Enzyme kinetics and computational modeling for systems biology.
Enzyme kinetics is a century-old area of biochemical research which is regaining popularity due to its use in systems biology. Computational models of biochemical networks depend on rate laws and kinetic parameter values that describe the behavior of enzymes in the cellular milieu. While there is a considerable body of enzyme kinetic data available from the past several decades, a large number of enzymes of specific organisms were never assayed or were assayed in conditions that are irrelevant to those models. The result is that systems biology projects are having to carry out large numbers of enzyme kinetic assays. This chapter reviews the main methodologies of enzyme kinetic data analysis and proposes using computational modeling software for that purpose. It applies the biochemical network modeling software COPASI to data from enzyme assays of yeast triosephosphate isomerase (EC 5.3.1.1).
Mendes
Pedro
P
Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom; School of Computer Science, The University of Manchester, Manchester, United Kingdom; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.
Messiha
Hanan
H
Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom; School of Chemistry, The University of Manchester, Manchester, United Kingdom.
Malys
Naglis
N
Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom; Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.
Hoops
Stefan
S
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004798:Enzymes / Q000378:metabolism*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D012984:Software; D014305:Triose-Phosphate Isomerase / Q000378:metabolism
D004798:Enzymes; D029701:Saccharomyces cerevisiae Proteins; D014305:Triose-Phosphate Isomerase