Tyrosinase and superoxide dismutase activities of peroxidase in the vacuoles of beet roots

In the absence of H₂O₂, isoforms of vacuolar phenol-dependent peroxidase (PO) in beet (Beta vulgaris) roots oxidized phenolic compounds like tyrosinases. Tyrosinase activity of PO manifested a clearly expressed pH-dependence with the optimum at pH of 8.0–9.0; peroxidase activity was the highest at pH 5.0–7.0. The inhibitory analysis confirmed a specificity of observed reactions. Along with tyrosinase activity, PO manifested SOD-like activity, which was also expressed in the absence of H₂O₂ and depended on some factors, for example, on the way of analyzed sample preparation. This activity appeared at a long-term dialysis and low temperature. SOD-like PO activity was observed in the presence of such substrates as 3,3′-diaminobenzidine and IAA. The results obtained allow a conclusion that vacuolar PO, as well as PO of other localization and origin is a polyfunctional enzyme, which, under definite conditions, can catalyze reactions of oxidase type.     

Catalytic mechanism of inulinase from Arthrobacter sp. S37

Detailed catalytic roles of the conserved Glu323, Asp460, and Glu519 of Arthrobacter sp. S37 inulinase (EnIA), a member of the glycoside hydrolase family 32, were investigated by site-directed mutagenesis and pH-dependence studies of the enzyme efficiency and homology modeling were carried out for EnIA and for D460E mutant. The enzyme efficiency (k_cat/K_m) of the E323A and E519A mutants was significantly lower than that of the wild-type due to a substantial decrease in k_cat, but not due to variations in K_m, consistent with their putative roles as nucleophile and acid/base catalyst, respectively. The D460A mutant was totally inactive, whereas the D460E and D460N mutants were active to some extent, revealing Asp460 as a catalytic residue and demonstrating that the presence of a carboxylate group in this position is a prerequisite for catalysis. The pH-dependence studies indicated that the pK_a of the acid/base catalyst decreased from 9.2 for the wild-type enzyme to 7.0 for the D460E mutant, implicating Asp460 as the residue that interacts with the acid/base catalyst Glu519 and elevates its pK_a. Homology modeling and molecular dynamics simulation of the wild-type enzyme and the D460E mutant shed light on the structural roles of Glu323, Asp460, and Glu519 in the catalytic activity of the enzyme.     

Ionization basis for activation of enzymes soluble in ionic liquids

BackgroundThe complex interactions between electrolytes and proteins have been studied for more than a century. However, understanding is not yet complete and does not provide a basis for predicting the activity of enzymes in ionic media. The use of ionic liquids (ILs) as reaction medium has opened up new opportunities for better understanding of the mechanism of enzymatic catalysis. Although a number of properties of ILs have been correlated with enzyme function, these relationships are not completely understood at a molecular level.MethodsWe propose that ILs must be able to promote ionization of protein ionizable groups in order to dissolve active enzymes. The biocompatible IL need to possess a functional group with large donor number and acceptor number in both cationic and anionic units, each of which is based on a high dielectric constant lead structure. We designed and synthesized two series of ILs and determined their ionizing–dissociating abilities and activities of lipases soluble in these new ILs.ResultsThe results showed that the ionizing–dissociating abilities of ILs paralleled the catalytic activity trend of lipases dissolved in the ILs. The activities of lipases soluble in the newly designed ILs were comparable to those in water.ConclusionsWe can conclude that ionizing–dissociating abilities of an IL can be used as a basis for predicting the activity of enzymes soluble in the IL.General significanceIonization basis for activation of enzymes gives a deeper understanding of the behavior of enzymes in non-aqueous media at a molecular level.     

Cytochrome c oxidase oxygen reduction reaction induced by cytochrome c on nickel-coordination surfaces based on graphene oxide in suspension

BackgroundThe electrochemical and spectroscopic investigation of bacterial electron-transfer proteins stabilized on solid state electrodes has provided an effective approach for functional respiratory enzyme studies.MethodsWe assess the biocompatibility of carboxylated graphene oxide (CGO) functionalized with Nickel nitrilotriacetic groups (CGO-NiNTA) ccordinating His-tagged cytochrome c oxidase (CcO) from Rhodobacter sphaeroides.ResultsKinetic studies employing UV–visible absorption spectroscopy confirmed that the immobilized CcO oxidized horse-heart cytochrome c (Cyt c) albeit at a slower rate than isolated CcO. The oxygen reduction reaction as catalyzed by immobilized CcO could be clearly distinguished from that arising from CGO-NiNTA in the presence of Cyt c and dithiothreitol (DTT) as a sacrificial reducing agent. Our findings indicate that while the protein content is about 3.7‰ by mass with respect to the support, the contribution to the oxygen consumption activity averaged at 56.3%.ConclusionsThe CGO-based support stabilizes the free enzyme which, while capable of Cyt c oxidation, is unable to carry out oxygen consumption in solution on its own under our conditions. The turnover rate for the immobilized CcO was as high as 240 O₂ molecules per second per CcO unit.General significanceIn vitro investigations of electron flow on isolated components of bacterial electron-transfer enzymes immobilized on the surface of CGO in suspension are expected to shed new light on microbial bioenergetic functions, that could ultimately contribute toward the improvement of performance in living organisms.     

Use of competitive dead-end inhibitors to determine the chemical mechanism of action of yeast alcohol dehydrogenase

In this work, we have postulated a comprehensive and unified chemical mechanism of action for yeast alcohol dehydrogenase (EC 1.1.1.1, constitutive, cytoplasmic), isolated from Saccharomyces cerevisiae. The chemical mechanism of yeast enzyme is based on the integrity of the proton relay system: His-51....NAD⁺....Thr-48....R.CH₂OH(H₂>O)....Zn$++,\; stretching\; from\; His-51\; on\; the\; surface\; of\; enzyme\; to\; the\; active\; site\; zinc\; atom\; in\; the\; substrate-binding\; site\; of\; enzyme.\; Further,\; it\; is\; based\; on\; extensive\; studies\; of\; steady-state\; kinetic\; properties\; of\; enzyme\; which\; were\; published\; recently.\; In\; this\; study,\; we\; have\; reported\; the\; pH-dependence\; of\; dissociation\; constants\; for\; several\; competitive\; dead-end\; inhibitors\; of\; yeast\; enzyme\; from\; their\; binary\; complexes\; with\; enzyme,\; or\; their\; ternary\; complexes\; with\; enzyme\; and\; NAD+or\; NADH;\; inhibitors\; include:\; pyrazole,\; acetamide,\; sodium\; azide,\; 2-fluoroethanol,\; and\; 2,2,2-trifluorethanol.\; The\; unified\; mechanism\; describes\; the\; structures\; of\; four\; dissociation\; forms\; of\; apoenzyme,\; two\; forms\; of\; the\; binary\; complex\; E.NAD+,\; three\; forms\; of\; the\; ternary\; complex\; E.NAD+.alcohol,\; two\; forms\; of\; the\; ternary\; complex\; E.NADH.aldehyde\; and\; three\; binary\; complexes\; E.NADH.\; Appropriate\; pK$_a values have been ascribed to protonation forms of most of the above mentioned complexes of yeast enzyme with coenzymes and substrates.     

Analysis of the Kinetics and Bistability of Ubiquinol:Cytochrome c Oxidoreductase

Ubiquinol:cytochrome c oxidoreductase, bc₁ complex, is the enzyme in the respiratory chain of mitochondria responsible for the transfer reducing potential from ubiquinol to cytochrome c coupled to the movement of charge against the electrostatic potential across the mitochondrial inner membrane. The complex is also implicated in the generation of reactive oxygen species under certain conditions and is thus a contributor to cellular oxidative stress. Here, a biophysically detailed, thermodynamically consistent model of the bc₁ complex for mammalian mitochondria is developed. The model incorporates the major redox centers near the Q_o- and Q_i-site of the enzyme, includes the pH-dependent redox reactions, accounts for the effect of the proton-motive force of the reaction rate, and simulates superoxide production at the Q_o-site. The model consists of six distinct states characterized by the mobile electron distribution in the enzyme. Within each state, substates that correspond to various electron localizations exist in a rapid equilibrium distribution. The steady-state equation for the six-state system is parameterized using five independent data sets and validated in comparison to additional experimental data. Model analysis suggests that the pH-dependence on turnover is primarily due to the pKa values of cytochrome b_H and Rieske iron sulfur protein. A previously proposed kinetic scheme at the Q_i-site where ubiquinone binds to only the reduced enzyme and ubiquinol binds to only the oxidized enzyme is shown to be thermodynamically infeasible. Moreover, the model is able to reproduce the bistability phenomenon where at a given overall flux through the enzyme, different rates of superoxide production are attained when the enzyme is differentially reduced.     

Discovery of a series of small molecules as potent histone deacetylase inhibitors

Abstract

A series of small molecules were designed and synthesized based on our previous virtual screening approach, which was performed to discover potent histone deacetylase inhibitors (HDACIs) with novel structures. The derived compounds were tested by Hela cell nucleus extract for enzyme inhibition assay. Tumor cell growth inhibition assays were performed using a series of tumor cell lines. Molecule 4h has the best performance among these compounds with enzyme inhibition IC₅₀ of 0.14?μM and tumor cell growth inhibition IC₅₀ of 1.85 (U937), 2.02 (HL60), 2.67 (K562). Docking studies showed that multiple H-bonds and hydrophobic interactions make 4h binding to the active site of HDAC. 4h has the advantage of low molecular weight, so a variety of structural modifications can be performed in our further studies.     

Potent inhibitory effects of benzyl and p-xylidine-bis dithiocarbamate sodium salts on activities of mushroom tyrosinase

A novel monofunctional benzyldithiocarbamate, C₆H₅CH₂NHCSSNa (I), and a bifunctional p-xylidine-bis(dithiocarbamate), NaSSCNHCH₂C₆H₄CH₂NHCSSNa (II), as sodium salts, were synthesized by reaction between p-xylylenediamine or benzylamine with CS₂ in the presence of NaOH. They were characterized by spectroscopic techniques such as ¹H NMR, IR, and elemental analysis. These water-soluble compounds were examined for their inhibition of both activities of mushroom tyrosinase (MT) from a commercial source of Agricus bisporus. l-3,4- Dihydroxyphenylalanine (L-DOPA) and l-tyrosine were used as natural substrates for the catecholase and cresolase enzyme reactions, respectively. Kinetic studies showed noncompetitive inhibition of I and mixed type inhibition of II on both activities of MT. The inhibition constant (K_I) of II was smaller than that of I. Raising the temperature from 27 to 37°C caused a decrease in K_I values of I and an increase in values of II. The binding process for inhibition of I was only entropy driven, which means that the predominant interaction in the active site of the enzyme is hydrophobic; meanwhile, the electrostatic interaction can be important for the inhibition of II due to the enthalpy driven binding process. Fluorescence studies showed a decrease of emission intensity without a shift of emission maximum in the presence of different concentrations of compounds. An extrinsic fluorescence study did not show any considerable change of the tertiary structure of MT. Probably, the conformation of inhibitor-bound MT is stable and inflexible compared with uninhibited MT.     

Organophosphorus compounds as active site-directed inhibitors of elastase

Four ethyl $\text{p}$-nitrophenyl alkylphosphonates were studied for the inhibition of elastase. A pH-dependence study using the assay substrate BOC-Ala-ONp or the phosphonate inhibitors showed the participation of an ionizing group with an apparent pK_a of 6.9 and a decrease of reaction or inhibition at higher pH. Out of the four compounds investigated ethyl $\text{p}$-nitrophenyl pentylphosphonate was found to be the best inhibitor of elastase as judged from the value of $\text{k}{}_2\text{K}{}_{\mathrm{<mtext>I</mtext>}}$. This value, which is the measure of inhibitory capacity, is the highest reported so far for the inhibition of elastase.     

Mechanism of action of α-galactosidase

The effect ofpH on K_m and V_max values of coconut α-galactosidase indicates the involvement of two ionizing groups with pK_a values of 3.5 and 6.5 in catalysis. Chemical modification has indicated the presence of two carboxyl groups, a tryptophan and a tyrosine, at or near the active site of α-galactosidase. Based on these facts a new mechanism of action for α-galactosidase is proposed in which the ionizing group with a pK_a of 3.5 is a carboxyl group involved in stabilizing a carbonium ion intermediate and the ionizing group with a pK_a of 6.5 is a carboxyl group perturbed due to the presence of a hydrophobic residues in its vicinity which donates a H⁺ ion in catalysis.     

Gas-liquid Chromatographic Determination of Carbohydrates in Tobacco

An enzyme which catalyzes the degradation of polyvinyl alcohol) (PVA) oxidized by secondary alcohol oxidase, in which hydroxyl groups of PVA are partially converted to carbonyl groups, has been purified from a fraction adsorbed on DEAE-Sephadex at pH 7.0 from PVA-degrading enzyme activities produced by a bacterial symbiotic mixed culture in a minimal medium containing PVA as a sole source of carbon and energy. The purified enzyme was electrophoretically homogeneous in the absence and presence of SDS.

The enzyme is a single polypeptide with a molecular weight of about 36,000 and has an isoelectric point of 5.1. The N- and C-terminal amino acid residues are both alanine. The enzyme is most active at pH 6.5 and at 40°C and is stable between pH 6.0 and 9.0 and at temperatures below 45°C. The enzyme is inhibited by Hg²⁺ and is restored by the addition of reduced glutathione, although p-chloromercuribenzoate has no effect.

The enzyme was active on oxidized PVA, but not on PVA and on various low molecular weight carbonyl compounds examined. The enzyme reaction on oxidized PVA resulted in a rapid decrease in viscosity, a fall of pH, and production of carboxylic acids. The enzyme, therefore, is considered to be an oxidized PVA hydrolase.

The enzyme shows a common antigenicity in immunodiffusion and neutralization reactions with antisera to an oxidized PVA hydrolase previously purified from another fraction adsorbed on SP-Sephadex at pH 7.0 from the PVA-degrading enzyme activities [Agric. Biol. Chem., 45, 63 (1981)]. The relations between these two oxidized PVA hydrolases are discussed.     

Entrapment of purified novel dextransucrase obtained from newly isolated Acetobacter tropicalis and its comparative study of kinetic parameters with free enzyme

Abstract

Purified Acetobacter tropicalis dextransucrase was immobilized in different matrices viz. calcium-alginate, κ-carrageenan, agar, agarose and polyacrylamide. Calcium-alginate was proved to be superior to the other matrices for immobilization of dextransucrase enzyme. Standardization of immobilization conditions in calcium-alginate resulted in 99.5% relative activity of dextransucrase. This is the first report with such a large amount of relative activity as compared to the previous reports. The immobilized enzyme retained activity for 11 batch reactions without a decrease in activity which suggested that enzyme can be used repetitively for 11 cycles. The dextransucrase was also characterized, which revealed that enzyme worked best at pH 5.5 and 37?°C for 30?min in both the free as well as immobilized state. Calcium-alginate immobilized dextransucrase of A. tropicalis showed the K_m and V_max values of 29?mM and 5000?U/mg, respectively. Free and immobilized enzyme produced 5.7?mg/mL and 2.6?mg/mL of dextran in 2?L bench scale fermenter under optimum reaction conditions. This immobilization method is very unconventional for purified large molecular weight dextran-free dextransucrase of A. tropicalis as this method is used usually for cells. Such reports on entrapment of purified enzyme are rarely documented.     

The inhibitory effect of some new synthesized xanthates on mushroom tyrosinase activities

Three iso-alkyldithiocarbonates (xanthates), as sodium salts, C₃H₇OCS₂Na (I), C₄H₉OCS₂Na (II) and C₅H₁₁OCS₂Na (III), were synthesized, by the reaction between CS₂ with the corresponding iso-alcohol in the presence of NaOH, and examined for inhibition of both cresolase and catecholase activities of mushroom tyrosinase (MT) from a commercial source of Agricus bisporus. 4-[(4-methylbenzo)azo]-1,2-benzendiol (MeBACat) and 4-[(4-methylphenyl)azo]-phenol (MePAPh) were used as synthetic substrates for the enzyme for the catecholase and cresolase reactions, respectively. Lineweaver-Burk plots showed different patterns of mixed and competitive inhibition for the three xanthates and also for cresolase and catecholase activities of MT. For cresolase activity, I and II showed a mixed inhibition pattern but III showed a competitive inhibition pattern. For catecholase activity, I showed mixed inhibition but II and III showed competitive inhibition. These new synthesized compounds are potent inhibitors of MT with K_i values of 9.8, 7.2 and 6.1 μM for cresolase inhibitory activity, and also 12.9, 21.8 and 42.2 μM for catecholase inhibitory activity for I, II and III, respectively. They showed a greater inhibitory potency towards the cresolase activity of MT. Both substrate and inhibitor can be bound to the enzyme with negative cooperativity between the binding sites (α>1) and this negative cooperativity increases with increasing length of the aliphatic tail in these compounds in both cresolase and catecholase activities. The cresolase inhibition is related to the chelating of the copper ions at the active site by a negative head group (S^? ) of the anion xanthate, which leads to similar values of K_i for all three xanthates. Different K_i values for catecholase inhibition are related to different interactions of the aliphatic chains of I, II and III with hydrophobic pockets in the active site of the enzyme.     

pH dependent changes in ADP and ATP affinity for the tight nucleotide-binding site of chloroplast coupling factor 1

The pH-dependence of ADP and ATP affinity for CF₁ tight nucleotide-binding sites was studied under conditions of equilibrium between bound and free labeled nucleotides. With the nucleotide/CF₁ ratio>1, the ATP content in tightly bound nucleotides depended only slightly on medium pH. With the nucleotide/CF₁ ratio approaching 1, tightly bound ATP content grew rapidly with decreasing pH. Calculations of ADP/ATP ratio in free and tightly bound nucleotides showed that decreasing the pH from 8.0 to 6.0 induced a 150 times greater affinity of the nucleotide-binding site for ATP than for ADP. The data indicates that ATP-ADP equilibrium at the CF₁ tight nucleotide-binding site depends on protonation of specific acid-base groups of the enzyme.Abbreviations CF₁, BF₁, and MF₁ coupling factors of chloroplasts, bacteria, and mitochondria, respectively - AdN adenine nucleotide     

The two cytochromes c in the facultative methylotroph Pseudomonas AM1

It was previously suggested that there is only one soluble cytochrome c in Pseudomonas AM1, having a molecular weight of 20000, a redox midpoint potential of about +260mV and a low isoelectric pint [Anthony (1975) Biochem. J. 146, 289–298; Widdowson & Anthony (1975) Biochem. J. 152, 349–356]. A more thorough examination of the soluble fraction of methanol-grown Pseudomonas AM1 has now revealed the presence of two different cytochromes c. These were both purified to homogeneity by acid treatment, ion-exchange chromatography, gel filtration, chromatography on hydroxyapatite and preparative isoelectric focusing. Molecular weights were determined by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis; midpoint redox potentials were determined directly by using platinum and calomel electrodes; isoelectric points were estimated by electrophoresis and by the behaviour of the two cytochromes on ion-exchange celluloses. The more abundant cytochrome c_H (λ_max. 550.5nm) had a low molecular weight (11000), a midpoint potential of about +294mV and a high isoelectric point, not being adsorbed on DEAE-cellulose in 20mm-Tris/HCl buffer, pH8.0. The less abundant cytochrome c_L (λ_max. 549nm) was about 30% of the total; it had a high molecular weight (20900), a midpoint potential of about +256mV and a low isoelectric point, binding strongly to DEAE-cellulose in 20mm-Tris/HCl buffer, pH8.0. The pH-dependence of the midpoint redox potentials of the two cytochromes c were very similar. There were four ionizations affecting the redox potentials in the pH range studied (pH4.0–9.5), two in the oxidized form (pK values about 3.5 and 5.5) and two in the reduced form (pK values about 4.5 and 6.5), suggesting that the ionizing groups involved may be the two propionate side chains of the haem. Neither of the cytochromes c was present in mutant PCT76, which was unable to oxidize or grow on C₁ compounds, although still able to grow well on multicarbon compounds such as succinate. Whether or not these two cytochromes c have separate physiological functions is not yet certain.     

Influence of the Drying Technique of Silica Gels on the Enzymatic Activity of Encapsulated Lipase

Recent studies by Reetz et al. (Reetz, M.T., Zonta, A. and Simpelkamp, J. (1996a) Biotechnology and Bioengineering, 49, 527-534) have shown that the catalytic activity of lipase encapsulated in sol-gel materials, in esterification reactions, depends on many parameters such as the presence of hydrophobic groups grafted on the gel network and of an organic component in the gel network. In the present study, we have examined the effect of the gel pore texture which can be modified by varying the drying technique, for a given silica precursor composition and hydrolysis-condensation procedure. For a given mixture of two silane precursors, propyltri-methoxysilane and tetramethoxysilane, we compared the effects of the presence or absence of an organic component such as polyvinyl alcohol, in combination with drying either by evaporation which leads to the formation of xerogels, or by supercritical drying in CO₂ which leads to the formation of aerogels. For this last technique, the exchange of liquid is also an important step and its effect on the enzyme activity has been examined. The gel pore texture was characterized by nitrogen absorption according to the Brunauer Emmett and Teller method. The catalytic activities of the materials were compared in the esterification of lauric acid by 1-octanol.     

Borate inhibits activation of inactive dinitrogenase reductase from Rhodospirillum rubrum

Borate and aminophenylboronic acid were tested as inhibitors of activation of inactive dinitrogenase reductase from Rhodospirillum rubrum. Inhibition was specific for activation because activity of the active form of the enzyme was not inhibited. Inhibition showed the pH-dependence expected if borate inhibits by binding to cis-hydroxy groups of the modifying group found on the inactive enzyme.     

Structural insight into the inhibition of acetylcholinesterase by 2,3,4, 5-tetrahydro-1, 5-benzothiazepines

Benzothiazepines 1–3 inhibited acetylcholinesterase (AChE; EC 3.1.1.7) enzyme in a concentration-dependent fashion with IC₅₀ values of 1.0 ± 0.002, 1.2 ± 0.005 and 1.3 ± 0.001 μM, respectively. By using linear-regression equations, Lineweaver-Burk, Dixon plots and their secondary replots were constructed which indicated that compounds 1–3 are non-competitive inhibitors of AChE with K_i values of 0.8 ± 0.04, 1.1 ± 0.002, and 1.5 ± 0.001 μM, respectively. Molecular docking studies revealed that all the compounds are completely buried inside the aromatic gorge of AChE, extending deep into the gorge of AChE. A comparison of the docking results of compounds 1–3 displayed that these compounds generally adopt the same binding mode in the active site of AChE. The superposition of the docked structures demonstrated that the non-flexible benzothiazepine always penetrate into the aromatic gorge through the six-membered ring A, which allowed the ligands to interact simultaneously with more than one subsites of the active center of AChE. The higher AChE inhibitory potential of compounds 1–3 was found to be the cumulative effect of hydrophobic contacts and π-π interactions between the ligands and AChE. The relatively high affinity of benzothiazepine 1 with AChE was found to be due to additional hydrogen bond in benzothiazepine 1-AChE complex. The results indicated that substitution of halogen and methyl groups by hydrogen at aromatic ring of the benzothiazepine decreased the affinity of these molecules towards enzyme that may be due to the polar non-polar repulsions of these moieties with the amino acid residues in the active site of AChE. The observed binding modes of benzothiazepines 1–3 in the active site of AChE explain the affinities of benzothiazepines and provide a rational basis for the structure-based drug design of benzothiazepines with improved pharmacological properties.     

Fatty acid synthetase complex: Selective inactivation by phenylmethylsulphonyl fluoride

Reaction of pigeon and rat liver fatty acid synthetases with phenylmethylsulphonyl fluoride at pH 7.0 results in rapid and complete loss of activity for fatty acid synthesis. Acetyl and malonyl transacylation, two reductions, dehydration and condensation-CO₂ exchange reactions are not appreciably altered in the modified enzyme. However, the deacylation of palmityl CoA is completely inhibited. Complete inactivation results in the incorporation of about 1.9 moles of ¹⁴C-phenylmethylsulphonyl groups/mole of the enzyme complex. These results suggest that either two moles of a fatty acyl deacylase or two deacylases with different fatty acyl chain length specificities may be functional in the enzyme complex.