title: A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency.
abstract: BACKGROUND
  The advantages of grouping enzymes into metabolons and into higher order structures have long been debated. To quantify these advantages, we have developed a stochastic automaton that allows experiments to be performed in a virtual bacterium with both a membrane and a cytoplasm. We have investigated the general case of transport and metabolism as inspired by the phosphoenolpyruvate:sugar phosphotransferase system (PTS) for glucose importation and by glycolysis.
  
  
  RESULTS
  We show that PTS and glycolytic metabolons can increase production of pyruvate eightfold at low concentrations of phosphoenolpyruvate. A fourfold increase in the numbers of enzyme EI led to a 40% increase in pyruvate production, similar to that observed in vivo in the presence of glucose. Although little improvement resulted from the assembly of metabolons into a hyperstructure, such assembly can generate gradients of metabolites and signaling molecules.
  
  
  CONCLUSIONS
  in silico experiments may be performed successfully using stochastic automata such as HSIM (Hyperstructure Simulator) to help answer fundamental questions in metabolism about the properties of molecular assemblies and to devise strategies to modify such assemblies for biotechnological ends.
authors: Epigenomics Programme, genopole, 91000 Evry, France. Patrick.Amar@lri.fr
authors: Patrick
authors: P
authors: Amar
authors: Guillaume
authors: G
authors: Legent
authors: Michel
authors: M
authors: Thellier
authors: Camille
authors: C
authors: Ripoll
authors: Gilles
authors: G
authors: Bernot
authors: Thomas
authors: T
authors: Nystrom
authors: Milton H
authors: MH
authors: Saier
authors: Vic
authors: V
authors: Norris
mesh_terms: D003198:Computer Simulation; D006019:Glycolysis / Q000502:physiology*; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000378:metabolism*; D019289:Pyruvic Acid / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D013269:Stochastic Processes
chemical_list: D019289:Pyruvic Acid; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System