Bravo2012 - Modelling blood coagulation factor Va inactivation by APC.

  public model
Short description
Mathematical model of blood coagulation factor Va and Va fragment inactivation by APC, reactions with Xa and prothrombinase-prothrombin complex formation.
Format
SBML (L2V4)
Related Publication
  • Modeling of human factor Va inactivation by activated protein C.
  • Bravo MC, Orfeo T, Mann KG, Everse SJ
  • BMC systems biology , 5/ 2012 , Volume 6 , pages: 45
  • Cell and Molecular Biology Program, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
  • Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modeling. Such models can potentially improve the design of therapeutics. The prothrombinase complex (composed of the protease factor (F)Xa and its cofactor FVa) plays a central role in this network as the main producer of thrombin, which catalyses both the activation of platelets and the conversion of fibrinogen to fibrin, the main substances of a clot. A key negative feedback loop that prevents clot propagation beyond the site of injury is the thrombin-dependent generation of activated protein C (APC), an enzyme that inactivates FVa, thus neutralizing the prothrombinase complex. APC inactivation of FVa is complex, involving the production of partially active intermediates and "protection" of FVa from APC by both FXa and prothrombin. An empirically validated mathematical model of this process would be useful in advancing the predictive capacity of comprehensive models of coagulation.A model of human APC inactivation of prothrombinase was constructed in a stepwise fashion by analyzing time courses of FVa inactivation in empirical reaction systems with increasing number of interacting components and generating corresponding model constructs of each reaction system. Reaction mechanisms, rate constants and equilibrium constants informing these model constructs were initially derived from various research groups reporting on APC inactivation of FVa in isolation, or in the presence of FXa or prothrombin. Model predictions were assessed against empirical data measuring the appearance and disappearance of multiple FVa degradation intermediates as well as prothrombinase activity changes, with plasma proteins derived from multiple preparations. Our work integrates previously published findings and through the cooperative analysis of in vitro experiments and mathematical constructs we are able to produce a final validated model that includes 24 chemical reactions and interactions with 14 unique rate constants which describe the flux in concentrations of 24 species.This study highlights the complexity of the inactivation process and provides a module of equations describing the Protein C pathway that can be integrated into existing comprehensive mathematical models describing tissue factor initiated coagulation.
Contributors
Matthew Roberts

Metadata information

isVersionOf
Gene Ontology blood coagulation
isDescribedBy
Curation status
Non-curated
Name Description Size Actions

Model files

Bravo2012.xml SBML L2V4 representation of Bravo2012 - Modelling blood coagulation factor Va inactivation by APC. 61.38 KB Preview | Download

Additional files

fig3C.jpg Figure 3 (solid lines): APC(0) = 5e-10 or 2e-9, Va(0) = 2e-8. tfinal = 1200. 15.21 KB Preview | Download
Bravo2012.cps Model COPASI file. Figure 3 requires reactions from table 1. Figures 4 and 5 require reactions from table 2. Figure 7 requires reactions from table 3. Encoded model contains all reactions and figures can be generated by changing the initial concentrations. Figure 3 (solid lines): APC(0) = 5e-10 or 2e-9, Va(0) = 2e-8. tfinal = 1200. Figure 4: APC(0) = 5e-10 or 2e-9, Va(0) = 200e-12, Xa(0) = 100e-12, Va:Xa(0) or 100e-12 oe 500e-12 or 750e-12, tfinal = 360 Figure 5: APC(0) = 2e-9, Va(0) = 20e-9, Xa*(0) = 30e-9 (?), R12_kon = 2.5e6 or 5e6 or 9.1e6 as opposed to 1.5e8, tfinal = 1200. Figure 7: APC(0) = 2e-9 or 20e-9, Va(0) = 20e-9, PT(0) = 1.4e-6, Va:PT(0) = 0 or 500e-9 or 700e-9, tfinal = 1200. Parameter scan can be used to change initial conditions. 137.72 KB Preview | Download
fig7B.png Figure 7: APC(0) = 2e-9 or 20e-9, Va(0) = 20e-9, PT(0) = 1.4e-6, Va:PT(0) = 0 or 500e-9 or 700e-9, tfinal = 1200. 19.54 KB Preview | Download
fig4B_test.jpg Figure 4: APC(0) = 5e-10 or 2e-9, Va(0) = 200e-12, Xa(0) = 100e-12, Va:Xa(0) = 100e-12 or 500e-12 or 750e-12, tfinal = 360 20.32 KB Preview | Download
fig3D.jpg Figure 3 (solid lines): APC(0) = 5e-10 or 2e-9, Va(0) = 2e-8. tfinal = 1200. 22.88 KB Preview | Download
fig3E.jpg Figure 3 (solid lines): APC(0) = 5e-10 or 2e-9, Va(0) = 2e-8. tfinal = 1200. 21.24 KB Preview | Download

  • Model originally submitted by : Matthew Roberts
  • Submitted: 02-Jul-2018 10:26:09
  • Last Modified: 02-Jul-2018 10:26:09
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 02-Jul-2018 10:26:09
    • Submitted by: Matthew Roberts
    • With comment: Edited model metadata online.