Thermodynamic Properties of Nucleotide Reductase Reactions

• Published in: Biochemistry (Easton) 2004-08, Vol.43 (30), p.9840-9845
• Main Author: Alberty, Robert A
• Format: Article
• Language: English
• Subjects: Adenosine Diphosphate - analogs & derivatives; Adenosine Diphosphate - chemistry; Aldehyde-Lyases - chemistry; Binding Sites; Catalysis; Hydrogen-Ion Concentration; Kinetics; Models, Chemical; Osmolar Concentration; Protons; Reducing Agents - chemistry; Ribonucleoside Diphosphate Reductase - chemistry; Ribonucleotide Reductases - chemistry; Ribosemonophosphates - chemistry; Substrate Specificity; Thermodynamics; Thioredoxins - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi049353r

Recent thermodynamic measurements have made it possible to calculate the apparent equilibrium constants of the ribonucleoside diphosphate reductase reaction and the ribonucleoside triphosphate reductase reaction with various reducing agents. Third law heat capacity measurements on crystals of d-ribose and other calorimetric measurements make it possible to calculate Δf G° for d-ribose and two species of d-ribose 5-phosphate. The experimental value of the apparent equilibrium constant K‘ for the deoxyribose-phosphate aldolase reaction makes it possible to calculate the standard Gibbs energies of formation Δf G° for two protonation states of 2‘-deoxy-d-ribose 5-phosphate. This shows that Δf G°(2‘-deoxy-d-ribose 5-phosphate2-) − Δf G°(d-ribose 5-phosphate2-) = 147.86 kJ mol-1 at 298.15 K and zero ionic strength in dilute aqueous solutions. This difference between reduced and oxidized forms is expected to apply to d-ribose, d-ribose 1-phosphate, ribonucleosides, and ribonucleotides in general. This expectation is supported by two other enzyme-catalyzed reactions for which apparent equilibrium constants have been determined. The availability of Δf G° values for the species of 2‘-deoxy-d-ribose and its derivatives makes it possible to calculate standard transformed Gibbs energies of formation of these reactants, apparent equilibrium constants for their reactions, changes in the binding of hydrogen ions in these reactions, and standard apparent reduction potentials of the half reactions involved as a function of pH and ionic strength at 298.15 K. The apparent equilibrium constant for ADP + thioredoxinred = 2‘-deoxyADP + H2O + thioredoxinox is 1.4 × 1011 at 298.15 K, pH 7, and 0.25 M ionic strength.