Stability constants nucleotide complexes

Table XIX contains stability constants for complexes of Ca2+ and of several other M2+ ions with a selection of phosphonate and nucleotide ligands (681,687-695). There is considerably more published information, especially on ATP (and, to a lesser extent, ADP and AMP) complexes at various pHs, ionic strengths, and temperatures (229,696,697), and on phosphonates (688) and bisphosphonates (688,698). The metal-ion binding properties of cytidine have been considered in detail in relation to stability constant determinations for its Ca2+ complex and complexes of seven other M2+ cations (232), and for ternary M21 -cytidine-amino acid and -oxalate complexes (699). Stability constant data for Ca2+ complexes of the nucleosides cytidine and uridine, the nucleoside bases adenine, cytosine, uracil, and thymine, and the 5 -monophosphates of adenosine, cytidine, thymidine, and uridine, have been listed along with values for analogous complexes of a wide range of other metal ions (700). Unfortunately comparisons are sometimes precluded by significant differences in experimental conditions.

Comparison of areas under individual peaks in the H NMR spectrum of dienPd(II)-nucleoside and nucleotide complexes permits evaluation of equilibrium stability constants for complex formation. Figure 5 shows the species distribution in a nearly equimolar solution of dienPd(II) and 5 -GMP and Figure 6 does the same for 5 -AMP. The difference between the distributions in Figure 5 and 6 results largely from the different absolute... 

Most of this section will be devoted to summarizing information relating to the stability constants reported for complexes of this group of Ca2+-binding ligands. However, we shall precede this main part with a short mention of a few relevant structures. Other properties of calcium phosphates and phosphonates will be mentioned in Sections VIII.B.4 and VIII.D below. An overall view of complexes of nucleosides, nucleotides, and nucleic acids is available (670). 

Stability Constants (LogU)K, at 298 K and I = 0.1M) for Phosphate, Phospho-nate, Nucleoside, and Nucleotide Complexes of Selected M2+ Cations... 

O Sullivan and Smithersi describe various protocols for determining dissociation constants (or, stability constants) of metal ion-nucleotide complexes. Morrison and Cleland have presented a kinetic method that has... 

The equilibrium constant of an enzyme-catalyzed reaction can depend greatly on reaction conditions. Because most substrates, products, and effectors are ionic species, the concentration and activity of each species is usually pH-dependent. This is particularly true for nucleotide-dependent enzymes which utilize substrates having pi a values near the pH value of the reaction. For example, both ATP" and HATP may be the nucleotide substrate for a phosphotransferase, albeit with different values. Thus, the equilibrium constant with ATP may be significantly different than that of HATP . In addition, most phosphotransferases do not utilize free nucleotides as the substrate but use the metal ion complexes. Both ATP" and HATP have different stability constants for Mg +. If the buffer (or any other constituent of the reaction mixture) also binds the metal ion, the buffer (or that other constituent) can also alter the observed equilibrium constant . ... 

An essential aspect to understanding the influence of metal ions on enzyme-catalyzed reactions is the knowledge of how tight different metal ions bind to a wide variety of substrates (particularly nucleotides and other phosphoryl-containingmolecular entities), products, and effectors and that binding phenomena are altered by the experimental conditions (e.g., the effects of pH, temperature, ionic strength, etc.). This necessitates the experimental determination of the stability constant (an association constant) for the metal ion-hgand complex. O Sulhvan and Smithers have reviewed the theory and the various techniques for such determinations and have provided values for many of the more common, biochemically relevant complexes. 

Preliminary rate measurements should allow one to make a plot of initial velocity Vq versus [metal ion], and this should provide information on the optimal metal ion concentration. (For many MgATP -dependent enzymes, the optimum is frequently 1-3 mM uncomplexed magnesium ion.) Then, by utilizing pubhshed values for formation constants (also known as stability constants) defining metal ion-nucleotide complexation, one can readily design experiments to keep free metal ion concentration at a fixed level. To compensate properly for metal ion complexation in ATP-dependent reactions, one must chose a buffer for which a stability constant is known. For example, in 25 mM Tris-HCl (pH 7.5), the stability constant for MgATP is approximately 20,000 M Thus, one can write the following equation ... 

The following table lists several frequently used stability constants for metal ion-nucleotide complexes. Because complexation is driven by neutrafization of electric charge on the components, one should immediately appreciate that the values apply only for the specified solution conditions. A more complete list is provided else-where. ... 

There was no change in the metal ion-phosphate interaction when the heterocyclic ring was substituted and the ribose residue replaced by deoxysugar (77, 76). According to the magnitude of the stability constants of the Mn2+, Co2+, Ni2+ and Zn2+ metal nucleotide complexes (Table 3) it can be concluded that the electronic structure of the metal ion seems to have little effect to the extent of binding. Rather, the... 

O Sullivan, W. J., and D. D. Perrin The stability constants of metal-adenine nucleotide complexes. Biochemistry 3, 18 (1964). 

Hodson and Azam (1977) have reported that up to 20% of the total ATP in seawater occurs in the free form. It is, however, difficult to say whether this finding was a product of sample manipulation. At least in bacterial cultures, it has been shown that nucleotides may be released into the medium (Chapmann et al., 1971). On the other hand, it is questionable whether ATP is stable enough to exist in solution over longer periods owing to its low stability constant or the possibility of complexation with divalent cations and fulvic acids (Tetas and Lowenstein, 1963 Hulett, 1970 Bulleid, 1978). 

As early as 1932 it was reported that an increase in the acidity of AMP was observed when borate was present [46). Twenty years later the complex reactions of borate with nucleosides were employed to separate mixtures of nucleosides and even nucleotides (see also sections on chromatography and electrophoresis). Only very little is known about whether or not borate interferes with biochemical reactions where nucleosides or nucleotides are involved. Thus, the stability constants of some boric nucleosides (72) are roughly in the same order of magnitude as the formation constants of earth alkaline or transition metal nucleotide complexes (62). It is therefore not unlikely that borate could influence to... 

Orotidine and its derivatives play an important role as intermediates in the metabolism of pyrimidine-nucleotides [91]. Its structure is shown in Figure 8 (top, left) it is closely related to uridine (see Figure 1), but due to the (C6)-carboxylate group it exists in solution mainly in the syn conformation [89]. The (C6)COOH group is very acidic for aqueous solution it was estimated that pATa = 0.5 0.3 [92]. Consequently, the stability constants of the orotidinate (Or ) complexes of Mg ", Cu ", and Zn " (only these metal ions have been studied [92]) are somewhat below of those measured for the corresponding M(Ac) complexes (see Table 1, column 7). There is no evidence for any significant chelate formation in aqueous solution [92]. Therefore, one may assume that all this also holds for the Cd(Or) complex, which gives as an estimate for its stability log cd(Or) = 1-0 0-3-... 

Table 14 Extent of intramolecular aromatic-ring stacking or hydrophobic adduct formation in ternary M(N)(L) complexes, where N = nucleotide and L = another ligand, as depicted for example in equilibrium (34) and as calculated from stability constants determined via potentio-metric (pot.) pH titrations Stability enhancement log zIm/n/l (analogous to eq. 14), intramolecular and dimensionless equilibrium constant Kj/st (eq. 34), and percentage of the closed M(N)(L)d species in aqueous solution at 25°C and / = 0.1 M (NaC104 or KNOs)." " For comparison some results obtained from H NMR shift experiments are also given.

R.M. Smith, Y. Chen, and A.E. Martell, "Critical Evaluation of Stability Constants for Nucleotide Complexes with Protons and Metal Ions and the accompaning Enthalphy Changes", in preparation. 

In the presence of an aromatic ligand such as bipyridyl or o-phenanthroline ternary complexes of the type nucleotide—M" —ligand form in aqueous solution with enhanced thermodynamic stability. The enhanced stability arises from rc-stacking interactions between the aromatic ligand and the heterocyclic base. In solution these interactions are evident from induced H NMR shifts and in the solid state the two bases are aligned parallel within van der Waals contact distances. Recently the extent of these stacking interactions for a number of Mn" and Zn" complexes of nucleoside triphosphates have been estimated in terms of intramolecular equilibrium constants. ... 

The experimentally measured water binding energies of nucleotides provide an important set of data required, for instance, to work out the energetics of DNA duplex formation. The Watson-Crick base pair interaction, in solution, is in constant competition with hydration of the individual bases. Thus, the duplex stability depends on the base-base interaction energy relative to the base-water and water-water interaction. Knowing all of the energetic contributions to a complex system such as solvated... 

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