Enzyme deactivation

Enzyme_Metal-Organic Framework Composites as Novel Approach for Microplastic Degradation

Plastic pollution is one of the main worldwide environmental concerns. Our lifestyle involves persistent plastic consumption, aggravating the low efficiency of wastewater treatment plants in its removal. Nano/microplastics are accumulated in living beings, pushing to identify new water remediation strategies to avoid their harmful effects. Enzymes (e. g., Candida rugosa-CrL) are known natural plastic degraders as catalysts in depolymerization reactions. However, their practical use is limited by their stability, recyclability, and economical concerns. Here, enzyme immobilization in metal-organic frameworks (CrL_MOFs) is originally presented as a new plastic degradation approach to achieve a boosted plastic decomposition in aqueous systems while allowing the catalyst cyclability. Bis-(hydroxyethyl)terephthalate (BHET) was selected as model substrate for decontamination experiments for being the main polyethylene terephthalate (PET) degradation product. Once in contaminated water, CrL_MOFs can eliminate BHET (37 %, 24 h), following two complementary mechanisms: enzymatic degradation (CrL action) and byproducts adsorption (MOF effect). As a proof-of-concept, the capacity of a selected CrL_MOF composite to eliminate the BHET degradation products and its reusability are also investigated. The potential of these systems is envisioned in terms of improving enzyme cyclability, reducing costs along with feasible co-adsorption of plastic byproducts and other harmful contaminants, to successfully remove them in a single step.

Whole-genome sequencing of Sphingobium baderi SC-1 and identification of a crucial 3-phenoxybenzoic acid-degrading gene

As an efficient degradation strain, Sphingobium baderi SC-1 can breakdown 3-phenoxybenzoic acid (3-PBA) with high proficiency. To investigate the internal factors that regulate this process, we conducted whole-genome sequencing and successfully identified the pivotal 3-PBA-degrading gene sca (1,230 bp). After sca was expressed in engineered bacteria, a remarkable degradation efficiency was observed, as 20 mg/L 3-PBA was almost completely decomposed within 24 h. The phenol was formed as one of the degradation products. Notably, in addition to their ability to degrade 3-PBA, the resting cells proficiently degraded 4'-HO-3-PBA and 3'-HO-4-PBA. In conclusion, we successfully identified and validated sca as the pivotal enzyme responsible for the efficient degradation of 3-PBA from Sphingomonas baderi, providing a crucial theoretical foundation for further explorations on the degradation potential of SC-1.

The behavior of cathepsin D during milk processing and its contribution to bitterness in a model fresh cheese

The bovine endopeptidase cathepsin D was investigated regarding its temperature-dependent inactivation and ability to form bitter peptides within a spiked model fresh cheese. Cathepsin D was found to be more susceptible than other milk endogenous peptidases to temperature treatments in skim milk. Inactivation kinetics revealed decimal reduction times of 5.6 min to 10 s in a temperature range from 60 to 80°C. High temperature and ultra-high temperature (UHT) treatments from 90 to 140°C completely inactivated cathepsin D within 5 s. A residual cathepsin D activity of around 20% was detected under pasteurization conditions (72°C for 20 s). Therefore, investigations were done to estimate the effect of residual cathepsin D activity on taste in a model fresh cheese. The UHT-treated skim milk was spiked with cathepsin D and acidified with glucono-δ-lactone to produce a model fresh cheese. A trained bitter-sensitive panel was not able to distinguish cathepsin D-spiked model fresh cheeses from the control model fresh cheeses in a triangle test. Model fresh cheese samples were also analyzed for known bitter peptides derived from casein fractions using a HPLC-tandem mass spectrometry (MS) approach. In accordance with the sensory evaluation, the MS analyses revealed that the bitter peptides investigated within the cathepsin D-spiked model fresh cheese were not found or were below the limit of detection. Even though cathepsin D may be present during the fermentation of pasteurized milk, it does not seem to be responsible for bitter peptide formation from milk proteins on its own.

Oriented bio-feeding control of the anaerobic biodegradation of ethinyl estradiol

Up to 95% of hormones are excreted into domestic wastewater with urine or feces, but their macromolecules are difficult to biodegrade. This project studies the treatment of Ethinyl Estradiol (EE₂) in swine wastewater in an Upstream Solids Reactor (USR), and explores a new method for oriented bio-feeding to regulate the anaerobic biodegradation process. It was found that the metabolism of lactic acid and propionic acid was accompanied by changes in EE₂ content, but lactic acid molecules were not readily bioavailable, so adding propionic acid was more suitable. However, controlling the pH to lower (4.73) and higher (8.73) values inhibited further fermentation of acetic acid and propionic acid, which was not favorable for the removal of EE₂. This is simply due to the fact that propionic acid as a carbon source changes the preference of the microbes for consuming EE₂. The order of the effect of addition of propionic acid on the removal of EE₂ was as follows: P₄₀₀>P₈₀₀>P₀>P₂₀₀ (addition of propionic acid). The P₄₀₀ removal efficiency increased from 60% to 85%. In the metabolism of EE₂, after oxidation, hydrolysis, ketosis, hydroxylation and enzymatic action, dienoic acid and oleic acid were generated, and there was no secondary pollution from EE₂ metabolites. In conclusion, feeding microorganisms with propionic acid can enhance the anaerobic biodegradation of EE₂, providing a new strategy for the anaerobic biodegradation and bioremediation of refractory pollutants.

Protein Stability: Enhancement and Measurement

This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.

An outlook on suicide enzyme inhibition and drug design

There have been recent renewed interests in the importance of suicide enzyme inhibition. The principal objective of this review is to investigate all types of suicide inhibitions for natural enzymes, artificial biocatalysts as well as therapeutic potential of enzyme suicide inhibition. It is discussed the suicide inhibition beneficial in drug design and treatments and non-beneficial achievements for some industrial enzymes such as HRP peroxidase enzyme. The design of biomimetic artificial enzymes explained to prevent inhibition by protecting the active site via environmental conditions. Suicide enzyme inhibition development can be the key mechanism against sever diseases such as SARS. In this report, suicide enzyme inactivation classes are classified based on target enzyme groups via their substrates.

Protein-inorganic calcium-phosphate supraparticles as a robust platform for enzyme co-immobilization

Immobilization of enzymes provides many benefits, including facile separation and recovery of enzymes from reaction mixtures, enhanced stability, and co-localization of multiple enzymes. Calcium-phosphate-protein supraparticles imbued with a leucine zipper binding domain (ZR ) serve as a modular immobilization platform for enzymes fused to the complementary leucine zipper domain (ZE ). The zippers provide high-affinity, specific binding, separating enzymatic activity from the binding event. Using fluorescent model proteins (mCherryZE and eGFPZE ), an amine dehydrogenase (AmDHZE ), and a formate dehydrogenase (FDHZE ), the efficacy of supraparticles as a biocatalytic solid support was assessed. Supraparticles demonstrated several benefits as an immobilization support, including predictable loading of multiple proteins, structural integrity in a panel of solvents, and the ability to elute and reload proteins without damaging the support. The dual-enzyme reaction successfully converted ketone to amine on supraparticles, highlighting the efficacy of this system.

New Method of Determining Kinetic Parameters for Decomposition of Hydrogen Peroxide by Catalase

The presented study investigates the kinetic properties of catalase during hydrogen peroxide decomposition reaction. A novel and simple method is hereby proposed for the determination of the enzyme deactivation rate constant (kd) and the decomposition of H2O2 reaction rate constant (kr). Available methods allow the kd constant to be determined only based on previously experimentally determined kr. The presented method differs from the conventional procedure. Known initial and final concentrations of hydrogen peroxide enable determination of both constants at the same time based on data from only one experiment. The correctness of the new method proposed here in determining the reaction rate constant was checked by comparing the obtained constant values with the calculated values according to the commonly used Aebi method. The method was used to analyze in detail the effect of pH (3–10) and temperature (10–45 °C) of the reaction medium on kinetic constants. The value of the constant kd increases together with the value of pH and temperature. In addition, the activation energy for decomposition reaction and deactivation reaction was found to be Er = 14 kJ mol−1 and Ed = 56.8 kJ mol−1 respectively.

Antioxidant and Antibacterial Peptides from Soybean Milk through Enzymatic- and Membrane-Based Technologies

Enzymatic hydrolysis of soybean milk proteins with cysteine protease papain was performed in an advanced bioreactor, operated with batch mode. In soybean milk protein hydrolysis reaction, enzyme and substrate ratio and reaction temperature were varied, ranging from 0.029:100–0.457:100 and 30–60 °C, respectively. The degree of hydrolysis of soybean milk proteins was increased with increase of enzyme and substrate (soybean milk protein) ratio. However, the degree of hydrolysis was increased due to change of reaction temperature from 30 °C to 60 °C with enzyme and substrate ratio 0.229:100 and was reduced when hydrolysis reaction was performed with enzyme and substrate ratio 0.11:100 at hydrolysis temperature 60 °C. Antioxidant capacity of enzyme-treated milk had a similar trend with degree of hydrolysis. In a later exercise, a membrane bioreactor was adopted for continuous production of antioxidant and antibacterial peptides from soybean milk. The membrane bioreactor was operated for 12 h with constant feeding. Ceramic-made tubular membrane with a pore size 20 nm was used. Application of static turbulence promoter in a membrane separation process was investigated and its positive effects, with respect to higher permeate flux and lower energy consumption in filtration process, were proven. Antioxidant capacity and antibacterial activity against Bacillus cereus of enzyme-hydrolyzed milk and permeate from membrane were confirmed.

Optimizing concentrations and contact times of cleaning and sanitizing agents for inactivating winery spoilage microorganisms

Microbial management is one of the most critical aspects of winery operations and is normally achieved via chemical control. This study sought to optimize winery cleaning and sanitation protocols for the management of winery spoilage microorganisms by applying multiple techniques commonly found in clinical health settings to winery-relevant conditions. The minimum inhibitory concentration and minimum biocidal concentration assay and a modified minimum biofilm inactivation assay were performed for three common winery spoilage yeast (S. cerevisiae, B. bruxellensis, Z. baili). Results indicate that inhibitory and biocidal concentrations vary dramatically between organisms but are largely in line with established application rates for inactivation of all cells in planktonic and biofilm physiologies. Dual-channel fluorescence staining was employed to determine minimum inactivation time for S. cerevisiae using two peracetic acid concentrations. Propidium Iodide and SYBR Green 1 stains were validated as a live/dead proxy (R2 = 0.99) and used to determine the contact time required to inactivate cell suspensions. Peracetic acid treatment trials indicate that S. cerevisiaepopulations are inactivated in five minutes or less at concentrations of 1−1.5 mg/L. In conjunction, these experiments provide insight for winemakers to critically think about cleaning and sanitation protocols and how to optimize these processes.

Enzyme kinetics approach to assess biocatalyst inhibition and deactivation caused by [bmim][Cl] ionic liquid during cellulose hydrolysis

The aim of this work was to study the inhibition and deactivation of commercial enzyme cocktail (Cellic® Htec2) in the presence of [bmim][Cl] ionic liquid employing model cellulosic substrate, carboxymethyl cellulose (CMC). It turned out from the experiments - relying on enzyme kinetics approach - that [bmim][Cl] could act as a competitive inhibitor. Furthermore, depending on the process conditions i.e. contact of enzyme solution with high concentration [bmim][Cl], severe biocatalyst inactivation should be also taken into account as a potential risk during the enzymatic cellulose hydrolysis even in as short process times as few minutes.

Protein Stability: Enhancement and Measurement

This article defines protein stability, emphasizes its importance and surveys the field of protein stabilization, with summary reference to a selection of 2009-2015 publications. One can enhance stability by, in particular, protein engineering strategies and by chemical modification (including conjugation) in solution. General protocols are set out on how to measure a given protein's (1) kinetic thermal stability, and (2) oxidative stability, and (3) how to undertake chemical modification of a protein in solution.

Storage and Lyophilization of Pure Proteins

This article outlines empirical procedures for the storage of pure proteins with preservation of high levels of biological activity. It describes simple and workable means of preventing microbial contamination and proteolytic degradation, and the use of various types of stabilizing additives. It sets out the principles of lyophilization (otherwise known as freeze-drying, a complex process comprising freezing, primary dying, and secondary drying stages). There follows a general procedure for the use of lyophilizer apparatus with emphasis on best practice and on pitfalls to avoid. The use of modulated differential scanning calorimetry to measure the glass transition temperature, a key parameter in the design and successful operation of lyophilization processes, is described.

Analysis of heterogeneity in nonspecific PEGylation reactions of biomolecules

The compositional heterogeneity associated with polymer conjugation reactions of biomolecules is analyzed for the particular case of nonspecific PEGylation reactions. It is shown that the distribution of the number of PEG moieties grafted to biomolecules such as proteins is a binomial-type function of two parameters-the reaction efficiency as well as the number of binding sites per biomolecule. The nature of this distribution implies that uniform compositions are favored for increasing number of coupling sites per biomolecule as well as for increasing efficiency of the modification process. Therefore, the binomial distribution provides a rationale for the pronounced heterogeneity that is observed for PEGylated small enzyme systems even at high coupling efficiencies. For the particular case of PEGylated trypsin it is shown that the heterogeneity results in a broad distribution of deactivation times that is captured by a stretched exponential decay model. The presented analysis is expected to apply to general modification processes of compounds in which partial functionalization of a fixed number of reactive sites is achieved by means of a nonspecific coupling reaction.

Bacterial versus fungal laccase: potential for micropollutant degradation

Relatively high concentrations of micropollutants in municipal wastewater treatment plant (WWTP) effluents underscore the necessity to develop additional treatment steps prior to discharge of treated wastewater. Microorganisms that produce unspecific oxidative enzymes such as laccases are a potential means to improve biodegradation of these compounds. Four strains of the bacterial genus Streptomyces (S. cyaneus, S. ipomoea, S. griseus and S. psammoticus) and the white-rot fungus Trametes versicolor were studied for their ability to produce active extracellular laccase in biologically treated wastewater with different carbon sources. Among the Streptomyces strains evaluated, only S. cyaneus produced extracellular laccase with sufficient activity to envisage its potential use in WWTPs. Laccase activity produced by T. versicolor was more than 20 times greater, the highest activity being observed with ash branches as the sole carbon source. The laccase preparation of S. cyaneus (abbreviated L_Sc) and commercial laccase from T. versicolor (L_Tv) were further compared in terms of their activity at different pH and temperatures, their stability, their substrate range, and their micropollutant oxidation efficiency. L_Sc and L_Tv showed highest activities under acidic conditions (around pH 3 to 5), but L_Tv was active over wider pH and temperature ranges than L_Sc, especially at near-neutral pH and between 10 and 25°C (typical conditions found in WWTPs). L_Tv was also less affected by pH inactivation. Both laccase preparations oxidized the three micropollutants tested, bisphenol A, diclofenac and mefenamic acid, with faster degradation kinetics observed for L_Tv. Overall, T. versicolor appeared to be the better candidate to remove micropollutants from wastewater in a dedicated post-treatment step.

Engineering protein stability

This article defines protein stability, emphasizes its importance and surveys some notable recent publications (2004-2008) in the field of protein stability/stabilization. Knowledge of the factors stabilizing proteins has emerged from denaturation studies and from study of thermophilic (and other extremophilic) proteins. One can enhance stability by protein engineering strategies, the judicious use of solutes and additives, immobilization, and chemical modification in solution. General protocols are set out on how to measure the kinetic thermal stability of a given protein and how to undertake chemical modification of a protein in solution.

Storage and lyophilisation of pure proteins

This article outlines empirical procedures for the storage of pure proteins with preservation of high levels of biological activity. It describes simple and workable means of preventing microbial contamination and proteolytic degradation, and the use of various types of stabilising additives. It sets out the principles of lyophilisation (otherwise known as freeze-drying, a complex process comprising freezing, primary drying and secondary drying stages), outlines a general procedure for the use of lyophiliser apparatus and mentions notable pitfalls to be avoided.

Partial nitrification/denitrification can be attributed to the slow response of nitrite oxidizing bacteria to periodic anoxic disturbances

This work aims to assess and model the behavior of both ammonium (AOB) and nitrite (NOB) oxidizing bacteria during the transition from completely anoxic to aerobic conditions. An enhanced aerobically grown culture containing AOB and NOB was subjected to anoxic conditions of varying durations from 1.5 to 12 h before its exposure to aerobic conditions. Experiments were carried out in both continuously stirred tank reactor (CSTR) and batch type reactors. Although the AOB did not exhibit any impact in their performance following the anoxic disturbance, the NOB were seriously inhibited presenting a period of reduced growth rate, which was proportional to the duration of the disturbance. This finding proves the previously postulated mechanism (NOB inhibition under periodic aerobic/anoxic operation) for achieving nitrogen removal via the partial nitrification/denitrification (PND) process as demonstrated in lab- and pilot-scale operating conditions. A mathematical model was developed to describe with sufficient accuracy the performance of AOB and NOB under aerobic, anoxic, and transient conditions in both CSTR and batch type systems. The model is able to describe the inhibitory effect of anoxic exposure to NOB by assuming enzyme deactivation (under anoxic conditions) and reactivation (adjustment of the NOB enzymatic mechanism) under aerobic conditions. The presented kinetic model is quite simple and general and therefore may be used for predicting the performance of mixed growth biological systems operating via the PND process.

Role of hydrodynamic shear on activity and structure of proteins

Proteins are important products used in industry. They may be enzymes which catalyze different reactions or they may be required for their biological activities as hormones, growth factors or therapeutics. During production and recovery, proteins are subjected to fluid forces which arise due to operations such as stirring, pumping and centrifugation. The resulting hydrodynamic shear forces may cause damage to the large molecular weight proteins, resulting in denaturation and inactivation of the protein. This is a major concern as it affects the overall efficiency of protein recovery and final yield of the product. A considerable amount of research has been devoted to studying the effects of hydrodynamic shear stress on proteins, especially with respect to the enzymes. Enzymes are subjected to shear stresses during their production in fermentors, during isolation and purification steps in downstream operations and also during their use in enzyme reactors, especially if stirred reactors are employed to perform enzyme catalysed reactions. The present review discusses the effects of fluid shear stress on proteins including enzymes. A brief description on deactivation has been included in order to understand the effect of shear on the deactivation kinetics of proteins. The model systems used to subject proteins to shear and some unit operations during protein processing or use wherein they are exposed to shear stresses have also been presented. The significance of shear effects in designing bioprocesses involving shear sensitive biocatalysts as well as suggestions for future work have also been given.

Functionally-stabilized proteins — A review

The maintenance or stabilization of protein or enzyme function is of vital importance in Biotechnology. Investigations of thermophilic organisms, studies of denaturation and the use of enzymes in organic solvents have each contributed to an understanding of protein stability. Enzymes can reliably and reproducibly be stabilized by variety of means including immobilization, use of additives, chemical modification in solution and protein engineering. Examples of each of these are discussed. With these recent advances it appears that a rational strategy for achieving a particular stabilized enzyme or protein may be within reach.

Substrate inactivation of enzymes in vitro and in vivo

Some enzymes are inactivated by their natural substrates during catalytic turnover, limiting the ultimate extent of reaction. These enzymes can be separated into three broad classes, depending on the mechanism of the inactivation process. The first type is enzymes which use molecular oxygen as a substrate. The second type is inactivated by hydrogen peroxide, which is present either as a substrate or a product, and are stabilized by high catalase activity. The oxidation of both types of enzymes shares common features with oxidation of other enzymes and proteins. The third type of enzyme is inactivated by non-oxidative processes, mainly reversible loss of cofactors or attached groups. Sub classes are defined within each broad classification based on kinetics and stoichiometry. Reaction-inactivation is in part a regulatory mechanism in vivo, because specific proteolytic systems give rapid turnover of such labelled enzymes. The methods for enhancing the stability of these enzymes under reaction conditions depends on the enzyme type. The kinetics of these inactivation reactions can be used to optimize bioreactor design and operation.