title: Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
abstract: Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.
authors.affiliation: Joint Center for Molecular Modeling (JCMM), Burnham Institute for Medical Research, La Jolla, CA 92037, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.forename: Ines
authors.initials: I
authors.lastname: Thiele
authors.forename: Dana
authors.initials: D
authors.lastname: Weekes
authors.forename: Zhanwen
authors.initials: Z
authors.lastname: Li
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaroszewski
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Ginalski
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.forename: John
authors.initials: J
authors.lastname: Wooley
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.forename: Bernhard
authors.initials: B
authors.lastname: Palsson
authors.forename: Andrei
authors.initials: A
authors.lastname: Osterman
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D049490:Systems Biology; D020124:Thermotoga maritima / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004798:Enzymes