A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway

Abstract

A database of thermodynamic properties is developed, which extends a previous database of glycolysis and tricarboxylic acid cycle by adding the reactions of the pentose phosphate pathway. The raw data and documented estimations of solution properties are made electronically available. The database is determined by estimation of a set of parameters representing species-level free energies of formation. The resulting calculations provide thermodynamic and network-based estimates of thermodynamic properties for six reactions of the pentose phosphate pathway for which estimates are not available in the preexisting literature. Optimized results are made available in ThermoML format. Because calculations depend on estimated hydrogen and metal cation dissociation constants, an uncertainty and sensitivity analysis is performed, revealing 23 critical dissociation constants to which the computed thermodynamic properties are particularly sensitive. DATABASE URL: http://www.biocoda.org/thermo

Figure 1.

Model-predicted versus experimental . Model predicted apparent equilibrium constants under defined experimental conditions (T, I, [Mg²⁺], [Ca²⁺], [Na⁺], [K⁺] and pH) are plotted versus experimental measurements for all data used in the analysis. Data points in the pentose phosphate pathway are shown as filled squares.

Figure 2.

Model-predicted versus experimental for the ribose-5-phosphate isomerase and ribuloase-phosphate 3-epimerase reactions. Open circles (GT-based ) are computed based on the Goldberg's database (25); filled squares (optimized ) are computed based on the optimized values of from Table 5.

Figure 3.

(A) Distribution of the product of uncertainty and sensitivity (US) for all pK values; (B) detailed distribution of the product >0.01.