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Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains

Petrides, A and Vinnicombe, G (2018) Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains. PLoS Computational Biology, 14. e1006107-. ISSN 1553-734X

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Abstract

© 2018 Petrides, Vinnicombe. http://creativecommons.org/licenses/by/4.0/ This paper is concerned with the potential multistability of protein concentrations in the cell. That is, situations where one, or a family of, proteins may sit at one of two or more different steady state concentrations in otherwise identical cells, and in spite of them being in the same environment. For models of multisite protein phosphorylation for example, in the presence of excess substrate, it has been shown that the achievable number of stable steady states can increase linearly with the number of phosphosites available. In this paper, we analyse the consequences of adding enzyme docking to these and similar models, with the resultant sequestration of phosphatase and kinase by the fully unphosphorylated and by the fully phosphorylated substrates respectively. In the large molecule numbers limit, where deterministic analysis is applicable, we prove that there are always values for these rates of sequestration which, when exceeded, limit the extent of multistability. For the models considered here, these numbers are much smaller than the affinity of the enzymes to the substrate when it is in a modifiable state. As substrate enzyme-sequestration is increased, we further prove that the number of steady states will inevitably be reduced to one. For smaller molecule numbers a stochastic analysis is more appropriate, where multistability in the large molecule numbers limit can manifest itself as multimodality of the probability distribution; the system spending periods of time in the vicinity of one mode before jumping to another. Here, we find that substrate enzyme sequestration can induce bimodality even in systems where only a single steady state can exist at large numbers. To facilitate this analysis, we develop a weakly chained diagonally dominant M-matrix formulation of the Chemical Master Equation, allowing greater insights in the way particular mechanisms, like enzyme sequestration, can shape probability distributions and therefore exhibit different behaviour across different regimes.

Item Type: Article
Uncontrolled Keywords: Enzymes Molecular Docking Simulation Phosphotransferases Protein Binding Protein Domains Stochastic Processes Substrate Specificity
Subjects: UNSPECIFIED
Divisions: Div F > Control
Depositing User: Cron Job
Date Deposited: 16 Apr 2018 20:10
Last Modified: 24 Oct 2019 14:33
DOI: 10.1371/journal.pcbi.1006107