Metal ion binding properties of dihydroxyacetone phosphate and glycerol 1-phosphate

Liang, Guangchao; Chen, Dong; Bastian, Matthias; Sigel, Helmut

doi:10.1021/ja00046a025

Cited by 27 publications

(48 citation statements)

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“…(vii) The results given in the lower part of Table 2 confirm the earlier conclusions (see the 15 discussed Cu(DHAP) and Cu(G1P) complexes [52,53]) that a reduced solvent polarity favors M 2+ -hydroxyl interactions.…”

supporting

confidence: 84%

“…Indeed, for Cu(DHAP) and Cu(G1P) it has been shown that in water containing 50% 1,4-dioxane (v/v) the chelated species in equilibrium (5) reach a formation degree of about 45% [52,53]. A similar chelate formation must be anticipated for the corresponding Cd 2+ complexes in solutions with a reduced dielectric constant or permittivity (ε).…”

Section: The Metal Ion Affinity Of Ribose-hydroxyl Groups Is Smallmentioning

confidence: 83%

“…However, the results log ∆ Cd/DHAP = 0.02 ± 0.05 and log ∆ Cd/G1P = -0.02 ± 0.06 (25°C; I = 0.1 M, NaNO 3 ) [52,53] are both zero within their error limits, and thus, no increased complex stability is observed and it must therefore be concluded that in aqueous solution equilibrium (5) [52,53].…”

Section: The Metal Ion Affinity Of Ribose-hydroxyl Groups Is Smallmentioning

confidence: 85%

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Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel

Skilandat

Sigel

et al. 2012

Metal Ions in Life Sciences

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Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromaticnitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono-to the di-and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono-or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

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supporting

confidence: 84%

Section: The Metal Ion Affinity Of Ribose-hydroxyl Groups Is Smallmentioning

confidence: 83%

Section: The Metal Ion Affinity Of Ribose-hydroxyl Groups Is Smallmentioning

confidence: 85%

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Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel

Skilandat

Sigel

et al. 2012

Metal Ions in Life Sciences

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“…a Value for glycerol-1-phosphate, 258C (Liang et al, 1992). The values for which no reference is given are estimated.…”

Section: Computational Softwarementioning

confidence: 99%

“…For instance, the acid and Mg complex dissociation constants of GAP are difficult to obtain because of its instability and conversion to the enolic form (DHAP). Based on the kinetic and structural analysis, Liang et al (1992) postulated that the pK a and pK d for GAP are probably closer to those of glycerol-1-phosphate than to DHAP (Tables III and IV). Therefore, these values were used in the present study.…”

Section: Uncertainty Of the Pk A And Pk D Valuesmentioning

confidence: 99%

Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

Vojinović

Stockar

2009

Biotech & Bioengineering

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Thermodynamic feasibility analysis (TFA) has been used as a tool capable of providing additional constraints to the mass balance-based methods of analysis of metabolic networks (e.g., flux balance analysis). Several publications have recently appeared in which TFA of different metabolic pathways from relatively simple to the genome-scale networks was described as a means of detecting the possible metabolic control steps. However, in order to perform TFA, many simplifying assumptions were necessary. On the other hand, it has been shown by applying TFA to the well-known pathway of glycolysis that erroneous simplifying assumptions may seriously bias the results of the analysis. A quantitative analysis of the influence of non-ideality of the biochemical system, pH, temperature, and complexation of the metabolites with Mg(2+) ions as well as a number of other factors on the TFA is reported. It is shown that the feasibility of glycolysis is very seriously limited by the reaction of oxidative phosphorylation of glyceraldehyde phosphate, and that the intracellular concentration of the main product of this reaction, biphosphoglycerate, must be anywhere from 10 to 100 times lower than published values. In addition, the driving force for this reaction, and consequently the feasibility of the entire pathway depend strongly on the intracellular pH and ionic strength and to a lesser extent on pMg and temperature. The analysis may also be influenced by uncertainties of the dissociation and magnesium complexation constants of glyceraldehyde phosphate. The analysis demonstrates the crucial importance of taking such factors into account when performing TFA. It also suggests an urgent need for experimental determinations of such factors as a prerequisite for sensible thermodynamic analysis of metabolism on a genome-wide scale.

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Complex Formation of Nickel(II) with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel¹,

Sigel²

2007

Nickel and Its Surprising Impact in Nature

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Metal ion binding properties of dihydroxyacetone phosphate and glycerol 1-phosphate

Cited by 27 publications

References 0 publications

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

Complex Formation of Nickel(II) with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

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