Thermodynamic properties of enzyme-catalyzed reactions involving cytosine, uracil, thymine, and their nucleosides and nucleotides

Abstract

The standard Gibbs energies of formation of species in the cytidine triphosphate series, uridine triphosphate series, and thymidine triphosphate series have been calculated on the basis of the convention that Δ f G° = 0 for the neutral form of cytidine in aqueous solution at 298.15 K at zero ionic strength. This makes it possible to calculate apparent equilibrium constants for a number of reactions for which apparent equilibrium constants have not been measured or cannot be measured because they are too large. This paper adds fifteen reactants to the database BasicBiochemData3 at MathSource that includes 199 reactants. The standard transformed Gibbs energies of formation of these fifteen reactants are used to calculate apparent equilibrium constants at 298.15 K, ionic strength 0.25 M, and pHs 5, 6, 7, 8, and 9 for thirty two reactions. The pKs, standard Gibbs energies of hydrolysis, and standard Gibbs energies of deamination are given for these fifteen reactants.

Thermodynamic Reaction Control of Nucleoside Phosphorolysis

“…This equilibrium constant exists irrespective of the (bio)catalyst used and K′ values for some substrates in NPase‐catalyzed reactions have been reported . Thus, according to the law of mass action, only the reaction conditions influence the final equilibrium concentrations and not the enzyme used for catalysis.…”

Kinetic mechanism and energetics of binding of phosphoryl group acceptors to Mycobacterium tuberculosis cytidine monophosphate kinase

“…Incidentally, it has been shown that Asp185 of E. coli CMK (corresponding to Asp187 in MtCMK) plays a more relevant role in catalysis than in NMP substrate binding [13]. It has also been pointed out that whether the a-phosphate of the substrate acceptor (e.g., CMP) is protonated in phosphoryl transfer reactions remains controversial as the local enzymatic environment can influence its pK a value [43,44]. Quantum mechanics calculations have suggested that UMP/CMP kinase from Dictyostelium discoideum follows a concerted phosphoryl transfer mechanism in which the a-phosphate group of CMP is protonated [45].…”

RNA Folding and Hydrolysis Terms Explain ATP Independence of RNA Interference in Human Systems

“…Hydrolysis energies were taken from previous experiments (Alberty, 2007), but we estimate that discrepancies up to 50% may arise since the systems in the experiments were at 25°C and possibly different ionic conditions. From Table 7 of Alberty (2007), the energy of hydrolysis of CMP, UMP, and TMP is 12.96 kJ/mol, or approximately 3.1 kcal/mol per bond.…”

“…From Table 7 of Alberty (2007), the energy of hydrolysis of CMP, UMP, and TMP is 12.96 kJ/mol, or approximately 3.1 kcal/mol per bond. Two phosphoester bonds are hydrolyzed in the processing of premiRNA, and thus we take this energy of hydrolysis to be 6.2 kcal/mol.…”

“…For the let-7 premiRNA, hydrolysis G ∆ is the energy change due to cleavage of 2 phosphoester bonds to release three new fragments, and can be approximated as -6.2 kcal/mol (Alberty, 2007). As mentioned in the previous section, we take 0 ≈ ∆ bind G as a first order approximation.…”