title: 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.
authors.affiliation: Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat Gan, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Stern
authors.forename: Dan Thomas
authors.initials: DT
authors.lastname: Major
authors.forename: Hugo Emilio
authors.initials: HE
authors.lastname: Gottlieb
authors.forename: Daniel
authors.initials: D
authors.lastname: Weizman
authors.forename: Alon Haim
authors.initials: AH
authors.lastname: Sayer
authors.forename: Eliav
authors.initials: E
authors.lastname: Blum
authors.forename: Bilha
authors.initials: B
authors.lastname: Fischer
mesh_terms: D002118:Calcium / Q000737:chemistry*; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D011199:Potentiometry
chemical_list: D015226:Dinucleoside Phosphates; D008274:Magnesium; D002118:Calcium