Role of nucleoside components and internucleotide phosphate groups of oligodeoxyribonucleotide template in its binding to human DNA polymerase alpha

Affinity labelling of human placenta DNA polymerase alpha (EC 2.7.7.7) with the reactive oligodeoxyribonucleotide d(pT)2pC[Pt2+(NH3)2OH](pT)7 was used for quantitative analysis of enzyme interaction with oligodeoxyribonucleotides as templates. Dissociation constants and Gibb's energy values for different oligothymidylates d(pT)nT where n = 1-14 have been evaluated by competitive experiments of these ligands with Pt2+ reagent. The data obtained prove the formation of one Me2+-dependent electrostatic contact and a hydrogen bond between the enzyme and one phosphate of these templates. One may suppose that the hydrophobic interaction of any other monomeric link of oligodeoxyribonucleotides with the enzyme template site takes place.     

Purification and characterization of DNA-dependent DNA-polymerase alpha from human placenta

A preparation of human placenta DNA polymerase with specific activity 6000 unit/mg was obtained. The protocol of the enzyme purification includes the crude extract preparation, the subsequent chromatographies on phosphocellulose, red sepharose, DEAE sepharose and hydroxylapatite. The isolated DNA polymerase belongs to alpha-type according to the large molecular mass (greater than 150 kDa), high sensitivity to N-ethylmaleimide, the profound inhibition of DNA polymerization activity by 200 mM KCl and the ability to catalyze DNA synthesis, using the deoxyribonucleic template and ribonucleic primer. The DNA polymerase preparations contain a few forms with Stokes radii 50-60 A and sedimentation coefficients 7.3-9.0 S as found from data of gel-filtration and ultracentrifugation in glycerol density gradient, accordingly. The existence of four various forms of DNA polymerase activity: 150, 170, 220, 480 kDa were revealed by native electrophoresis. The four steps of purification result in DNA polymerase preparation that was shown by electrophoresis to contain 15-20% of protein possessing the polymerase activity. However the preparation obtained seems to be a "chromatographically pure substance", according to following ion-exchange and affinity chromatographies. The other proteins without polymerase activity are suggested to be the components of the replicative complex of human placenta cells.     

Highly selective affinity labeling of the primer-binding site of E. coli DNA polymerase I

Membrane-associated phosphoinositidase C activity has been identified in Dictyostelium discoideum using phosphatidylinositol 4,5-bisphosphate as exogenous substrate. Maximal activity was observed with 0.4 mM phosphatidylinositol 4,5-bisphosphate at pH 7.0. The enzyme was stimulated

by micromolar concentrations of free calcium with maximal activity at 100 μM.     

Structure-function analysis of mononucleotides and short oligonucleotides in the priming of enzymatic DNA synthesis

The reversed-phase chromatography technique was employed in the measurement of DNA synthesis at the primers d(pT)n, r(pU)n, d(pA)n, and r(pA)n (n = 1-16) in the presence of template poly(dA) or poly(dT). DNA synthesis was catalyzed by Escherichia coli DNA polymerase I Klenow fragment, Physarum polycephalum DNA polymerase beta-like, P. polycephalum DNA polymerase alpha, and human placenta DNA polymerase alpha. Values of Km and Vmax were measured as functions of the primer chain lengths. It was found that all mononucleotides and small oligonucleotides served as primers of DNA synthesis. Values of the logarithm of both Km and Vmax increased linearly until primers had attained a chain length of 9-12 nucleotides, where a break was observed. The incremental as well as the absolute values of Km were interpreted in terms of free binding energies. These together with other data indicate that the 3'-ultimate nucleotide of the primer contributes a decisive amount of free energy of binding to DNA polymerase both from the nucleoside and from the phosphate moiety. The incremental increase is due to a complementary interaction between bases of primer and template buried in the binding cleft of the polymerase. It is also the ultimate nucleotide that determines whether the ribonucleotide or the deoxyribonucleotide is an efficient primer. It is of interest that the major results seem preserved for all four DNA polymerases. An energetic model for the binding of the template-primer was proposed and compared with available crystallographic data.     

The separation of subunits of phenylalanyl-tRNA-synthetase from Escherichia coli MRE-600 by means of affinity chromatography in dissociation conditions

The method of affinity chromatography on sepharose with immobilized tRNA in the presence of urea was developed for separating the subunits of phenylalanyl-tRNA synthetase from E. coli MRE-600 (subunit structure alpha 2 beta 2). Specific binding of large beta-subunits of the enzyme on immobilized tRNA testifies the localization of the tRNA-binding center on the beta-subunit of phenylalanyl-tRNA synthetase. Separately alpha- and beta-subunits of the enzyme exhibit no catalytic activity. Incubation of the mixture of alpha- and beta-subunits in conditions leading to reassociation of the oligomeric structure results in restoration of catalytic activity of the enzyme. In the presence of urea resin with immobilised analogs of ATP binds alpha- and beta-subunits of the enzyme. This testifies the presence of nucleotide-binding sites on both subunits. The possibility of using the affinity chromatography method to separate non-identical subunits of different enzymes is discussed.     

Light microscope immunolocation of Bacillus thuringiensis kurstaki delta-endotoxin in the midgut and Malpighian tubules of the tobacco budworm, Heliothis virescens

Light microscope immunofluorescence was used to localize the membrane binding of Bacillus thuringiensis kurstaki 63-kDa delta-endotoxin in Heliothis virescens midgut and Malpighian tubules. Staining was observed along all exposed mucosal (apical microvillar) plasma membranes. Interpretation of the serosal (basal) plasma membrane staining was complicated because the basal lamina also stained. The results suggest that the toxin binds to all exposed plasma membranes without apparent specificity for particular membrane domains.     

Caspase-2: What do we know today?

Apoptosis (programmed cell death) is essential process in multicellular organisms. Apoptosis plays an important role in cell differentiation, damaged cell elimination, and immune system homeostasis. The review focuses on various mechanisms of signal transduction through caspase-2, which is thought to be one of the most enigmatic proteases involved in apoptosis. Caspase-2 is activated upon stimulation by various factors, including genotoxic stress, death receptor ligation, endoplasmic reticulum stress, metabolic changes, and a number of others. In addition, caspase-2 can act as a tumor suppressor and has been implicated in the cell response to oxidative stress and neurodegenerative progression during ischemic brain injury. Thus, the variety of pathways triggered by caspase-2 sets the enzyme apart from other members of the family and suggests a prominent role in apoptosis. The review analyzes the various functions of this unique caspase and discusses the possible applications of the available knowledge about it in modern oncology and medicine.     

Photoaffinity labeling of mouse fibroblast enzymes by a base excision repair intermediate. Evidence for the role of poly(ADP-ribose) polymerase-1 in DNA repair

To examine the interaction of mammalian base excision repair (BER) enzymes with DNA intermediates formed during BER, we used a novel photoaffinity labeling probe and mouse embryonic fibroblast cellular extracts. The probe was formed in situ, using an end-labeled oligonucleotide containing a synthetic abasic site; this site was incised by apurinic/apyrimidinic endonuclease creating a nick with 3'-hydroxyl and 5'-reduced sugar phosphate groups at the margins, and then a dNMP carrying a photoreactive adduct was added to the 3'-hydroxyl group. With near-UV light (312 nm) exposure of the extract/probe mixture, six proteins were strongly labeled. Four of these include poly(ADP-ribose) polymerase-1 (PARP-1) and the BER participants flap endonuclease-1, DNA polymerase beta, and apurinic/apyrimidinic endonuclease. The amount of the probe cross-linked to PARP-1 was greater than that cross-linked to the other proteins. The specificity of PARP-1 labeling was examined using various competitor oligonucleotides and DNA probes with alternate structures. PARP-1 labeling was stronger with a DNA representing a BER intermediate than with a nick in double-stranded DNA. These results indicate that proteins interacting preferentially with a photoreactive BER intermediate can be selected from the crude cellular extract.