The structure of MESSI biological systems
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Abstract: We introduce a general framework for biological systems, called MESSI systems, that describe Modifications of type Enzyme-Substrate or Swap with Intermediates, and we prove general results based on the network structure. Many post-translational modification networks are MESSI systems. For example: the motifs in [Feliu and Wiuf (2012a)], sequential distributive and processive multisite phosphorylation networks, most of the examples in [Angeli et al. (2007)], phosphorylation cascades, two component systems as in [Kothamachu et al. (2015)], the bacterial EnvZ/OmpR network in [Shinar and Feinberg (2010)], and all linear networks. We show that, under mass-action kinetics, MESSI systems are conservative. We simplify the study of steady states of these systems by explicit elimination of intermediate complexes and we give conditions to ensure an explicit rational parametrization of the variety of steady states (inspired by [Feliu and Wiuf (2013a, 2013b), Thomson and Gunawardena (2009)]). We define an important subclass of MESSI systems with toric steady states [P'erez Mill'an et al. (2012)] and we give for MESSI systems with toric steady states an easy algorithm to determine the capacity for multistationarity. In this case, the algorithm provides rate constants for which multistationarity takes place, based on the theory of oriented matroids.
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Cited in
(34)- Gröbner bases of reaction networks with intermediate species
- Families of polynomials in the study of biochemical reaction networks
- Parametric toricity of steady state varieties of reaction networks
- Symbolic analysis of multiple steady states in a MAPK chemical reaction network
- Identifiability from a few species for a class of biochemical reaction networks
- Monostationarity and multistationarity in tree networks of Goldbeter-Koshland loops
- Testing binomiality of chemical reaction networks using comprehensive Gröbner systems
- Regions of multistationarity in cascades of Goldbeter-Koshland loops
- Multistationarity questions in reduced versus extended biochemical networks
- Multistationarity in the space of total concentrations for systems that admit a monomial parametrization
- Parameter regions that give rise to \(2\lfloor \frac{n}{2} \rfloor +1\) positive steady states in the \(n\)-site phosphorylation system
- Algebra and geometry in the study of enzymatic cascades
- Joining and decomposing reaction networks
- The multistationarity structure of networks with intermediates and a binomial core network
- Efficiently and effectively recognizing toricity of steady state varieties
- The kinetic space of multistationarity in dual phosphorylation
- Bistability of sequestration networks
- Identifying the parametric occurrence of multiple steady states for some biological networks
- Transition graph decomposition for complex balanced reaction networks with non-mass-action kinetics
- Parameter Region for Multistationarity in \({\boldsymbol{n-}}\)Site Phosphorylation Networks
- MESSI
- Graph-based, dynamics-preserving reduction of (bio)chemical systems
- A deficiency-based approach to parametrizing positive equilibria of biochemical reaction systems
- Sign-sensitivities for reaction networks: an algebraic approach
- Multistability of small zero-one reaction networks
- Absolute concentration robustness: algebra and geometry
- Lower bounds for positive roots and regions of multistationarity in chemical reaction networks
- Analysis of mass-action systems by split network translation
- Emergence of oscillations in a mixed-mechanism phosphorylation system
- Computing weakly reversible deficiency zero network translations using elementary flux modes
- Multistationarity in structured reaction networks
- Symbolic Proof of Bistability in Reaction Networks
- Maximum likelihood estimation of log-affine models using detailed-balanced reaction networks
- Homeostasis and injectivity: a reaction network perspective
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