Generating rate equations for complex enzyme systems by a computer-assisted systematic method
Open Access
- 4 August 2009
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 10 (1), 238
- https://doi.org/10.1186/1471-2105-10-238
Abstract
While the theory of enzyme kinetics is fundamental to analyzing and simulating biochemical systems, the derivation of rate equations for complex mechanisms for enzyme-catalyzed reactions is cumbersome and error prone. Therefore, a number of algorithms and related computer programs have been developed to assist in such derivations. Yet although a number of algorithms, programs, and software packages are reported in the literature, one or more significant limitation is associated with each of these tools. Furthermore, none is freely available for download and use by the community. We have implemented an algorithm based on the schematic method of King and Altman (KA) that employs the topological theory of linear graphs for systematic generation of valid reaction patterns in a GUI-based stand-alone computer program called KAPattern. The underlying algorithm allows for the assumption steady-state, rapid equilibrium-binding, and/or irreversibility for individual steps in catalytic mechanisms. The program can automatically generate MathML and MATLAB output files that users can easily incorporate into simulation programs. A computer program, called KAPattern, for generating rate equations for complex enzyme system is a freely available and can be accessed at http://www.biocoda.org.Keywords
This publication has 29 references indexed in Scilit:
- BISEN: Biochemical Simulation EnvironmentBioinformatics, 2009
- Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenaseBiochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2008
- Detailed Enzyme Kinetics in Terms of Biochemical Species: Study of Citrate SynthasePLOS ONE, 2008
- A Biophysical Model of the Mitochondrial Respiratory System and Oxidative PhosphorylationPLoS Computational Biology, 2005
- A Two-Step Computer-Assisted Method for Deriving Steady-State Rate EquationsBiochemical and Biophysical Research Communications, 1999
- A slide rule for deriving the rate equations of enzyme catalysed reactions with mechanisms involving up to six enzyme-containing intermediatesJournal of Theoretical Biology, 1974
- A slide rule for deriving the rate equations of enzyme catalysed reactions with unbranched mechanismsJournal of Theoretical Biology, 1974
- A simplified schematic method for deriving steady-state rate equations using a modification of the “theory of graphs” procedureBiochemical and Biophysical Research Communications, 1970
- The simulation and analysis by digital computer of biochemical systems in terms of kinetic models IV. Automatic derivation of enzymic rate lawsJournal of Theoretical Biology, 1968
- The simulation and analysis by digital computer of biochemical systems in terms of kinetic models: III. Generator programmingJournal of Theoretical Biology, 1967