L-Arginine and zinc ion effect on recognition and hydrolysis rate of adenosine 5′-triphosphate

Zn²⁺ can interact with adenosine 5′-triphosphate (ATP) by electrostatic and coordination interactions, and the interaction sites between Zn²⁺ and ATP vary at different pH in the ATP–Zn²⁺ binary system. Non-covalent interactions exist between the carboxyl of arginine (Arg) and Zn²⁺, which led to competition between ATP and Arg to interact with Zn²⁺ in the ATP–Zn²⁺–Arg ternary system. Kinetics studies show that the hydrolysis rate constant of ATP in the ATP–Zn²⁺ binary system was 2.44?×?10^?2?min^?1, about 11-fold faster than that (2.27?×?10^?3?min^?1) in the ATP–Zn²⁺–Arg ternary system. This may be attributed to coordination interactions between the carboxyl of Arg and Zn²⁺ and the decreased activity of zinc ion toward the phosphate groups via nucleophilic attack. A mechanism that the hydrolysis occurred through an addition–elimination mechanism is proposed.     

Recognition and catalytic hydrolysis of adenosine 5′-triphosphate by cadmium(II) and L-glutamic acid

Interactions among Cd²⁺, glutamic acid (Glu), and adenosine 5′-triphosphate (ATP) have been studied by potentiometric pH titration, IR, Raman, fluorescence, and NMR methods. In the Cd²⁺–ATP binary system, the main interaction sites are the α-, β-, and γ-phosphate groups, N-1, and/or N-7. Cd²⁺ binds to the N-1 site at relatively low pH and binds to the N-7 site of adenosine ring of ATP with increasing pH. In the Cd²⁺–Glu–ATP ternary system, ATP mainly binds to Cd²⁺ by the triphosphate chain. Oxygens of Glu coordinate with Cd²⁺ to form a complex to catalyze ATP hydrolysis. Hydrolysis of ATP catalyzed by the CdGlu complex was studied at pH 7.0 and 80°C by ³¹P-NMR spectrometry. Kinetics studies showed that the rate constant of ATP hydrolysis was 0.0199?min^?1 in the ternary system, which is 9.9-fold faster than that in the ATP solution (2.01?×?10^?3?min^?1). Hydrolysis occurs through an addition–elimination reaction mechanism with Cd²⁺ regulating the recognition and catalytic hydrolysis of ATP; water participates in the hydrolysis reaction of ATP at different steps with different functions in the ternary system.     

Thermodynamic parameters for the interaction of adenosine 5′-diphosphate,and adenosine 5′-triphosphate with Mg2+ from 323.15 to 398.15 K

The interaction of adenosine 5-diphosphate (ADP) and adenosine 5-triphosphate (ATP) with Mg²⁺ in water has been studied calorimetrically at 323.15, 348.15, 373.15, and 398.15 K for ATP and at 348.15 and 373.15 K for ADP. The enthalpies of reaction of Mg²⁺ with ADP and ATP were obtained from the heats of mixing of aqueous solutions of tetramethylammonium salts of ADP and ATP with MgCl₂ solutions in an isothermal flow calorimeter. Equilibrium constant (K), enthalpy change (H°), entropy change (S°), and heat capacity change (Cp°) values were calculated for the interaction: Mg²⁺+L^n–=MgL^2–n and Mg²⁺+MgL^2–n=Mg₂L^4–n, where n=4 for L=ATP and n=3 for L=ADP. The results are consistent with those at lower temperatures. For the two nucleotides studied, the above two reactions are endothermic and entropy-driven in the temperature range studied. Large Cp° values for the interaction of Mg²⁺ with ADP with ATP indicate the involvement of phosphate groups of nucleotides in the coordination of Mg²⁺. The coordination of the first and second Mg²⁺ ions involves the phosphate chain in both ADP and ATP. No evidence was found for the involvement of the adenine ring or the ribose moiety in the coordination of Mg²⁺ with these nucleotides. Approximate values of logK, H°, and S°, and Cp° for the self-association of ADP and ATP in the presence of Mg²⁺ are also given.     

The first chemical synthesis of pyrazofurin 5′-triphosphate

As an archetype C-nucleoside, pyrazofurin possesses broad-spectrum antiviral and antitumor activities. However, the presence of the acidic enol in the nucleobase of pyrazofurin poses a huge challenge to the conventional NTP synthetic methods. On the basis of a selective phosphorylation method and the P(V)-N activation strategy, the first chemical synthesis of pyrazofurin 5′-triphosphate (PTP) was accomplished, which will greatly facilitate the investigation on the interactions of viral RNA polymerases and PTP, an important cellular metabolite of pyrazofurin.     

Deprotonation energetics of adenine,adenosine, 5′-adenosine monophosphate and adenosine triphosphate in water from EMF and spectrophotometric measurements

The deprotonation constants of adenine (ADE) [K₁ and K₂], adenosine (ADO) [K₁ and K₂], 5-adenosine monophosphate (5-AMP) [K₁, K₂ and K₃] and adenosine triphosphate (ATP) [K₃ and K₄] have been obtained for aqueous soutions from emf measurements on cells such as Pt, H₂ (g, 1 atm)/HA(m₁), NaA(m₂), KI(m₃)/AgI-Ag (where HA is the corresponding acid of ADE, ADO, 5-AMP and ATP) at different temperatures. The pK values were fitted by the temperature equation: pK=AT¹+B+CT by the least squares method and the related thermodynamic quantities viz. G ^o , TS ^o and H ^o were calculated from the coefficients A, B and C.     

Efficient method for the synthesis of dideoxyuridine-5′-triphosphate fluorescent derivative

An approach to the synthesis of a fluorescent labeled dideoxyuridine triphosphate derivative using the pentafluorophenyl ester of a dicarbocyanine dye was suggested. The use of the dye pentafluorophenyl ester instead of N-oxysuccinimidyl one has the advantage of giving significantly higher yield of the fluorescent labeled dideoxyuridine-5??-triphosphate derivative.     

A critical study of the application of ultraviolet spectroscopy to the self-association of adenine,adenosine and 5′-AMP in aqueous solution

UV spectra of adenine, adenosine and 5′-AMP in aqueous solution have been measured over the concentration range 1 × 10⁻⁶−5 × 10⁻² M. The apparent molar absorptivity of these compounds changes upon concentration, showing two hypochromic effects at c < 5 × 10⁻³ M and c &>; 5 × 10⁻³ M, respectively, which may be explained in terms of self-association.A method for calculating self-association constants from these experimental data is developed, based on an association model in which the first hypochromic effect is interpreted in terms of formation of dimers, with an equilibrium constant K₂, and the second effect is interpreted in terms of formation of polymers, with an equilibrium constant K_n. The value of K₂ is of the order of magnitude of 10⁴ for the three compounds. The value of K_n is dependent on the model chosen for the analysis of the second effect, having an order of magnitude of 10².The features of the self-association model are discussed, as well as the method for calculating self-association parameters from experimental data.     

Investigations into the electrooxidation of guanosine-5′-triphosphate at the pyrolytic graphite electrode

The electrochemical oxidation of guanosine-5-triphosphate has been investigated in phosphate-containing electrolytes in the pH range 1.5–10.9 at a pyrolytic graphite electrode by cyclic sweep voltammetry, spectral studies, bulk electrolysis and related techniques. In this pH range, the oxidation occurred in a single well-defined peak (I_a). The peak potential of oxidation peaks (E_p) was found to be dependent on pH, concentration and sweep rate. The kinetics of the UV-absorbing intermediates was followed spectrophotometrically and the decay of the intermediate occurred in a pseudo-first-order reaction. The first-order rate constants for the disappearance of the UV-absorbing intermediate have also been calculated. The products of the electrode reaction were characterized by HPLC and GC/MS. A tentative mechanism for the formation of the products has also been suggested.     

Generation of cytidine 5′-triphosphate using adenylate kinase

A membrane-enclosed enzyme reactor containing adenylate kinase (E.C. 2.7.4.3, rabbit muscle) and pyruvate kinase (E.C. 2.7.1.40) converts cytidine 5′-monophosphate (CMP) and phosphoenolpyruvate (PEP) to cytidine 5′-triphosphate (CTP) and pyruvate on a gram scale.     

Ternary complexes in solution. Comparison of the coordination tendency of some biologically important zwitterionic buffers toward the binary complexes of Cu(II) and adenosine 5′-mono-, 5′-di-, and 5′-triphosphate

Summary Potentiometric equilibrium measurements have been made at 25.0±0.1 °C and ionic strengthI=0.1 mol dm^–3 KNO₃ for the interaction of adenosine 5-mono-, 5-di-, and 5-triphosphate (AMP,ADP andATP) and Cu(II) with biologically important secondary ligand zwitterionic buffers (N,N-bis-(2-hydroxyethyl)-2-aminoethanesulphonic acid (BES), N-tris-(hydroxymethyl)-methyl-2-aminoethanesulphonic acid (TES), N,N-bis-(2-hydroxyethyl)-glycine (Bicine) andtris-(hydroxymethyl)-methylaminopropane sulphonic acid (TAPS)) in a 1:1:1 ratio and the formation of various 1:1:1 mixed ligand complex species inferred from the potentiometricpH titration curves. Initial estimates of the formation constants of the resulting species and the acid dissociation constants ofAMP,ADP,ATP, and secondary ligands have been refined with the SUPERQUAD computer program. Negative and positive logK values were obtained for the ternary systems studied. In some Cu(II) ternary systems studied the interligand interactions or some cooperativity between the coordinate ligands, possibly H bond formation, has been found to be most effective in deciding the stability of the ternary complexes formed in solution. Stabilities of mixed ligand complexes increase in the orderAMP<ADP<ATP. The trend in stability constants of the mixed-ligand complexes of the title zwitterionic buffer ligands is found to beTAPS>Bicine>TES>BES.

---

Ternäre Komplexe in Lösung. Vergleich der Koordinationstendenz einiger biologisch wichtiger zwitterionischer Puffer an binäre Komplexe von Cu(II) und Adenosin-5-mono-, -5-di- und-5-triphosphat

Zusammenfassung Die Wechselwirkungen zwischen Adenosin-5-mono, -5-di- und-5-triphosphat (AMP,ADP undATP), Cu(II) und biologisch wichtigen zwitterionischen Puffern mit Sekundärligandeigenschaften (N,N-bis-(2-Hydroxyethyl)-2-aminoethansulfonsäure (BES), N-tris-(Hydroxymethyl)-methyl-2-aminoethansulfonsäure (TES), N,N-bis-(2-Hydroxyethyl)-glycin (Bicin) undtris-(Hydroxymethyl)-methylaminopropansulfonsäure (TAPS) im Verhältnis 1:1:1 wurden mittels potentiometrischer Gleichgewichtsmessungen bei 25.0±0.1 °C undI=0.1 mol·dm^–3 KNO₃ untersucht. Die Titrationskurven lassen auf verschiedene Komplexe mit gemischten Liganden im Verhältnis von 1:1:1 schließen. Erste Abschätzungen der Bildungskonstanten der entstehenden Produkte und der Dissoziationskonstanten vonAMP,ADP,ATP und der Sekundärliganden wurden mit HIlfe des Programms SUPERQUAD verfeinert. Für die untersuchten ternären Systeme wurden negative und positive Werte für logK erhalten. In einigen der Cu(II)-Komplexe wird die Stabilität des ternären Systems in Lösung hauptsächlich durch Wechselwirkungen zwischen den Liganden, möglicherweise durch die Ausbildung von Wasserstoffbrückenbindungen, bestimmt. Die Stabilität der Komplexe steigt in der ReihenfolgeAMP<ADP<ATP. Der entsprechende Trend der Stabilitätskonstanten bei den gemischten Komplexen mit den im Titel genannten zwitterionischen Puffern lautetTAPS>Bicin>TES>BES.

     

In vitro nonenzymatic glycation of guanosine 5′-triphosphate by dihydroxyacetone phosphate

Dihydroxyacetone phosphate (DHAP) is a glycolytic intermediate that has been found to be significantly elevated in the erythrocytes of diabetic patients and patients with triosephosphate isomerase deficiency. DHAP spontaneously breaks down to methylglyoxal, a potent glycating agent that reacts with proteins and nucleic acids in vivo to form advanced glycation endproducts (AGEs). Like methylglyoxal, DHAP itself is also a glycating metabolite, capable of condensing with proteins and altering their structure or function. The objective of this investigation was to evaluate the susceptibility of nucleotides to nonenzymatic attack by DHAP, and to determine the factors influencing the rate and extent of nucleotide glycation by this sugar. Of the four nucleotide triphosphates (ATP, CTP, GTP and UTP) that were studied, only GTP was reactive, forming a wide range of UV and fluorescent products with DHAP. Increases in temperature and nucleotide concentration enhanced the rate and extent of GTP glycation by DHAP and promoted the heterogeneity of AGEs. Capillary electrophoresis, HPLC, and mass spectrometry allowed for a thorough analysis of the glycated products and demonstrated that the reaction of DHAP with GTP occurred via the classical Amadori pathway.     

The effect of replacing a benzene ring with a saturated six-membered ring on the mesomorphic properties of 4,4′-disubstituted diphenyldiacetylenes

We present new results of experimental investigations of azimuthal director reorientation dynamics for a nematic liquid crystal on solid substrates. Two types of substrate with weak anchoring were studied: glass/polystyrene and glass/UV‐activated dye. Slow and fast relaxation processes were observed in both cases under the action of a strong ‘in‐plane’ electric field. The slow surface reorientation and memory effects were controlled by two parameters: the electric voltage and the excitation time. It was established that the increase of the excitation time results in a slowing of the relaxation of the system to the initial state after turning off the electric field. A phenomenological model of a gliding of easy axes is proposed to explain the slow relaxation process.     

A multinuclear NMR study on the microscopic ionization constants of adenosine-5′-triphosphate in aqueous solution

A ¹H, ¹³C and ³¹P NMR study of adenosine-5′-triphosphate has been performed as a function of pH. The examination of the chemical shifts allowed the proposal of an ionization scheme in which the third deprotonation takes place both on the adenine ring and on the phosphate group in a ratio of about 2:1. Furthermore, an analysis of carbon relaxation times supports this mechanism of ionization and confirms that the adenine ring binds the proton both on the NH₂ group and the N₇ nitrogen atom.     

A multifunctional probe based on the use of labeled aptamer and magnetic nanoparticles for fluorometric determination of adenosine 5’-triphosphate

A multifunctional fluorescent probe is synthesized for the determination of adenosine 5′-triphosphate (ATP). The 6-carboxyfluorescein-labeled aptamer (FAM-aptamer) was bound to the surface of magnetite nanoparticles coated with polydopamine (Fe₃O₄@PDA) by π-π stacking interaction to form the multifunctional probe. The probe has three functions including recognition, magnetic separation, and yielding a fluorescent signal. In the presence of ATP, FAM-aptamer on the surface of the probe binds to ATP and returns to the solution. Thus, the fluorescence of the supernatant is enhanced and can be related to the concentration of ATP. Fluorescence intensities were measured at excitation/emission wavelengths of 494/526 nm. Response is linear in the 0.1–100 μM ATP concentration range, and the detection limit is 89 nM. The probe was applied to the quantitation of ATP in spiked human urine and serum samples, with recoveries ranging between 94.8 and 102%.

Open image in new window

Graphical abstract A multifunctional fluorescent probe based on the use of FAM-aptamer and Fe₃O₄@PDA is described for the determination of ATP in spiked human urine and serum samples. FAM-aptamer: 6-carboxyfluorescein-labeled aptamer; Fe₃O₄@PDA: magnetite nanoparticles coated with polydopamine. ATP: adenosine 5′-triphosphate.

     

Separation of Cytidine 5′-triphosphate Biosynthesized from Cytidine 5′-monophosphate on Ion-exchange Resin and HPLC Analysis of Cytidine Compounds

Conditions were studied in the biosynthesis of cytidine 5′-triphosphate (CTP) from cytidine 5′-monophosphate (CMP). A 201 × 7 anion ion-exchange resin was applied for the separation of CTP from CMP. Adsorption isotherm and elution conditions (eluant, eluant concentration, flow rate, sample volume loaded) were investigated. At the same time, a new high-performance liquid chromatography on an anion ion-exchange column WAX-1 with UV detector at 260 nm was developed to measure CMP, cytidine 5′-diphosphate (CDP), and CTP. The retention time for CMP, CDP, and CTP are 0.723, 1.448, and 4.432 min, respectively. This new rapid high-performance liquid chromatography (HPLC) method for the analysis of cytidine compounds in biological sample has a wide linear range with high precision and repeatability.     

Stepwise conformational transition of crystalline disodium adenosine 5′-triphosphate with relative humidity as studied by high resolution solid state 13C and 31P NMR

Stepwise conformational transition of disodium adenosine 5′-triphosphate (Na₂ATP) crystals as a function of relative humidity (RH), was examined by means of high resolution solid state NMR spectroscopy. The presence of two types of molecules, A and B, with altered conformations in an asymmetric unit, is evident from both ³¹P and ¹³C NMR spectra, irrespective of the three different crystalline forms, mono-, di- and trihydrates, in which, cell parameters changed linearly with RH. Hydration-dependent conformational transition from the monohydrate (RH 0–10%) through dihydrate (20–40%) to trihydrate (60–90%), was well monitored by stepwise upfield displacements of the C1′ ¹³C signals of ribose moiety (molecule B), although, the corresponding peak for the molecule A, is almost unchanged. This means that, adaptation of stepwise structural transitions to the linear expansion of cell parameters is almost entirely ascribed to the conformational readjustment of the molecule B, together with varying proportion of two types of hydrate forms, at the RH range of 20–40%. We consider that, small clusters or thin layers are formed in the beginning of the transition and subsequently, the number of them, rather than the size or thickness increases, because the phosphorous spin–lattice relaxation times, T₁^P, for the three phosphorous nuclei, including those of mixed state, of the two hydrate forms, turned out to be similar due to sufficient fast spin diffusion rates among them. Since only one direction of the cell parameters is changed, as determined by the previous X-ray diffraction study, we conclude that thin layer type micro crystals might be produced during the stepwise transition. Further, it was found that, these molecules acquired motional flexibility mainly at the bound water molecules, together with increased relative humidity, as determined by a variety of relaxation parameters.     

Furanose ring conformations in a 1′-alkynyl C-nucleoside and the dinucleotide

A large-scale synthesis was carried out for alkynyl C-nucleotide oligomers in order to clarify the structural details of the artificial DNA. A liquid-phase synthesis by means of phosphoramidite methodology enabled us to handle ～0.1 g of the DNA oligomers possessing a pseudouracil derivative (T*) as a non-natural nucleobase. ¹H NMR measurements in aqueous media were carried out for the oligomers, succeeded in the accurate assignments of the protons accompanying with determination of the coupling constants (J values). These J values revealed that average conformation of the alkynylribose rings in the DNA was substantially biased toward the S-type conformers (²T₁/E₁/^OT₁). X-ray crystal analysis of the non-natural nucleoside also supported the S-type conformation (²E/²T₁) as seen in natural B-DNA.     

Determination of the rates of formation and hydrolysis of the Schiff bases formed by pyridoxal 5′-phosphate and copolypeptides containing l-lysine

We determined the apparent rate constants of formation (k₁) and hydrolysis (k₂) of the Schiff bases formed between pyridoxal 5′-phosphate (PLP) and l-lysine and l-alanine copolymers of different compositions, as well as those formed between PLP and l-lysine and l-glutamic acid copolymers, at various pH values, a temperature of 25 °C and an ionic strength of 0.1 M. The k₁ values obtained in neutral and acidic media were independent of the copolymer composition. The efficiency of the intramolecular acid catalysis for the formation of the Schiff bases was found to be somewhat higher than that of PLP—primary amine systems (the slope of the Brøwted plot was α=0.77). The most stable of the Schiff bases studied was that with a protonated imine nitrogen and phosphate group and a unprotonated pyridine nitrogen.