A Database of Thermodynamic Properties of the Reactions of Glycolysis, the Tricarboxylic Acid Cycle, and the Pentose Phosphate Pathway

Overview

Journal Database (Oxford)

Specialty Biology

Date 2011 Apr 13

PMID 21482578

Citations 17

Authors

Xin Li

Fan Wu

Feng Qi

Daniel A Beard

Affiliations

Soon will be listed here.

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

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References

Casazza J, Veech R . The interdependence of glycolytic and pentose cycle intermediates in ad libitum fed rats. J Biol Chem. 1986; 261(2):690-8. View

DATTA A, RACKER E . Mechanism of action of transketolase. I. Properties of the crystalline yeast enzyme. J Biol Chem. 1961; 236:617-23. View

Godt R, Maughan D . On the composition of the cytosol of relaxed skeletal muscle of the frog. Am J Physiol. 1988; 254(5 Pt 1):C591-604. DOI: 10.1152/ajpcell.1988.254.5.C591. View

Kummel A, Panke S, Heinemann M . Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol. 2006; 2:2006.0034. PMC: 1681506. DOI: 10.1038/msb4100074. View

Vinnakota K, Wu F, Kushmerick M, Beard D . Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways. Methods Enzymol. 2009; 454:29-68. PMC: 2761843. DOI: 10.1016/S0076-6879(08)03802-0. View

Vojinovic V, von Stockar U . Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways. Biotechnol Bioeng. 2009; 103(4):780-95. DOI: 10.1002/bit.22309. View

Tewari Y, Steckler D, Goldberg R, Gitomer W . Thermodynamics of hydrolysis of sugar phosphates. J Biol Chem. 1988; 263(8):3670-5. View

Glaser L, Brown D . Purification and properties of d-glucose-6-phosphate dehydrogenase. J Biol Chem. 1955; 216(1):67-79. View

HORECKER B, Hurwitz J . The purification of phosphoketopentoepimerase from Lactobacillus pentosus and the preparation of xylulose 5-phosphate. J Biol Chem. 1956; 223(2):993-1008. View

10.

Li X, Dash R, Pradhan R, Qi F, Thompson M, Vinnakota K . A database of thermodynamic quantities for the reactions of glycolysis and the tricarboxylic acid cycle. J Phys Chem B. 2010; 114(49):16068-82. PMC: 3299200. DOI: 10.1021/jp911381p. View

11.

Mavrovouniotis M . Identification of localized and distributed bottlenecks in metabolic pathways. Proc Int Conf Intell Syst Mol Biol. 1993; 1:275-83. View

12.

Henry C, Broadbelt L, Hatzimanikatis V . Thermodynamics-based metabolic flux analysis. Biophys J. 2006; 92(5):1792-805. PMC: 1796839. DOI: 10.1529/biophysj.106.093138. View

13.

LARSSON-RAZNIKIEWICZ M . Complex formation between 3-phospho-D-glyceric acid and divalent metal ions. Eur J Biochem. 1972; 30(3):579-83. DOI: 10.1111/j.1432-1033.1972.tb02129.x. View

14.

Villet R, Dalziel K . The nature of the carbon dioxide substrate and equilibrium constant of the 6-phosphogluconate dehydrogenase reaction. Biochem J. 1969; 115(4):633-8. PMC: 1185187. DOI: 10.1042/bj1150633. View

15.

Wu F, Yang F, Vinnakota K, Beard D . Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology. J Biol Chem. 2007; 282(34):24525-37. DOI: 10.1074/jbc.M701024200. View

16.

Merrill D, McAlexander J, Guynn R . Equilibrium constants under physiological conditions for the reactions of D-3-phosphoglycerate dehydrogenase and L-phosphoserine aminotransferase. Arch Biochem Biophys. 1981; 212(2):717-29. DOI: 10.1016/0003-9861(81)90416-1. View

17.

AXELROD B, Jang R . Purification and properties of phosphoribo-isomerase from alfalfa. J Biol Chem. 1954; 209(2):847-55. View

18.

Alberty R . Thermodynamic properties of weak acids involved in enzyme-catalyzed reactions. J Phys Chem B. 2006; 110(10):5012-6. DOI: 10.1021/jp0545086. View

19.

Alberty R . Calculation of thermodynamic properties of species of biochemical reactants using the inverse Legendre transform. J Phys Chem B. 2006; 109(18):9132-9. DOI: 10.1021/jp044162j. View

20.

Yang F, Beard D . Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: a case study of acetaminophen and ethanol toxic interaction. Biophys Chem. 2005; 120(2):121-34. DOI: 10.1016/j.bpc.2005.10.013. View