Team:KULeuven/Model/Cell Death

From 2008.igem.org

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[[Image:CellDeath_CellDesigner_new.png|800px|center|Cell Death]]
[[Image:CellDeath_CellDesigner_new.png|800px|center|Cell Death]]
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==== Matlab ([ SBML file])====
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==== Matlab ([https://static.igem.org/mediawiki/2008/3/36/CellDeath_Matlab_Final.zip SBML file])====
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[[Image:CellDeath_Matlab_Final.jpg|800px|center|Cell Death]]

Revision as of 13:37, 22 August 2008

  dock/undock dropdown  

Pictogram celldeath.png

Contents

Cell Death

Position in the system

The Cell Death subsystem receives input from two other subsystems, namely:

LuxR is the component repressing the regulation of CcdB, the toxic product causing cell death. There the LuxR production is constitutive, no protein controls the gene regulation of LuxR, but the amount of LuxR available to repress the transcripion of the CcdB gene is controlled by HSL (Homoserine lactone).

If the inverter subsystem produces HSL (occurs when no light is detectable), this will forms a complex with LuxR. This will diminish the amount of LuxR available to repress the CcdB transcription and initiate cell death. When waiting long enough the amount of HSL becomes critical.

If however the pulse generator becomes active (by the filter), it will produce a pulse of lactonase, which will then bind to the HSL, reacting to an hydroxy-acid. As opposed to HSL, this hydroxy-acid will no longer form a complex with LuxR. This increase in LuxR lowers the CcdB production. The challenge is to generate a pulse of lactonase high enough to neutralise all HSL present in the cell.

Describing the system

Cell Death.jpg

ODE's

Parameters

Remark: update parameters to repressive promotor

Parameter values (Cell Death)
Name Value Comments Reference
Degradation Rates
dLuxR 0.0010 s-1
dLuxR_HSL 0.0010 s-1 complex of HSL and LuxR degrades, giving back HSL
dRNA_LuxR 0.00227 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dCcdB 7.7E-5 s-1 [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
dRNA_CcdB 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dHSL 1.02E-6 s-1 [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Association/Dissociation/Reaction Rates
kass (HSL+LuxR) 1E6 s-1 association rate of HSL with LuxR. Chosen to be relatively (to the other rate constants) high and such that Kdiss (HSL + LuxR) equals 10-6
kdiss (HSL+LuxR) 1 s-1 dissociation rate of the HSL-LuxR complex
kass (HSL+lactonase) 1E6 s-1 association rate of HSL with lactonase
kdiss (HSL+lactonase) 446.5 s-1 dissociation rate of the HSL-lactonase complex
kcat (HSL:hydroxy-acid) 29 s-1 catalytic transformation of HSL to an hydroxy-acid, lactonase is the enzyme [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]
Dissociation Constants
KHSL_LuxR 1E-6 [M]/L kdiss / kass (HSL+LuxR) [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
KHSL_LuxR 4.05E-6 [M]/L binding HSL_LuxR on LuxPromotor [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]
Hill Cooperativity
nHSL_LuxR 2.08 [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]
Transcription Rates
kmRNA_LuxR (constitutive promotor) 0.025 s-1 see Constitutive Promotors & E. coli transcription Rates
kmRNA_CcdB 0.025 s-1 maximal transcription rate for CcdB RNA (no LuxR repressor present)

[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6T39-3Y6HKD6-BK-1&_cdi=4941&_user=877992&_orig=search&_coverDate=08%2F30%2F1995&_sk=998379998&view=c&wchp=dGLbVtz-zSkzS&md5=49efd14150c71e668eabdef225220ce3&ie=/sdarticle.pdf This paper] says that synthesis of even a few molecules of the shorter CcdB protein is probably lethal.

Models

CellDesigner (SBML file)

Cell Death

Matlab (SBML file)

Remark: not yet up to date to latest (final) version

Cell Death


Simulations

todo

Sensitivity Analysis

todo

New Cell Death

Describing the system

ODE's

parameters

Parameter values (Cell Death)
Name Value Comments Reference
Degradation Rates
dLuxR 0.0010 s-1
dLuxR_HSL 0.0010 s-1 complex of HSL and LuxR degrades, giving back HSL
dRNA_LuxR 0.00227 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dCcdB 7.7E-5 s-1 [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
dRNA_CcdB 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dHSL 1.02E-6 s-1 [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Association/Dissociation/Reaction Rates
kass (HSL+LuxR) 1E6 s-1 association rate of HSL with LuxR. Chosen to be relatively (to the other rate constants) high and such that Kdiss (HSL + LuxR) equals 10-6
kdiss (HSL+LuxR) 1 s-1 dissociation rate of the HSL-LuxR complex
kass (HSL+lactonase) 1E6 s-1 association rate of HSL with lactonase
kdiss (HSL+lactonase) 446.5 s-1 dissociation rate of the HSL-lactonase complex
kcat (HSL:hydroxy-acid) 29 s-1 catalytic transformation of HSL to an hydroxy-acid, lactonase is the enzyme [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]
Dissociation Constants
KHSL_LuxR 1E-6 [M]/L kdiss / kass (HSL+LuxR) [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
KHSL_LuxR 4.05E-6 [M]/L binding HSL_LuxR on LuxPromotor [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]
Hill Cooperativity
nHSL_LuxR 2.08 [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]
Transcription Rates
kmRNA_LuxR (constitutive promotor) 0.025 s-1 see Constitutive Promotors & E. coli transcription Rates
kmRNA_CcdB 0.025 s-1 maximal transcription rate for CcdB RNA (no LuxR repressor present)

Models

CellDesigner (SBML file)

Cell Death

Matlab (SBML file)

Cell Death
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