title: Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae.
abstract: Mathematical models have become a necessary tool for organizing the rapidly increasing amounts of large-scale data on biochemical pathways and for advanced evaluation of their structure and regulation. Most of these models have addressed specific pathways using either stoichiometric or flux-balance analysis, or fully kinetic Michaelis-Menten representations, metabolic control analysis, or biochemical systems theory. So far, the predictions of kinetic models have rarely been tested using direct experimentation. Here, we validate experimentally a biochemical systems theoretical model of sphingolipid metabolism in yeast. Simulations of metabolic fluxes, enzyme deletion and the effects of inositol (a key regulator of phospholipid metabolism) led to predictions that show significant concordance with experimental results generated post hoc. The model also allowed the simulation of the effects of acute perturbations in fatty-acid precursors of sphingolipids, a situation that is not amenable to direct experimentation. The results demonstrate that modelling now allows testable predictions as well as the design and evaluation of hypothetical 'thought experiments' that may generate new metabolomic approaches.
authors.affiliation: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Alvarez-Vasquez
authors.forename: Kellie J
authors.initials: KJ
authors.lastname: Sims
authors.forename: L Ashley
authors.initials: LA
authors.lastname: Cowart
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Okamoto
authors.forename: Eberhard O
authors.initials: EO
authors.lastname: Voit
authors.forename: Yusuf A
authors.initials: YA
authors.lastname: Hannun
mesh_terms: D003198:Computer Simulation; D005227:Fatty Acids / Q000378:metabolism; D007294:Inositol / Q000378:metabolism / Q000494:pharmacology; D008954:Models, Biological; D019308:Palmitic Acid / Q000378:metabolism; D010171:Palmitoyl Coenzyme A / Q000378:metabolism; D010743:Phospholipids / Q000378:metabolism; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D013107:Sphingolipids / Q000378:metabolism*
chemical_list: D005227:Fatty Acids; D010743:Phospholipids; D013107:Sphingolipids; D010171:Palmitoyl Coenzyme A; D019308:Palmitic Acid; D007294:Inositol