Nucleotides complexes with metal ions

The method of circular dichroism has been applied in investigations that have determined the reactions between Pt(II) compound and nucleosides, nucleotides, and DNA. Many antimicrobial preparations are excellent ligands. The activity of some of the antimicrobial preparations has been based on their complexing with metal ions. For example, increased effectiveness of tetracycline has been observed after its coordination with Ca. The complex is more lipophilic and very oil-soluble, which explains its transportation through the cell membrane. The opposite situation occurs when the ion-metal is toxic and the coordinated antibiotic serves as carrier through the membrane. 

Building towards models relevant for polymeric DNA and RNA, nucleotides contain a phosphate attached at the 5 or 3 position. The 5 -nucleotides are most commonly studied, for which the phosphate has a pAa 6 for the first protonation step. Unless otherwise noted, throughout this chapter nucleotide will refer to the 5 -phosphate linkage. In nucleotides, metal-phosphate coordination competes with metal-base interactions. Chelate complexes with both phosphate and base coordination can occur when sterically allowed. Thus, transition metal complexes with purine monophosphates tend to exhibit metal coordination to the base N7 position, with apparent hydrogen bonding of coordinated waters to the phosphate. By contrast, more ionic Mg" binds preferentially to the phosphate groups in nucleotide monophosphates. In di- and tri-phosphate complexes such as metal-ATP compounds, the proximity of multiple phosphates generally favors polyphosphate chelate complexes with metal ions. 

Structure of binary complexes of mono- and poly-nucleotides with metal ions of the first transition group. H. Pezzano and F. Podo, Chem. Rev., 1980, 80, 365-401 (389). 

Hartman, K. A., Jr. The infrared spectra of some complexes of metal ions with nucleosides and nucleotides. Biochim. Biophys. Acta 138, 192 (1967). 

In aqueous solution, nucleotides and their metal ion complexes are known to undergo a degree of self-association via base stacking. The tendency for this decreases with the number of phosphate groups present A > AMP > ADP > ATP. 

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. 

It is not an exaggeration to say that electrospray has introduced a new era, not only for the analytical mass spectroscopist, but also for the more physically oriented researcher interested in physical measurements involving the above ions, which are of such great importance in condensed-phase ion chemistry. In particular, gas-phase ions produced by electrospray allow, for the first time, thermochemical measurements involving ions of biochemical significance such as protonated peptides, deprotonated nucleotides, and metal ion complexes with peptides and proteins. It is to be expected that such data will be of importance in the development of theoretical modeling of the state of these systems in the condensed phase.34,35... 

Fig. 2.7. Characteristic rate constants (s 1) for substitution of inner-sphere H20 of various aqua ions. Note The substitution rates of water in complexes ML(H20)m will also depend on the symmetry of the complex (adapted from Frey, C.M. and Stuehr, J. (1974). Kinetics of metal ion interactions with nucleotides and base free phosphates in H. Sigel (ed.), Metal ions in biological systems (Vol. 1). Marcel Dekker, New York, p. 69).

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.

The structure of cobalamin is more complex than that of folic acid (Figure 15.2 and 15.3). At its heart is a porphyrin ring containing the metal ion cobalt at its centre. In catalytic reactions the cobalt ion forms a bond with the one-carbon group, which is then transferred from one compound to another. Vitamin B12 is the prosthetic group of only two enzymes, methylmalonyl-CoAmutase and methionine synthase. The latter enzyme is particularly important, as it is essential for the synthesis of nucleotides which indicates the importance of vitamin B12 in maintenance of good health. 

The topologically defined region(s) on an enzyme responsible for the binding of substrate(s), coenzymes, metal ions, and protons that directly participate in the chemical transformation catalyzed by an enzyme, ribo-zyme, or catalytic antibody. Active sites need not be part of the same protein subunit, and covalently bound intermediates may interact with several regions on different subunits of a multisubunit enzyme complex. See Lambda (A) Isomers of Metal Ion-Nucleotide Complexes Lock and Key Model of Enzyme Action Low-Barrier Hydrogen Bonds Role in Catalysis Yaga-Ozav /a Plot Yonetani-Theorell Plot Induced-Fit Model Allosteric Interaction... 

Exchange-inert complexes of Co(III) with nucleotides that have proven to be extremely useful as chirality probes because the different coordination isomers are stable and can be prepared and separated In addition, these nucleotides can be used as dead-end inhibitors of enzyme-catalyzed reactions and, since Co(III) is diamagnetic, a number of spectroscopic protocols can be utilized. See Exchange-Inert Complexes Chromium-Nucleotide Complexes Metal Ion-Nucleotide Interactions... 

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 . ... 

A metal-nucleotide complex that exhibits low rates of ligand exchange as a result of substituting higher oxidation state metal ions with ionic radii nearly equal to the naturally bound metal ion. Such compounds can be prepared with chromium(III), cobalt(III), and rhodi-um(III) in place of magnesium or calcium ion. Because these exchange-inert complexes can be resolved into their various optically active isomers, they have proven to be powerful mechanistic probes, particularly for kinases, NTPases, and nucleotidyl transferases. In the case of Cr(III) coordination complexes with the two phosphates of ATP or ADP, the second phosphate becomes chiral, and the screw sense must be specified to describe the three-dimensional configuration of atoms. 

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