A database of thermodynamic quantities for the reactions of glycolysis and the tricarboxylic acid cycle. J Phys Chem B 2010 Dec 16;114(49):16068-82
Date
05/08/2010Pubmed ID
20446702Pubmed Central ID
PMC3299200DOI
10.1021/jp911381pScopus ID
2-s2.0-77956568325 (requires institutional sign-in at Scopus site) 25 CitationsAbstract
Analysis of biochemical systems requires reliable and self-consistent databases of thermodynamic properties for biochemical reactions. Here a database of thermodynamic properties for the reactions of glycolysis and the tricarboxylic acid cycle is developed from measured equilibrium data. Species-level free energies of formation are estimated on the basis of comparing thermodynamic model predictions for reaction-level equilibrium constants to previously reported data obtained under different experimental conditions. Matching model predictions to the data involves applying state corrections for ionic strength, pH, and metal ion binding for each input experimental biochemical measurement. By archiving all of the raw data, documenting all model assumptions and calculations, and making the computer package and data available, this work provides a framework for extension and refinement by adding to the underlying raw experimental data in the database and/or refining the underlying model assumptions. Thus the resulting database is a refinement of preexisting databases of thermodynamics in terms of reliability, self-consistency, transparency, and extensibility.
Author List
Li X, Dash RK, Pradhan RK, Qi F, Thompson M, Vinnakota KC, Wu F, Yang F, Beard DAAuthor
Ranjan K. Dash PhD Professor in the Biomedical Engineering department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Citric Acid CycleDatabases as Topic
Glycolysis
Models, Chemical
Thermodynamics