical and chemical properties. The morphology of NV-NF-Ms-OH was studied by scanning electron microscopy (SEM). The suitability for enzyme binding was proven by designing a palette of different surface functionalization to enable both reversible and irreversible enzyme immobilization. NV-NF-Ms-OH were successfully functionalized with vinyl sulfone (281 ± 20 μmol/g), carboxyl (560 ± 50 μmol/g), and amine groups (281 ± 20 μmol/g) and applied for the immobilization of two enzymes of biotechnological interest. Galactose oxidase was immobilized on vinyl sulfone-activated materials and carboxyl-activated materials, while laccase was immobilized onto amine-activated materials. These preliminary results are a promising basis for the application of nonwoven membranes in enzyme technology.

Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization

Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.

Mammalian Cell Interaction with Periodic Surface Nanostructures

Here, we report on the nanopatterning of different aromatic polymer substrates achieved by KrF excimer laser treatment. The conditions for the construction of the laser-induced periodic surface structures, the so-called LIPSS pattern, were established by optimized laser fluence and a number of pulses. The polymer substrates were polyethylene naphthalate (PEN), polyethersulfone (PES), and polystyrene (PS), which were chosen since they are thermally, chemically, and mechanically resistant polymers with high absorption coefficients at the excimer laser wavelength. The surface morphology of the treated substrates was investigated by atomic force microscopy and scanning electron microscopy, and the roughness and effective surface area on the modified samples were determined. Elemental concentration was characterized by energy-dispersive (EDX) analysis, surface chemistry was determined with X-ray photoelectron spectroscopy (XPS). The samples with the formation of LIPSS induced by 10 mJ·cm⁻² with 1000, 3000, and 6000 pulses were used for subsequent in vitro cytocompatibility tests using human cells from osteosarcoma (U-2 OS). The LIPSS pattern and its ability of significant cell guidance were confirmed for some of the studied samples. Cell morphology, adhesion, and proliferation were evaluated. The results strongly contribute to the development of novel applications using nanopatterned polymers, e.g., in tissue engineering, cell analysis or in combination with metallization for sensor construction.

Combining a Genetically Engineered Oxidase with Hydrogen-Bonded Organic Frameworks (HOFs) for Highly Efficient Biocomposites

Enzymes incorporated into hydrogen-bonded organic frameworks (HOFs) via bottom-up synthesis are promising biocomposites for applications in catalysis and sensing. Here, we explored synthetic incorporation of d-amino acid oxidase (DAAO) with the metal-free tetraamidine/tetracarboxylate-based BioHOF-1 in water. N-terminal enzyme fusion with the positively charged module Zbasic2 strongly boosted the loading (2.5-fold; ≈500 mg enzyme gmaterial-1 ) and the specific activity (6.5-fold; 23 U mg-1 ). The DAAO@BioHOF-1 composites showed superior activity with respect to every reported carrier for the same enzyme and excellent stability during catalyst recycling. Further, extension to other enzymes, including cytochrome P450 BM3 (used in the production of high-value oxyfunctionalized compounds), points to the versatility of genetic engineering as a strategy for the preparation of biohybrid systems with unprecedented properties.

Intraparticle Kinetics Unveil Crowding and Enzyme Distribution Effects on the Performance of Cofactor-Dependent Heterogeneous Biocatalysts

Multidimensional kinetic analysis of immobilized enzymes is essential to understand the enzyme functionality at the interface with solid materials. However, spatiotemporal kinetic characterization of heterogeneous biocatalysts on a microscopic level and under operando conditions has been rarely approached. As a case study, we selected self-sufficient heterogeneous biocatalysts where His-tagged cofactor-dependent enzymes (dehydrogenases, transaminases, and oxidases) are co-immobilized with their corresponding phosphorylated cofactors [nicotinamide adenine dinucleotide phosphate (NAD(P)H), pyridoxal phosphate (PLP), and flavin adenine dinucleotide (FAD)] on porous agarose microbeads coated with cationic polymers. These self-sufficient systems do not require the addition of exogenous cofactors to function, thus avoiding the extensive use of expensive cofactors. To comprehend the microscopic kinetics and thermodynamics of self-sufficient systems, we performed fluorescence recovery after photobleaching measurements, time-lapse fluorescence microscopy, and image analytics at both single-particle and intraparticle levels. These studies reveal a thermodynamic equilibrium that rules out the reversible interactions between the adsorbed phosphorylated cofactors and the polycations within the pores of the carriers, enabling the confined cofactors to access the active sites of the immobilized enzymes. Furthermore, this work unveils the relationship between the apparent Michaelis-Menten kinetic parameters and the enzyme density in the confined space, eliciting a negative effect of molecular crowding on the performance of some enzymes. Finally, we demonstrate that the intraparticle apparent enzyme kinetics are significantly affected by the enzyme spatial organization. Hence, multiscale characterization of immobilized enzymes serves as an instrumental tool to better understand the in operando functionality of enzymes within confined spaces.

Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies

The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.

Leloir glycosyltransferases enabled to flow synthesis: Continuous production of the natural C-glycoside nothofagin

C‐glycosyltransferase (CGT) and sucrose synthase (SuSy), each fused to the cationic binding module Z_basic2, were co‐immobilized on anionic carrier (ReliSorb SP400) and assessed for continuous production of the natural C‐glycoside nothofagin. The overall reaction was 3ʹ‐C‐β‐glycosylation of the polyphenol phloretin from uridine 5ʹ‐diphosphate (UDP)‐glucose that was released in situ from sucrose and UDP. Using solid catalyst optimized for total (∼28 mg/g) as well as relative protein loading (CGT/SuSy = ∼1) and assembled into a packed bed (1 ml), we demonstrate flow synthesis of nothofagin (up to 52 mg/ml; 120 mM) from phloretin (≥95% conversion) solubilized by inclusion complexation in hydroxypropyl β‐cyclodextrin. About 1.8 g nothofagin (90 ml; 12–26 mg/ml) were produced continuously over 90 reactor cycles (2.3 h/cycle) with a space‐time yield of approximately 11 mg/(ml h) and a total enzyme turnover number of up to 2.9 × 10³ mg/mg (=3.8 × 10⁵ mol/mol). The co‐immobilized enzymes exhibited useful effectiveness (∼40% of the enzymes in solution), with limitations on the conversion rate arising partly from external liquid–solid mass transfer of UDP under packed‐bed flow conditions. The operational half‐life of the catalyst (∼200 h; 30°C) was governed by the binding stability of the glycosyltransferases (≤35% loss of activity) on the solid carrier. Collectively, the current study shows integrated process technology for flow synthesis with co‐immobilized sugar nucleotide‐dependent glycosyltransferases, using efficient glycosylation from sucrose via the internally recycled UDP‐glucose. This provides a basis from engineering science to promote glycosyltransferase applications for natural product glycosides and oligosaccharides.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

Quantitative measurements of free and immobilized RgDAAO Michaelis-Menten constant using an electrochemical assay reveal the impact of covalent cross-linking on substrate specificity

Challenges facing enzyme-based electrochemical sensors include substrate specificity, batch to batch reproducibility, and lack of quantitative metrics related to the effect of enzyme immobilization. We present a quick, simple, and general approach for measuring the effect of immobilization and cross-linking on enzyme activity and substrate specificity. The method can be generalized for electrochemical biosensors using an enzyme that releases hydrogen peroxide during its catalytic cycle. Using as proof of concept RgDAAO-based electrochemical biosensors, we found that the Michaelis-Menten constant (K_m) decreases post immobilization, hinting at alterations in the enzyme kinetic properties and thus substrate specificity. We confirm the decrease in K_m electrochemically by characterizing the substrate specificity of the immobilized RgDAAO using chronoamperometry. Our results demonstrate that enzyme immobilization affects enzyme substrate specificity and this must be carefully evaluated during biosensor development.

Design of the Enzyme-Carrier Interface to Overcome the O2 and NADH Mass Transfer Limitations of an Immobilized Flavin Oxidase

Understanding how the immobilization of enzymes on solid carriers affects their performance is paramount for the design of highly efficient heterogeneous biocatalysts. An efficient supply of substrates onto the solid phase is one of the main challenges to maximize the activity of the immobilized enzymes. Herein, we apply advanced single-particle analysis to decipher the optimal design of an immobilized NADH oxidase (NOX) whose activity depends both on O₂ and NADH concentrations. Carrier physicochemical properties and its functionality along with the enzyme distribution across the carrier were implemented as design variables to study the effects of the intraparticle concentration of substrates (O₂ and NADH) on the activity. Intraparticle O₂-sensing analysis revealed the superior performance of the enzyme immobilized at the outer surface in terms of effective supply of O₂. Furthermore, the co-immobilization of NADH and NOX within the tuned surface of porous microbeads increases the effective concentration of NADH in the surroundings of the enzyme. As a result, the optimal spatial organization of NOX and its confinement with NADH allow a 100% recovery of the activity of the soluble enzyme upon the immobilization process. By engineering these variables, we increase the NADH oxidation activity of the heterogeneous biocatalyst by up to 650% compared to NOX immobilized under suboptimal conditions. In conclusion, this work highlights the rational design and engineering of the enzyme-carrier interface to maximize the efficiency of heterogeneous biocatalysts.

Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes

The possibility of immobilizing a protein with antigenic properties on a solid support offers significant possibilities in the development of immunosensors and vaccine formulations. For both applications, the orientation of the antigen should ensure ready accessibility of the antibodies to the epitope. However, an experimental assessment of the orientational preferences necessarily proceeds through the preparation/isolation of the antigen, the immobilization on different surfaces and one or more biophysical characterization steps. To predict a priori whether favorable orientations can be achieved or not would allow one to select the most promising experimental routes, partly mitigating the time cost towards the final product. In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. These calculations can account for the experimental observation that direct immobilization on gold gives sufficient exposure of the epitope to obtain a response in immunochemical assays.

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation

Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells, or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics, and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating local protein flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian dynamics simulations. The impact of protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e., residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.