Categorization of enzyme deactivations using a series-type mechanism

Combinatorial High-Throughput Screening of Complex Polymeric Enzyme Immobilization Supports

Recent advances have demonstrated the promise of complex multicomponent polymeric supports to enable supra-biological enzyme performance. However, the discovery of such supports has been limited by time-consuming, low-throughput synthesis and screening. Here, we describe a novel combinatorial and high-throughput platform that enables rapid screening of complex and heterogeneous copolymer brushes as enzyme immobilization supports, named combinatorial high-throughput enzyme support screening (CHESS). Using a 384-well plate format, we synthesized arrays of three-component polymer brushes in the microwells using photoactivated surface-initiated polymerization and immobilized enzymes in situ. The utility of CHESS to identify optimal immobilization supports under thermally and chemically denaturing conditions was demonstrated usingBacillus subtilisLipase A (LipA). The identification of supports with optimal compositions was validated by immobilizing LipA on polymer-brush-modified biocatalyst particles. We further demonstrated that CHESS could be used to predict the optimal composition of polymer brushes a priori for the previously unexplored enzyme, alkaline phosphatase (AlkP). Our findings demonstrate that CHESS represents a predictable and reliable platform for dramatically accelerating the search of chemical compositions for immobilization supports and further facilitates the discovery of biocompatible and stabilizing materials.

Easy and Versatile Technique for the Preparation of Stable and Active Lipase-Based CLEA-like Copolymers by Using Two Homofunctional Cross-Linking Agents: Application to the Preparation of Enantiopure Ibuprofen

An easy and versatile method was designed and applied successfully to obtain access to lipase-based cross-linked-enzyme aggregate-like copolymers (CLEA-LCs) using one-pot, consecutive cross-linking steps using two types of homobifunctional cross-linkers (glutaraldehyde and putrescine), mediated with amine activation through pH alteration (pH jump) as a key step in the process. Six lipases were utilised in order to assess the effectiveness of the technique, in terms of immobilization yields, hydrolytic activities, thermal stability and application in kinetic resolution. A good retention of catalytic properties was found for all cases, together with an important thermal and storage stability improvement. Particularly, the CLEA-LCs derived from Candida rugosa lipase showed an outstanding behaviour in terms of thermostability and capability for catalysing the enantioselective hydrolysis of racemic ibuprofen ethyl ester, furnishing the eutomer (S)-ibuprofen with very high conversion and enantioselectivity.

Kinetic Modeling, Thermodynamic Approach and Molecular Dynamics Simulation of Thermal Inactivation of Lipases from Burkholderia cepacia and Rhizomucor miehei

The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation was investigated using eight inactivation models at a temperature range of 40–70 °C. Kinetic modeling showed that the first-order model and Weibull distribution were the best equations to describe the residual activity of Lipase PS and Palatase, respectively. The results obtained from the kinetic parameters, decimal reduction time (D and t_R), and temperature required (z and z’) indicated a higher thermal stability of Lipase PS compared to Palatase. The activation energy values (Ea) also indicated that higher energy was required to denature bacterial (34.8 kJ mol⁻¹) than fungal (23.3 kJ mol⁻¹) lipase. The thermodynamic inactivation parameters, Gibbs free energy (ΔG^#), entropy (ΔS^#), and enthalpy (ΔH^#) were also determined. The results showed a ΔG^# for Palatase (86.0–92.1 kJ mol⁻¹) lower than for Lipase PS (98.6–104.9 kJ mol⁻¹), and a negative entropic and positive enthalpic contribution for both lipases. A comparative molecular dynamics simulation and structural analysis at 40 °C and 70 °C were also performed.

Experimental and mathematical modeling approaches for biocatalytic post-consumer poly(ethylene terephthalate) hydrolysis

The environmental impact arising from poly(ethylene terephthalate) (PET) waste is notable worldwide. Enzymatic PET hydrolysis can provide chemicals that serve as intermediates for value-added product synthesis and savings in the resources. In the present work, some reaction parameters were evaluated on the hydrolysis of post-consumer PET (PC-PET) using a cutinase from Humicola insolens (HiC). The increase in PC-PET specific area leads to an 8.5-fold increase of the initial enzymatic hydrolysis rate (from 0.2 to 1.7 mmol L^-1 h^-1), showing that this parameter plays a crucial role in PET hydrolysis reaction. The effect of HiC concentration was investigated, and the enzymatic PC-PET hydrolysis kinetic parameters were estimated based on three different mathematical models describing heterogeneous biocatalysis. The model that best fits the experimental data (R² = 0.981) indicated 1.68 mg_protein mL^-1 as a maximum value of the enzyme concentration to optimize the reaction rate. The HiC thermal stability was evaluated, considering that it is a key parameter for its efficient use in PET degradation. The enzyme half-life was shown to be 110 h at 70 ºC and pH 7.0, which outperforms most of the known enzymes displaying PET hydrolysis activity. The results evidence that HiC is a very promising biocatalyst for efficient PET depolymerization.

Immobilization of Aspergillus oryzae β-galactosidase in cation functionalized agarose matrix and its application in the synthesis of lactulose

Aspergillus oryzae β-galactosidase was immobilized in in-house quaternary ammonium agarose (QAA) and used for the first time in the synthesis of lactulose. A biocatalyst was obtained with a specific activity of 24,690 IU_H∙g^-1; protein immobilization yield of 97% and enzyme immobilization yield of 76% were obtained at 30 °C in 10 mM phosphate buffer pH 7 for standard size agarose at 100 mg_protein∙g_support^-1 which the maximum protein load of QAA. Highest yield and specific productivity of lactulose were 0.24 g∙g^-1 and 9.78 g∙g^-1 h^-1 respectively, obtained at pH 6, 100 IU_H∙g lactose^-1 enzyme/lactose ratio and 12 lactose/fructose molar ratio. In repeated-batch operation with the immobilized enzyme, the cumulative mass of lactulose per unit mass of contacted protein and cumulative specific productivity were higher than obtained with the soluble enzyme since the first batch. After enzyme activity exhaustion, the enzyme was desorbed and QAA support was reused without alteration in its maximum enzyme load capacity and without detriment in yield, productivity and selectivity in the batch synthesis of lactulose with the resulting biocatalyst. This significantly decreases the economic impact of the support, presenting itself as a distinctive advantage of immobilization by ionic interaction.

Alkali-stable GH11 endo-β-1,4 xylanase (XynB) from Bacillus subtilis strain CAM 21: application in hydrolysis of agro-industrial wastes, fruit/vegetable peels and weeds

GH11 endo-xylanases, due to their inherent structural and biochemical properties, are the key to efficient bioconversion of lignocellulosic biomass into value-added products. A GH11 endo-xylanase (XynB) from Bacillus subtilis strain CAM 21 was cloned, over-expressed and purified (Mw∼24 kDa) using Ni-NTA affinity chromatography. XynB showed optimum activity at pH 7.0 and 50°C and was stable (>88%) in a broad range of pH (4-11). The apparent Km_, K_cat and K_cat/Km of XynB were 2.9 mg/ml, 1961.2/sec, and 675.62 ml/mg/sec, respectively using birchwood xylan as substrate. XynB was a classical endo-xylanase as it hydrolyzed birchwood xylan to xylo-oligosaccharides and not xylose. Kinetic stability of XynB at 45-53°C was between 43-182 min. Secondary structure analysis of XynB using far-UV CD spectroscopy revealed presence of 51.85% β strands and 2.64% α helix and was consistent with the homology modeling studies. XynB hydrolyzed the xylan extracted from agro-industrial wastes and fruit/vegetable peels by releasing up to 670 mg/g of reducing sugars. The xylan extracted from weeds (Ageratum conyzoides, Achyranthes aspera and Tridax procumbens) had characteristic signatures of hemicelluloses and after XynB hydrolysis showed cracks, peeling and release of up to 135.2 mg/g reducing sugars.

In Situ Immobilization of Enzymes in Biomimetic Silica

In this chapter we describe different strategies for enzyme immobilization in biomimetic silica nanoparticles. Synthesis of this type of support is performed under mild and biocompatible conditions and has been proven suitable for the immobilization and stabilization of a range of enzymes and enzymatic systems in nanostructured particles. Immobilization occurs by entrapment while the silica matrix is formed via catalysis of a polyamine molecule and the presence of silicic acid. Parameters such as enzyme, polyamine molecule, or source of Si concentration have been tailored in order to maximize enzymatic loads, stabilities, and specific activities of the catalysts. We provide different approaches for the immobilization and co-immobilization of enzymes that could be potentially extensible to other biocatalysts.

Parameters for the Evaluation of Immobilized Enzymes Under Process Conditions

The characterization of immobilized enzymes allows the evaluation of the immobilization process itself and also the projection of the immobilized enzyme performance under process operation conditions. Based on such characterization, strategies for support functionalization and enzyme immobilization into the activated support can be selected, determining the best conditions for conducting such steps in view of the intended use of the biocatalyst, establishing a linkage between biocatalyst production and biocatalyst use. The determination of the catalytic potential of the immobilized enzyme under operational conditions is a priceless parameter that takes into account both activity and stability, including the effect of both mass transfer limitations (diffusional restrictions) and intrinsic enzyme inactivation upon the immobilization process.

Considerations when Measuring Biocatalyst Performance

As biocatalysis matures, it becomes increasingly important to establish methods with which to measure biocatalyst performance. Such measurements are important to assess immobilization strategies, different operating modes, and reactor configurations, aside from comparing protein engineered variants and benchmarking against economic targets. While conventional measurement techniques focus on a single performance metric (such as the total turnover number), here, it is argued that three metrics (achievable product concentration, productivity, and enzyme stability) are required for an accurate assessment of scalability.

Novel thermostable enzymes from Geobacillus thermoglucosidasius W-2 for high-efficient nitroalkane removal under aerobic and anaerobic conditions

In this study, a thermophilic facultative anaerobic strain Geobacillus thermoglucosidasius W-2 was found to degrade nitroalkane under both aerobic and anaerobic conditions. Bioinformatical analysis revealed three putative nitroalkane-oxidizing enzymes (Gt-NOEs) genes from the W-2 genome. The three identified proteins Gt2929, Gt1378, and Gt1208 displayed optimal activities at high temperatures (70, 70, and 80 °C, respectively). Among these, Gt2929 exhibited excellent degradation capability, pH stability, and metal ion tolerance for nitronates under aerobic condition. Interestingly, under anaerobic condition, only Gt1378 still maintained high activity for 2-nitropropane and nitroethane, indicating that the W-2 strain utilized various pathways to degrade nitronates under aerobic and anaerobic conditions, respectively. Taken together, the first revelation of thermophilic nitroalkane-degrading mechanism under both aerobic and anaerobic conditions provides guidance and platform for biotechnological and industrial applications.

Design of stable magnetic hybrid nanoparticles of Si-entrapped HRP

Hybrid and composite nanoparticles represent an attractive material for enzyme integration due to possible synergic advantages of the structural builders in the properties of the nanobiocatalyst. In this study, we report the synthesis of a new stable hybrid nanobiocatalyst formed by biomimetic silica (Si) nanoparticles entrapping both Horseradish Peroxidase (HRP) (EC 1.11.1.7) and magnetic nanoparticles (MNPs). We have demonstrated that tailoring of the synthetic reagents and post immobilization treatments greatly impacted physical and biocatalytic properties such as an unprecedented ~280 times increase in the half-life time in thermal stability experiments. The optimized nanohybrid biocatalyst that showed superparamagnetic behaviour, was effective in the batch conversion of indole-3-acetic acid, a prodrug used in Direct Enzyme Prodrug Therapy (DEPT). Our system, that was not cytotoxic per se, showed enhanced cytotoxic activity in the presence of the prodrug towards HCT-116, a colorectal cancer cell line. The strategy developed proved to be effective in obtaining a stabilized nanobiocatalyst combining three different organic/inorganic materials with potential in DEPT and other biotechnological applications.

Effect of intense pulsed light on the deactivation of lipase: Enzyme-deactivation kinetics and tertiary structural changes by fragmentation

The effect of intense pulsed light (IPL) irradiation on Chromobacterium viscosum lipase was investigated with a primary focus on catalytic activity and molecular structure. During IPL irradiation, lipase activity decreased significantly with increasing pulse fluence (F_p) and exposure time (t_e). IPL-induced deactivation kinetics were further elucidated based on a two-step series-type deactivation model (constant deactivation rate k₁ >k₂). F_p was found to be the dominant variable affecting the degree of lipase deactivation, and residual activity was not associated with increasing t_e below a certain F_p energy density (2.66 mJ/cm²), implying a critical threshold for IPL-induced deactivation of lipase. From the results of fluorescence spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), we determined that IPL-induced deactivation was caused by fragmentation, leading to lipase tertiary structural changes. Furthermore, the results of FindPept analysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) indicated that the internal sensitive bonds of lipase were cleaved preferentially by IPL, such that IPL irradiation induced site-sensitive fragmentation and peptide bond cleavage.

Understanding the functional properties of bio-inorganic nanoflowers as biocatalysts by deciphering the metal-binding sites of enzymes

The biomineralisation of metal phosphates is a promising approach to develop more efficient nanobiocatalysts; however, the interactions between the protein and the inorganic mineral are poorly understood. Elucidating which protein regions most likely participate in the mineral formation will guide the fabrication of more efficient biocatalysts based on metal-phosphate nanoflowers. We have biomineralised the lipase from Thermomyces lanuginosus using three calcium, zinc and copper phosphates to fabricate different types of bio-inorganic nanoflowers. To better understand how the biomineralisation process affects the enzyme properties, we have computationally predicted the protein regions with a higher propensity for binding Ca²⁺, Cu²⁺ and Zn²⁺. These binding sites can be considered as presumable nucleation points where the biomineralisation process starts and explain why different metals can form bio-inorganic nanoflowers of the same enzyme with different functional properties. The formation of calcium, copper and zinc phosphates in the presence of this lipase gives rise to nanoflowers with different morphologies and different enzymatic properties such as activity, stability, hyperactivation and activity-pH profile; these functional differences are supported by structural studies based on fluorescence spectroscopy and can be explained by the different locations of the predicted nucleation sites for the different metals. Among the three metals used herein, the mineralisation of this lipase with zinc-phosphate enables the fabrication of bio-inorganic nanoflowers 34 times more stable than the soluble enzyme. These bio-inorganic nanoflowers were reused for 8 reaction cycles achieving 100% yield in the hydrolysis of p-nitrophenol butyrate but losing more than 50% of their initial activity after 6 operational cycles. Finally, this heterogeneous biocatalyst was more active and enantioselective than the soluble enzyme (ee = 79%(R)) towards the kinetic resolution of rac-1-phenylethyl acetate yielding the R enantiomer with ee = 84%.

Aroma Release in Wine Using Co-Immobilized Enzyme Aggregates

Aroma is a remarkable factor of quality and consumer preference in wine, representing a distinctive feature of the product. Most aromatic compounds in varietals are in the form of glycosidic precursors, which are constituted by a volatile aglycone moiety linked to a glucose residue by an O-glycosidic bond; glucose is often linked to another sugar (arabinose, rhamnose or apiose). The use of soluble β-glycosidases for aroma liberation implies the addition of a precipitating agent to remove it from the product and precludes its reuse after one batch. An attractive option from a technological perspective that will aid in removing such constraints is the use of immobilized glycosidases. Immobilization by aggregation and crosslinking is a simple strategy producing enzyme catalysts of very high specific activity, being an attractive option to conventional immobilization to solid inert supports. The purpose of this work was the evaluation of co-immobilized β-glycosidases crosslinked aggregates produced from the commercial preparation AR2000, which contains the enzymes involved in the release of aromatic terpenes in Muscat wine (α-l-arabinofuranosidase and β-d-glucopyranosidase). To do so, experiments were conducted with co-immobilized crosslinked enzyme aggregates (combi-CLEAs), and with the soluble enzymes, using an experiment without enzyme addition as control. Stability of the enzymes at the conditions of winemaking was assessed and the volatiles composition of wine was determined by SPE-GC-MS. Stability of enzymes in combi-CLEAs was much higher than in soluble form, 80% of the initial activity remaining after 60 days in contact with the wine; at the same conditions, the soluble enzymes had lost 80% of their initial activities after 20 days. Such higher stabilities will allow prolonged use of the enzyme catalyst reducing its impact in the cost of winemaking. Wine treated with combi-CLEAs was the one exhibiting the highest concentration of total terpenes (18% higher than the control) and the highest concentrations of linalool (20% higher), nerol (20% higher) and geraniol (100% higher), which are the most important terpenes in determining Muscat typicity. Co-immobilized enzymes were highly stable at winemaking conditions, so their reutilization is possible and technologically attractive by reducing the impact of enzyme cost on winemaking cost.

Effect of Water Content on the Thermal Inactivation Kinetics of Horseradish Peroxidase Freeze-Dried from Alkaline pH

The thermal inactivation of horseradish peroxidase freeze-dried from solutions of different pH (8, 10 and 11.5, measured at 25 C) and equilibrated to different water contents was studied in the temperature range from 110 to 150 C. The water contents studied (0.0, 1.4, 16.2 and 25.6 g water per 100 g of dry enzyme) corresponded to water activities of 0.0, 0.11, 0.76 and 0.88 at 4 C. The kinetics were well described by a double exponential model. The enzyme was generally more stable the lower the pH of the original solution, and for all pH values, the maximum stability was obtained at 1.4 g water/100 g dry enzyme. Values of z were generally independent of water content and of the pH of the original solution, and in the range of 15–25 °C, usually found in neutral conditions, with the exception of the enzyme freeze dried from pH 11.5 and equilibrated with phosphorus pentoxide, where a z-value of the stable fraction close to 10 C was found.

Improving the thermostability and stress tolerance of an archaeon hyperthermophilic superoxide dismutase by fusion with a unique N-terminal domain

The superoxide dismutase from the archaeon Sulfolobus solfataricus (SOD Ss ) is a well-studied hyperthermophilic SOD with crystal structure and possible thermostability factors characterized. Previously, we discovered an N-terminal domain (NTD) in a thermophilic SOD from Geobacillus thermodenitrificans NG80-2 which confers heat resistance on homologous mesophilic SODs. The present study therefore aimed to further improve the thermostability and stress tolerance of SOD Ss via fusion with this NTD. The recombinant protein, rSOD Ss , exhibited improved thermophilicity, higher working temperature, improved thermostability, broader pH stability, and enhanced tolerance to inhibitors and organic media than SOD Ss without any alterations in its oligomerization state. These results suggest that the NTD is an excellent candidate for improving stability of both mesophilic and thermophilic SOD from either bacteria or archaea via simple genetic manipulation. Therefore, this study provides a general, feasible and highly useful strategy for generating extremely thermostable SODs for industrial applications.

Vault Nanoparticles Packaged with Enzymes as an Efficient Pollutant Biodegradation Technology

Vault nanoparticles packaged with enzymes were synthesized as agents for efficiently degrading environmental contaminants. Enzymatic biodegradation is an attractive technology for in situ cleanup of contaminated environments because enzyme-catalyzed reactions are not constrained by nutrient requirements for microbial growth and often have higher biodegradation rates. However, the limited stability of extracellular enzymes remains a major challenge for practical applications. Encapsulation is a recognized method to enhance enzymatic stability, but it can increase substrate diffusion resistance, lower catalytic rates, and increase the apparent half-saturation constants. Here, we report an effective approach for boosting enzymatic stability by single-step packaging into vault nanoparticles. With hollow core structures, assembled vault nanoparticles can simultaneously contain multiple enzymes. Manganese peroxidase (MnP), which is widely used in biodegradation of organic contaminants, was chosen as a model enzyme in the present study. MnP was incorporated into vaults via fusion to a packaging domain called INT, which strongly interacts with vaults' interior surface. MnP fused to INT and vaults packaged with the MnP-INT fusion protein maintained peroxidase activity. Furthermore, MnP-INT packaged in vaults displayed stability significantly higher than that of free MnP-INT, with slightly increased Km value. Additionally, vault-packaged MnP-INT exhibited 3 times higher phenol biodegradation in 24 h than did unpackaged MnP-INT. These results indicate that the packaging of MnP enzymes in vault nanoparticles extends their stability without compromising catalytic activity. This research will serve as the foundation for the development of efficient and sustainable vault-based bioremediation approaches for removing multiple contaminants from drinking water and groundwater.

Novel extracellular medium-chain-length polyhydroxyalkanoate depolymerase from Streptomyces exfoliatus K10 DSMZ 41693: a promising biocatalyst for the efficient degradation of natural and functionalized mcl-PHAs

Cloning and biochemical characterization of a novel extracellular medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase from Streptomyces exfoliatus K10 DSMZ 41693 are described. The primary structure of the depolymerase (PhaZSex2) includes the lipase consensus sequence (serine-histidine-aspartic acid) which is known for serine hydrolases. Secondary structure analysis shows 7.9 % α-helix, 43.9 % β-sheet, 19.4 % β-turns, and 31.2 % random coil, suggesting that this enzyme belongs to the α/β hydrolase fold family, in agreement with other PHA depolymerases and lipases. The enzyme was efficiently produced as an extracellular active form in Rhodococcus and purified by two consecutive hydrophobic chromatographic steps. Matrix-assisted laser desorption-time-of-flight (MALDI-TOF) analysis of the purified enzyme revealed a monomer of 27.6 kDa with a midpoint transition temperature of 44.2 °C. Remarkably, the activity is significantly enhanced by low concentrations of nonionic and anionic detergents and thermal stability is improved by the presence of 10 % glycerol. PhaZSex2 is an endo-exohydrolase that cleaves both large and small PHA molecules, producing (R)-3-hydroxyoctanoic acid monomers as the main reaction product. Markedly, PhaZSex2 is able to degrade functionalized polymers containing thioester groups in the side chain (PHACOS), releasing functional thioester-based monomers and oligomers demonstrating the potentiality of this novel biocatalyst for the industrial production of enantiopure (R)-3-hydroxyalkanoic acids.

Laccase immobilization over multi-walled carbon nanotubes: Kinetic, thermodynamic and stability studies

The biocatalytic performance of immobilized enzyme systems depends mostly on the intrinsic properties of both biomolecule and support, immobilization technique and immobilization conditions. Multi-walled carbon nanotubes (MWCNTs) possess unique features for enzyme immobilization by adsorption. Enhanced catalytic activity and stability can be achieved by optimization of the immobilization conditions and by investigating the effect of operational parameters. Laccase was immobilized over MWCNTs by adsorption. The hybrid material was characterized by Fourier transformed infrared (FTIR) spectroscopy, scanning and transmission electron microscopy (SEM and TEM, respectively). The effect of different operational conditions (contact time, enzyme concentration and pH) on laccase immobilization was investigated. Optimized conditions were used for thermal stability, kinetic, and storage and operational stability studies. The optimal immobilization conditions for a laccase concentration of 3.75μL/mL were a pH of 9.0 and a contact time of 30min (522 Ulac/gcarrier). A decrease in the thermal stability of laccase was observed after immobilization. Changes in ΔS and ΔH of deactivation were found for the immobilized enzyme. The Michaelis-Menten kinetic constant was higher for laccase/MWCNT system than for free laccase. Immobilized laccase maintained (or even increased) its catalytic performance up to nine cycles of utilization and revealed long-term storage stability.

Click synthesis of ionic strength-responsive polyphosphazene hydrogel for reversible binding of enzymes

A chemically crosslinkable cationic polyphosphazene was synthesized and fabricated into hydrogels via thiol–ene click chemistry for reversible enzyme binding.

Operational stability of naringinase PVA lens-shaped microparticles in batch stirred reactors and mini packed bed reactors-one step closer to industry

The immobilization of naringinase in PVA lens-shaped particles, a cheap and biocompatible hydrogel was shown to provide an effective biocatalyst for naringin hydrolysis, an appealing reaction in the food and pharmaceutical industries. The present work addresses the operational stability and scale-up of the bioconversion system, in various types of reactors, namely shaken microtiter plates (volume ⩽ 2 mL), batch stirred tank reactors (volume <400 mL) and a packed-bed reactor (PBR, 6.8 mL). Consecutive batch runs were performed with the shaken/stirred vessels, with reproducible and encouraging results, related to operational stability. The PBR was used to establish the feasibility for continuous operation, running continuously for 54 days at 45°C. The biocatalyst activity remained constant for 40 days of continuous operation. The averaged specific productivity was 9.07 mmol h(-1) g enzyme(-1) and the half-life of 48 days.