Developing a colorimetric assay for Fe(II)/2-oxoglutarate-dependent dioxygenase.

The Fe(II)/2-oxoglutarate-dependent dioxygenases (2-OGDs) catalyze the oxidation of substrates ranging from small molecules to large biomolecules with concomitant oxidation of co-substrate (2-oxoglutarate) into succinate. In the present study, we reported a coupled colorimetric assay that can be generally applied to measure the activities of all members of 2-OGDs family. Succinyl-CoA synthetase is employed as the coupling enzyme to transform succinate produced from 2-OGDs catalysis to form succinyl-CoA with concomitant hydrolysis of ATP to form ADP and orthophosphate. Orthophosphate can be quantitated by reacting it with molybdic acid forming a blue pigment. As a proof of concept, kinetic parameters of ectoine hydroxylase obtained using this method are compared to a traditional time- and labor-consuming HPLC based method. As 2-OGDs family enzymes are important drug targets due to their impressive versatility in catalyzing numerous oxidative reactions that are still very challenging using synthetic chemistry, colorimetric method detailed in the manuscript has the potential to enable the practice of high throughput drug screening for 2-OGDs.

Identification of novel biomarker and therapeutic target candidates for diagnosis and treatment of follicular carcinoma.

Distinguishing follicular carcinoma from follicular adenoma, based on cytomorphological features, has always been challenging to cytopathologists. Identification of biomarkers for improving diagnostic accuracy is important for clinical management. Meanwhile, it is critical to identify therapeutic target candidates for treatment of follicular carcinoma. Currently, no reliable diagnostic protein biomarkers and therapeutic targets are available. To explore novel protein biomarker and therapeutic target candidates, a liquid chromatography-tandem mass spectrometry approach was applied to analyze control, follicular adenoma, and follicular carcinoma using formalin-fixed, paraffin-embedded tissue samples. The proteomics analysis revealed 80 protein biomarker candidates for diagnosis of thyroid follicular carcinoma. The candidates were prioritized into three categories and ranked within each category. Using the proteomics data and bioinformatics results, the top seven biomarker candidates were coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial (CHCHD2), succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (SUCLG2), stomatin-like protein 2, mitochondrial (STOML2), ES1 protein homolog, mitochondrial (C21orf33), fumarate hydratase, mitochondrial (FH), 3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10), and electron transfer flavoprotein subunit beta (ETFB); and the top seven therapeutic target candidates were insulin receptor (INSR), Myc proto-oncogene protein (MYC), peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A), gastrin (GAST), N-myc proto-oncogene protein (MYCN), transforming growth factor beta-1 (TGFB1), and interleukin-4 (IL4). Immunohistochemical staining of SUCLG2 and ETFB is highly consistent with the discovery of proteomics, revealing that SUCLG2 has a sensitivity of 75% and a specificity of 80% to distinguish follicular carcinoma from follicular adenoma based on a specific cut-off score calculated from the IHC staining percentage and intensity. BIOLOGICAL SIGNIFICANCE: Distinguishing follicular carcinoma from follicular adenoma, based on cytomorphological features, has always been challenging to cytopathologists. Fourteen biomarker candidates were identified. Two of them were validated with Immunohistochemical staining. The Identification of biomarkers for improving diagnostic accuracy is important for clinical management.

Affinity chromatography of acyl-CoA utilizing enzymes on Procion Red-agarose.

The dye Procion Red HE3B immobilized on agarose and available as Matrex Gel Red A is shown to bind citrate synthase and succinate thiokinase from a number of diverse organisms. Salt-gradient elution removes the enzymes in high yields and with substantial purification. The elution profiles follow a pattern similar to that of the molecular size variations of the enzymes.

Heme synthesis in Crithidia deanei: influence of the endosymbiote.

The activity of the following enzymes involved in the biosynthesis of porphyrins was determined in endosymbiote-free and endosymbiote-containing Crithidia deanei grown in a chemically defined medium: succinyl Coenzyme A synthetase (Suc.CoA-S), 5-aminolevulinate synthetase (ALA-S), 4,5-dioxovaleric acid transaminase (DOVA-T), 5-aminolevulinate dehydratase (ALA-D), porphobilinogenase (PBGase), deaminase and heme synthetase (Heme-S). The amount of 5-aminolevulinic acid (ALA) and porphobilinogen, porphyrins and heme was also determined. ALA and PBG were detected in C. deanei. The levels of free porphyrins was low. Heme concentration was nil. The activity of ALA-D, deaminase and PBGase was not detected in C. deanei. The activity of Suc.CoA-S and ALA-S were twice higher in symbiote-containing than in aposymbiotic C. deanei. Aposymbiotic cells had a higher activity of DOVA-T than symbiote-containing cells. The level of Heme-S, measured using protoporphyrin as substrate, was twice as high in symbiote-containing than in symbiote-free cells.

The direct assay of kinases and acyl-CoA synthetases by HPLC: application to nucleoside diphosphate kinase and succinyl-CoA synthetase.

A general procedure is described for developing and validating HPLC-based assays for nucleotide-utilizing enzymes. The method is comparable in sensitivity to spectrophotometric, enzyme-coupled assays and is applicable to any enzymatic reaction involving coenzyme A and its esters, or the common nucleoside tri-, di-, and/or monophosphates. Nucleotide products of the enzymatic reactions are directly quantitated from their uv absorbances. A typical HPLC-based assay involves running an enzymatic reaction for a fixed time, stopping the reaction by adding acid, and using HPLC to quantitate the amount(s) of nucleotide reactant(s) converted to product(s). Nucleotides containing the same base can be separated under isocratic conditions using a 5-microns C-18, reversed-phase column, and a mobile phase at pH 5 containing 100 mM potassium phosphate, 20 mM acetate, 5 mM tetrabutylammonium ion as an ion-pairing agent, and sufficient acetonitrile to keep the run time within 10 min. Separation of nucleotides containing different bases can usually be accomplished under isocratic conditions by the proper choice of the pH within the range of 3 to 7. A microcomputer is used to control all system hardware and to automate collection and processing of chromatographic data. Application of the general method to development of assays for nucleoside diphosphate kinase and succinyl-CoA synthetase is described. The assay for nucleoside diphosphate kinase quantitates UTP formed from UDP and ATP as substrates. The assay for succinyl-CoA synthetase measures succinyl-CoA after HPLC separation of reactants and products at pH 4 where succinyl-CoA is stable to chemical hydrolysis.

Studies of the process of renaturation and assembly of Escherichia coli succinyl-CoA synthetase from its alpha and beta subunits.

Succinyl-CoA synthetase catalyzes the substrate-level phosphorylation step of the tricarboxylic acid cycle. The enzyme, as isolated from Escherichia coli, has an alpha 2 beta 2 subunit structure. It is known that substrate-binding sites are distributed between both subunit types and that the active enzyme is the nondissociating tetramer. This paper describes a study of the process of assembly of the enzyme from its denatured constituent subunits. Starting with equimolar mixtures of the subunits that are prepared in denaturing conditions (6 M urea, 5% acetic acid), rapid renaturation to produce virtually a fully active enzyme occurs after neutralization and dilution under suitable conditions. This process occurs most efficiently in the presence of either ATP or Pi, indicating that occupation of the phosphoryl-binding site on the refolding alpha subunit facilitates productive intrasubunit interactions. We have determined conditions of protein concentration, pH, temperature, final urea concentration, and buffer compositions that optimize both the rate and extent of production of active enzyme. The final refolded product is indistinguishable from the native species with respect to its specific catalytic activity, size, and other physical properties. To probe further the mechanism and route of renaturation, we have shown that the rate of appearance of activity has first-order dependence on each of the two subunits. The step that determines the rate of assembly is thus bimolecular, such as the association of structural monomers to form a dimeric transient species. The highly specific mutual interactions between the refolding transient species of subunits must be essential for the correct assembly of this enzyme from the two gene products in vivo.

Characterization of hydrogenosomes and their role in glucose metabolism of Neocallimastix sp. L2.

In the anaerobic fungus Neocallimastix sp. L2 fermentation of glucose proceeds via the Embden-Meyerhof-Parnas pathway. Enzyme activities leading to the formation of succinate, lactate, ethanol, and formate are associated with the cytoplasmic fraction. The enzymes 'malic enzyme,' NAD(P)H:ferredoxin oxidoreductase, pyruvate:ferredoxin oxidoreductase, hydrogenase, acetate:succinate CoA transferase and succinate thiokinase leading to the formation of H2,CO2, acetate, and ATP are localized in microbodies. Thus, these organelles are identified as hydrogenosomes. In addition, the microbodies contain the O2-scavenging enzymes NADH- and NADPH oxidase, while NAD(P)H peroxidase, catalase, or superoxide dismutase could not be detected. In cell-free extracts from zoospores of Neocallimastix sp. L2 the specific activities of hydrogenosomal enzymes as well as the quantities of these proteins are 2- to 6-fold higher than in mycelium extracts. These findings suggest that hydrogenosomes perform an important role--especially in zoospores--as H2-evolving, ATP-generating and O2-scavenging organelles.