Macromolecular derivatives of NAD+ in heart nuclei: poly adenosine diphosphoribose and adenosine diphosphoribose proteins.

Rates of poly (ADP-R) formation from NAD⁺ were determined in isolated pigeon heart and liver nuclei. In heart nuclei K_m for NAD⁺ was 330 μM. On a DNA basis rates were more than twice in heart nuclei than in liver nuclei. The polymer poly (ADP-R) was identified in both nuclear systems by isolation, digestion with snake venom phosphodiesterase and chromatographic separation of phosphoribosyl-AMP and AMP. ADP-R binds to macromolecular nuclear components to form ADP-R derivatives, which upon digestion with snake venom phosphodiesterase yield only AMP, distinguishing these ADP-R compounds from poly (ADP-R).     

Turnip Yellow Mosaic Virus RNA as a Substrate of the Transfer RNA Nucleotidyltransferase II. Incorporation of Cytidine 5'-Monophosphate and Determination of a Short Nucleotide Sequence at the 3' End of the RNA

Turnip yellow mosaic virus (TYMV) RNA treated with snake venom phosphodiesterase accepts cytidine 5′-monophosphate and adenosine 5′-monophosphate (AMP) when it is incubated in the presence of cytidine 5′-triphosphate (CTP), adenosine 5′-triphosphate, and Escherichia coli transfer RNA nucleotidyltransferase; untreated TYMV RNA accepts only AMP. When α ³²PCTP was used for terminal labeling, the nearest neighbor analyses and the anallyses after action of various nucleases showed that the sequence of five nucleotides at the 3′ end of TYMV RNA is: pGpCpApCpC. A nuclease present in commerical preparations of snake venom phosphodiesterase leads to the fragmentation of TYMV RNA, the 3′ end of which is found in a fragment having a sedimentation constant close to 5s.     

The isolation and identification of a novel intermediate in ubiquinone-6 biosynthesis by Saccharomyces cerevisiae.

The reaction product obtained from HeLa cell nuclei incubated with [³H]NAD was specifically hydrolyzed with snake venom phosphodiesterase. Analysis of the hydrolyzed product revealed that it is a homopolymer consisting of 4–5 repetition of ADP-ribose units. The [³H]poly ADP-ribosylated histone fraction was anslyzed by urea-acetic acid polyacrylamide gel electrophoresis. The radioactive peak was clearly separated from the stained histone H1 band, while a slight overlap was observed. When chromatographed on a SP-Sephadex C-50 column, more than 90% of the radioactivity of [³H]poly(ADP-ribose) was eluted in accordance with histones but not with nonhistone contaminants. On a sodium dodecyl sulfate polyacrylamide gel electrophoresis, a major radioactive peak appeared at a position very close to the histone Hl band, which disappeared by the treatment with alkali prior to electrophoresis. A selective extraction of histone Hl with 5% perchloric acid showed that histone Hl contained about 85% of the radioactivity incorporated into whole histones.     

Adenylyl-(5′, 2′)-adenosine 5′-Phosphate ((2′-5′) pA-A) in Crude Crystals of 5′-Adenylic Acid Isolated from Nuclease P1 (Penicillium Nuclease) Digest of Technical Grade Yeast RNA

Adenylyl (5′,2′)-adenosine 5′-phosphate ((2′-5′)pA-A) was detected in crude crystals of 5′-AMP prepared from Penicillium nuclease (nuclease P₁) digest of a technical grade yeast RNA. While (3′–5′)A-A was split by nuclease P₁, spleen phosphodiesterase, snake venom phosphodiesterase or alkali, (2′–5′)A-A was not split by a usual level of nuclease P₁ or spleen phosphodiesterase. Nuclease P₁ digests of 12 preparations of technical grade yeast RNA tested were confirmed to contain (2′–5′)pA-A. Its content was about 1 to 2% of the AMP component of each RNA preparation. As poly(A) was degraded completely by the Penicillium enzyme into 5′-AMP without formation of any appreciable amount of (2′–5′)pA-A, the technical grade RNA is supposed to contain 2–5′ phosphodiester linkages in addition to 3′–5′ major linkages.     

Determination of diadenosine tetraphosphate (Ap4A) levels in subpicomole quantities by a phosphodiesterase luciferin-luciferase coupled assay: Application as a specific assay for diadenosine tetraphosphatase

A coupled enzymatic assay for diadenosine 5′, 5?-P¹, P⁴-tetraphosphate(Ap₄A) is described. Luciferin-luciferase produces light by consuming the ATP that is liberated by the action of snake venom phosphodiesterase on Ap₄A. The procedure is linear with Ap₄A levels ranging from 0.02 to 2 pmol. The pool size of Ap₄A in human leukemic cells was determined by acid extraction of the cells followed by initial fractionation of the extract on a DEAE-cellulose column and application of the phosphodiesterase luciferin-luciferase coupled assay. The method was also used to follow the purification of a diadenosine tetraphosphate-degrading enzyme (diadenosine tetraphosphatase, Ap₄Aase) from mouse ascites tumor cells. The partially purified enzyme had a K_m of 2.8 μm for Ap₄A when applying the coupled enzymatic assay for the determination of initial rate kinetics.     

Identification of a protein linked to the ends of adenovirus DNA.

A DNA-protein complex from human adenoviruses has been further characterized by electron microscopy, radiochemical labeling and analytical ultracentrifugation. Preparations of the complex contain a large percentage of forms of DNA which are either circular or oligomeric and are readily distinguishable from preparations of pronase-treated adenovirus DNA by analytical ultracentrifugation in cesium chloride gradients containing 4 M guanidinium chloride. The protein component has been iodinated in vitro with ¹²⁵I using Bolton and Hunter reagent, and SDS-polyacrylamide gel analysis of the labeled protein indicates that it has an apparent molecular weight of 55,000 daltons. DNAase I digestion of the DNA-protein complex labeled with ³²PO₄ results in release of a ³²PO₄-labeled protein which remains labeled even after boiling in 1% SDS and 1% mercaptoethanol. Subsequent digestion of this entity with snake venom phosphodiesterase leads to release of ³²P₄-labeled 5′-phosphate deoxynucleotides. Digestion of the DNA-protein complex with Eco R1 and analysis of the isolated restriction fragments indicates that the protein is present on each terminal fragment. We conclude that there is a protein of 55,000 daltons directly attached to each 5′ end of molecule probably via a covalent linkage. We propose that the protein functions during DNA replication by facilitating priming of the progeny strands, thus allowing the 5′ ends of the DNA to be replicated.     

Nucleotide sequence of U-2 ribonucleic acid. The sequence of the 5'-terminal oligonucleotide.

The nucleotide sequences were determined for the 5'-oligonucleotides obtained by complete pancreatic RNase digestion (P25) and complete T1 RNase digestion (T27) of U-2 RNA. Complete digestion of oligonucleotide P25 with snake venom phosphodiesterase produced pm3 2,2,7G, pAm, pUm, and pCp in approximately equimolar ratios. Partial digestion of these oligonucleotides with snake venom phosphodiesterase produced -Um-C-Gp and pAm-Um, indicating the sequence of the 3'-terminal portion of the 5'-oligonucleotide is pAm-Um-C-Gp. The 5'-terminal oligonucleotide did not contain a 5'-phosphate and no free nucleoside was released from the 5' end by venom phosphodiesterase digestion. Since free pm3 2,2,7G was released by digestion with nucleotide pyrophosphatase and limited digestion with snake venom phosphodiesterase, this nucleotide is apparently linked to pAm in a pyrophosphate linkage. Mass spectrometry and thin layer chromatography in borate systems showed the ribose of m3 2, 2, 7G contains no 2'O-methyl residue. Moreover, the finding that the ribose of m3 2, 2, 7G was oxidized by NaIO4 and reduced by KB3H4 in intact U-2 RNA rules out other linkages involving the 2' and 3' positions. Accordingly, it is concluded that the structure of the 5'-terminal pentanucleotide of U-2 RNA is(see article).     

Base Modified Oligodeoxynucleotides. II. Increase of Stability to Nucleases by 5-Alkyl-, 5-(1-Alkenyl)-, and 5-(1-Alkynyl)-pyrimidines

Abstract

The effect of pyrimidine base substitution on the sensitivity of oligonucleotides to nucleases has been studied with two series of self complementary deoxyoligonucleotides containing n-alkyl, n-(1-alkenyl) or n-(1-alkynyl) groups at C5 of pyrimidines, (dA-r⁵dU)₁₀ and (dG-r^sdC)₆. The rate of hydrolysis by snake venom phosphodiesterase and in human serum decreased with increasing length and unsaturation of the substituent.     

Cloning and characterisation of novel cystatins from elapid snake venom glands

Snake venoms contain a complex mixture of polypeptides that modulate prey homeostatic mechanisms through highly specific and targeted interactions. In this study we have identified and characterised cystatin-like cysteine-protease inhibitors from elapid snake venoms for the first time. Novel cystatin sequences were cloned from 12 of 13 elapid snake venom glands and the protein was detected, albeit at very low levels, in a total of 22 venoms. One highly conserved isoform, which displayed close sequence identity with family 2 cystatins, was detected in each elapid snake. Crude Austrelaps superbus (Australian lowland copperhead) snake venom inhibited papain, and a recombinant form of A. superbus cystatin inhibited cathepsin L ≅ papain > cathepsin B, with no inhibition observed for calpain or legumain. While snake venom cystatins have truncated N-termini, sequence alignment and structural modelling suggested that the evolutionarily conserved Gly-11 of family 2 cystatins, essential for cysteine protease inhibition, is conserved in snake venom cystatins as Gly-3. This was confirmed by mutagenesis at the Gly-3 site, which increased the dissociation constant for papain by 10⁴-fold. These data demonstrate that elapid snake venom cystatins are novel members of the type 2 family. The widespread, low level expression of type 2 cystatins in snake venom, as well as the presence of only one highly conserved isoform in each species, imply essential housekeeping or regulatory roles for these proteins.     

Crystal structure of phospholipase PA2-Vb,a protease-activated receptor agonist from the Trimeresurus stejnegeri snake venom

Phospholipase A₂ (PLA₂) is an important component in snake venoms. Here, an acidic PLA₂, designated PA2-Vb was isolated from the Trimeresurus stejnegeri snake venom. PA2-Vb acts on a protease-activated receptor (PAR-1) to evoke Ca²⁺ release through the inositol 1,4,5-trisphosphate receptor (IP₃R) and induces mouse aorta contraction. PAR-1, phospholipase C and IP₃R inhibitors suppressed PA2-Vb-induced aorta contraction. The crystal structure reveals that PA2-Vb has the typical fold of most snake venom PLA₂. Several PEG molecules bond to a positively charged pocket. The finding offers a novel pharmacological basis of the structure for investigating the PAR-1 receptor and suggests potential applications for PA2-Vb in the vascular system.     

Evidence for adenylylation/deadenylylation control of the glutamine synthetases of Rhodospirillum tenue and Rhodocyclus purpureus

The phylogenetically related phototrophic bacteria Rhodospirillum tenue and Rhodocyclus purpureus modulate activity of their glutamine synthetases by adenylylation/deadenylylation. Evidence for covalent modification includes the inhibitory effect of Mg²⁺ on the activity of glutamine synthetase extracted from cells of either species grown on excess ammonia, and the lack of Mg²⁺ inhibition of activity of the enzyme isolated from N₂-(R. tenue) or glutamine (R. purpureus)-grown cells. In addition, snake venom phosphodiesterase treatment of glutamine synthetase from either species grown on excess ammonia relieved Mg²⁺ inhibition of the enzyme (as measured via the -glutamyl transferase assay), and changed the cation specificity from Mn²⁺ to Mg²⁺ (in the biosynthetic assay).     

Biphasic effect on platelet aggregation by phospholipase a purified from Vipera russellii snake venom

A basic phospholipase A was isolated from Vipera russellii snake venom. It induced a biphasic effect on washed rabbit platelets suspended in Tyrode's solution. The first phase was a reversible aggregation which was dependent on stirring and extracellular calcium. The second phase was an inhibitory effect on platelet aggregation, occurring 5 min after the addition of the venom phospholipase A without stirring or after a recovery from the reversible aggregation. The aggregating phase could be inhibited by indomethacin, tetracaine, papaverine, creatine phosphate/creatine phosphokinase, mepacrine, verapamil, sodium nitroprusside, prostaglandin E₁ or bovine serum albumin. The venom phospholipase A released free fatty acids from synthetic phosphatidylcholine and intact platelets. $\text{p-}\text{Bromophenacyl}$ bromide-modified venom phospholipase A lost its phospholipase A enzymatic and platelet-aggregating activities, but protected platelets from the aggregation induced by the native enzyme. The second phase of the venom phospholipase A action showed a different degree of inhibition on platelet aggregation induced by some activators in following order: $\text{arachidonic acid}\text{>}\text{collagen}\text{>}\text{thrombin}\text{>}\text{ionophore A}\text{23187}$. The longer the incubation time or the higher the concentration of the venom phospholipase A, the more pronounced was the inhibitory effect. The venom phospholipase A did not affect the thrombin-induced release reaction which was caused by intracellular Ca²⁺ mobilization in the presence of EDTA, but inhibited collagen-induced release reaction which was caused by Ca²⁺ influx from extracellular medium. The inhibitory effect of the venom phospholipase A and also lysophosphatidylcholine or arachidonic acid could be antagonized or reversed by bovine serum albumin. It was concluded that the first stimulatory phase of the venom phospholipase A action might be due to arachidonate liberation from platelet membrane. The second phase of inhibition of platelet aggregation and the release of ATP might be due to the inhibitory action of the split products produced by this venom phospholipase A.     

Vanillic acid as a novel specific inhibitor of snake venom 5′-nucleotidase: A pharmacological tool in evaluating the role of the enzyme in snake envenomation

Vanillic acid has been investigated for its inhibitory effect on Naja naja, Daboia russellii, and Trimeresurus malabaricus venom 5′-nucleotidase activity. Trimeresurus malabaricus venom 5′-nucleotidase activity was 1.3- and 8.0-fold higher than that of N. naja and D. russellii venoms, respectively. Substrate specificity studies showed that for all the venoms tested, 5′-AMP was the preferred substrate for 5′-nucleotidase. This indicates the central role of adenosine in snake envenomation. Vanillic acid selectively and specifically inhibited 5′-nucleotidase activity among several enzymes present in the three venoms tested. The inhibitor was competitive, as the inhibition was relieved by increased substrate concentration. It appears that the COOH group in vanillic acid is the determining factor for inhibition as vanillin, a structurally similar compound with respect to vanillic acid, had no inhibitory activity. This study for the first time exemplifies vanillic acid as a pharmacological tool in evaluating the role of 5′-nucleotidase in snake envenomation.     

Protein kinase associated with chromatin and changes in substrate-specificity during germination of wheat seeds

Protein kinase activity was associated with chromatin in wheat ( Triticum aestivum L. cv. Mukakomugi) embryos. The kinase activity did not change significantly during germination, whereas the activity of poly (ADP-ribose) synthetase decreased significantly. The protein kinase activity in chromatin was inhibited by NAD, NADH, and ADP-ribose, and was enhanced by treatment of the chromatin with snake venom phosphodiesterase or soybean trypsin inhibitor. The activity in chromatin was not stimulated by cyclic AMP. Different subfractions of the histones, H1 and H2, were mainly phosphorylated in germ and 3 day-germinated seedling chromatins. The histones, H3 and H4, seemed unable to accept phosphate from ATP in the in vitro reaction system. Different acidic non-histone chromosomal proteins were phosphorylated in germ and 3-day-germinated seedling chromations, and germ-specific and seedling-specific acidic non-histone chromosomal proteins seemed unable to accept phosphate from ATP.     

Properties and applications of immobilized snake venom NAD glycohydrolase

The NAD glycohydrolase (NADase) from Bungarus fasciatus snake venom was adsorbed on concanavalin A-Sepharose, and demonstrated to retain both hydrolase and transglycosidase activities in the bound form. The matrix-bound enzyme was stable to repeated washing with buffer and storage at 4°C. The bound enzyme exhibited the same K_m value for hydrolysis of nicotinamide-1,N⁶-ethenoadenine dinucleotide as previously measured with the soluble, purified form of the enzyme. The bound NADase was used repeatedly for a preparative-scale synthesis of 3-acetylpyridine adenine dinucleotide. It was further demonstrated that the immobilized enzyme could be prepared directly from crude snake venom, thus avoiding the time required for purification. The application of the immobilized snake venom NADase for the preparation of pyridine nucleotide coenzyme analogs has many advantages over procedures used previously for analog synthesis.     

RNA Synthesis in Isolated Nuclei of the Dinoflagellate Crypthecodinium cohnii

Atypical eukaryotic RNA polymerase activity was demonstrated in nuclei of Crypthecodinium cohnii, a eukaryote devoid of histones. Nuclei were isolated from growing cultures of this dinoflagellate and assayed for endogenous RNA polymerase (EC 2.7.7.6) activity. There was a biphasic response to Mg²⁺ with optima at ? 0.01 and 0.02 M MgCl₂, but in contrast to other eukaryotic RNA polymerases, this enzyme activity was inhibited by low MnCl₂ concentrations. In the presence of 0.01 M MgCl₂ the optimum (NH₄)₂SO₄ concentration was 0.025 M, a concentration at which the nuclei were lysed. Incorporation of [₃H]UMP into RNA was inhibited by actinomycin D and dependent on the presence of undegraded DNA, and the reaction product was sensitive to ribonuclease and KOH digestion. Omission of one or more ribonucleoside triphosphates greatly reduced the incorporation. Only a slight enhancement of RNA polymerase activity resulted from the addition of various amounts of native and denatured calf thymus DNA. Spermine caused a marked inhibition while spermidine had little effect on RNA synthesis in the nuclei. Under the optimum conditions described in the present paper the nuclei incorporated ? 3 pmoles of [₃H]UMP/muml; DNA at 25 C for 15 min, and ? 80% of this activity was inhibited by the eukaryotic RNA polymerase II inhibitor, α-amanitin (20 m?/ml). A unique situation therefore exists in C. cohnii nuclei, in which absence of histones (a prokaryotic trait) is combined with α-amanitin-sensitive RNA polymerase activity (a eukaryotic trait).     

Inhibition of brain glutamate decarboxylase by 2-keto-4-pentenoic acid, a metabolite of allylglycine.

Abstract— 2-Keto-4-pentenoic acid, a potent inhibitor of brain glutamate decarboxylase (Orlowski et al., 1977) was prepared by oxidative deamination of l -allylglycine with snake venom l -amino acid oxidase. In the presence of glutamate the keto acid is a competitive inhibitor of the enzyme with respect to glutamate; its K_i is 2.4 ± 10^?6m . After preincubation of brain glutamate decarboxylase with 2-keto-4-pentenoic acid in the absence of glutamate, a slow and incomplete reactivation is obtained by prolonged dialysis, Sephadex gel-filtration, and dilution, suggesting the formation of a slowly dissociating enzyme-inhibitor complex and partial inactivation of the enzyme. In vivo inhibition of brain glutamate decarboxylase after administration of allylglycine is maximal after 2-8 h with activity returning to normal after 16 h. The inhibition of the enzyme after administration of d -allylglycine was greatest in the cerebellum and the medulla-pons area, the sites of the highest activity of d -amino acid oxidase. These results are interpreted as strongly supporting the postulate that allylglycine-induced inhibition of brain glutamate decarboxylase is due to the in vivo formation of 2-keto-4-pentenoic acid.     

Snake inhibitors of phospholipase A2 enzymes

Phospholipase A₂ (PLA₂) enzymes consist of a large family of proteins which share the same enzymatic function and display considerable sequence homology. These enzymes have been identified and characterised in mammalian tissue and snake venoms. Numerous physiological functions have been attributed to mammalian PLA₂s and they are nontoxic. In comparison, venom PLA₂s are toxic and induce a variety of pharmacological effects that are probably mediated via membrane receptors. Snake PLA₂ inhibitors (PLIα), with a similar structure to the M-type receptor, have been identified as soluble complexes in the serum of viperinae and crotalinae snakes. These inhibitors showed selective binding to crotalid group II PLA₂s and appeared to be restricted to the serum of this snake family. Analysis of PLA₂ binding to recombinant fragments of PLIα indicated that the CRD region was most likely responsible for enzyme inhibition. A second type of inhibitor, PLIβ, has been identified in serum from one viperid snake and consists of a leucine-rich structure. The third type of inhibitor, PLIγ, was found in the serum of five snake families and contains a pattern of cysteine residues that define a three-finger structure. PLIγ inhibitors isolated from the serum of Elapidae, Hydrophidae, Boidae and Colubridae families were able to inhibit a broad range of enzymes including the nontoxic mammalian group IB and IIA PLA₂s, and bee venom group III PLA₂. However, differences in the binding affinities indicated specificity for particular PLA₂s. A different representation has emerged for crotalid and viperid snakes. Their PLIγs did not inhibit bee venom group III, mammalian group IB and IIA enzymes. Furthermore, inhibition data for the γ-type inhibitor from Crotalus durissus terrificus (CICS) showed that this inhibitor was specific for viperid β-neurotoxins and did not inhibit β-neurotoxins from elapids [1]. Further studies are required to determine if this phenomenon is true for all γ-type inhibitors from Crotalidae snakes. The relative distribution of these inhibitors, their specificities and the structural features involved in binding are discussed in this review.     

Enzymatic hydrolysis of nucleoside phosphoramidates

The nucleoside phosphoramidate thymidine-5′-phospho-α-naphthylamidate and thymidine-3′-phospho-α-naphthylamidate were prepared as fluorogenic substrates for the study of enzymatic hydrolysis of the PN bond. With these new substrates, the rate and specificity of hydrolysis of the PN bond of the nucleoside phosphoramidate by snake venom and spleen phosphodiesterase could be studied. It was found that the 5′-phosphoramidate was hydrolyzed by snake venom phosphodiesterase and the 3′-phosphoramidate was hydrolyzed only by the spleen phosphodiesterase. Thus, the specificity requirement for PN bond cleavage is similar to that of the P0 bond cleavage, even though the rate is much slower.     

1,3,4-Oxadiazole-2(3H)-thione and its analogues: A new class of non-competitive nucleotide pyrophosphatases/phosphodiesterases 1 inhibitors

A series of 1,3,4-oxadiazole-2 (3H)-thiones and 1,3,4-thiadiazole-2 (3H)-thiones were synthesized and evaluated for their inhibitory activities against the two nucleotide pyrophosphatase phosphodiesterase 1 enzymes. Dixon, as well as Lineweaver–Burk plots, and their secondary replots have indicated that the inhibition was of pure non-competitive type, against both snake venom and pure human recombinant enzymes as the V_max values decreases without affecting the K_m values. 5-[4-(t-Butyldimethylsilyloxy)-phenyl]-1,3,4-thiadiazole-2 (3H)-thione (17) and [4-(t-butyldimethylsilyloxy)-phenyl]-1,3,4-oxadiazole-2 (3H)-thione (1) were found to be the most active compounds with IC₅₀ values 66.47 and 368 μM, respectively. The K_i values were 100 μM and 360 μM against the snake venom and human recombinant NPP1 enzyme, respectively. Most active compounds were found to be non-toxic in neutrophil viability assay.