Highly sensitive simultaneous bioluminescent measurement of acetate kinase and pyruvate phosphate dikinase activities using a firefly luciferase-luciferin reaction and its application to a tandem bioluminescent enzyme immunoassay.

We have developed a simultaneous bioluminescent measurement of acetate kinase (AK) and pyruvate phosphate dikinase (PPDK) activities and its application to a tandem enzyme immunoassay. The principle of the proposed assay is as follows. In the first step, AK generates ATP from ADP and acetylphosphate, and the ATP is determined by the firefly luciferase-luciferin reaction. In the second step, the bioluminescent intensity from AK is eliminated by adding glucose and ADP-dependent hexokinase, which forms AMP from ADP. At the same time, the PPDK catalyzes the interconversion of AMP, diphosphate, and phosphoenolpyruvate to ATP, phosphate and pyruvate. The ATP formed by PPDK is also determined by the firefly luciferase-luciferin reaction. The detection limits (at blank + 3SD) of AK and PPDK were 1.03 x 10(-20) and 2.05 x 10(-20) mol per assay, respectively. The method was applicable to a bioluminescent enzyme immunoassay for the assay of insulin and C-peptide in the same sample.     

An optimized luciferase bioluminescent assay for coenzyme A

A new bioluminescent method for coenzyme A (CoA) quantification is described. It is based on the enzymatic conversion of dehydroluciferyl-adenylate (L-AMP) into dehydroluciferyl-coenzyme A (L-CoA) by firefly luciferase (E.C. 1.13.12.7) (LUC), which causes a flash of light that can be measured in a luminometer. The method was subjected to optimization using experimental design methodologies to obtain optimum values for the concentrations of L-AMP ([L-AMP]), luciferase ([LUC]), ATP ([ATP]) and luciferin ([LH₂]). This method has a linear response over the range of 0.25–4 μM of CoA, with a limit of detection (LOD) of 0.24 μM and a limit of quantification (LOQ) of 0.80 μM. The assay has a relative standard deviation of about 7%. By coupling this optimized procedure to bioluminescent detection, a sensible and robust method can be obtained for the analysis of CoA.     

Bioluminescence and exogenous compounds: physico-chemical basis for bioluminescent assay

Bioluminescent systems are convenient objects to study mechanisms of influence of exogenous molecules on living organisms. Classification of physical and physico-chemical mechanisms of the effects of luminous bacteria Photobacterium leiognathi on bioluminescent reactions is suggested. Five mechanisms are discussed: (1) change of electron-excited states' population and energy transfer, (2) change of efficiency of S-T conversion in the presence of external heavy atom, (3) change of rates of coupled reactions, (4) interactions with enzymes and variation of enzymatic activity, (5) nonspecific effects of electron acceptors. Effects of various groups of chemical compounds are discussed according to the classification suggested. The compounds are: a series of fluorescent dyes, organic oxidizers, organic and inorganic heavy-atom containing compounds, and metallic salts. Applications of fluorescence time-resolved and steady-state techniques, as well as bioluminescence kinetics study, are discussed. The patterns of exogenous compounds' influence form a physico-chemical basis for bioluminescent ecological assay.     

Production of recombinant bleaching enzymes from thermophilic microorganisms in fungal hosts

Cost-effective production of enzymes for industrial processes makes the appropriate selection of the host-vector expression system critical. We have developed two systems for the bulk production of bleaching enzymes from thermophiles. Kluyveromyces lactis has been developed as a secretion host employing expression vectors based on the 2μ-like plasmid pKD1 of Kluyveromyces drosophilarium. Our second system involves the filamentous fungus Trichoderma reesei. Fusion and nonfusion vectors have been constructed using the strong cellobiohydrolase 1 (cbh1) promoter. The KEX2 protease cleavage site and a 6 × HIS-tag have been incorporated to facilitate both cleavage and purification of the mature foreign proteins.     

Toxicity biomonitoring of degradation byproducts using freeze-dried recombinant bioluminescent bacteria

A toxicity biomonitoring system using freeze-dried recombinant bioluminescent bacteria was implemented to diagnose the biotreatment of 2,4,5-trichlorophenol and its degradation byproducts of using a cell-free culture broth of Phanerochaete chrysosporium. The cellular toxicity was measured by the bioluminescence of constitutive bioluminescent bacteria, such as Photobacterium phosphoreum and GC2, while information on the toxicity caused by unknown byproducts was obtained using the specific bioluminescent responses of stress-inducible bioluminescent bacteria, which included DPD2540 (membrane-damage sensitive), TV1061 (protein-damage sensitive), DPD2794 (DNA-damage sensitive), and DPD2511 (oxidative-damage sensitive) strains. An overall decrease in the cellular toxicity was observed as the treatment progressed, i.e. as 2,4,5-trichlorophenol disappeared. On the other hand, bioluminescent responses from DPD2511, DPD2540, and TV1061 increased as degradation progressed, most probably due to the formation of byproducts causing oxidative-, membrane-, and protein-damage. In conclusion, this toxicity biomonitoring method may be applied to evaluate the toxicities of degradation byproducts of the other environmental processes to provide more information about the mode of the byproducts’ toxicity.     

Purification of human leucocyte pyruvate kinase

The M2 form of pyruvate kinase (M2-PK) was purified from human leucocytes by a new method involving a succession of two different Dyematrex agarose chromatographies. The main step consisted of an orange dye affinity column with elution by fructose-1,6-diphosphate. This purification procedure allowed us to obtain M2-PK with a specific activity of 433 I.U./mg of protein, i.e. a 188-fold purification with an overall yield of 33%. The homogeneity of this preparation was verified by sodium dodecyl sulphate polyacrylamide gel electrophoresis and double immunodiffusion in Ouchterlony plates. Anti-M2-PK antibodies obtained from rabbit neutralized the enzyme activity. Their specificity with regard to other types of PK showed that anti-M2-PK also reacted with M1-PK but not with R-PK.     

Rapid and highly sensitive detection of Escherichia coli O157:H7 in food with loop-mediated isothermal amplification coupled to a new bioluminescent assay

Testing for bioluminescent pyrophosphate is a convenient method of DNA detection without complex equipments, but it is insufficiently sensitive and offers no particular time advantage over other rapid detection methods. The shortcomings of the traditional bioluminescent pyrophosphate method have been addressed by using 2-deoxyadenosine-5-(α-thio)-triphosphate (dATPαS) instead of dATP for LAMP, thus reducing the high background signal and generating a constant background value. In this study, LAMP coupled to a novel bioluminescent pyrophosphate assay was developed to detect E. coli O157:H7. The new method has a limit of detection of <10 copies/μL or 5 CFU/mL; its sensitivity is higher than that of the conventional LAMP assay. Moreover, a food-borne pathogen can be detected when a single DNA template is included in the LAMP assay, making it 100 times more sensitive than the traditional LAMP method. Three hundred food samples were tested with this assay and the accuracy of detection was verified with a culture method and MALDI Biotyper. The assay only took 90–120 min and detected <10 copies of the pathogen. This method had the advantages of rapidity, sensitivity, and simplicity, so it is very competitive for the rapid and highly sensitive detection of food-borne pathogens.     

Mass spectrometric analysis reveals O-methylation of pyruvate kinase from pancreatic cancer cells

Pyruvate kinase (PK) is an important glycolytic enzyme that catalyzes the dephosphorylation of phosphoenolpyruvate to pyruvate. Human PK isozyme M2 (PKM2), a splice variant of M1, is overexpressed in many cancer cells, and PKM2 has been investigated as a potential tumor marker for diagnostic assays and as a target for cancer therapy. To facilitate identification and characterization of PK, we studied the enzyme from pancreatic cancer cells and normal pancreatic duct cells by electrophoresis and mass spectrometry, and identified multiple O-methylated residues from PK. These findings advance our knowledge of the biochemical properties of PK and will be important in understanding its biological function in cells.

Fluorescence detection techniques for protein kinase assay

Traditional methods for protein kinase (PK) assay are mainly based on use of ³²P-labeled adenosine triphosphate (ATP); applications of such methods are, however, hampered by radioactive waste and short half-life of ³²P-labeled ATP. Therefore non-radioactive methods, such as fluorescence detection techniques are good alternative. In this review, we describe the principles of four fluorescence techniques (fluorescence intensity endpoint measurement, fluorescence resonance energy transfer (FRET), fluorescence polarization (FP), and fluorescence lifetime imaging) and provide an overview of applications of these fluorescence detection techniques in protein kinase assay, underlining their relative advantages and limitations. Research trends in this field are also highlighted. Figure Schematic representation of kinase assay based on direct fluorescence polarization measurements. The fluorescent peptide, on phosphorylation by kinase, binds to a phosphospecific antibody, which leads to a high FP value     

Detection of small RNA molecules by a combination of branched rolling circle amplification and bioluminescent pyrophosphate assay

Polyfluorinated compounds (PFCs) are a relatively new and diverse set of compounds analyzed as contaminants in food. Their unique physical-chemical properties dictate the methods used for their analysis. Current analyses of the more volatile PFCs involve gas chromatography–mass spectrometry; liquid chromatography–tandem mass spectrometry is generally used for the less volatile PFCs. Considerations in the analysis of PFCs in foods include contamination from the widespread presence of materials that contain various PFCs, endogenous interfering compounds, and matrix effects. Future opportunities for research on PFCs in food exist, particularly in the areas of biological molecule–PFC interactions and the effects of food processing on these interactions. Future research will be facilitated by the synthesis of a wider variety of analytical standards.     

A sensitive bioluminescent assay of alcohol dehydrogenase in human serum and tissue extracts

Conclusions With the aid of a sensitive bioluminescence assay, alcohol dehydrogenase activity can be measured in the plasma of chronic alcoholics and patients with other drug-related liver-disorders. Suitable reagents for the assay are commercially available but must be compared regarding sensitivity and stability before routine determinations are introduced in clinical practice.

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Bestimmung der Alkoholdehydrogenase-Aktivität in menschlichem Serum und Gewebeextrakten mit Hilfe einer empfindlichen Bioluminescenz-Methode

     

Conjugated polymer nanoparticles for biochemical protein kinase assay

Sensitive and reliable monitoring of kinase activity was reported by using highly efficient fluorescence resonance energy transfer of conjugated polymer nanoparticles (CPNs) to a rhodamine labelled peptide substrate.     

Cloning and Sequence Analysis of Novel DNA Polymerases from Thermophilic Geobacillus Species Isolated from Hot Springs in Turkey: Characterization of a DNA Polymerase I from Geobacillus kaue Strain NB

The complete coding sequences of the polA genes from seven thermophilic Geobacillus species, isolated from hot springs of G?nen and Hisaralan in Turkey, were cloned and sequenced. The polA genes of these Geobacillus species contain a long open reading frame of 2,637 bp encoding DNA polymerase I with a calculated molecular mass of 99 kDa. Amino acid sequences of these Geobacillus DNA polymerases are closely related. The multiple sequence alignments show all include the conserved amino acids in the polymerase and 5'-3' exonuclease domains, but the catalytic residues varied in 3'-5' exonuclease domain of these Geobacillus DNA polymerases. One of them, DNA polymerase I from Geobacillus kaue strain NB (Gkaue polI) is purified to homogeneity and biochemically characterized in vitro. The optimum temperature for enzymatic activity of Gkaue polI is 70 °C at pH 7.5-8.5 in the presence of 8 mM Mg(2+) and 80-100 mM of monovalent ions. The addition of polyamines stimulates the polymerization activity of the enzyme. Three-dimensional structure of Gkaue polI predicted using homology modeling confirmed the conservation of all the functionally important regions in the polymerase active site.     

Development of a peptide inhibitor-based cantilever sensor assay for cyclic adenosine monophosphate-dependent protein kinase

A highly sensitive nanomechanical cantilever sensor assay based on an electrical measurement has been developed for detecting activated cyclic adenosine monophosphate (cyclic AMP)-dependent protein kinase (PKA). Employing a peptide derived from the heat-stable protein kinase inhibitor (PKI), a magnetic bead system was first selected as a vehicle to immobilize the PKI-(5-24) peptide for capturing PKA catalytic subunit and the activity assay was applied for indirectly assessing the binding. Synergistic interactions of adenosine triphosphate (ATP) and the peptide inhibitor with the kinase were then investigated by a solution phase capillary electrophoretic assay, and by surface plasmon resonance technology which involved immobilization of the peptide inhibitor. After systemically evaluated by a homogeneous direct binding assay, the ATP-dependent recognition of the catalytic subunit of PKA by PKI-(5-24) was successfully transferred on to the nanomechanical cantilevers at protein concentrations of 6.6 pM-66 nM, exhibiting much higher sensitivity and wider dynamic range than the conventional activity assay. Thus, direct assessment of activated kinases using the cantilever sensor system functionalized with specific peptide inhibitors holds great promise in analytical applications and clinical medicine.     

Green polymers from Geobacillus thermodenitrificans DSM465--candidates for molecularly imprinted materials

Novel molecular recognition materials were prepared from water soluble proteins from thermophile G. thermodenitrificans DSM465 by an alternative molecular imprinting method. Water soluble proteins from G. thermodenitrificans DSM465 were converted into the molecularly imprinted materials by adopting 9-EA as a print molecule. The molecularly imprinted protein membranes recognized As in preference to Gs. The adsorption isotherms led to the conclusion that molecular recognition sites toward As were constructed by the presence of 9-EA during the membrane preparation process. The affinity constant between As and the molecular recognition site thus constructed was determined to be 1.75 x 10(5) mol(-1) dm(3). The results obtained in the present study suggest that water soluble proteins from G. thermodenitrificans DSM465 is one of environmentally-friendly 'green' polymers to be converted into molecular recognition materials by applying an alternative molecular imprinting method.     

Computational simulation of ligand docking to L-type pyruvate kinase subunit

Computational blind docking approach was used for mapping of possible binding sites in L-type pyruvate kinase subunit for peptides, RRASVA and the phosphorylated derivative RRAS(P_i)VA, which model the phosphorylatable N-terminal regulatory domain of the enzyme. In parallel, the same docking analysis was done for both substrates of this enzyme, phosphoenolpyruvate (PEP) and adenosine diphosphate (ADP), and for docking of fructose 1,6-bisphosphate (FBP), which is the allosteric activator of the enzyme. The binding properties of the entire surface of the protein were scanned and several possible binding sites were identified in domains A and C of the protein, while domain B revealed no docking sites for peptides or for substrates or the allosteric regulator. It was found that the docking sites of different ligands were partially overlapping, pointing to the possibility that some regulatory effects, observed in the case of L-type pyruvate kinase, may be caused by the competition of different ligands for the same binding sites.