Nucleotides, ionic

Several classes of vitamins are related to, or are precursors of, coenzymes that contain adenine nucleotides as part of their structure. These coenzymes include the flavin dinucleotides, the pyridine dinucleotides, and coenzyme A. The adenine nucleotide portion of these coenzymes does not participate actively in the reactions of these coenzymes rather, it enables the proper enzymes to recognize the coenzyme. Specifically, the adenine nucleotide greatly increases both the affinity and the speeifieity of the coenzyme for its site on the enzyme, owing to its numerous sites for hydrogen bonding, and also the hydrophobic and ionic bonding possibilities it brings to the coenzyme structure. 

The first one consists of 11-12 water molecules per nucleotide unit, which are coordinated directly to sites of the DNA double helix. Two of these water molecules are bound very tightly to the ionic phosphate residue and cannot be removed without completely destroying the structure of DNA. There are four other water molecules... 

Monomeric actin binds ATP very tightly with an association constant Ka of 1 O M in low ionic strength buffers in the presence of Ca ions. A polymerization cycle involves addition of the ATP-monomer to the polymer end, hydrolysis of ATP on the incorporated subunit, liberation of Pi in solution, and dissociation of the ADP-monomer. Exchange of ATP for bound ADP occurs on the monomer only, and precedes its involvement in another polymerization cycle. Therefore, monomer-polymer exchange reactions are linked to the expenditure of energy exactly one mol of ATP per mol of actin is incorporated into actin filaments. As a result, up to 40% of the ATP consumed in motile cells is used to maintain the dynamic state of actin. Thus, it is important to understand how the free energy of nucleotide hydrolysis is utilized in cytoskeleton assembly. 

Figure 1. Simplified schematic of receptor-mediated signal transduction in neutrophils. Binding of ligand to the receptor activates a guanine-nucleotide-binding protein (G protein), which then stimulates phospholipase C. Phosphatidylinositol 4,5-bis-phosphate is cleaved to produce diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG stimulates protein kinase C. IP3 causes the release of Ca from intracellular stores, which results in an increase in the cytosolic Ca concentration. This increase in Ca may stimulate protein kinase C, calmodulin-dependent protein kinases, and phospholipase A2. Protein phosphorylation events are thought to be important in stimulating degranulation and oxidant production. In addition, ionic fluxes occur across the plasma membrane. It is possible that phospholipase A2 and ionic channels may be governed by G protein interactions. ...

The membrane-bound preparation from kidney is easily solubilized in non-ionic detergent and analytical ultracentrifugation shows that the preparation consists predominantly (80 85%) of soluble af units with 143000 [28]. The soluble a)S unit maintains full Na,K-ATPase activity, and can undergo the cation or nucleotide induced conformational transitions that are observed in the membrane-bound preparation. A cavity for occlusion of 2K or 3Na ions can be demonstrated within the structure of the soluble a)S unit [29], as an indication that the cation pathway is organized in a pore through the aji unit rather than in the interphase between subunits in an oligomer. 

If the nucleoside is treated with a threefold excess of phosphoryltristriazole and subsequently with a mixture of triethylamine and water, the ionic nucleotide phosphoric triazolide can be obtained [46]... 

F. H. Westheimer (1987) has provided a detailed survey of the multifarious ways in which phosphorus derivatives function in living systems (Table 4.7). The particular importance of phosphorus becomes clear when we remember that the daily turnover of adenosine triphosphate (ATP) in the metabolic processes of each human being amounts to several kilograms Phosphate residues bond two nucleotides or deoxynucleotides in the form of a diester, thus making possible the formation of RNA and DNA the phosphate always contains an ionic moiety, the negative charge of which stabilizes the diester towards hydrolysis and prevents transfer of these molecules across the lipid membrane. 

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.

Most HPLC applications involving biomolecules utilize aqueous mobile phases. Critical parameters include both ionic strength and pH. Common solutes include TRIS, sodium phosphate, sodium acetate, and sodium chloride. Slightly alkaline pHs are preferable, for stability reasons. Specific examples of mobile phases include 50 mM TRIS, 25 mM KC1, and 5 mM MgCl2 (pH 7.2) for nucleotides, and 50 mM NaH2P04 (pH 7.0) and 20 mMTRIS and 0.1 M sodium acetate (pH 7.5) for both peptides and amino acids. All of these mobile phases are suitable for reverse phase or ion exchange applications. 

In even more disadvantageous circumstances, the thermal decomposition does not yield a single defined product, but a complex mixture that results in almost useless spectra, e.g., in case of highly polar natural products such as saccharides, nucleotides, and peptides or in case of ionic compounds such as organic salts or metal complexes. 

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. 

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. 

The adenine nucleotide translocase, integral to the inner membrane, binds ADP3 - in the intermembrane space and transports it into the matrix in exchange for an ATP4 molecule simultaneously transported outward (see Fig. 13-1 for the ionic forms of ATP and ADP). Because this antiporter moves four negative charges out for every three moved in, its activity is favored by the... 

Nucleotide A nucleic acid monomer consisting of three parts a nitrogenous base, a ribose sugar, and an ionic phosphate group. 

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