InterJournal Complex Systems, 366
Status: Accepted
Manuscript Number: [366]
Submission Date: 501
Revised On: 10305
Modelling bacterial hyperstructures with cellular automata
Author(s): Lois Le Sceller ,Camille Ripoll ,Maurice Demarty ,Armelle Cabin-Flamand ,Thomas Nystrom ,Milton Saier ,Vic Norris

Subject(s): CX.04.02.4, BG.51

Category: Article

Abstract:

The physiology of prokaryotic and eukaryotic cells has been proposed to be determined at the level of hyperstructures [Norris et al. 1999] or modules [Hartwell et al. 1999] that would constitute a level intermediate between macromolecules and whole cells. Non-equilibrium hyperstructures include assemblies of genes, mRNA, enzymes and lipids brought together to fulfil a particular function and dismissed when no longer needed [Norris, et al. 1999]. For example, enzymes in the same or related metabolic pathways that are actively engaged in processing their substrates may have an increased probability of co-localization. To determine the values of the parameters governing the formation of hyperstructures in the membrane and cytoplasm of bacteria, we have constructed a program that, in its present version, simulates the dynamics of the formation of hyperstructures comprising enzymes responsible for the transport and metabolism of sugars due to changes in the affinities of its enzymes for one another. These changes result from the binding of enzymes to their substrates and result in increased diffusion coefficients [Norris et al. 1999]. In essence, the program uses cellular automata to represent both the cytoplasm in 3-D and the surrounding cytoplasmic membrane in 2-D. Each unit volume of the bacterium corresponds to a cellular automaton that can contain an enzyme (or, according to the size of the unit volume, another molecule such as a lipid or a stretch of nucleic acid). The diffusion process of each enzyme in either the membrane or the cytoplasm is based on models of the diffusion of gas molecules on lattices. Up to 20 different types of enzymes in the cytoplasm and 1 type of membrane receptor can be studied using this program which we have applied here to the relatively well-understood system of glucose transport and metabolism in Escherichia coli [Saier 2000].

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