Study of fumarase activity in non-conventional media. Part I

Fumarase catalysed hydration of fumarate was investigated in water/organic solvent one-phase systems. The organic solvents used were ethylene glycol, glycerol and dimethylformamide. The effects of the amount of organic solvent on the maximum velocity (V_max), the Michaelis-Menten constant (K_M) and the equilibrium constant (K_eq) were studied in all the reaction media. Together with a denaturing power of the solvent evidenced by a systematic decrease of V_max also a surprising decrease of the K_M was registered as the percentage of organic solvent in the reaction media was increased. While the equilibrium constant of the reaction (K_eq = [l-malate]/[fumarate]) decreased when the percentage of organic solvent was raised. An interpretation of these facts was given. Time-dependent denaturation was also investigated and glycerol resulted the less denaturing of the solvents used, while the aprotic DMF exhibited the highest deactivation.     

Carboxypeptidase Y-Catalyzed Reaction in Systems Containing Organic Solvent

The effect of organic solvents on carboxypeptidase Y (a serine carboxypeptidase from yeast)-catalyzed hydrolysis of amino acid ester and peptide synthesis from N-acyl amino acid ester and amino acid amide was investigated.

The K_m value of ester hydrolysis increased with an increase in the solvent content. Dioxane was the most effective and dimethyl sulfoxide (DMSO) the least, whilst K_cat showed a tendency to increase slightly in N, N-dimethylformamide (DMF) and DMSO. For dioxane and acetonitrile (MeCN) a maximum was observed.

In peptide formation from Fua-Phe-OEt and Gly-NH₂, dioxane and MeCN supported high product yield at molar fractions smaller than ca. 0.05 but the yield decreased significantly at higher fractions, although a relatively constant selectivity (ratio of the peptide bond formed to the ester consumed) was maintained. DMSO gave rather low peptide yields and selectivity even at lower molar fractions. DMF showed an intermediate tendency.

An apparent saturation parameter of the amine component was evaluated and the dissociation constant of a complex between acyl-enzyme and amino acid amide (K_n), as well as the rate constant of aminolysis exerted by the amino acid amide bound correctly on the enzyme (K_n), was calculated by initial rate analysis of peptide formation. In contrast to K_m values, K_n decreased with increasing concentrations of organic cosolvent. while a suppressive effect was observed (except for DMSO) on the K_n parameter.

Effects of the solvent practically immiscible in water was also studied by use of the enzyme physically “immobilized” on glass beads.     

Biocatalysis of lipoxygenase in selected organic solvent media

The biocatalysis of purified soybean lipoxygenase (LOX) (EC 1.13.11.12), using linoleic acid as a substrate model, was investigated in selected organic solvent media, including chloroform, dichloromethane, hexane, iso-octane, octane and toluene. The results indicated that there was a 2.6-fold increase in LOX activity in the monophasic iso-octane medium compared to that obtained in the aqueous medium. The results also showed that there was an increase of 2.2- and 1.8-fold in LOX activity in the monophasic reaction media of octane and hexane, respectively. However, an inhibitory effect on enzyme activity was observed when the monophasic reaction media of toluene, chloroform and dichloromethane were used. In addition, the results showed that the optimum concentration of octane and iso-octane in the biphasic medium containing the organic solvent and Tris–HCl buffer solution, was determined to be 3.5% and 4%, respectively, for LOX activity. Moreover, the biocatalysis of LOX in a ternary micellar system, containing either 3.5% octane or 4% iso-octane, Tris–HCl buffer solution and an emulsifier, resulted in an overall increase in enzyme activity. The K_m and V_max values, substrate specificity, optimum protein concentration, optimum reaction temperature as well as the enzymatically catalyzed end-products were investigated for LOX biocatalysis in both ternary micellar systems.     

A kinetic study of almond-β-glucosidase catalysed synthesis of hexyl-glycosides in low aqueous media: Influence of glycosyl donor and water activity

A variety of alkyl and aryl glycosides were investigated as substrates for almond β-glucosidase catalysed synthesis of hexyl-β- -glycosides in low aqueous hexanol media. The rate-limiting step in the organic media was determined to be the glycosylation of the enzyme. The kinetic constants V_max, K_m (glycosyl donor) and V_max/K_m were all influenced by the water activity and they all increased in value with increasing water activity. The increase in V_max/K_m was mainly determined by the increase in V_max and a plot of log(V_max/K_m) versus water activity resulted in a straight line with similar slopes for all glycosides but with different absolute values and thus the most reactive substrate p-nitrophenyl glucoside was the best one in the entire water activity range studied (0.53–0.96). The preference for the two competing acceptors, hexanol and water, was not affected by the aglycon part of the glucoside. Surprisingly, the ratio between trans glycosylation and hydrolysis increased with increasing water activity. A decrease in water activity caused an increase in equilibrium yield of hexyl glycoside, as expected, but was not beneficial for the kinetically controlled yield.     

Denaturation capacity: a new quantitative criterion for selection of organic solvents as reaction media in biocatalysis.

The process of reversible denaturation of several proteins (alpha-chymotrypsin, trypsin, laccase, chymotrypsinogen, cytochrome c and myoglobin) by a broad series of organic solvents of different nature was investigated using both our own and literature data, based on the results of kinetic and spectroscopic measurements. In all systems studied, the denaturation proceeded in a threshold manner, i.e. an abrupt change in catalytic and/or spectroscopic properties of dissolved proteins was observed after a certain threshold concentration of the organic solvent had been reached. To account for the observed features of the denaturation process, a thermodynamic model of the reversible protein denaturation by organic solvents was developed, based on the widely accepted notion that an undisturbed water shell around the protein globule is a prerequisite for the retention of the native state of the protein. The quantitative treatment led to the equation relating the threshold concentration of the organic solvent with its physicochemical characteristics, such as hydrophobicity, solvating ability and molecular geometry. This equation described well the experimental data for all proteins tested. Based on the thermodynamic model of protein denaturation, a novel quantitative parameter characterizing the denaturing strength of organic solvents, called the denaturation capacity (DC), was suggested. Different organic solvents, arranged according to their DC values, form the DC scale of organic solvents which permits theoretical prediction of the threshold concentration of any organic solvent for a given protein. The validity of the DC scale for this kind of prediction was verified for all proteins tested and a large number of organic solvents. The experimental data for a few organic solvents, such as formamide and N-methylformamide, did not comply with equations describing the denaturation model. Such solvents form the group of so-called 'bad' solvents; reasons for the occurrence of 'bad' solvents are not yet clear. The DC scale was further extended to include also highly nonpolar solvents, in order to explain the well-known ability of enzymes to retain catalytic activity and stability in biphasic systems of the type water/water-immiscible organic solvent. It was quantitatively demonstrated that this ability is accounted for by the simple fact that nonpolar solvents are not sufficiently soluble in water to reach the inactivation threshold concentration.     

Heat Effects of Dehydration of Human Serum Albumin in Hydrophilic Organic Solvents

A thermochemical model for describing the transfer of water from the protein phase to the organic solvent liquid phase and for determining how the solvation ability of organic solvents affects this process was developed. Enthalpy changes on the interaction of dried and hydrated human serum albumin (HSA) with hydrophilic organic solvents (dimethyl sulfoxide, formamide, ethanol, methanol and acetic acid) and water were measured by isothermal calorimetry at 25 °C. The initial hydration level of human serum albumin was varied in the entire water content range from 0–30 % [g water/g HSA]. The dependence of the interaction enthalpies on the initial water content is complex. The interaction enthalpies of the dried HSA with organic solvents are exothermic. At low water contents (less than 0.1 g/g), there is a sharp increase in the interaction enthalpy values. At the highest water contents (more than 0.2 g/g), the interaction enthalpies are endothermic for acetic acid and formamide and exothermic for DMSO, methanol, and ethanol. These thermochemical data were analyzed in conjunction with the results for the water adsorption in organic solvents to calculate the molar enthalpies of dehydration of HSA in organic liquids. It was found that the dehydration enthalpy changes may be endothermic or exothermic depending on the initial water content and the water solvation enthalpy value. From the results obtained, it can be concluded that: (i) only the solvation of water by hydrophilic organic solvent determines the changes in the dehydration enthalpy values, and (ii) the data for the enthalpies of solvation of water by the solvent at infinite dilution reflect this effect.     

Comparative molecular field analysis and QSAR on substrates binding to cytochrome p450 2D6

In this study, we utilized comparative molecular field analysis (CoMFA) to gain a better understanding of the steric and electrostatic features of the cytochrome P450 2D6 (CYP2D6) active site. The training set consists of 24 substrates with reported K_M values from liver microsomal CYP2D6 spanning an activity range of almost three log units. The low energy conformers were fit by root mean square (RMS) to minaprine at the site of metabolism and to the protonated nitrogen. In this manner, we constructed two CoMFA models, one model with a distance constraint and another without. The model with the distance parameter (non-crossvalidated R²=0.99) was approximately equal to the CoMFA without a distance parameter (non-cross-validated R²=0.98). Validation of our CoMFA was accomplished by predicting the K_M values of 15 diverse CYP2D6 substrates not in the original training set resulting in a predictive R²=0.62. Finally, we also pursued correlations of pK_a and log P with CYP2D6 substrate K_M in an effort to investigate other physicochemical properties.     

Kinetic characterization of chiral biocatalysis of cycloarenes by the camphor 5-monooxygenase enzyme system

Redox enzyme mediated biocatalysis has the potential to regio- and stereo-specifically oxidize hydrocarbons producing valuable products with minimal by-product formation. In vitro reactions of the camphor (cytochrome P-450) 5-monooxygenase enzyme system with naphthalene-like substrates yield stereospecifically hydroxylated products from nonactivated hydrocarbons. Specifically, the enzyme system catalyzes the essentially stereospecific conversion of the cycloarene, tetralin (1,2,3,4-tetrahydronaphthalene) to (R)-1-tetralol ((R)-(−)-1,2,3,4-tetrahydro-1-naphthol). It is shown that this reaction obeys Michaelis–Menten kinetics and that interactions between the enzyme subunits are not affected by the identity of the substrate. This subunit independence extends to the efficiency of NADH usage by the enzyme system—subunit ratios do not effect efficiency, but substrate identity does. Tetralin is converted at an efficiency of 13±3%, whereas (R)-1-tetralol is converted at 7.8±0.7%. A model of this system based on Michaelis–Menten parameters for one subunit (Pdx: K_M=10.2±2 μM) and both substrates (tetralin: K_M=66±26 μM, ν_max=0.11±0.04 s⁻¹, and (R)-1-tetralol: K_M=2800±1300 μM, ν_max=0.83±0.22 s⁻¹) is presented and used to predict the consumption and production of all substrates, products and cofactors.     

Histidine 454 plays an important role in polymerization of human glutamate dehydrogenase

Although previous chemical modification studies have suggested several residues to be involved in the maintenance of the quaternary structure of glutamate dehydrogenase (GDH), there are conflicting views for the polymerization process and no clear evidence has been reported yet. In the present study, cassette mutagenesis at seven putative positions (Lys333, Lys337, Lys344, Lys346, Ser445, Gly446, and His454) was performed using a synthetic human GDH gene to examine the polymerization process. Of the mutations at the seven different sites, only the mutagenesis at His454 results in depolymerization of the hexameric GDH into active trimers as determined by HPLC gel filtration analysis and native gradient polyacrylamide gel electrophoresis. The mutagenesis at His454 has no effects on expression or stability of the protein. The K_M values for NADH and 2-oxoglutarate were 1.5-fold and 2.5-fold greater, respectively, for the mutant GDH than for wild-type GDH, indicating that substitution at position 454 had appreciable effects on the affinity of the enzyme for both NADH and 2-oxoglutarate. The V_max values were similar for wild-type and mutant GDH. The k_cat/K_M value of the mutant GDH was reduced up to 2.8-fold. The decreased efficiency of the mutant, therefore, results from the increase in K_M values for NADH and 2-oxoglutarate. The results with cassette mutagenesis and HPLC gel filtration analysis suggest that His454 is involved in the polymerization process of human GDH.     

Hydrolytic reactions in two-phase systems. Effect of water-immiscible organic solvents on stability and activity of acid phosphatase, beta-glucosidase, and beta-fructofuranosidase.

The stability and activity of three hydrolytic enzymes, acid phosphatase (EC 3.1.3.2), beta-fructofuranosidase (EC 3.2.1.26), and beta-glucosidase (EC 3.2.1.4), were studied at 30 degrees C in two-phase systems. They were prepared with equal quantities of buffered water and a water-immiscible organic solvent. Low-molecular-weight acetates and paraffins were tested in this investigation. The kinetic constant of storage inactivation was correlated with the logarithm of solvent polarity. Enzyme stability in the presence of organic phases, whose log P value was included in 1.2-2.2, was greater than the one measured in pure buffered aqueous media. On the other hand, a dramatic enzyme denaturation took place making use of solvents at higher log P-value. Experiments carried out during the 24-h operation clarified that the reaction yield does not depend solely on solvent polarity. Acid phosphatase and beta-glucosidase, which are less resistant than beta-fructofuranosidase to temperature and shear in buffered solutions, showed especially significant enhancement of catalytic activity when hydrolysis was performed with the addition of acetates (50% v/v).     

Biocatalysis of tyrosinase using catechin as substrate in selected organic solvent media

The enzymatic activity of mushroom tyrosinase was investigated using catechin as substrate in selected organic solvent media. The results showed that optimal tyrosinase activity was obtained at pH 6.2, 6.6, 6.0 and 6.2 in the organic solvent media of heptane, toluene, dichloromethane, and dichloroethane, respectively, and at a temperature between 25°C and 27.5°C. In addition, the kinetic studies showed that the K_m values were 5.38, 1.03, 2.52 and 4.03 mM, for the tyrosinase-catechin biocatalysis in the reaction media of heptane, toluene, dichloromethane, and dichloroethane, respectively, while the corresponding V_max values were 1.22×10⁻³, 0.33×10⁻³, 1.47×10⁻³ and 1.20×10⁻³ δA per μg protein per second, respectively. The use of acetone as co-solvent for the tyrosinase-catechin biocatalysis showed that acetone concentrations ranging from 5% to 30% (v/v) in the heptane reaction medium produced a decrease of 4.3% to 96.7% in tyrosinase activity. The results also indicated that the presence of 12.5% acetone in the reaction medium of dichloromethane, and 22.0% in those of toluene and dichloroethane produced a maximal increase of 42.6%, 92.1% and 71.8%, respectively, in tyrosinase activity. However, the overall findings indicated that additional increases in acetone concentration resulted in an inhibition of tyrosinase activity.     

Catalysis by Laccase (From Coriolus uersicolor) in Microheterogeneous Media of the Water/Organic Solvent/Surfactant Type

Catalysis by laccase from Coriolus uersicolor solubilized in the ternary systems of surfactant/water/organic solvent type, namely, Aerosol OT/water/octane, Brij 56/water/cyclohexane and egg lecithin/water/octane + pentanol + methanol mixture, has been studied. The laccase activity is found to depend, in principle, not only on the water/surfactant molar ratio, but on the surfactant concentration (with its hydration degree being constant) as well. The following inferences should be emphasized. Firstly, in all the systems under study, the catalytic activity (k_cat) of laccase entrapped into surfactant reversed micelles increases more than 50 times (when the surfactant concentration is extrapolated to zero) compared with the k_cat value in aqueous solution. Secondly, the catalytic activity (k_cat) of laccase entrapped in hydrated Aerosol OT aggregates, having lamellar, reversed cylindrical (hexagonal) and reversed micellar structure, depends greatly on the aggregate type. In other words, the phase transitions, i.e. an alteration in the packing of hydrated Aerosol OT molecules, evokes a sharp reversible change in the enzymatic activity. Thirdly, in the same phase, the catalytic activity of the solubilized enzyme depends on the linear dimensions of water cavities inside the surfactant aggregates (i.e. on the water content in the system under study). All these effects, regulating enzymatic activity, are probably caused by an alteration of the conformational mobility of laccase molecules incorporated into the inner polar cavities inside the surfactant aggregates.     

Development of immunosensors for the analysis of 1-naphthol in organic media

Immunosensor systems have been developed for the rapid determination of 1-naphthol. In this work, the comparison of performance of immunosensors working in aqueous and organic media was done. Direct, indirect and capture formats were studied. Immunoreagents were immobilized on controlled pore glass (CPG), hidroxysuccinimide agarose gel or on azlactone Protein A/G supports. The Protein A/G-based sensor showed the best performance. In aqueous media, a LOD of 16.2 microg l(-1) and a DR of 33.7-586.6 microg l(-1) were achieved employing Tween 20 at a concentration ranging from 0.01 to 0.05% v/v. Maximum sensitivity was reached with 0.025% of surfactant. Binary mixtures of methanol or acetonitrile with aqueous buffer and ternary mixtures of methanol/isopropanol or ethyl acetate/methanol with the same buffer were studied as organic media. The mixture 50% MeOH-50% 20 mM sodium phosphate, pH 8, with 0.05% (v/v) Tween 20 resulted to be the best. A detection limit of 12.0 microg l(-1) and a dynamic range of 53.6-17,756.0 microg l(-1) were reached. The recycling of Protein A/G-based sensor working in this media was about 300 assays. Preconcentration factors around 250 were achieved using methanol as extracting solvent. It has been demonstrated that the technique can be successful in carrying out the analysis of low solubility in water analytes, such as 1-naphthol. The sensors developed can use higher concentrations of organic solvent (up to 50% methanol) compared to ELISA. On the other hand, the advantage of preconcentration can also be taken for the use of the same procedure as recommended for standard sample treatments.     

Predicting enzyme behavior in nonconventional media: correlating nitrilase function with solvent properties

The insolubility of nitrile substrates in aqueous reaction mixture decreases the enzymatic reaction rate. We studied the interaction of fourteen water miscible organic solvents with immobilized nitrile hydrolyzing biocatalyst. Correlation of nitrilase function with physico-chemical properties of the solvents has allowed us to predict the enzyme behavior in such non-conventional media. Addition of organic solvent up to a critical concentration leads to an enhancement in reaction rate, however, any further increase beyond the critical concentration in the latter leads to the decrease in catalytic efficiency of the enzyme, probably due to protein denaturation. The solvent dielectric constant (epsilon) showed a linear correlation with the critical concentration of the solvent used and the extent of nitrile hydrolysis. Unlike alcohols, the reaction rate in case of aprotic solvents could be linearly correlated to solvent log P. Further, kinetic analysis confirmed that the affinity of the enzyme for its substrate (K (m)) was highly dependent upon the aprotic solvent used. Finally, the prospect of solvent engineering also permitted the control of enzyme enantioselectivity by regulating enantiomer traffic at the active site.     

Activity and stability of native and modified alanine aminotransferase in cosolvent systems and denaturants

Alanine aminotransferase (ALT) is used in clinical diagnostics, amino acid synthesis and in biosensors. Here we describe the stabilization of soluble porcine ALT by chemical modification with mono- and bis-imidates. The apparent transition temperatures (‘T_m’, the temperature where 50% of initial activity was lost in 10 min) for native and DMS-modified ALT were 46 and 56 °C respectively. The effects of water-miscible organic solvents (methanol, dimethylformamide, dimethylsulphoxide and 1,4-dioxane) on the activity/stability of native and modified forms were determined. In all systems studied, an abrupt decrease in ALT catalytic activity was observed on reaching a certain threshold concentration of the organic solvent. The modified derivatives were more organotolerant than native enzyme. Comparison of the apparent V_max and K_m for 2-oxoglutarate as substrate, determined in 10% (v/v) organic solvent, with the results of thermal inactivation studies showed that the solvents have different effects on ALT's catalytic parameters and on its conformational stability. At 35 °C with no organic solvent the dimethylsuberimidate (DMS)-modified derivative's half-life was 16 times greater than that for native enzyme; in 30% (v/v) solvent at 35 °C, the DMS-modified ALT's half-life was up to 4.6 times greater than native enzyme's. DMS-modified ALT was also more stable in urea and guanidine HCl, and its refolding was more noticeable, than that of native enzyme.     

Amyloid Fibrillation of Insulin under Water-Limited Conditions

Amyloid fibrillation in water-organic mixtures has been widely studied to understand the effect of protein-solvent interactions on the fibrillation process. In this study, we monitored insulin fibrillation in formamide and its methyl derivatives (formamide, N-methyl formamide, N,N-dimethyl formamide) in the presence and absence of water. These model solvent systems mimic the cellular environment by providing denaturing conditions and a hydrophobic environment with limited water content. Thioflavin T (ThT) assay revealed that binary mixtures of water with formamide and its methyl derivatives enhanced fibrillation rates and β-sheet abundance, whereas organic solvents suppressed insulin fibrillation. We utilized solution small-angle x-ray scattering (SAXS) and differential scanning calorimetry (DSC) to investigate the correlation between protein-solvent interactions and insulin fibrillation. SAXS experiments combined with simulated annealing of the protein indicated that the degree of denaturation of the hydrophobic core region at residues B11–B17 determines the fibrillation rate. In addition, DSC experiments suggested a crucial role of hydrophobic interactions in the fibrillation process. These results imply that an environment with limited water, which imitates a lipid membrane system, accelerates protein denaturation and the formation of intermolecular hydrophobic interactions during amyloid fibrillation.     

Multi-competitive enzymatic reactions in organic media: Application to the determination of lipase alcohol specificity

Multicompetitive reactions catalyzed by lipases in organic media were used for the determination of lipase specificity towards alcohols. The competitive factors (, defined as the ratio of the kinetic powers, k_cat/K_m, for two substrates in competition for the enzyme active site) were estimated in a one-step experiment and a scale of specificity was easily deduced. The specificity towards the alcohol chain length and degree of substitution of seventeen commercial lipase preparations was investigated. The results show that, like fatty acids, alcohols greatly influence the reaction rates of lipase catalyzed reactions in organic solvents. Five groups of alcohol specificity are proposed after using the statistical method of principal component analysis.     

Prebiotic phosphorylation of nucleosides in formamide.

A possible prebiotic phosphorylation method has been investigated in which formamide served as the reaction medium. Nucleotides and nucleotide derivatives were formed when nucleosides were allowed to react with different orthophosphate, hydrogen phosphate or dihydrogen phosphate salts or with different condensed phosphate salts. The reaction products obtained from the phosphorylation of adenosine were 2'3' and 5'-AMPs, 2',5' and 3',5'-ADPs and 2',3'-cyclic AMP. The extent of phosphorylation in formamide exceeded 50% under favorable conditions after 15 days at 70 degrees. The acidic dihydrogen phosphates and condensed hydrogen phosphates proved to be the best phosphorylating agents. The presence of water in the medium decreased the yield of nucleotide derivatives, but some phosphorylation of adenosine was detected using dihydrogen phosphate in formamide containing water. The phosphorylation reactions were also observed for deoxynucleosides. Little decompression of the nucleosides was detected during the reaction time needed to form nucleotide derivatives. The facility with which phosphorylation takes place in formamide under very mild conditions may justify further studies both of prebiotic phosphorylation and synthetic phosphorylation using this solvent.     

Kinetic study of sphingomyelin hydrolysis for ceramide production

Kinetic study of sphingomyelin hydrolysis catalyzed by Clostridium perfringens phospholipase C was, at the first time, conducted for ceramide production. Ceramide has the major role in maintaining the water-retaining properties of the epidermis. Hence, it is of great commercial potential in cosmetic and pharmaceutical industries such as in hair and skin care products. The enzymatic hydrolysis of sphingomyelin has been proved to be a feasible method to produce ceramide. The kinetic performance of sphingomyelin hydrolysis in the optimal two-phase (water:organic solvent) reaction system was investigated to elucidate the possible reaction mechanism and also to further improve the hydrolysis performance. Enzyme in solution had less thermal stability than the enzyme powder and the immobilized enzyme. The thermal inactivation of phospholipase C in all the three forms did not follow the first order reaction at 65 °C. The reactions for both the soluble and immobilized enzymes followed Michaelis–Menten kinetics. K_m's for the soluble and immobilized enzymes were 1.07 ± 0.32 and 1.26 ± 0.19 mM, respectively. The value of V_max was markedly decreased by the immobilization without much change in K_m, as if the immobilization functioned as the non-competitive inhibition. Ceramide as product activated the hydrolysis reaction, however, and its addition mainly caused the increase in the affinity of the enzyme–substrate complex.