Dudziuk2019 - Biologically sound formal model of Hsp70 heat induction

  public model
Model Identifier
BIOMD0000000843
Short description
This is a mathematical model of Hsp70 induction. To model heat shock effects, the model incorporates temperature dependencies in transcirption to Hsp70 mRNA and in dissociation of transcriptional complexes, in addition to a formal expression relating temperature to protein denaturation.
Format
SBML (L2V4)
Related Publication
  • Biologically sound formal model of Hsp70 heat induction.
  • Dudziuk G, Wronowska W, Gambin A, Szymańska Z, Rybiński M
  • Journal of theoretical biology , 10/ 2019 , Volume 487 , pages: 74-101 , PubMed ID: 31181241
  • ICM, University of Warsaw, ul. Tyniecka 15/17, Warsaw 02-630, Poland. Electronic address: g.dudziuk@icm.edu.pl.
  • A proper response to rapid environmental changes is essential for cell survival and requires efficient modifications in the pattern of gene expression. In this respect, a prominent example is Hsp70, a chaperone protein whose synthesis is dynamically regulated in stress conditions. In this paper, we expand a formal model of Hsp70 heat induction originally proposed in previous articles. To accurately capture various modes of heat shock effects, we not only introduce temperature dependencies in transcription to Hsp70 mRNA and in dissociation of transcriptional complexes, but we also derive a new formal expression for the temperature dependence in protein denaturation. We calibrate our model using comprehensive sets of both previously published experimental data and also biologically justified constraints. Interestingly, we obtain a biologically plausible temperature dependence of the transcriptional complex dissociation, despite the lack of biological constraints imposed in the calibration process. Finally, based on a sensitivity analysis of the model carried out in both deterministic and stochastic settings, we suggest that the regulation of the binding of transcriptional complexes plays a key role in Hsp70 induction upon heat shock. In conclusion, we provide a model that is able to capture the essential dynamics of the Hsp70 heat induction whilst being biologically sound in terms of temperature dependencies, description of protein denaturation and imposed calibration constraints.
Contributors
Grzegorz, Johannes Meyer, Krishna Kumar Tiwari

Metadata information

hasProperty
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated


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Dudziuk2019.xml SBML L2V4 Representation of Dudziuk2019 - Biologically sound formal model of Hsp70 heat induction 76.17 KB Preview | Download

Additional files

Dudziuk2019.sedml SED-ML file of Dudziuk2019 - Biologically sound formal model of Hsp70 heat induction 6.82 KB Preview | Download
Dudziuk2019.cps COPASI file of Dudziuk2019 - Biologically sound formal model of Hsp70 heat induction 102.61 KB Preview | Download

  • Model originally submitted by : Grzegorz
  • Submitted: Jun 28, 2019 10:38:23 AM
  • Last Modified: Nov 7, 2019 12:49:15 PM
Revisions
  • Version: 7 public model Download this version
    • Submitted on: Nov 7, 2019 12:49:15 PM
    • Submitted by: Johannes Meyer
    • With comment: Automatically added model identifier BIOMD0000000843
  • Version: 5 public model Download this version
    • Submitted on: Jun 28, 2019 10:38:23 AM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Submitted for public release
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Curator's comment:
(added: 07 Nov 2019, 12:48:51, updated: 07 Nov 2019, 12:48:51)
Reproduced plot of Figure D3 in the original publication. Model simulated and data obtained using COPASI 4.24 (Build 197). Plot produced using Wolfram Mathematica 11.3.