Modeling the effect of temperature and pH on activity of enzymes: the case of phytases

Minimizing anti-nutritional factors in wet protein extraction from Swedish faba beans through the application of response surface methodology

Faba beans, rich in protein and ideal for Swedish cultivation, are limited in food industry use due to anti-nutritional factors (ANFs) that hinder nutrient absorption. An extraction method was developed in our study to mitigate ANFs in faba beans, using aqueous alkaline methods and isoelectric precipitation with differential salt concentration. This method yielded 15.8 g of protein per 100 g of flour, with a protein concentration exceeding 83% of the total extract. It reduced ANFs like phytic acid (28.0%), lectins (87.5%), vicine (98.5%), and convicine (99.7%). Extraction conditions were optimized using response surface methodology, identifying pH 6, 2 h, and 20 °C as the most effective parameters, achieving an 86% reduction in phytic acid, closely matched the model's predictions (R2 = 0.945). This method effectively reduced ANFs, offering a sustainable approach for producing proteins suitable for diverse food products, including plant-based alternatives.

Mathematical Description of the Enzymatic Activity of Proteins with Ionizable Groups Exhibiting Deviations from the Henderson-Hasselbalch Equation

The ionization equilibrium implied in the calculation of the specific activity is classically described through the Henderson-Hasselbalch equation. An extension for the description of anomalous ionization profiles using the Hill equation is presented in this communication. The proposed framework was applied to the description of the specific enzymatic activity curve as a function of pH of five enzymes presenting different ionization states in their active site. The developed equation improves the description of relative enzymatic curves that deviate from the bell curve predicted by the application of the Henderson-Hasselbalch equation, regardless of the ionization scheme related to the active site.

Pulse-Cereal Blend Extrusion for Improving the Antioxidant Properties of a Gluten-Free Flour

Extrusion is an interesting technological tool that facilitates pulse formulation into flour mixtures, with tailored fibre content, total antioxidant capacity (TAC) and glycemic index (GI) among other components in final formulas. The gluten-free (GF) market has significantly grown during the last years. GF products have evolved from specialty health foods to products targeted to the general population and not only associated to celiac consumers. This study evaluates how temperature, cereal base (rice/corn) and pulse concentration affect extruded flour properties and which conditions are more efficient to develop a gluten-free flour with high TAC and low GI. Additionally, it evaluated the effect of this optimal formula after the baking process. The results showed an increase of total phenol (TP) and antioxidant activity with extrusion, with a temperature-dependent effect (130 °C ≥ 120 °C ≥ 110 °C), which may imply an enhanced bioaccessibility of phenolics compounds after extraction. Extrusion increased GI in comparison to native flour; however, a dough temperature of 130 °C resulted in a significantly (p ≤ 0.05) lower GI than that observed for 110-120 °C doughs, probably associated to the pastification that occurred at higher temperatures, which would decrease the degree of gelatinization of the starches and therefore a significant (p ≤ 0.05) GI reduction. Corn-lentil flour showed higher antioxidant properties and lower GI index in comparison with rice-lentil blends. The formulation of the optimal blend flour into a baked product (muffin) resulted in a significant loss of antioxidant properties, with the exception of the reducing power (FRAP), although the final antioxidant values of the baked product were in the range of the original native flour blend before any process.

An integrated modular framework for modeling the effect of ammonium on the sialylation process of monoclonal antibodies produced by CHO cells

BACKGROUND

Monoclonal antibodies (mABs) have emerged as one of the most important therapeutic recombinant proteins in the pharmaceutical industry. Their immunogenicity and therapeutic efficacy are influenced by post-translational modifications, specifically the glycosylation process. Bioprocess conditions can influence the intracellular process of glycosylation. Among all the process conditions that have been recognized to affect the mAB glycoforms, the detailed mechanism underlying how ammonium could perturb glycosylation remains to be fully understood. It was shown that ammonium induces heterogeneity in protein glycosylation by altering the sialic acid content of glycoproteins. Hence, understanding this mechanism would aid pharmaceutical manufacturers to ensure consistent protein glycosylation.

METHODS

Three different mechanisms have been proposed to explain how ammonium influences the sialylation process. In the first, the inhibition of CMP-sialic acid transporter, which transports CMP-sialic acid (sialylation substrate) into the Golgi, by an increase in UDP-GlcNAc content that is brought about by the augmented incorporation of ammonium into glucosamine formation. In the second, ammonia diffuses into the Golgi and raises its pH, thereby decreasing the sialyltransferase enzyme activity. In the third, the reduction of sialyltransferase enzyme expression level in the presence of ammonium. We employed these mechanisms in a novel integrated modular platform to link dynamic alteration in mAB sialylation process with extracellular ammonium concentration to elucidate how ammonium alters the sialic acid content of glycoproteins.

RESULTS

Our results show that the sialylation reaction rate is insensitive to the first mechanism. At low ammonium concentration, the second mechanism is the controlling mechanism in mAB sialylation and by increasing the ammonium level (< 8 mM) the third mechanism becomes the controlling mechanism. At higher ammonium concentrations (> 8 mM) the second mechanism becomes predominant again.

CONCLUSION

The presented model in this study provides a connection between extracellular ammonium and the monoclonal antibody sialylation process. This computational tool could help scientists to develop and formulate cell culture media. The model illustrated here can assist the researchers to select culture media that ensure consistent mAB sialylation.

Single step immobilization of CMCase within agarose gel matrix: Kinetics and thermodynamic studies

In the current study, CMCase from Bacillus licheniformis KIBGE-IB2 was immobilized within the matrix of agarose gel through entrapment technique. Maximum immobilization yield (%) of the enzyme was obtained when 2.0 % agarose was used. The activation energy (E_a) of the enzyme increased from 16.38 to 44.08 kJ mol^-1 after immobilization. Thermodynamic parameters such as activation energy of deactivation (ΔG_d), enthalpy (ΔH_d) and entropy (ΔS_d) of deactivation, deactivation rate constant (K_d), half-life (t_1/2), D-value and z-value were calculated for native/free and immobilized CMCase. The maximum reaction rate (V_max) of the native enzyme was found to be 8319.47 U ml^-1 min^-1, which reduced to 7218.1 U ml^-1 min^-1after immobilization process. However, the Michaelis-Menten constant (K_m) value of the enzyme increased from 1.236 to 2.769 mg ml^-1 min^-1 after immobilization. Immobilized enzyme within agarose gel matrix support can be reuse up to eight reaction cycles. Broad stability profile and improved catalytic properties of the immobilized CMCase indicated that this enzyme can be a plausible candidate to be used in various industrial processes.

Horseradish peroxidase-mediated decolourization of Orange II: modelling hydrogen peroxide utilization efficiency at different pH values

Enzymatic decolourization of azo-dyes could be a cost-competitive alternative compared to physicochemical or microbiological methods. Stoichiometric and kinetic features of peroxidase-mediated decolourization of azo-dyes by hydrogen peroxide (P) are central for designing purposes. In this work, a modified version of the Dunford mechanism of peroxidases was developed. The proposed model takes into account the inhibition of peroxidases by high concentrations of P, the substrate-dependant catalatic activity of peroxidases (e.g. the decomposition of P to water and oxygen), the generation of oxidation products (OP) and the effect of pH on the decolourization kinetics of the azo-dye Orange II (OII). To obtain the parameters of the proposed model, two series of experiments were performed. In the first set, the effects of initial P concentration (0.01-0.12 mM) and pH (5-10) on the decolourization degree were studied at a constant initial OII concentration (0.045 mM). Obtained results showed that at pH 9-10 and low initial P concentrations, the consumption of P was mainly to oxidize OII. From the proposed model, an expression for the decolourization degree was obtained. In the second set of experiments, the effect of the initial concentrations of OII (0.023-0.090 mM), P (0.02-4.7 mM), HRP (34-136 mg/L) and pH (5-10) on the initial specific decolourization rate (q₀) was studied. As a general rule, a noticeable increase in q₀ was observed for pHs higher than 7. For a given pH, q₀ increased as a function of the initial OII concentration. Besides, there was an inhibitory effect of high P concentrations on q₀. To asses the possibility of reusing the enzyme, repeated additions of OII and P were performed. Results showed that the enzyme remained active after six reuse cycles. A satisfactory accordance between the change of the absorbance during these experiments and absorbances calculated using the proposed model was obtained. Considering that this set of data was not used during the fitting procedure of the model, the agreement between predicted and experimental absorbances provides a powerful validation of the model developed in the present work.

DNA extraction in Echinococcus granulosus and Taenia spp. eggs in dogs stool samples applying thermal shock

The extraction of DNA in taeniid eggs shows complications attached to the composition of stool samples and the high resistance of eggs to degradation. The objective of this study was to test a method of DNA extraction in taeniid eggs by applying a thermal shock to facilitate the chemical-enzymatic degradation of these elements. A group of six tubes containing 1 ml of dog stool sample was spiked with eggs of Echinococcus granulosus and another group of six with Taenia pisiformis. Samples were floated with supersaturated sugar solution and centrifuged. The upper portion of each tube (500 μl) was aspirated and deposited in 1.5 ml tubes. Three tubes from each group were incubated at -20 °C and then at 90 °C, the remaining three from each group, incubated at room temperature. Proteinase K and lysis buffer were added to each tube and incubated for 12 h at 58 °C. The lysis effect was evaluated by microscopy at 3, 6 and 12 h and integrity by electrophoresis in 1% agarose gels. With the same experimental scheme, the thermal shock effect was evaluated in extractions of 1, 2, 3 and 4 eggs of each species and the DNA was quantified. Additionally, the protocol was applied in samples of 4 dogs diagnosed with natural infection by Taeniidae worms. Finally, all the extractions were tested by PCR amplification. Both E. granulosus and T. pisiformis eggs showed a similar response in the tests. In samples without treatment, the lysis effect was poor and showed no differences over time, but in those subjected to thermal shock, eggs degradation increased with time. In both treatments, there was no DNA loss integrity. The protocol applied to limited amounts of eggs yielded PCR products in 100% of the samples exposed to thermal shock, allowing PCR amplifications up to 1 egg. In non-exposed samples, the results were not replicable. However, DNA quantification showed low values in both treatments. In turn, DNA extractions with thermal shock in infected dog samples finally yielded PCR amplifications in 100%. It was concluded that thermal shock facilitates the DNA extraction for molecular analysis in taeniid eggs. The technique is effective extracting DNA even from a single egg and also to analyze natural infections samples with a relatively simple implementation.

Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library

BACKGROUND

Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance.

RESULTS

Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-β-d-galactopyranoside, pNP-β-d-xylopyranoside, pNP-α-l-arabinopyranoside or pNP-α-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a β-galactosidase (74%) and (2) a β-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The β-galactosidase- and β-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the β-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50 °C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant α-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding α-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' α-glucosidase activity.

CONCLUSION

Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.

Mechanistic Modeling of the Effects of Acidosis on Thrombin Generation

Supplemental Digital Content is available in the text.

Published ahead of print April 2, 2015

BACKGROUND:

Acidosis, a frequent complication of trauma and complex surgery, results from tissue hypoperfusion and IV resuscitation with acidic fluids. While acidosis is known to inhibit the function of distinct enzymatic reactions, its cumulative effect on the blood coagulation system is not fully understood. Here, we use computational modeling to test the hypothesis that acidosis delays and reduces the amount of thrombin generation in human blood plasma. Moreover, we investigate the sensitivity of different thrombin generation parameters to acidosis, both at the individual and population level.

METHODS:

We used a kinetic model to simulate and analyze the generation of thrombin and thrombin–antithrombin complexes (TAT), which were the end points of this study. Large groups of temporal thrombin and TAT trajectories were simulated and used to calculate quantitative parameters, such as clotting time (CT), thrombin peak time, maximum slope of the thrombin curve, thrombin peak height, area under the thrombin trajectory (AUC), and prothrombin time. The resulting samples of parameter values at different pH levels were compared to assess the acidosis-induced effects. To investigate intersubject variability, we parameterized the computational model using the data on clotting factor composition for 472 subjects from the Leiden Thrombophilia Study. To compare acidosis-induced relative parameter changes in individual (“virtual”) subjects, we estimated the probabilities of relative change patterns by counting the pattern occurrences in our virtual subjects. Distribution overlaps for thrombin generation parameters at distinct pH levels were quantified using the Bhattacharyya coefficient.

RESULTS:

Acidosis in the range of pH 6.9 to 7.3 progressively increased CT, thrombin peak time, AUC, and prothrombin time, while decreasing maximum slope of the thrombin curve and thrombin peak height (P < 10^–5). Acidosis delayed the onset and decreased the amount of TAT generation (P < 10^–5). As a measure of intrasubject variability, maximum slope of the thrombin curve and CT displayed the largest and second-largest acidosis-induced relative changes, and AUC displayed the smallest relative changes among all thrombin generation parameters in our virtual subject group (1-sided 95% lower confidence limit on the fraction of subjects displaying the patterns, 0.99). As a measure of intersubject variability, the overlaps between the maximum slope of the thrombin curve distributions at acidotic pH levels with the maximum slope of the thrombin curve distribution at physiological pH level systematically exceeded analogous distribution overlaps for CT, thrombin peak time, and prothrombin time.

CONCLUSIONS:

Acidosis affected all quantitative parameters of thrombin and TAT generation. While maximum slope of the thrombin curve showed the highest sensitivity to acidosis at the individual-subject level, it may be outperformed by CT, thrombin peak time, and prothrombin time as an indicator of acidosis at the subject-group level.

Soaking and extrusion effects on physicochemical parameters, phytic acid, nutrient content and mineral bio-accessibility of whole rice grain

A combination of soaking and extrusion processes of whole rice grain was studied. The effects of temperature (35-55 °C) and time (24-48 h) of soaking treatment on phytic acid (PA), protein and ashes losses using a factorial design were evaluated. Taking into account ash, protein and PA losses, whole rice was soaked 24 h at 45 °C and extruded using a Brabender single screw extruder. Effects of extrusion temperature (160-190 °C) and moisture content (14-19 g/100 g) on product characteristics were evaluated using surface response methodology. Values corresponding to the different responses were: Expansion (1.64-3.28), Specific Volume (5.68-11.06 cm(3)/g), Water absorption (3.41-4.43 mL/g) and Solubility (45.44-66.20 g/100 g). The content of PA was reduced from 740.09 to 163.47 mg/100 g (77%) after both processes, resulting in a higher mineral bio-accessibility, and a 7.3% decrease of protein digestibility. Total soluble phenolics and trolox equivalent antioxidant capacity (TEAC) were affected according to the treatment. Both treatments were important to obtain a nutritionally improved whole grain product.

A new and general model to describe, characterize, quantify and classify the interactive effects of temperature and pH on the activity of enzymes

The common approachvs.the modern approach to analyze the effects of temperature and pH on the activity of enzymes.

Cultivation Conditions for Phytase Production from Recombinant Escherichia coli DH5α

Response surface methodology (RSM) was used to optimize the cultivation conditions for the production of phytase by recombinant Escherichia coli DH5α. The optimum predicted cultivation conditions for phytase production were at 3 hours seed age, a 2.5% inoculum level, an L-arabinose concentration of 0.20%, a cell concentration of 0.3 (as measured at 600 nm) and 17 hours post-induction time with a predicted phytase activity of 4194.45 U/mL. The model was validated and the results showed no significant difference between the experimental and the predicted phytase activity (P = 0.305). Under optimum cultivation conditions, the phytase activity of the recombinant E. coli DH5α was 364 times higher compared to the phytase activity of the wild-type producer, Enterobacter sakazakii ASUIA279. Hence, optimization of the cultivation conditions using RSM positively increased phytase production from recombinant E. coli DH5α.

Activity stabilization of Aspergillus niger and Escherichia coli phytases immobilized on allophanic synthetic compounds and montmorillonite nanoclays

The aim of this work was to study the stabilization of the activity of two commercial microbial phytases (Aspergillus niger and Escherichia coli) after immobilization on nanoclays and to establish optimal conditions for their immobilization. Synthetic allophane, synthetic iron-coated allophanes and natural montmorillonite were chosen as solid supports for phytase immobilization. Phytase immobilization patterns at different pH values were strongly dependent on both enzyme and support characteristics. After immobilization, the residual activity of both phytases was higher under acidic conditions. Immobilization of phytases increased their thermal stability and improved resistance to proteolysis, particularly on iron-coated allophane (6% iron oxide), which showed activation energy (E(a)) and activation enthalpy (ΔH(#)) similar to free enzymes. Montmorillonite as well as allophanic synthetic compounds resulted in a good support for immobilization of E. coli phytase, but caused a severe reduction of A. niger phytase activity.