Literature DB >> 24334389

Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws.

Adám M Halász1, Hong-Jian Lai1, Meghan McCabe Pryor2, Krishnan Radhakrishnan3, Jeremy S Edwards4.   

Abstract

True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady-state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here, we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher-dimensional space. We show that the linearized version of the steady-state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1.

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Year:  2013        PMID: 24334389      PMCID: PMC4090023          DOI: 10.1109/TCBB.2013.41

Source DB:  PubMed          Journal:  IEEE/ACM Trans Comput Biol Bioinform        ISSN: 1545-5963            Impact factor:   3.710


  28 in total

1.  Heterogeneities in EGF receptor density at the cell surface can lead to concave up scatchard plot of EGF binding.

Authors:  Kapil Mayawala; Dionisios G Vlachos; Jeremy S Edwards
Journal:  FEBS Lett       Date:  2005-06-06       Impact factor: 4.124

2.  Quantifying crosstalk among interferon-γ, interleukin-12, and tumor necrosis factor signaling pathways within a TH1 cell model.

Authors:  David J Klinke; Ning Cheng; Emily Chambers
Journal:  Sci Signal       Date:  2012-04-17       Impact factor: 8.192

3.  Quantification of short term signaling by the epidermal growth factor receptor.

Authors:  B N Kholodenko; O V Demin; G Moehren; J B Hoek
Journal:  J Biol Chem       Date:  1999-10-15       Impact factor: 5.157

4.  Spatio-temporal modeling of signaling protein recruitment to EGFR.

Authors:  Ming-yu Hsieh; Shujie Yang; Mary Ann Raymond-Stinz; Jeremy S Edwards; Bridget S Wilson
Journal:  BMC Syst Biol       Date:  2010-05-06

5.  Stochastic simulations of ErbB homo and heterodimerisation: potential impacts of receptor conformational state and spatial segregation.

Authors:  M-Y Hsieh; S Yang; M A Raymond-Stinz; S Steinberg; D G Vlachos; W Shu; B Wilson; J S Edwards
Journal:  IET Syst Biol       Date:  2008-09       Impact factor: 1.615

Review 6.  Systems biology of vascular endothelial growth factors.

Authors:  Feilim Mac Gabhann; Aleksander S Popel
Journal:  Microcirculation       Date:  2008-11       Impact factor: 2.628

7.  Sensitivity analysis predicts that the ERK-pMEK interaction regulates ERK nuclear translocation.

Authors:  K Radhakrishnan; J S Edwards; D S Lidke; T M Jovin; B S Wilson; J M Oliver
Journal:  IET Syst Biol       Date:  2009-09       Impact factor: 1.615

8.  Monotone and near-monotone biochemical networks.

Authors:  Eduardo D Sontag
Journal:  Syst Synth Biol       Date:  2007-07-04

9.  Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction.

Authors:  Michelle N Costa; Krishnan Radhakrishnan; Bridget S Wilson; Dionisios G Vlachos; Jeremy S Edwards
Journal:  PLoS One       Date:  2009-07-23       Impact factor: 3.240

10.  An empirical Bayesian approach for model-based inference of cellular signaling networks.

Authors:  David J Klinke
Journal:  BMC Bioinformatics       Date:  2009-11-09       Impact factor: 3.169

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  4 in total

1.  The impact of high density receptor clusters on VEGF signaling.

Authors:  Ye Chen; Christopher Short; Adám M Halász; Jeremy S Edwards
Journal:  Electron Proc Theor Comput Sci       Date:  2013

2.  A technique for determining the signs of sensitivities of steady states in chemical reaction networks.

Authors:  Eduardo D Sontag
Journal:  IET Syst Biol       Date:  2014-12       Impact factor: 1.615

3.  Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

Authors:  Marcus Rosenblatt; Jens Timmer; Daniel Kaschek
Journal:  Front Cell Dev Biol       Date:  2016-05-11

4.  Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.

Authors:  Anna Fiedler; Sebastian Raeth; Fabian J Theis; Angelika Hausser; Jan Hasenauer
Journal:  BMC Syst Biol       Date:  2016-08-22
  4 in total

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