Studies of Mg2+/Ca2+ complexes of naturally occurring dinucleotides: potentiometric titrations, NMR, and molecular dynamics

Abstract

Dinucleotides (Np(n)N'; N and N' are A, U, G, or C, n = 2-7) are naturally occurring physiologically active compounds. Despite the interest in dinucleotides, the composition of their complexes with metal ions as well as their conformations and species distribution in living systems are understudied. Therefore, we investigated a series of Mg(2+) and Ca(2+) complexes of Np(n)N's. Potentiometric titrations indicated that a longer dinucleotide polyphosphate (N is A or G, n = 3-5) linker yields more stable complexes (e.g., log K of 2.70, 3.27, and 3.73 for Ap(n)A-Mg(2+), n = 3, 4, 5, respectively). The base (A or G) or ion (Mg(2+) or Ca(2+)) has a minor effect on K(M)(ML) values. In a physiological medium, the longer Ap(n)As (n = 4, 5) are predicted to occur mostly as the Mg(2+)/Ca(2+) complexes. (31)P NMR monitored titrations of Np(n)N's with Mg(2+)/Ca(2+) ions showed that the middle phosphates of the dinucleotides coordinate with Mg(2+)/Ca(2+). Multidimensional potential of mean force (PMF) molecular dynamics (MD) simulations suggest that Ap(2)A and Ap(4)A coordinate Mg(2+) and Ca(2+) ions in both inner-sphere and outer-sphere modes. The PMF MD simulations additionally provide a detailed picture of the possible coordination sites, as well as the cation binding process. Moreover, both NMR and MD simulations showed that the conformation of the nucleoside moieties in Np(n)N'-Mg(2+)/Ca(2+) complexes remains the same as that of free mononucleotides.

Adenosine/guanosine-3′,5′-bis-phosphates as biocompatible and selective Zn2+-ion chelators. Characterization and comparison with adenosine/guanosine-5′-di-phosphate

“…Based on our earlier free energy simulations of metal ion binding in dinucleotides we expect a significant barrier to metal-ion dissociation from the nucleotide. 39 Therefore, we consider the final complexation state of the simulation to be representative of the preferred binding mode. The Zn 2+ -binding in the case of d( pAp) is markedly different than that of ADP (Fig.…”

Characterization of Complexes of Nucleoside-5′-Phosphorothioate Analogues with Zinc Ions

“…Likewise, pK a values of AP 3 (β-S)A were highly similar to the parent dinucleotide, AP 3 A. 39 However, pK a values of the thiophosphate group in ADP-β-S, GDP-β-S, and ATP-γ-S were more acidic by about 1 log unit as compared to those of their parent nucleotides (Table 1), because of the higher polarizibility of the sulfur atom as compared to oxygen, inducing greater stability of the thiophosphate anion. These results are consistent with the literature.…”

“…The p K a values of ADP, GDP, and ATP, which we determined, were consistent with literature (Table ). ,, p K a values of the protons in the guanine and adenine nucleobases at N7–H + and N1–H + protons, respectively were not affected by the sulfur modification at the phosphate chain (Table ). Likewise, p K a values of AP 3 (β-S)A were highly similar to the parent dinucleotide, AP 3 A . However, p K a values of the thiophosphate group in ADP-β-S, GDP-β-S, and ATP-γ-S were more acidic by about 1 log unit as compared to those of their parent nucleotides (Table ), because of the higher polarizibility of the sulfur atom as compared to oxygen, inducing greater stability of the thiophosphate anion.…”

Development of holistic analytical methods for disease biomarker discovery and the study of drug efficasy in autoimmune disease

“…In addition to the identification of unknowns there are also classes of known, and well biologically described, metabolites (sugar phosphate, carboxylic acids, nucleotides, nucleosides, phosphorylated compounds, aminoacids and CoA derivatives) that exhibit rather challenging separation/detection problems due to strong ionic interactions with the free silanol groups, metals (172)(173)(174)(175)(176) and glass substrates with these particularly evident in chromatographic-mass spectrometry-based methodologies. These metabolites are intermediates in the most important catabolic and anabolic functions of the cell.…”