Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks.
The architecture of the cellular metabolic network is almost completely available from several databases. This has paved the way for computational analyses. Whereas kinetic modelling is still restrained to small metabolic sub-systems for which enzyme-kinetic details are known, so-called structural modelling techniques can be applied to complete metabolic networks even if the kinetics and regulation of the underlying enzymes is still unknown. Structural modelling requires detailed information on the presence of metabolic enzymes in a specific cell type of interest and the thermodynamics of the reactions, determining their direction under cellular conditions. If compartments are distinguished the sub-cellular compartmentation of reactions and enzymes and the membrane transporters exchanging metabolites between cellular compartments must be included. All this information cannot be taken from a single data base but has to be compiled from various Bioinformatics resources. Here we present an approach towards the organization of Bioinformatics data that enables the flux-balance analysis of comprehensive compartmentalized metabolic networks of eukaryotic cells with special focus on human hepatocytes.
Gille
Christoph
C
Medical School (Charité), Institute of Biochemistry, Humboldt University Berlin, Monbijoustrasse 2, 10117 Berlin, Germany. christoph.gille@charite.de
Hoffmann
Sabrina
S
Holzhütter
Hermann-Georg
HG
D001219:Aspartate Aminotransferases / Q000378:metabolism; D002451:Cell Compartmentation; D002468:Cell Physiological Phenomena; D002477:Cells / Q000201:enzymology / Q000378:metabolism; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D003625:Data Collection; D016208:Databases, Factual; D004798:Enzymes / Q000378:metabolism; D005057:Eukaryotic Cells / Q000502:physiology*; D022781:Hepatocytes / Q000201:enzymology* / Q000378:metabolism*; D006801:Humans; D020407:Internet; D008954:Models, Biological; D012984:Software; D013347:Subcellular Fractions / Q000737:chemistry; D013816:Thermodynamics; D014584:User-Computer Interface
D004798:Enzymes; D001219:Aspartate Aminotransferases