A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency.

Patrick Amar 1, * Guillaume Legent Michel Thellier Camille Ripoll 2 Gilles Bernot 3 Thomas Nystrom Milton H Saier Vic Norris
* Corresponding author
1 LRI - Laboratoire de Recherche en Informatique
2 GTCV - Glycobiologie et transports chez les végétaux
3 Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe BIOINFO
Laboratoire I3S - MDSC - Modèles Discrets pour les Systèmes Complexes
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. CONCLUSION: 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.
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https://hal.inria.fr/hal-00643746
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Submitted on : Tuesday, November 22, 2011 - 4:51:12 PM
Last modification on : Tuesday, December 17, 2019 - 2:07:30 AM

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Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, et al.. A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency.. BMC Systems Biology, BioMed Central, 2008, 2, pp.27. ⟨10.1186/1752-0509-2-27⟩. ⟨hal-00643746⟩

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