Effects of small particle numbers on long-term behaviour in discrete biochemical systems

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Abstract
Motivation: The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. Results: We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. Availability and implementation:http://www.biosys.uni-jena.de/Services.html. Contact:bashar.ibrahim@uni-jena.de or dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online.

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