Distinct effect of a cationic surfactant on the transient and steady state phases of 2-naphthyl acetate hydrolysis catalyzed by α-chymotrypsin

Results obtained on the effect of addition of dodecyltrimethylammonium bromide (DTAB) upon the α-chymotrypsin (α-CT) catalyzed hydrolysis of 2-naphthyl acetate (2-NA) under steady state conditions for the acyl–enzyme intermediate are compared with those previously obtained in the transient (pre-steady state or “burst”) phase. It is found that, while in the transient phase there is no effect of DTAB addition on the kinetic parameters at concentrations below the critical micelle concentration (CMC) of the surfactant, super-activity is observed when the acyl–enzyme intermediate reaches the steady state condition. This difference implies that the surfactant does not modify either the formation or the decomposition of the enzyme–substrate complex (transient phase) but notably increases the rate of disruption of the acyl–enzyme intermediate.     

Studies on nitrite reductase in barley

Summary Nitrite reductase from barley seedlings was purified 50–60 fold by ammonium sulphate precipitation and gel filtration. No differences were established in the characteristics of nitrite reductases isolated in this way from either leaf or root tissues. The root enzyme accepted electrons from reduced methyl viologen, ferredoxin, or an unidentified endogenous cofactor. Enzyme activity in both tissues was markedly increased by growth on nitrate. This activity was not associated with sulphite reductase activity. Microbial contamination could not account for the presence of nitrite reductase activity in roots. Nitrite reductase assayed in vitro with reduced methyl viologen as the electron donor was inhibited by 2,4-dinitrophenol but not by arsenate.Abbreviations DNP 2,4-dinitrophenol - DEAE diethyl amino ethyl     

Cyclohexane-1,2-dione hydrolase: A new tool to degrade alicyclic compounds

Alicyclic alcohols are naturally occurring compounds which can be degraded by microorganisms via cleavage of the ring C–C bond. Denitrifying Azoarcus sp. strain 22Lin grows on cyclohexane-1,2-diol which serves as electron donor and carbon source. The diol is converted to cyclohexane-1,2-dione followed by hydrolysis to the corresponding semialdehyde and oxidation to adipate. The latter two reactions are catalyzed by the thiamine diphosphate-dependent flavoenzyme cyclohexane-1,2-dione hydrolase, the first α-ketolase known so far. Biochemical and structural properties of this new member of the thiamine diphosphate enzyme family will be presented.     

Metabolomics for biotransformations: Intracellular redox cofactor analysis and enzyme kinetics offer insight into whole cell processes

For redox reactions catalyzed by microbial cells the analysis of involved cofactors is of special interest since the availability of cofactors such as NADH or NADPH is often limiting and crucial for the biotransformation efficiency. The measurement of these cofactors has usually been carried out using spectrophotometric cycling assays. Today LC‐MS/MS methods have become a valuable tool for the identification and quantification of intracellular metabolites. This technology has been adapted to measure all four nicotinamide cofactors (NAD, NADP, NADH, and NADPH) during a whole cell biotransformation process catalyzed by recombinant Escherichia coli cells. The cells overexpressing an alcohol dehydrogenase from Lactobacillus brevis were used for the reduction of methyl acetoacetate (MAA) with substrate‐coupled cofactor regeneration by oxidation of 2‐propanol. To test the reliability of the measurement the data were evaluated using a process model. This model was derived using the measured concentrations of reactants and cofactors for initiation as well as the kinetic constants from in vitro measurements of the isolated enzyme. This model proves to be highly effective in the process development for a whole cell redox biotransformation in predicting both the right concentrations of cofactors and reactants in a batch and in a CSTR process as well as the right in vivo expression level of the enzyme. Moreover, a sensitivity analysis identifies the cofactor regeneration reaction as the limiting step in case for the reduction of MAA to the corresponding product (R)‐methyl 3‐hydroxybutyrate. Using the combination of in vitro enzyme kinetic measurements, measurements of cofactors and reactants and an adequate model initiated by intracellular concentrations of all involved reactants and cofactors the whole cell biotransformation process can be understood quantitatively. Biotechnol. Bioeng. 2009; 104: 251–260 © 2009 Wiley Periodicals, Inc.     

Ascorbate increases the synthesis of procollagen hydroxyproline by cultured fibroblasts from chick embryo tendons without activation or prolyl hydroxylase

An improved procedure was developed to extract prolyl hydroxylase from tendon cells of chick embryos with detergent, and improved assays were developed for both the activity of the enzyme and the amount of enzyme protein. Freshly isolated tendon cells were found to contain approx. 100 μg of enzyme protein per 10⁸ cells and 40–50% of the enzyme protein was active. When the cells were cultured, they were found to contain the same amount of enzyme protein by only 15–20% of the enzyme protein was active. Gel filtration of cell extracts indicated that the active form of prolyl hydroxylase in freshly isolated tendon cells and in cultured tendon cells had the same apparent size and the same activity per μg of immunoreactive protein as enzyme which was shown to be a tetramer. The inactive form was found to have about the same apparent size as subunits of the enzyme.When freshly isolated cells were incubated for 2 h in the presence of 40 μg per ml of ascorbate, there was a slight increase in the rate of hydroxyproline synthesis. In cultured cells, ascorbate at a concentration of 40 μg per ml caused a 2-fold increase in the rate of hydroxyproline synthesis within 30 min. However, ascorbate did not increase the activity of prolyl hydroxylase in extracts from either cell system. Therefore it appears that the influence of ascorbate on synthesis of procollagen hydroxyproline by the cells studied here must be ascribed to a cofactor effect on the hydroxylation reaction similar to that observed with purified enzyme, and it does not involve “activation” of inactive enzyme protein to active enzyme as has been observed in cultures of L-929 and 3T6 mouse fibroblasts.     

Purification and partial characterisation of tentatively classified acid phosphatase from the earthworm Eisenia veneta

In order to use leakage of lysosomal acid phosphatase (AP) as a biomarker of stress to earthworms, more information about AP’s in earthworms are needed. This paper describes the details about tentatively classified APs in the earthworm Eisenia veneta. Two isoenzymes (enzyme I and II) of acid phosphatase (AP) and one alkaline phosphatase (enzyme III) from the earthworm E. veneta were separated by gel filtration. All three enzymes were further purified and concentrated on a Con A Sepharose 4B column. Enzyme I was inhibited by tartrate, showed an optimal pH range between 4.0 and 5.0 and was assumed to be of lysosomal origin. Enzyme II was the major enzyme showing the highest activity of the three enzymes. It was expected to be a lysosomal AP under physiological conditions. Enzyme II had a molecular mass 113 kDa and was composed of apparently identical polypeptide chains of 36 kDa each. This enzyme was inhibited by tartrate, showed an optimal pH in the range 6.0–7.5 and was slowly degraded at temperatures above 40°C. Enzyme III is not inhibited by tartrate and has a pH-optimum >9. The subcellular location under physiological conditions was assumed to be the cytosol.     

Mathematical modelling of cancer cell invasion of tissue: local and non-local models and the effect of adhesion

The ability to invade tissue is one of the hallmarks of cancer. Cancer cells achieve this through the secretion of matrix degrading enzymes, cell proliferation, loss of cell–cell adhesion, enhanced cell–matrix adhesion and active migration. Invasion of tissue by the cancer cells is one of the key components in the metastatic cascade, whereby cancer cells spread to distant parts of the host and initiate the growth of secondary tumours (metastases). A better understanding of the complex processes involved in cancer invasion may ultimately lead to treatments being developed which can localise cancer and prevent metastasis. In this paper we formulate a novel continuum model of cancer cell invasion of tissue which explicitly incorporates the important biological processes of cell–cell and cell–matrix adhesion. This is achieved using non-local (integral) terms in a system of partial differential equations where the cells use a so-called “sensing radius” R to detect their environment. We show that in the limit as R→0 the non-local model converges to a related system of reaction–diffusion–taxis equations. A numerical exploration of this model using computational simulations shows that it can form the basis for future models incorporating more details of the invasion process.     

The influence on enzyme activity of storage of tissue blocks at −70° C

Summary Blocks of tissue from various organs of the rat have been chilled by precipitate immersion in n-hexane cooled to –70° C, and then stored at –70° C. At various intervals (up to 14 days) after chilling, cryostat sections were prepared from these blocks and assayed for the activity of a variety of enzymes. Enzyme activity was measured by scanning and integrating microdensitometry. With the exception of acid phosphatase and cytochrome oxidase, all enzymes assayed were stable for at least 7 days after storage at –70° C and most were stable for 14 days. Storage of fresh-frozen sections at –30° C in the cabinet of the cryostat, for up to 24 h, had little effect on enzyme activity.     

Two Novel Human Members of an Emerging Mammalian Gene Family Related to Mono-ADP-Ribosylating Bacterial Toxins

Mono-ADP-ribosylation is one of the posttranslational protein modifications regulating cellular metabolism, e.g., nitrogen fixation, in prokaryotes. Several bacterial toxins mono-ADP-ribosylate and inactivate specific proteins in their animal hosts. Recently, two mammalian GPI-anchored cell surface enzymes with similar activities were cloned (designated ART1 and ART2). We have now identified six related expressed sequence tags (ESTs) in the public database and cloned the two novel human genes from which these are derived (designatedART3andART4). The deduced amino acid sequences of the predicted gene products show 28% sequence identity to one another and 32–41% identity vs the muscle and T cell enzymes. They contain signal peptide sequences characteristic of GPI anchorage. Southern Zoo blot analyses suggest the presence of related genes in other mammalian species. By PCR screening of somatic cell hybrids and byin situhybridization, we have mapped the two genes to human chromosomes 4p14–p15.1 and 12q13.2–q13.3. Northern blot analyses show that these genes are specifically expressed in testis and spleen, respectively. Comparison of genomic and cDNA sequences reveals a conserved exon/intron structure, with an unusually large exon encoding the predicted mature membrane proteins. Secondary structure prediction analyses indicate conserved motifs and amino acid residues consistent with a common ancestry of this emerging mammalian enzyme family and bacterial mono(ADP-ribosyl)transferases. It is possible that the four human gene family members identified so far represent the “tip of an iceberg,” i.e., a larger family of enzymes that influences the function of target proteins via mono-ADP-ribosylation.     

Microbial enzymes for aromatic compound hydroxylation

Redox enzymes are ubiquitous in all living organisms. In fact, oxidation and reduction reactions are fundamental for the transformation of cellular and external compounds both for cell reproduction and for energy production. Redox enzymes share a common characteristic that is the capacity of transferring electrons to and from molecules. In addition, microorganisms contain many oxidative enzymes, and because they are relatively easier to cultivate and study, they have been investigated in details, in particular for potential use in biotechnological field. One important reaction that oxidative enzymes perform is the introduction of one or two oxygen atoms on aromatic compounds. The most representative classes of enzymes that perform this reaction are oxygenases/hydroxylases, peroxidases, and laccases; they differ in many aspects: the metal present in the active site, the used reductive cofactor, the final oxidant, and the number of electrons transferred in each step. Their essential features and mechanisms of action have been the subject of several studies, together with some structural analyses. This review reports recent developments and summarizes some of the most interesting results concerning both structural requirements and mechanisms implicated in aromatic hydroxylation.     

The enzymology of sulfur metabolism in phototrophic bacteria — A review

Summary The two functions of sulfur metabolism in phototrophic bacteria are to supply electrons for photosynthesis and to supply sulfur for biosynthetic purposes. The pathways for both functions may be partly identical. For the electron-supplying pathway the following enzymes are needed: a sulfide-oxidizing enzyme, a sulfur-oxidizing enzyme system, APS reductase, ADP sulfurylase and — in the case of thiosulfate utilization — thiosulfate reductase. Assimilatory reactions are catalyzed by ATP sulfurylase, APS kinase, sulfotransferases, PAPS reductase, sulfite reductase and o-acetylserine sulfhydrylase. Paper read at the Symposium on the Sulphur Cycle, Wageningen, May 1974.     

On-line electrocatalyzed luminol chemiluminescence determination of d-glucose and dissolved oxygen in simulated mammalian cell bioreactor perfusion fluid using solid phase reagent modules

On-line instrumentation and methods for the chemiluminescence based real-time monitoring of d-glucose and O₂ levels in mammalian cell bioreactor perfusion fluid are described. The unit processes required for the analysis include: pH adjustment using solid phase flow-through modules, immobilized enzyme catalyzed oxidation of glucose by molecular oxygen to produce hydrogen peroxide, controlled release of luminol using a solid phase flow-through module, electrocatalyzed luminescence using gold electrodes, and photodetection of chemiluminescent emissions. Calibration curves for d-glucose and dissolved O₂ in simulated bioreactor perfusion fluid have been generated using fully integrated reagentless test systems from 0–800 mg l^–1 and 0–10 mg l^–1, respectively.     

Continuous asymmetric ketone reduction processes with recombinant Escherichia coli

The reduction of methyl acetoacetate was carried out in continuously operated biotransformation processes catalyzed by recombinant Escherichia coli cells expressing an alcohol dehydrogenase from Lactobacillus brevis. Three different cell types were applied as biocatalysts in three different cofactor regeneration approaches. Both processes with enzyme-coupled cofactor regeneration catalyzed by formate dehydrogenase or glucose dehydrogenase are characterized by a rapid deactivation of the biocatalyst. By contrast the processes with substrate-coupled cofactor regeneration by alcohol dehydrogenase catalyzed oxidation of 2-propanol could be run over a period of 7 weeks with exceedingly high substrate and cosubstrate concentrations of up to 2.5 and 2.8 mol L(-1), respectively. Even under these extreme conditions, the applied biocatalyst showed a good stability with only marginal leakage of intracellular cofactors.     

Antagonistic Interactions between Stress Factors during the Growth of Microorganisms under Conditions Simulating the Parameters of Their Natural Ecotopes

Two stress factors, hypoxia (microaerobic conditions) and a high salt concentration, if applied simultaneously to aerobic microorganisms, display an antagonistic mode of interaction. As a result, the NaCl level that is usually optimal for moderate halophiles (5–6 %) becomes optimal for the growth of weak halophiles (Rhodococcus erythropolis and Shewanella sp. CN32); the halotolerant yeast Yarrowia lypolytica acquires halophilic properties (with a growth optimum at a NaCl concentration of 10%), and the growth rate of the extremely halophilic Halobacterium salinarum increases at supraoptimal salt concentrations (25–34%). This phenomenon is apparently due to multiple changes in metabolic reactions. In particular, high salt concentrations suppress respiration and the formation of enzymes (superoxide dismutase and catalase) that protect the cell from toxic oxygen species. Therefore, establishment of microaerobic conditions compensates for the loss of these protective mechanisms and enables cell growth at higher salt concentrations than under aerobic conditions. Of some importance can also be the increase in the intracellular concentrations of osmoprotectants caused by the suppression of their intracellular oxidation. The implications of this phenomenon for the ecophysiology of microorganisms (including oil-oxidizing species) and for the classification of weak and moderate halophiles are discussed.     

Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions

Several novel enzyme reactions have recently been discovered in the aromatic metabolism of anaerobic bacteria. Many of these reactions appear to be catalyzed by oxygen-sensitive enzymes by means of highly reactive radical intermediates. This contribution deals with two key reactions in this metabolism: the ATP-driven reductive dearomatisation of the benzene ring and the reductive removal of a phenolic hydroxyl group. The two reactions catalyzed by benzoyl-CoA reductase (BCR) and 4-hydroxybenzoyl-CoA reductase (4-HBCR) are both mechanistically difficult to achieve; both are considered to proceed in ‘Birch-like’ reductions involving single electron and proton transfer steps to the aromatic ring. The problem of both reactions is the extremely high redox barrier for the first electron transfer to the substrate (e.g., −1.9 V in case of a benzoyl-CoA (BCoA) analogue), which is solved in the two enzymes in different manners. Studying these enzymatic reactions provides insights into general principles of how oxygen-dependent reactions are replaced by alternative processes under anoxic conditions.     

X-ray crystallographic snapshots of reaction intermediates in pyruvate oxidase and transketolase illustrate common themes in thiamin catalysis

Thiamin diphosphate (ThDP)-dependent enzymes play pivotal roles in intermediary metabolism of virtually all organisms. Although extensive mechanistic work on cofactor models and various enzymes has served as a guide to understand general principles of catalysis, high-resolution structural information of reaction intermediates along the catalytic pathway was scarcely available until recently. Here, we review cryocrystallographic studies on the prototypical ThDP enzymes pyruvate oxidase and transketolase, which provided exciting insights into the chemical nature and structural features of several key intermediates and into the stereochemical course of substrate processing. The structures revealed a conserved (S)-configuration at the C2alpha stereocenter of the initially formed tetrahedral intermediate in the different enzymes with the scissile C2alpha–C2beta bond being directed perpendicular to the aromatic ring plane of the thiazolium portion of ThDP confirming the proposed maximum overlap mechanism. Elimination of the respective leaving groups (carbon dioxide, sugar phosphates) appears to be driven – amongst other factors such as stereoelectronic control – by strain relief as the C2–C2alpha bond, which connects C2 of ThDP with the carbonyl of the substrate, substantially deviates from planarity and relaxes to an in-plane conformation only after bond fission to give an enamine-type intermediate with considerable delocalization of the free electron pair onto the thiazolium ring. Except for the apparent flexibility of the cofactor itself, no major structural rearrangements are detectable indicating that the enzyme active centers are poised for catalysis. The structures also provide the basis for understanding the origins of substrate and reaction specificity.     

Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK

[NiFe] hydrogenases are key enzymes for the energy and redox metabolisms of different microorganisms. Synthesis of these metalloenzymes involves a complex series of biochemical reactions catalyzed by a plethora of accessory proteins, many of them required to synthesize and insert the unique NiFe(CN)₂CO cofactor. HypC is an accessory protein conserved in all [NiFe] hydrogenase systems and involved in the synthesis and transfer of the Fe(CN)₂CO cofactor precursor. Hydrogenase accessory proteins from bacteria-synthesizing hydrogenase in the presence of oxygen include HupK, a scaffolding protein with a moderate sequence similarity to the hydrogenase large subunit and proposed to participate as an intermediate chaperone in the synthesis of the NiFe cofactor. The endosymbiotic bacterium Rhizobium leguminosarum contains a single hydrogenase system that can be expressed under two different physiological conditions: free-living microaerobic cells (∼12 μm O₂) and bacteroids from legume nodules (∼10–100 nm O₂). We have used bioinformatic tools to model HupK structure and interaction of this protein with HypC. Site-directed mutagenesis at positions predicted as critical by the structural analysis have allowed the identification of HupK and HypC residues relevant for the maturation of hydrogenase. Mutant proteins altered in some of these residues show a different phenotype depending on the physiological condition tested. Modeling of HypC also predicts the existence of a stable HypC dimer whose presence was also demonstrated by immunoblot analysis. This study widens our understanding on the mechanisms for metalloenzyme biosynthesis in the presence of oxygen.     

DFT and MP2 studies on the C2C2α bond cleavage in thiamin catalysis

Thiamin diphosphate (ThDP), the biologically active derivative of vitamin B₁, is an important cofactor of several enzymes that catalyze the oxidative and non-oxidative conversion of α-keto acids. The final step of non-oxidative decarboxylation of pyruvate by pyruvate decarboxylase – the liberation of acetaldehyde – requires deprotonation of the α-hydroxyl group and cleavage of the C2–C2α bond of the transitory 2-(1-hydroxyethyl)-ThDP intermediate. It has been proposed that the cofactor 4′-amino/imino function is essentially involved in the deprotonation of the α-hydroxyl group. Proton transfer and C2–C2α cleavage may occur in a stepwise manner, or, alternatively in a concerted mechanism. Here, density functional theory (DFT) calculations as well as second order Møller–Plesset perturbation theory (MP2) studies were performed on a simple model for the enzyme using the program package Gaussian 03. Calculations favor a stepwise mechanism with initial formation of the C2α alkoxide, followed by C2–C2α bond cleavage.     

Stereochemical aspects of cholinesterase catalysis

Proceeding from the sterochemical regularities of the nucleophilic substitution reaction at the carbonyl group and the assumption that the spatial structure of the active center of cholinesterases is complementary to the molecule of the ester substrates for these enzymes, some general features of the stereoselectivity phenomena in the reactions of acetylcholinesterase (EC 3.1.1.7) and butyrylcholinesterase (EC 3.1.1.8) with organophosphorus inhibitors are discussed. For these enzymes the models of the active center are proposed in terms of different binding sites and the catalytic center. On the basis of this model, the stereochemical pecularities and the physicochemical background of the stereoselectivity effects on enzyme inhibition, reactivation, and “aging” reactions can be understood. Knowledge of the absolute configuration of several chiral organophosphorus inhibitors also makes it possible to determine the absolute spatial arrangement of the hydrophobic binding sites on the active surface of cholinesterases.     

Structure–function relationships in 3α-hydroxysteroid dehydrogenases: a comparison of the rat and human isoforms

3α-Hydroxysteroid dehydrogenases (3α-HSDs) inactivate steroid hormones in the liver, regulate 5α-dihydrotestosterone (5α-DHT) levels in the prostate, and form the neurosteroid, allopregnanolone in the CNS. Four human 3α-HSD isoforms exist and correspond to AKR1C1–AKR1C4 of the aldo-keto reductase (AKR) superfamily. Unlike the related rat 3α-HSD (AKR1C9) which is positional and stereospecific, the human enzymes display varying ratios of 3-, 17-, and 20-ketosteroid reductase activity as well as 3α-, 17β-, and 20α-hydroxysteroid oxidase activity. Their k_cat values are 50–100-fold lower than that observed for AKR1C9. Based on their product profiles and discrete tissue localization, the human enzymes may regulate the levels of active androgens, estrogens, and progestins in target tissues. The X-ray crystal structures of AKR1C9 and AKR1C2 (human type 3 3α-HSD, bile acid binding protein and peripheral 3α-HSD) reveal that the AKR1C2 structure can bind steroids backwards (D-ring in the A-ring position) and upside down (β-face inverted) relative to the position of a 3-ketosteroid in AKR1C9 and this may account for its functional plasticity. Stopped-flow studies on both enzymes indicate that the conformational changes associated with binding cofactor (the first ligand) are slow; they are similar in both enzymes but are not rate-determining. Instead the low k_cat seen in AKR1C2 (50-fold less than AKR1C9) may be due to substrate “wobble” at the plastic active site.