Team:Newcastle/Modelling/Degradation

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We assumed that the species have the following inital concentrations. We took these values by running the model when there is no arabinose.
[[Image:Team_Newcastle_iGEM_2009_Degradation_Model_1.png|400px]]
[[Image:Team_Newcastle_iGEM_2009_Degradation_Model_1.png|400px]]
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When the arabinose concentration is increased to 1000nM, Hin levels decrease sharply in 15 minutes.
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[[Image:Team_Newcastle_iGEM_2009_Degradation_Model_2.png|400px]]
[[Image:Team_Newcastle_iGEM_2009_Degradation_Model_2.png|400px]]
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The reaosn for this decrease is very obvious. Arabibose binds to AraR protein which normally repress sppB expression and sspB exprssion increases. As a result Hin proteins are targeted for degradation.
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[[Image:Team_Newcastle_iGEM_2009_Degradation_Model_3.png|400px]]
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We haven't gone into much detail about the rate parameters of the ClpXP degradation system. We assumed that the system would degrade a 0.2 protein per second. However we changed this parameter between 0.1 and 0,8 at 100 intervals. Range of sspB and Hin concentrations are displayed below against 100 different values of the protein degradation speed of ClpXP system.
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Revision as of 13:41, 17 October 2009

Degradation Model

We used the degradation as another control in our Stochastic Switch construct in additon to IPTG and Xylose. While IPTG and Xylose control the expression of Hin, we designed an arabinose inducable degradation for Hin protein.

SspB protein regulated by arabinose binds to the modified ssrA tag and targets the Hin for degradation by ClpXP system.

Team Newcastle iGEM 2009 Degradation Model 7.png

We assumed that the species have the following inital concentrations. We took these values by running the model when there is no arabinose.

Team Newcastle iGEM 2009 Degradation Model 1.png

When the arabinose concentration is increased to 1000nM, Hin levels decrease sharply in 15 minutes.

Team Newcastle iGEM 2009 Degradation Model 2.png

The reaosn for this decrease is very obvious. Arabibose binds to AraR protein which normally repress sppB expression and sspB exprssion increases. As a result Hin proteins are targeted for degradation.

Team Newcastle iGEM 2009 Degradation Model 3.png

We haven't gone into much detail about the rate parameters of the ClpXP degradation system. We assumed that the system would degrade a 0.2 protein per second. However we changed this parameter between 0.1 and 0,8 at 100 intervals. Range of sspB and Hin concentrations are displayed below against 100 different values of the protein degradation speed of ClpXP system.

Team Newcastle iGEM 2009 Degradation Model 4.png


Team Newcastle iGEM 2009 Degradation Model 5.png Team Newcastle iGEM 2009 Degradation Model 6.png Team Newcastle iGEM 2009 Degradation Model 8.gif



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