Thermodynamic calculations of biochemical reaction systems at specified pH, pMg, and change in binding of hydrogen and magnesium ions

Abstract

Each metabolite in biochemical reaction may be available as an equilibrated mixture of different charged ions, and it is termed as "metabolite species." At equilibrium, each metabolite is represented as pseudoisomer group of metabolite species. At constant pH condition, the number of hydrogen and magnesium ions in a particular biochemical reactant is constant. The conventional thermodynamic property does not signify the biochemical systems precisely. Therefore, transformed thermodynamic Gibbs free energy change of reactions must be used for biochemical systems. Gibbs free energy of formation (ΔG ′0 f ) of pseudoisomers of different biochemical reactants in glycolysis is calculated based on pK a . Transformed Gibbs energy change of all biochemical reactions involved in glycolysis is calculated by incorporating pH, pMg, ionic strength, and change in binding of H + and Mg 2+ ions. The transformed Gibbs free energy change of all biochemical reactions in glycolysis (Δ r G ′0 ) is calculated and compared with standard Gibbs free energy change of reaction (Δ r G 0 ).The results indicated that there is difference in values of (Δ r G ′0 ) and (Δ r G 0 ). Hence, it is shown that the thermodynamic property G is not sufficient to provide a criterion for the spontaneity of biochemical reaction. At equilibrium, G′ must be minimized rather than G at constant pH and pMg.KEYWORDS ionic strength, metabolite species, pH and pMg, reactions in glycolysis, thermodynamic feasibility

How Does Mg2+(aq) Interact with ATP(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

“…Overall, phosphorylation and dephosphorylation processes are strongly affected by the presence of divalent metal cations, particularly by Mg 2+ (aq) , the cation with the highest ATP (aq) binding affinity, 25,34 and by hydration effects inherent to the aqueous environment of the cell. 46,48−50 In this way, metal− ligand coordination at the phosphate chain is involved in dephosphorylation (hydrolysis) or phosphorylation at specific phosphate units via charge redistribution and conformational changes, 24,46 with the relatively small size of the Mg 2+ (aq) ion facilitating coordination. 51 These bonding interactions should result in charge redistribution at the P−O−P bond 39 and differences in electron BEs of the α-, β-, and γ-phosphates in ATP (aq) and Mg 2+ −ATP (aq) .…”

“…Despite a single phosphate unit seemingly being involved in phosphorylation and dephosphorylation reactions, Mg 2+ (aq) complexation to multiple sites in the phosphate chain is required for the overall reaction to proceed. − In the absence of enzymes, α-, β-, and γ-phosphate are expected to be equally involved in Mg 2+ (aq) association to ATP (aq) . ,, In enzyme-bound ATP (aq) , the β- and γ-phosphate units are most likely to interact with Mg 2+ (aq) . The binding constants associated with specific Mg 2+ –ATP (aq) ion pairing motifs alter the Gibbs free energy of hydrolysis, as they determine the concentration of each of the species involved in the reaction.…”

“… 26 , 44 , 45 In enzyme-bound ATP (aq) , the β- and γ-phosphate units are most likely to interact with Mg 2+ (aq) . 46 The binding constants associated with specific Mg 2+ –ATP (aq) ion pairing motifs alter the Gibbs free energy of hydrolysis, 47 as they determine the concentration of each of the species involved in the reaction.…”