A specific radiochemical assay for pyrroline-5-carboxylate dehydrogenase

Previous studies of pyrroline-5-carboxylate dehydrogenase have been conducted using a spectrophotometric method to monitor substrate-dependent NAD(P)H production. For the assay of the mammalian enzyme, the spectrophotometric assay was found to be unacceptable for kinetic studies as the production of NAD(P)H was nonlinear with time and protein concentration. An assay which measures radiolabeled glutamate production by this enzyme in the presence of NAD+ from radiolabeled pyrroline-5-carboxylate has been developed. Separation of substrate from product is achieved by column chromatography using Dowex 50 cation-exchange resin. The product isolated by this procedure was identified as glutamate. This new assay is linear with time and protein concentration and gives reproducible results. The assay is not influenced by competing enzyme activities, such as glutamate dehydrogenase, in a liver homogenate so that quantitative conversion of pyrroline-5-carboxylate to glutamate is observed.     

A radiochemical assay for a NADP+-specific gamma-glutamate semialdehyde dehydrogenase extracted from mitochondrial membrane of rat intestinal epithelial cells

A radiochemical assay has been developed for a NADP+-specific gamma-glutamate semialdehyde dehydrogenase from rat intestinal epithelial cells. The spectrophotometric assay utilized to measure the enzyme in bacterial cell homogenates is not sensitive enough for homogenates from rat mitochondria, which require an assay that can measure as little as 0.5 nmol NADPH formed/min/ml extract. The assay described here is sensitive to 0.1 nmol product formed/min/ml of extract and employs the use of [3H]pyrroline 5-carboxylate which is phosphorylated and oxidized by the enzyme to gamma-[3H]glutamyl phosphate, a product that decomposes to [3H]pyrrolidone 5-carboxylate. The latter product is separated from the substrate by ion-exchange chromatography. In order to correct for any product loss during separation by ion-exchange [14C]pyrrolidone 5-carboxylate is added as an internal standard to the deproteinized assay mixture. Under the assay conditions described mammalian gamma-glutamate semialdehyde dehydrogenase activity is linear with respect to time and protein concentration. Comparison between the kinetic parameters reported for the bacterial enzyme and those reported here for the mammalian enzyme indicate similarities in the pH optima as well as a requirement for phosphate. Kinetic studies on mammalian enzyme yield apparent Km values of 1.8 mM for pyrroline 5-carboxylate, 0.2 mM for NADP+, and 11.3 mM for phosphate.     

A microassay for heme oxygenase activity using thin-layer chromatography.

A sensitive and facile assay for heme oxygenase (HO) has been developed. The basis of the assay is the detection of [14C]bilirubin formation in a coupled enzyme assay involving HO and biliverdin reductase actions, respectively. Separation of substrate from product is accomplished by thin-layer chromatography with subsequent quantitation by liquid scintillation counting of radioactive material present on chromatograms. As little as 20 micrograms of total cellular protein derived from cells growing in a standard 25-cm2 culture flask is sufficient for detection of HO enzyme activity using this assay. The reaction is inhibited by tin-protoporphyrin (10 microM final concentration), a specific inhibitor of HO. The linearity of the enzyme reaction with respect to incubation time and amount of protein used was established. Comparison of the new HO assay with a spectrophotometric assay was made, and good agreement of the results from both methods was found. The assay described here should facilitate measurements of this important heme-degrading enzyme in tissue culture studies and cases where limited amounts of material are available.     

Firefly luciferase luminescence assays using scintillation counters for quantitation in transfected mammalian cells

The firefly enzyme luciferase catalyzes the luminescent reaction of luciferin with ATP and oxygen. The luciferase gene has recently been cloned and proposed as a reporter gene in procaryotic and eucaryotic cells. We present here a luciferase activity assay which relies on luminescence detection using a standard scintillation counter. This technique is simple, fast, inexpensive, and still very sensitive: as little as 0.02 pg (250,000 molecules) of enzyme is readily detected. The technique is optimized for the luciferase assay in mammalian cell lysates. Thus, the luciferase gene may become a very useful tool for gene regulation studies.     

Bisphenol-A Can Inhibit the Enzymatic Activity of Human Superoxide Dismutase

Bisphenol-A (BPA), a synthetic xenoestrogen, is currently being used to produce a wide variety of consumer products. Humans as well as animals are exposed to this ubiquitous compound through ingestion, inhalation, and dermal exposure. The effect of this compound on superoxide dismutase (SOD), an antioxidant enzyme, isolated from human blood was studied using an enzyme inhibition assay. The mode of interaction of BPA on SOD was investigated using modeling and docking studies. Purified human SOD from erythrocytes was used to study the enzyme inhibition assay of BPA. Molecular level interactions of BPA on SOD were also analyzed by modeling and docking studies. Our study demonstrates that BPA has an inhibitory effect on SOD. The docking results showed that it could bind to the active site residues of SOD and could interfere with the catalytic activity of the enzyme. Our study reveals for the first time that BPA can directly inhibit the enzymatic activity of human SOD and thus impairs the free radical scavenging mechanism.     

Continuous spectrophotometric assay for beta-glucuronidase

A continuous spectrophotometric assay has been developed for detecting beta-glucuronidase activity. In the assay, Para-nitrophenyl beta-D-glucuronide is cleaved to yield a chromophoric product. With the commercial E. coli enzyme, it is demonstrated that the reactions can be continuously monitored by the increase of absorbance at 405 nm. The method is highly sensitive and able to detect less than 1.4 x 10(-4) U/mL of the enzyme activity in solution. Such a new assay offers significant advantages over the existing discontinuous methods and should be useful for both routine enzyme assay and accurate kinetic studies.     

Development of a solid-phase assay for analysis of matrix metalloproteinase activity.

Proteases play fundamentally important roles in normal physiology and disease pathology. Methods for detection of active proteolysis may greatly aid in the diagnosis of disease progression, and suggest modes of therapeutic intervention. Most assays for proteolytic potential are limited by a lack of specificity and/or quantification. We have developed a solid-phase activity assay for members of the matrix metalloproteinase (MMP) family that is specific and can be used to quantify active enzyme concentration. The assay has two principal components: a capture antibody that immobilizes the MMP without perturbing the enzyme active site, and a fluorescence resonance energy transfer substrate for monitoring proteolysis at low enzyme concentrations. The assay was standardized for MMP-1, MMP-3, MMP-13, and MMP-14. The efficiency of the assay was found to be critically dependent upon the quality of the antibodies, the use of substrates exhibiting high specific activities for the enzymes, and enzyme samples that are fresh. The assay was applied to studies of constitutive and induced MMP activity in human melanoma cells. Analysis of several melanoma cell lines, and comparison with prior studies, correlated higher constitutive MMP-13 activity with higher levels of the cell surface receptor CD44. Ligands to two different melanoma cell surface receptors (the alpha2beta1 integrin or CD44) were found to induce different proteolytic profiles, suggesting that the extracellular matrix can modulate melanoma invasion. Overall, the solid-phase MMP activity assay was found to be valuable for analysis of protease activity in cellular environments. The solid-phase assay is suitably flexible to allow studies of virtually any proteolytic enzyme for which appropriate substrates and antibodies are available.     

A time-resolved, internally quenched fluorescence assay to characterize inhibition of hepatitis C virus nonstructural protein 3-4A protease at low enzyme concentrations

The hepatitis C virus (HCV) nonstructural protein 3 (NS3) with its cofactor NS4A is a pivotal enzyme for the replication of HCV. Inhibition of NS3-4A protease activity has been validated as an antiviral target in clinical studies of inhibitors of the enzyme. We have developed a sensitive time-resolved fluorescence (TRF) assay capable of detecting very low NS3-4A concentrations. A depsipeptide substrate is used that contains a europium-cryptate moiety and an efficient quenching group, QSY-7. The TRF assay is at least 30-fold more sensitive than a fluorescence energy transfer (FRET) assay and allows evaluation of NS3 protease inhibitors in reactions catalyzed by low enzyme concentrations (30 pM). Use of low enzyme concentrations allows for accurate measurement of inhibition by compounds with subnanomolar inhibition constants. The inhibitory potency of the potent protease inhibitor, BILN-2061, is significantly greater than previously reported. The ability to accurately determine inhibitory potency in reactions with low picomolar concentrations of NS3-4A is crucially important to allow valid comparisons between potent inhibitors. Studies of the interaction of NS3 with its NS4A cofactor at low enzyme concentration also reveal that the protease activity is salt dependent. This salt dependence of the enzyme activity is not present when high enzyme concentrations are used in the FRET assay.     

Bacterial complementation as a means to test enzyme–ligand interactions

A bacterial complementation assay has been developed for the rapid screening of a large number of compounds to identify those that inhibit an enzyme target for structure-based inhibitor design. The target enzyme is the hypoxanthine phosphoribosyltransferase (HPRT). This enzyme has been proposed as a potential target for inhibitors that may be developed into drugs for the treatment of diseases caused by several parasites. The screening assay utilizes genetically deficient bacteria complemented by active, recombinant enzyme grown in selective medium in microtiter plates. By comparing absorbance measurements of bacteria grown in the presence and absence of test compounds, the effect of the compounds on bacterial growth can be rapidly assayed. IC₅₀ values for inhibition of bacterial growth are a reflection of the ability of the compounds to bind and/or inhibit the recombinant enzyme. We have tested this bacterial complementation screening assay using recombinant HPRT from the parasites Plasmodium falciparum and Trypanosoma cruzi, as well as the human enzyme. The results of these studies demonstrate that a screening assay using bacterial complement selection can be used to identify compounds that target enzymes and can become an important part of structure-based drug design efforts. Received: 4 December 1997 / Received revision: 17 March 1998 / Accepted: 26 March 1998     

Design and synthesis of 3-pyrrol-3-yl-3H-isobenzofuran-1-ones as inhibitors of human cytosolic phospholipase A2alpha

A series of 3-pyrrol-3-yl-3H-isobenzofuran-1-ones was synthesized and assessed for the ability to inhibit cytosolic phospholipase A(2)alpha (cPLA(2)alpha). Several of these compounds were found to be active in both a cell based assay and an isolated enzyme assay. The most potent inhibitor was the thiazolidine-2,4-dione substituted derivative 35. With IC(50)-values of 0.7 muM and 7.3 muM in the cellular and isolated enzyme assay, respectively, it possesses similar inhibitory potency as the known cPLA(2)alpha inhibitor arachidonyltrifluoromethyl ketone (AACOCF(3)). Structure-activity relationship studies revealed that the evaluated isobenzofuran-1-ones seem to exert their cellular activities not only by a direct interaction with the enzyme but also by other as yet unknown mechanisms.     

Characterization of dolichyl diphosphate phosphatase from rat liver

Dolichyl diphosphate phosphatase (DolPPase) has been characterized in rat liver. Subcellular distribution studies indicate that the enzyme is localized in the endoplasmic reticulum. The in vitro enzymatic activity is stimulated by EDTA, due to release of inhibition by trivalent cations found in the assay tubes. All di- and trivalent cations tested were inhibitory, with the trivalent ions Al3+ and Fe3+ showing greater than 70% inhibition at a concentration of 10 microM. The assay requires the presence of a detergent for optimal activity, with Triton X-100 giving maximum activity at 0.1%. The substrate specificity of DolPPase toward polyprenyl diphosphates has been determined and indicates that there is little preference of the enzyme for substrates of different chain length, and either stereochemical orientation or degree of saturation of the alpha-isoprene unit. Km values of 11-14 microM were obtained for all substrates tested. Preliminary studies on the transmembrane topology of the DolPPase using latency assays, indicate that the active site of the enzyme may reside on the cytoplasmic face of the endoplasmic reticulum.     

Demonstration of a cell-associated, inactive precursor of an exocellular protease produced by Pseudomonas aeruginosa

The enzymatically active form of protease 1, the major exocellular protein produced by Pseudomonas aeruginosa strain 34362, has been shown to exist exclusively exocellularly with no significant cell-associated activity. However, the presence of a cell-associated, enzymatically inactive protein which is serologically cross-reactive with, and convertible to, active enzyme has been demonstrated. One method of conversion of "precursor" to active enzyme is via limited proteolysis. Two assay systems for precursor were developed, one a radioimmune assay, and the other a proteolytic activation procedure. Localization studies suggest that the association while more tenacious than classical periplasmic enzymes is still an ionic rather than a covalent one. Kinetics of production studies showed to precursor to be synthesized early in the growth cycle and to accumulate prior to the rapid release of the active enzyme. Molecular weight studies showed only slight changes produced upon activation.     

β-D-galactosidase activity of viable, non-culturable coliform bacteria in marine waters

The β-D-galactosidase activity of viable but non-culturable (vnc) Escherichia coli cells in seawater was investigated using a rapid fluorimetric enzyme assay. Results from microcosm studies showed that loss of culturability did not necessarily result in loss of the ability to produce the galactosidase enzyme. Even when no culturable cells were detected, a positive enzyme assay response was observed and the activity of the inducible enzyme over time more closely reflected the number of vnc cells present.     

A high-throughput fluorescence resonance energy transfer-based assay for DNA ligase

DNA ligase is the enzyme that catalyzes the formation of the backbone phosphodiester bond between the 5'-PO(4) and 3'-OH of adjacent DNA nucleotides at single-stranded nicks. These nicks occur between Okazaki fragments during replication of the lagging strand of the DNA as well as during DNA repair and recombination. As essential enzymes for DNA replication, the NAD(+)-dependent DNA ligases of pathogenic bacteria are potential targets for the development of antibacterial drugs. For the purposes of drug discovery, a high-throughput assay for DNA ligase activity is invaluable. This article describes a straightforward, fluorescence resonance energy transfer-based DNA ligase assay that is well suited for high-throughput screening for DNA ligase inhibitors as well as for use in enzyme kinetics studies. Its use is demonstrated for measurement of the steady-state kinetic constants of Haemophilus influenzae NAD(+)-dependent DNA ligase and for measurement of the potency of an inhibitor of this enzyme.     

A spectrophotometric method for the assay of phospholipase D activity

Phosphatidylcholine phosphatidohydrolase (EC 3.1.4.4, phospholipase D) catalyzes the hydrolysis of phosphatidylcholine to phosphatidic acid and choline. We have developed a spectrophotometric assay for phospholipase D using choline kinase, pyruvate kinase, and lactate dehydrogenase to couple the release of choline with the oxidation of NADH. The assay was linear both with time and with enzyme concentration. The assay should prove useful for continuous monitoring of enzyme activity, determination of initial rates of reaction, and detailed kinetic studies of phospholipase D. The method is limited to analysis of purified preparations of phospholipase D lacking competing activities to the coupled system.     

Radioactive method for the assay of glycogen phosphorylases

A new assay for glycogen phosphorylase (EC 2.4.1.1) is presented. This assay employs a filter paper technique in which newly formed glycogen-¹⁴C is precipitated on paper squares using 66% ethanol while other radioactivity is removed by washing. It is rapid and reproducible and may be employed with crude as well as purified enzyme preparations. An additional advantage of the method is the potential for increased sensitivity. It should find utility for assay of extremely small tissue samples and should be useful in kinetic studies.     

A continuous spectrophotometric assay for cyclic 3′,5′-nucleotide phosphodiesterase

In the course of studies on cyclic nucleotide phosphodiesterase, the need for an assay which was both sensitive and continuous was realized. Most of the methods available for monitoring phosphodiesterase either depend on the use of accessory enzymes, and are accordingly subject to intrinsic limitations, or are not capable of continuously monitoring the enzymatic reaction. The present paper describes a new spectrophotometric assay for cyclic nucleotide phosphotidesterase which is highly reproducible, rapid, simple, and more sensitive than many of the previously published assays for this enzyme. The method is sensitive enough to detect the enzymatic conversion of 75 pmol of cAMP to 5′-AMP per minute. This assay is based on the fact that the hydrolysis of cyclic nucleotides to the corresponding 5′-phosphate ester by phosphodiesterase makes available an additional titratable proton of the 5′-phosphate group. By incorporating phenol red into the assay mixture, the rate of proton production can be continuously measured by monitoring the decrease in absorbance of the basic chromophore of phenol red at 560 nm. The primary advantages of the spectrophotometric assay described here are: (a) it provides initial velocity measurements, and thus is ideally suited to studying the kinetic properties of partially purified preparations of enzyme, and (b) it does not require the tedious and time-consuming purification of commercially available substrates which is often required when radioisotopic assays are used in detailed kinetic studies. The chief limitations are: (a) the sensitivity is not sufficient to accurately monitor the “low K_m” enzyme, and (b) the use of the assay to quantitate revoveries throughout extensive purification, where different buffer salts at different pH values are used, would require that the enzyme be dialyzed prior to assay.     

Photometric method for routine determination of kcat and carbamylation of rubisco

Ribulose bisphosphate carboxylase (rubisco) is the first enzyme in photosynthetic CO₂ assimilation. It is also the single largest sink for nitrogen in plants. Several parameters of rubisco activity are often measured including initial activity upon extraction, degree of carbamylation, catalytic constant of the enzyme (k_cat), and the total amount of enzyme present in a leaf. We report here improvements of the photometric assay of rubisco in which rubisco activity is coupled to NADH oxidation which is continuously monitored in a photometer. The initial lag usually found in this assay was eliminated by assaying rubisco activity at pH 8.0 instead of 8.2, using a large amount of phosphoglycerate kinase, and adding monovalent cations to the assay buffer. We found that when using the photometric assay, the ratio of activity found initially upon extraction divided by the activity after incubating with CO₂ and Mg²⁺ reflects the degree of carbamylation as determined by ¹⁴carboxyarabinitol bisphosphate/¹²carboxyarabinitol bisphosphate competition. We developed methods for measuring the catalytic constant of rubisco as well as the total amount of enzyme present using the photometric assay and carboxyarabinitol 1,5-bisphosphate. We believe that the photometric assay for activity will prove more useful than the ¹⁴CO₂ assay in many studies.Abbreviations CA1P 2-carboxyarabinitol 1-phosphate - GAP glyceraldehyde 3-phosphate - OD optical density - PGA 3-phosphoglycerate - rubisco ribulose-1,5-bisphosphate carboxylase/oxygenase - RuBP ribulose 1,5-bisphosphate     

A sensitive enzyme-linked immunosorbent assay for dihydrofolate reductase.

A competitive enzyme-linked immunosorbent assay (ELISA) has been developed for the enzyme, dihydrofolate reductase. The sensitivity of the assay system approximates 3 ng of immunoreactive enzyme protein which is comparable to the sensitivity achieved in the radioimmunoassay (RIA) for this enzyme. The mean coefficient of variation for within--and between--assay precision was less than 13%. The assay appears to be specific and valid as the concentration of the enzyme is the same whether measured by ELISA or [3H]-methotrexate binding. Since this method, like the RIA, measures the mass concentration of enzyme protein, in conjunction with a [3H]-methotrexate binding assay it will be useful for quantitating functional as well as non-functional immunoreactive forms of the enzyme.     

Immobilized DNA hairpins for assay of sequential breaking and joining of DNA backbones

Immobilized DNA hairpins are exploited in a novel approach to assay DNA ligases and nucleases. A fundamental characteristic of the assay is that a fluorophore at the remote terminus of the hairpin reports on the integrity of the DNA backbone. The functionality of the protocol is confirmed using ATP- and NAD+-dependent DNA ligases and the nicking enzyme N.BbvCIA. The assay format is amenable to high-throughput analysis and quantitation of enzyme activity, and it is shown to be in excellent agreement with the more laborious electrophoretic approaches that are widely used for such analyses. Significantly, the assay is used to demonstrate sequential breaking and rejoining of a specific nucleic acid. Thus, a simple platform for biochemically innovative studies of pathways in cellular nucleic acid metabolism is demonstrated.