Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function.

A high-affinity RNA aptamer to human activated protein C (APC) was selected from a pool of random sequences using in vitro selection. Activated protein C, a trypsin-like serine protease plays an important role along with thrombin as a regulator in blood clotting cascade. After seven rounds of selection and amplification, a single predominant nucleic acid sequence APC-167, a 167-base oligonucleotide with a random sequence core of 120 bases, was obtained. The selected aptamer did not bind to thrombin or factor Xa and thus demonstrated specificity to APC. Furthermore, this aptamer was a non-competitive inhibitor to the cleavage reaction of a fluorogenic substrate catalyzed by APC. The inhibition constant (Ki) of APC-167 was 83 nM. The 99-base oligonucleotide (APC-99) derived from APC-167 by deleting both primer binding sites, was also found to inhibit APC strongly (Ki = 137 nM). Two stem-loop structures and at least one G x U wobble base pair in the stem were elucidated as important structural motifs for binding.

Catalytic activities of hammerhead ribozymes with a triterpenoid linker instead of stem/loop II.

A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem/loop II. In a previous study we demonstrated that a minizyme with high-level activity forms a dimeric structure with a common stem II (Amontov and Taira, J. Am. Chem. Soc., 118 (1996) 1624-1628). As a continuation of this study, we recently examined whether a short oligonucleotide linker at stem/loop II could be replaced by a triterpenoid linker and whether the resulting minizymes with bulky hydrophobic groups would form dimeric structures. In contrast to the minizyme with high-level activity that we characterized in the previous study, minizymes that contained a triterpenoid group had low cleavage activities. The nature of the dependence of the activity on the concentration of ribozyme revealed that these minizymes with a triterpenoid group do not form dimeric structures. Thus, the low activities of these structures can be attributed to their failure to form dimers.

Characterization of several kinds of dimer minizyme: simultaneous cleavage at two sites in HIV-1 tat mRNA by dimer minizymes.

A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two different sites simultaneously. In order to examine the properties of different kinds of minizyme, we constructed a number of minizymes with short oligonucleotide linkers (2-5 bases) instead of stem-loop II and examined their cleavage activities against HIV-1 tat mRNA. Analyses of melting curves, as well as Arrhenius plots, revealed that, in general, the longer the oligonucleotide linkers, the more stable and more active were the dimer minizymes. All minizymes examined cleaved the target substrate at two sites simultaneously. The activity of the dimer minizyme with a 5 nt linker was higher than that of the parental hammerhead ribozyme because the latter full-sized ribozyme was able to cleave at one site only.

Dependence on Mg2+ ions of the activities of dimeric hammerhead minizymes.

A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem/loop II. In a previous study we demonstrated that a minizyme with high-level activity forms a dimeric structure with a common stem II [Amontov and Taira (1996) J. Am. Chem. Soc. 118, 1624-1628]. We now demonstrate that the stability of the dimeric structure is influenced by Mg2+ ions. We found that the dependence on Mg2+ ions of the activity of homodimeric minizyme (a dimer with two identical binding sites) has composite biphasic characteristics. When the concentration of Mg2+ ions reached a specific critical level, the dependence on the concentration of Mg2+ ions lost its tendency to reach a plateau. In the case of the heterodimeric minizyme (a dimer with two different binding sites), we investigated the kinetic behavior of two different forms of the dimer, namely, free dimer and the complex of the dimer with an uncleavable substrate. The kinetic behavior of the free heterodimer was very similar to that of the homodimeric minizyme. In contrast, in the presence of the uncleavable substrate at a concentration as high as that of the minizyme, the curve for the dependence on Mg2+ ions showed normal saturation kinetics. While, at low concentrations of Mg2+ ions, the activity of the heterodimers was much higher when the dimeric structure was stabilized by the presence of the uncleavable substrate, at high concentrations of Mg2+ ions, this difference in activity became less and less significant. Thus, high concentrations of Mg2+ ions were able to stabilize the dimeric minizymes in the absence of the uncleavable substrate.

Interaction of ATP with acetyl-CoA carboxylase from rat liver. The role of the polyphosphate chain. Affinity labelling with alkylating amides of ATP and ADP.

The interaction of a number of ATP analogs with a modified triphosphate moiety as well as 2-chloro-ethyl-amino derivatives of nucleotides, 4(N-2-chloroethyl-N-methylamino)-benzyl-gamma-amide of ATP and the corresponding ADP beta-amide with acetyl-CoA carboxylase (EC 6.4.1.2.) from rat liver has been studied. Halophosphonate derivatives of ATP have been synthesized from bromomethylene diphosphonic acid and found to be reversible inhibitors of the enzyme. ATP and ADP alkylating amides have proved to form a reversible complex with the ATP-binding site and to modify a group in the acetyl-CoA-binding site. The bicarbonate ion accelerates the process of inactivation. The estimate of the distance between the ATP-binding site and the acetyl-CoA-binding site ranges within 0.8-1.2 nm.

Affinity labelling of rat liver acetyl-CoA carboxylase by a 2',3'-dialdehyde derivative of ATP.

The interaction of rat liver acetyl-CoA carboxylase with a 2',3'-dialdehyde derivative of ATP (oATP) has been studied. The degree of the enzyme inactivation has been found to depend on the oATP concentration and the incubation time. ATP was proved to be the only substrate which protected the inactivation. Acetyl-CoA did not effect inactivation, while HCO3- accelerated the process. Ki values for oATP in the absence and presence of HCO3- were 0.35 +/- 0.04 and 0.5 +/- 0.06 mM, and those of the modification constant (kmod) were 0.11 and 0.26 min-1 respectively. oATP completely inhibited the [14C]ADP in equilibrium ATP exchange and did not effect the [14C]acetyl-CoA in equilibrium malonyl-CoA exchange. Incorporation of approximately 1 equivalent of [3H]oATP per acetyl-CoA carboxylase subunit has been shown. No recovery of the modified enzyme activity has been observed in Tris or beta-mercaptoethanol containing buffers, and treatment with NaB3H4 has not led to 3H incorporation. The modification elimination of the ATP triphosphate chain. The results indicated the affinity modification of acetyl-CoA carboxylase by oATP. It was shown that the reagent apparently interacted selectively with the epsilon-amino group of lysine in the ATP-binding site to form a morpholine-like structure.

[Acetyl-CoA-carboxylase: modification of ATP-binding site of the active center by 2',3'-dialdehyde derivative of ATP]. / Atsetil-CoA-karboksilaza: modifikatsiia ATP-sviazyvaiushchego uchastka aktivnogo tsentra 2',3'-dial'degidnym proizvodnym ATP.

The interaction of rat liver acetyl-CoA carboxylase with a 2',3'-dialdehyde derivative of ATP (oATP) has been studied. The degree of the enzyme inactivation has been found to depend on the oATP concentration and the incubation time. ATP was the only reaction substrate which provided protection from inactivation. Acetyl-CoA did not affect inactivation, while HCO3- accelerated the process. Ki values for oATP in the absence and the presence of HCO3- were 0.35 +/- 0.04 and 0.5 +/- 0.06 mM, and those of the modification constant (k) were 0.11 and 0.26 min-1, respectively. oATP completely inhibited the reaction of [14C]ADP in equilibrium ATP exchange, whereas produced actually no effect on [14C]acetyl-CoA equilibrium with malonyl-CoA exchange. Incorporation of about one equivalent of [3H]oATP per acetyl-CoA carboxylase subunit has been shown. No restoration of the modified enzyme activity has been observed in Tris or beta-mercaptoethanol containing buffers, and treatment with NaB[3H]4 has not led to 3H incorporation. The modification process involves elimination of the triphosphate chain of oATP. The results obtained indicate the affinity character of oATP-mediated modification of acetyl-CoA carboxylase. The reagent apparently interacts selectively with the epsilon-amino group of lysine in the ATP-binding site to form a morpholine-like structure.

[Interaction of acetyl-CoA-carboxylase from the rat liver with alkylating amides of ATP and ADP]. / Issledovanie vzaimodeistviia atsetil-CoA-karboksilazy pecheni krysy s alkiliruiushchimi amidami ATP i ADP.

The interaction of 4-(N-chloroethyl-N-methylamino)-benzyl-gamma-amide ATP (I) and the corresponding beta-amide of ADP (II) with rat liver acetyl-CoA carboxylase was studied. Both analogs were shown to cause affinity modification of the enzyme. ATP and GoAS Ac protected the enzyme against inactivation. HCO3- increased the rate of carboxylase inactivation by analogs I and II (2.5- and 1.5-fold, respectively). The alkylating amides did not influence the rate of the bicarbonate-dependent [14C]-ADP-ATP exchange and inhibited the enzyme-catalyzed reaction of [14C]-CoAs Ac----CoAS Mal exchange, which testifies to the localization of the modified group in the CoAS Ac-binding site of the enzyme active center. Based on the affinity modification and analog size, it was found that the distance between the ATP- and CoAS Ac-binding sites of the enzyme active center can vary from 0.8 to 1.2 nm.

[Interaction of acetyl-CoA carboxylase from the rat liver with analogs of activated carbon dioxide and ATP]. / Vzaimodeistvie atsetil-CoA-karboksilazy pecheni krys s analogami aktivirovannoi uglekisloty i ATP.

The interaction of rat liver Ac-CoA-carboxylase with reactive and stable analogs of carbon dioxide and phosphoric acid mixed anhydrides--hypothetic intermediate of the enzyme reaction--has been studied. Carbamoylphosphate showed substrate properties, whereas phosphonacetic acid and beta-oxopropyl-alpha, alpha-diphosphonate inhibited this enzyme (Ki 3.0 and 3.5 mM correspondingly). The analog of another possible intermediate in the reaction of ATP and carbon dioxide, Appp (CH2COOH) also inhibited Ac-CoA-carboxylase (Ki = 0.7 mM).

The 5'-O-phosphonomethyl analog of ATP. Studies of substrate properties in ligase-dependent reactions.

The 5-O-phosphonomethyl analog of ATP (ATPc) and its interaction with different enzymes, catalysing synthesis of C-O-, C-S-, C-N- and C-C-bond were investigated. It was shown ATPc to have substrate properties and to be involved in all studied ligase-dependent reactions. Kinetic parameters of the interaction of alternative substrate - ATPc with all studied enzymes were established and the comparison of ATPc with other phosphonate analogs of ATP was performed.

[Organophosphate analogs of biologically active compounds. XIV. Halophosphonate analogs of ATP as acetyl CoA carboxylase inhibitors]. / Fosfororganicheskie analogi biologicheski aktivnykh soedinenii. XIV. Galoidfosfonatnye analogi ATP kak ingibitory Ac CoA-karboksilazy.

Halophosphonate ATP analogues pp[CHBr]pA and p[CHBr]ppA synthesised from bromomethylenebisphosphonate and adenosine derivatives, proved to be effective competitive inhibitors of Ac-CoA-carboxylase (CE 6.4.1.2) from rat liver (Ki = 0,2 mM). The inhibitory effects of both analogues were reversible and higher than those of some other ATP analogues. Another enzyme, Ac-CoA-synthetase (CE 6.2.1.1), with a different mode of ATP-cleavage showed wider specificity to ATP-analogues than Ac-CoA-carboxylase.

[Isolation and some properties of immobilized cystathionine-beta-synthase]. / Poluchenie i nekotorye svoistva immobilizovannoi tsistationin-beta-sintazy.

Covalent binding of the pyridoxal phosphate-dependent lyase--cystathionine-beta-synthase from chicken liver--by CNBr-activated Sepharose 4B and 6B resulted in catalytically active preparations of immobilized enzyme. Immobilized cystathionine-beta-synthase was shown to possess a higher stability as compared to the native enzyme. The maximum of activity of the obtained preparations was revealed at high temperatures (63 degrees), whereas the native enzyme had the temperature optimum at 40 degrees. The pH optimum of the enzyme activity was markedly shifted towards the alkaline region. The substrate specificity of the immobilized enzyme remained essentially unchanged.