Team:Newcastle/Modelling/KinAExpression

From 2009.igem.org

(Difference between revisions)
(KinA Expression Model)
(KinA Expression Model)
 
Line 95: Line 95:
<b>The KinA Expression Model is available for download as follows:</b>
<b>The KinA Expression Model is available for download as follows:</b>
-
* [[:Image:KinAExp (SBML and Copasi).zip|KinA Expression Model (SBML and COPASI]]
+
* [[:Image:KinAExp (SBML and Copasi).zip|KinA Expression Model (SBML and COPASI)]]
 +
 
 +
<br>
===Results===
===Results===

Latest revision as of 01:49, 22 October 2009


KinA Expression Model

Under normal conditions, LacI represses KinA.

TeamNewcastleKinAExpLacIKinA.png


However, in the presence of IPTG, KinA can be expressed, as IPTG binds to LacI, deactivating it. Equations (a) and (b) describes how IPTG binds to LacI, forming LacI*, which is the deactivated form of LacI

TeamNewcastleKinAExpLacIIPTG1.png


Over time, the deactivated form of LacI, LacI* may degrade. This is also taken into consideration while building the model.

TeamNewcastleKinAExpDeactivatedLacIDegradation.png


Protein synthesis requires two steps, transcription and translation, and is further illustrated in Figure 1, below.

TeamNewcastleKinAExpTranscriptiontranslation.png
Figure 1: Transcription and Translation


Referring to Figure 1, the following equations can be written:

Transcription of LacI,
TeamNewcastleKinAExpLacITranscription.png


Translation of LacI,
TeamNewcastleKinAExpLacITranslation.png


where mRNA_LacI is inducing the formation of LacI.


Transcription of KinA,
TeamNewcastleKinAExpKinATranscription.png


where LacI is repressing mRNA_KinA, therefore a lower concentration of LacI would result in a higher concentration of mRNA_KinA.


Translation of KinA,
TeamNewcastleKinAExpKinATranslation.png


where mRNA_KinA is inducing the formation of KinA.


As parameters such as transcription and translation rates could not be found in literature, the following equations were used to calculate the transcription and translation rates whenever possible.

TeamNewcastleSporeTuneTranscriptionRate.png


TeamNewcastleSporeTuneTranslationRate.png


Using the transcription and translation rate equations as seen above, the rates were calculated for the components Spo0A, Spo0B, Spo0F and KinA, and the results are reported in the table below.

TeamNewcastleSporeTuneTranscriptionTranslateRate.png
Table 1: Transcription and Translation Rates


For components where information on the CDS length could not be found, we used the value 0.1 for both the translation and transcription rate.

Also, the values for the various rate constants could not be found in literature either. Therefore, the following values were used:

kforward = 0.001

kreverse = 0.05

Other parameters and formulas which were used in this model are as follows:

Protein Degradation Rate = 0.0012

mRNA Degradation Rate = 0.0058


TeamNewcastleSporeTuneFunctions.png
Table 2: Functions used in the KinA Expression and Sporulation Tuning Models


The CDS lengths was found on the [http://www.ncbi.nlm.nih.gov/Genbank/ GenBank] using the accession number, AL009126.

These parameters and functions were also used in the Sporulation Tuning Model.

The KinA Expression Model is available for download as follows:


Results

The above equations were modelled in COPASI, and the following graphs show the behaviour of the system over time at different IPTG concentrations.


IPTG concentration = 1000 nmol/fl
TeamNewcastleKinAExpPic1.png
Figure 1.1


In Figure 1.1, at a IPTG concentration of 1000nmol/fl, due to the high concentration of LacI*, it is difficult to view the results for the other species, such as, KinA, LacI, mRNA_KinA, and mRNA_LacI as they are all concentrated at the bottom.


TeamNewcastleKinAExpPic2.png
Figure 1.2


Figure 1.2 shows the behaviour of KinA, LacI, mRNA_KinA and mRNA_LacI more clearly, at the IPTG concentration of 1000nmol/flu.

From Figure 1.1 and 1.2, it is observed that the concentration of LacI* is significantly higher than the other species when the IPTG concentration is set at 1000nmol/fl. Looking at Figure 1.2, while the concentration of KinA is increasing, it is still lower than that of LacI.


IPTG concentration = 3000 nmol/fl
TeamNewcastleKinAExpPic3.png
Figure 2.1


Comparing Figure 1.1 and 2.1, though the IPTG concentration in Figure 2.1 is 3000nmol/fl, the LacI* concentration is not particularly different.


TeamNewcastleKinAExpPic4.png
Figure 2.2


As the IPTG concentration increases from 1000 to 3000nmol/fl, the KinA concentration is greater than the LacI concentration. However, upon a closer look, the KinA concentration did not increase due to the higher IPTG concentration. The KinA concentration is now higher than the LacI concentration because the LacI concentration decreased.

IPTG concentration = 5000 nmol/fl
TeamNewcastleKinAExpPic5.png
Figure 3.1


Once again, as obsered in Figure 1.1 and 2.1, the concentration of LacI* in Figure 3.1 seems to reach the similar concentrations although the concentration of IPTG has been increased in each case. This seems to say that the concentration of LacI* has reached a threshold concentration.


TeamNewcastleKinAExpPic6.png
Figure 3.2


The KinA concentration in Figure 3.2 is greater than that of LacI once again. However, KinA concentration seems to be stagnant at approximately 90nmol/fl, while the LacI concentration constantly decreases with increased IPTG concentration. Therefore, the IPTG concentration only seems to affect the LacI concentration.


Other Models

See Sporulation Tuning Model
See Sin Operon Model





News

Events

Social Net

  • Newcastle iGEM Twitter
  • [http://www.facebook.com/home.php#/group.php?gid=131709337641 Newcastle on Facebook]
  • [http://www.youtube.com/user/newcastle2009igem Newcastle Youtube Channel]