Phosphorothioate analogues of 5-phosphoribosyl 1-diphosphate: 31P nuclear magnetic resonance study

31P nuclear magnetic resonance (NMR) has been used to study the 1-phosphorothioate analogues of 5-phosphoribosyl 1-diphosphate (P-Rib-PP). Comparison of the proton-decoupled spectra of 5-phosphoribosyl 1-O-(2-thiodiphosphate) (P-Rib-PP beta S) and the SP diastereomer of 5-phosphoribosyl 1-O-(1-thiodiphosphate) (P-Rib-PP alpha S) with the parent molecule revealed a characteristic large downfield chemical shift change for the resonance signal associated with the thiophosphate group (delta delta approximately 40-50 ppm) and an increase in the magnitude of the phosphate-thiophosphate spin-spin coupling constant (delta J alpha beta approximately 10 Hz). Both these changes are consistent with the observed effects of sulfur substitution on the behavior of the adenosine nucleotides, particularly ADP [Jaffe, E. K., & Cohn, M. (1978) Biochemistry 17, 652-657]. High-field 31P NMR has also been used to demonstrate the diastereomeric purity of P-Rib-PP alpha S (Sp diastereomer) and the greater lability of this analogue when compared with both P-Rib-PP beta S and P-Rib-PP. Sulfur substitution was found to cause a large decrease in the apparent pKa associated with the thiophosphate moiety of P-Rib-PP beta S (delta pKa approximately 1.4 units) and also to enhance the sensitivity of the thiophosphate chemical shift to protonation and, in particular, to Mg2+ binding, compared with P-Rib-PP. The potential application of the phosphorothioate analogues as probes of the reactions catalyzed by the phosphoribosyltransferase enzymes is discussed.     

Formation, characterization and partial purification of a Tn5 strand transfer complex

DNA transposition reactions typically involve a strand transfer step wherein the transposon ends are covalently joined by the transposase protein to a short target site. There is very little known about the transposase-DNA interactions that direct this process, and thus our overall understanding of the dynamics of DNA transposition reactions is limited. Tn5 presents an attractive system for defining such interactions because it has been possible to solve the structure of at least one Tn5 transposition intermediate: a transpososome formed with pre-cleaved ends. However, insertion specificity in the Tn5 system is low and this has hampered progress in generating target-containing transpososomes that are homogeneous in structure (i.e. where a single target site is engaged) and therefore suitable for biochemical and structural analysis. We have developed a system where the Tn5 transpososome integrates almost exclusively into a single target site within a short DNA fragment. The key to establishing this high degree of insertion specificity was to use a target DNA with tandem repeats of a previously characterized Tn5 insertion hotspot. The target DNA requirements to form this strand transfer complex are evaluated. In addition, we show that target DNAs missing single phosphate groups at specific positions are better substrates for strand transfer complex formation relative to the corresponding unmodified DNA fragments. Moreover, utilization of missing phosphate substrates can increase the degree of target site selection. A method for concentrating and partially purifying the Tn5 strand transfer complex is described.     

Analogues of ribose 5-phosphate and 5-phosphoribosyl pyrophosphate. The preparation and properties of ribose 5-phosphorothioate and 5-phosphoribosyl 1-methylenediphosphonate

1. 5-Phosphoribosyl 1-methylenediphosphonate was isolated after reaction of ribose 5-phosphate and O-adenylyl methylenediphosphonate with 5-phosphoribosyl pyrophosphate synthetase from Ehrlich ascites-tumour cells. 2. The analogue reacted with adenine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase and nicotinamide phosphoribosyltransferase [K(m) (analogue)/K(m) (5-phosphoribosyl pyrophosphate) 0.17, 0.19 and 6.3 respectively; V(max.) (analogue)/V(max.) (5-phosphoribosyl pyrophosphate) 0.011, 0.26 and 1.1 respectively]. 3. The analogue was not a substrate for 5-phosphoribosyl pyrophosphate amidotransferase or orotate phosphoribosyltransferase. 4. Ribose 5-phosphorothioate was synthesized by allowing ribose to react with thiophosphoryl chloride in triethyl phosphate. The analogue was a substrate for 5-phosphoribosyl pyrophosphate synthetase from Ehrlich ascites-tumour cells. When this reaction was coupled to either adenine phosphoribosyltransferase or hypoxanthine phosphoribosyltransferase, adenosine 5'-phosphorothioate or inosine 5'-phosphorothioate was formed respectively.     

The F1-ATPase from Streptococcus cremoris: isolation, purification and partial characterization

1. The F1-ATPase from the plasma membrane of Streptococcus cremoris HA was released by low ionic shock wash and purified by gel filtration and ion exchange chromatography. 2. The specific activity of the purified F1-ATPase was 25.8 mumol Pi/mg protein/min. 3. Km for ATP was 0.80 mM, and Ki for ADP as a competetive inhibitor 0.40 mM. 4. The purified F1-ATPase consisted of five subunits, alpha, beta, gamma, delta and epsilon, with molecular masses of 47.0, 45.0, 29.5, 22.0 and 13.0 kDa, respectively. 5. The isoelectric point of the enzyme complex was found to be 4.4.     

Ubiquitin: preparative chemical synthesis, purification and characterization

An improved total synthesis of ubiquitin has been achieved by the Fmoc/t-butyl solid-phase methodology using NGPmc protection of the Arg residues. Optimization of the purification protocol has offered the material in substantial quantity (90 mg) in an overall yield of 4.2%. Characterization of the isolated products has opened the way to the studies of the folding pathway and the preparation of structural analogues.     

Determination of 5-phosphoribosyl 1-pyrophosphate in mouse liver

Optimum conditions for the determination of 5-phosphoribosyl 1-pyrophosphate (PP-ribose-P) in mouse liver are described. PP-Ribose-P is extracted from frozen liver powder with a solution of 182 μm [¹⁴C]adenine (10 μCi/μmole), 3.36 mm 2,3-diphosphoglycerate and 21.3 mm Tris-Cl buffer (pH 7.4) for 20 sec at 100°C. The amount of PP-ribose-P in the extract is calculated from the radioactivity incorporated into AMP, ADP, and ATP during a 60 min incubation at 37°C with adenine phosphoribosyltransferase and 2.5 mm CaCl₂.     

Human placental sialidase: partial purification and characterization

A sialidase [EC 3.2.1.18] has been partially purified from human placenta by means of procedures comprising Con A-Sepharose adsorption, ammonium sulfate precipitation, sucrose density gradient centrifugation, and high-pressure liquid chromatography on a Shim pack Diol 300 column. On high-pressure liquid chromatography, most of the beta-galactosidase that comigrated with the sialidase on sucrose density gradient centrifugation was removed. The sialidase was purified 3,600-fold from the preparation obtained by Con A-Sepharose adsorption. The enzyme liberated the sialic acid residues from (alpha 2-3) and (alpha 2-6) sialyllactose, colomic acid, fetuin, and transferrin, but not from bovine submaxillary mucin. The enzyme also hydrolyzed gangliosides GM3, GD1a, and GD1b in the presence of sodium cholate as a detergent, but GM1 and GM2 were less susceptible to the enzyme. The optimum pHs for 4-methylumbelliferyl-N-acetylneuraminate, sialyllactose, fetuin, and GM3 lay between 4.0 and 5.0.     

Alcalase rapeseed inhibitors: purification and partial characterization

Extensive rapeseed protein hydrolysate obtained sequentially with Alcalase and Flavourzyme showed inhibitory activity towards Alcalase. Inhibitory activity decreased as the hydrolytic process progressed probably by heat denaturation and/or partial protease degradation. Alcalase rapeseed inhibitors were purified by gel filtration and subsequent ion exchange chromatography. They are composed of peptides of 8.4 and 6.1 kDa linked by interchain disulphide bonds, as observed by reducing SDS-PAGE, with a native molecular weight of 18 kDa. Aminoacid composition of the inhibitors was characterized by the high proportion of methionine (4.2%) and cysteine (4.6%). Alcalase inhibitors were partially resistant to heat treatment; after heating at 70 degrees C for 45 minutes more than 50% of the original inhibitory activity remained in the purified protein but after heating at 90 degrees C for 5 minutes, inhibitory activity decreased very fast to a basal level. The possible relation of these protease inhibitors with the 2S albumin storage proteins is discussed.     

Zebra chorionic gonadotropin: partial purification and characterization

Six samples of pregnant zebra (z) serum from the first and second trimesters of pregnancy were analyzed by RIA and shown to have chorionic gonadotropin levels comparable to that of the mare (0.9-5.3 micrograms/ml); first trimester levels in most cases were higher than second trimester levels. A pool of the sera (10 ml) was fractionated by methods previously employed for the purification of equine (e) and donkey (d) chorionic gonadotropin to achieve a concentration of the zebra chorionic gonadotropin (zCG). A yield of 1.0 mg of glycoprotein was obtained. HPLC analysis of the material indicated the content of zCG to be about 7%. Its molecular size as judged by Ve/Vo values is smaller than eCG, greater than ovine LH, and about the same as equine LH. The zCG was tested in RIAs for LH and eCG, radioreceptor assays (RRA) for LH and FSH, and the rat testis Leydig cell assay for LH. Comparisons were made with equine and donkey chorionic gonadotropin, and equine and zebra LH. The results, preliminary because the preparation is not of high purity, showed that zCG is bioactive as an LH; immunologically similar to eCG, eLH, dCG, and zLH; and competes in RRAs for LH but not FSH receptors. It differs, therefore, from eCG and eLH--which have high levels of intrinsic FSH activity, and is more like dCG, dLH, and zLH--all of which have minimal if any FSH activity.     

Sheep liver beta-N-acetylhexosaminidase: partial purification, characterization and photodynamic inactivation

Sheep liver beta-N-acetylhexosaminidase was purified over 20-fold by conventional methods. The enzyme possessed activity against both p-nitrophenly-beta-D-N-acetylglucosaminide and p-nitrophenyl-beta-D-N-acetylgalactosaminide as substrates. On the basis of a variety of physical and chemical analyses including pH stability, substrate inhibition studies and photodynamic inactivation, it was concluded that both the beta-N-acetylglucosaminidase and beta-N-acetylgalactosaminidase activities reside within the same molecule.     

Nitrate reductase from yeast: cultivation,partial purification and characterization

Summary Several yeast strains were assayed for occurence of nitrate reductase after growth in a defined medium with nitrate as the sole nitrogen source, Candida boidinii DSM 70026, showing the highest specific activity, was further investigated. The procedures for yeast fermentation and nitrate reductase purfication are described in detail. Nitrate reductase from this yeast was characterized as NAD(P)H: nitrate oxidoreductase (E.C.1.6.6.2). The enzyme activity with NADH (NADPH) was highest at pH 7.0 (7.1) and 30° C (25° C). The values of K _m determinations with NADH/NADPH were both 4 × 10^–4 mol/l; values for the substrate inhibition constant (K _i) were 6 × 10^–4 mol/l. The molecular mass of the native enzyme was estimated by gel permeation chromatography to be approximately 350 kDa. Offprint requests to: R. Gromes     

Phosphorothioate analogues of oligodeoxyribonucleotide: synthesis and activity as inhibitors of replication of human immunodeficiency virus

The modifications of oligodeoxyribonucleotides include replacement of the other chain either all-PS (S-ODNs), or end-capped with several PS (SO-ODNs) groups at both 3'- and 5'-ends. A general synthesis of phosphorothioate analogues of oligodeoxyribonucleotides is described using the new phosphite. In assays of HIV, oligomers (S-ODNs) with complete replacement of phosphodiesters with phosphorothioate groups were found to be very active. Finally of particular interest is S-ODNs-rev or tat (20mers) which possessed slightly higher anti-HIV activity than S-dC28 itself. By contrast, the unmodified oligomers (ODNs) as well as SO-ODNs did not have any inhibitory effect.     

Identification, purification, and partial characterization of plasma protein kinases

Two isomeric forms of protein kinases, FI and FII, were isolated from human plasma. These two isomeric enzymes were isolated to apparent homogeneity on NaDodSO4-PAGE by using (NH4)2SO4 fractionation, DEAE-cellulose, hydroxylapatite, Affi-Gel blue, and high-pressure liquid column chromatography. Polyclonal antibodies were obtained from immunized rabbits and both enzymes cross-reacted with each other. Furthermore, immunoaffinity-purified anti-FI and anti-FII antibodies inhibited the enzyme activity of both FI and FII. These enzymes are cyclic nucleotides, Ca2+, calmodulin and phosphatidylserine-independent enzymes which can phosphorylate exogenously added histone, casein, protamine, phosvitin, and platelet surface proteins. The phosphorylated proteins of intact platelets by these enzymes in the presence of exogenously added [gamma-32P]ATP ranged in apparent molecular weights from 13.5K to 200K, as estimated by their mobility during NaDodSO4-PAGE. Trypsin removed the label from the platelet surface phosphoproteins without affecting the intracellularly located phosphoproteins labeled endogenously by 32PO4-prelabeling of intact platelets. These observations raise the possibility that these enzymes could play a role in modulating the properties of platelets through phosphorylation of the platelet surface proteins.     

Protein-diet-induced elevation of 5-phosphoribosyl 1-diphosphate concentrations in mouse liver associated with increased syntheses of various nucleotides and the possible involvement of glucagon

Postprandial elevation of 5-phosphoribosyl 1-diphosphate (PPRibP) concentration in the mouse liver (Lalanne, M. and Henderson, J.F. (1975) Can. J. Biochem. 53,394-399) was further studied regarding the effects of protein intake and the underlying mechanisms. The extent and duration of the increase depended on the quantity and quality of proteins ingested. The order of effectiveness of various diets was as follows: 60% casein greater than 20% egg albumin greater than 20% casein greater than 20% gelatin = 20% gluten greater than 20% zein greater than 0% casein. Hepatic purine and pyrimidine biosyntheses de novo, as measured by labelled tracer incorporation, increased with increasing protein intake. Nicotinic acid incorporation into NAD increased equally, whether casein-containing or casein-free diets were given. Therefore, the increase of PPRibP level may be brought about by increase in its synthesis. Administration of glucagon or epinephrine similarly elevated the hepatic level of PPRibP. Somatostatin, known to inhibit secretion of pancreatic hormones, suppressed the casein-diet-dependent PPRibP level increase. Colchicine markedly inhibited the casein-diet- and glucagon-dependent responses, but not the epinephrine effect. It is likely that glucagon is a major factor in mediation of the protein-diet-dependent PPRibP level increase and that the cytoskeleton is involved in the glucagon-mediated response.     

Inactivation of mevalonate 5-diphosphate decarboxylase by phosphorothioate analogues of ATP

Mevalonate 5-diphosphate decarboxylase is inactivated by several nucleoside phosphorothioates and the order of effectiveness as inactivators is: (Rp) ATP beta S greater than (Sp) ATP beta S approximately equal to ADP beta S approximately equal to AMPS greater than ATP gamma S. Mevalonate 5-diphosphate protects the enzyme against inactivation and, to a lower extent, so does ATP. As dithiothreitol prevents the enzyme inactivation, these results are interpreted as being the consequence of the interaction of the above mentioned analogues with functional thiol groups of the enzyme.     

Rat kidney histamine N-methyltransferase: purification and partial characterization

Histamine N-methyltransferase (HMT, EC 2.1.1.8) was purified 8,420-fold in 44% yield from rat kidney. The basic steps in the purification included differential centrifugation, calcium phosphate adsorption, DEAE cellulose chromatography, and affinity chromatography on an S-adenosylhomocysteine-agarose matrix. The resulting protein was homogeneous as determined by gel electrophoresis and was stable for at least five months at -80 degrees C. The apparent molecular weight of the enzyme was found to be 31,500 as determined by gel filtration through Sephadex G-100 and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isoelectric point of the enzyme was determined to be 5.4. The Km's for histamine and S-adenosyl-L-methionine were 12.4 +/- 1.3 microM and 10.2 +/- 0.5 microM, respectively. When S-adenosyl-L-methionine was the variable substrate, the Ki's for S-adenosyl-L-homocysteine and S-adenosyl-D-homocysteine were 31.9 +/- 3.4 microM and 32.0 +/- 3.5 microM, respectively. When histamine was the variable substrate, the Ki for S-adenosyl-L-homocysteine was 11.8 +/- 0.6 microM. Comparison of physico-chemical and catalytic properties of the rat kidney and the guinea pig enzymes suggest that these proteins have similar structural and catalytic characteristics.     

Maize leaf adenylate kinase : purification and partial characterization

Adenylate kinase (EC 2.7.4.3) from leaves of maize (Zea mays) was purified to homogeneity using (NH₄)₂SO₄ fractionation, followed by chromatography on DEAE-cellulose, hydroxyapatite, Sephadex G-75SF, and Green A dye-ligand columns. The purified enzyme had specific activity of about 1,550 micromoles ADP produced per minute per milligram protein, and the ratio of velocities of the reverse (utilization of ATP) to forward (formation of ATP) reaction was about 1.5. The M_r value of adenylate kinase, determined by electrophoresis in dissociating conditions and by gel filtration, was 29,000 and 31,000 respectively, suggesting monomeric nature of the enzyme. Purified preparations were stable for at least 1 month at 0 to 4°C. Magnesium ions were essential for activity of adenylate kinase in both directions of the reaction. Optimal rates in the forward direction were observed at the magnesium to ADP ratio of about 0.6 to 0.8. For the reverse reaction, ATP served as a substrate only when complexed with magnesium, while AMP reacted as a free species. The enzyme preferentially utilized adenine ribonucleotides in both directions of the reaction. The nucleoside triphosphate-binding site of adenylate kinase was fairly nonspecific with regard to nucleotide species. On the other hand, the primary amino group of either adenine and cytosine moieties was essential for effective binding to the nucleoside monophosphate site of the enzyme.     

Soluble NADH-cytochrome b5 reductase from rabbit liver cytosol: partial purification and characterization.

A soluble form of NADH-cytochrome b5 reductase (NADH: ferricytochrome b5 oxidoreductase, EC 1.6.2.2) was found in the cytosolic fraction of rabbit liver. The partially purified enzyme was strictly specific for NADH. It catalyzed the reduction of several substrates such as the methemoglobin-ferrocyanide complex (Hegesh, E. and Avron, M. (1967) Biochim. Biophys. Acta 146, 91-101) (apparent Km: 8 micrometer), potassium ferricyanide (apparent Km: 10 micrometer) and ferricytochrome b5 (apparent Km: 15 micrometer). Upon acrylamide gel isoelectro-focusing followed by specific staining, the enzyme was resolved into four bands (isoelectric pH: 7.05, 6.70, 6.50 and 6.30). The optimum pH of activity with ferricytochrome b5 as a substrate was 6.5. The estimated molecular weight was 25 000--30 000. The enzyme was unsensitive to cyanide. It was strongly inhibited by p-hydroxymercuribenzoate. The cytosolic liver cytochrome b5 reductase was immunologically related to the soluble cytochrome b5 reductase from human and rabbit red-cells, and to the microsomal cytochrome b5 reductase from rabbit liver.