Team:Newcastle/Modelling/Degradation

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. Hence the width of the pulse for Hin expression can easily be adjusted by arabinose.

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



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



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



The reason for this decrease is very obvious. Arabinose binds to AraR protein which normally repress SppB expression and SspB expression increases. As a result Hin proteins are targeted for degradation.



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.



The diagran below shows the concentration of total Hin proteins (proteins that are free and bound to sspB) against SspB protein. X-axis represents SspB and Y-axis represents Hin. As it can be seen when SspB reached to its maximum level, Hin has its the lowest values,



We also wanted to investigate how different levels of arabinose effect the system. In the diagram below each line represents Hin levels against different arabinose concentration. Arabinose levels are changed between 0nM and 10000nM with 20 intervals with 500nM interval step. The top line is when the arabinose concentration is 0nM and the bottom line is when arabinose concenration 10000nM. In the later case, Hin proteins are degraded in 7-8 minutes.



Finally this animation shows the increase and decrease in each species' concentration. The volume of the balls corerspond to their concentrations.



Reactions
We used COPASI to prepare this model. The tool has its own format to represent the recations.
 * ->:Irreversible reactions
 * = :Reversible reactions
 * Modifiers are listed after ; character



Model
Model can be downloaded in SBML format.

SBML Model