Team:Freiburg/Modeling/Parameter analysis
From 2008.igem.org
(Difference between revisions)
Line 42: | Line 42: | ||
<tr> | <tr> | ||
<td> | <td> | ||
- | [[image:Freiburg2008_TR_SIA@r.png|thumb|left|400px]] | + | [[image:Freiburg2008_TR_SIA@r.png|thumb|left|400px|'''Figure 2:''' TCR densities in time for a set of parameters]] |
</td> | </td> | ||
<td> | <td> | ||
Line 79: | Line 79: | ||
<br><br> | <br><br> | ||
In the calculations for the plots below the same parameters as above were chosen except for '''k'''<sub>on</sub> repectively '''k'''<sub>don</sub>. The black lines represents active TCR densities in time for different '''k'''<sub>on</sub> repectively '''k'''<sub>don</sub>. | In the calculations for the plots below the same parameters as above were chosen except for '''k'''<sub>on</sub> repectively '''k'''<sub>don</sub>. The black lines represents active TCR densities in time for different '''k'''<sub>on</sub> repectively '''k'''<sub>don</sub>. | ||
- | |||
<table> | <table> | ||
<tr> | <tr> | ||
- | < | + | <td>[[image:Freiburg2008_TA_Kon_0-2.png|thumb|400px'''Figure 3.1:''' TCR activity in time for different binding rates (k<sub>on</sub>)]]</td> <td></td> |
- | < | + | <td>[[image:Freiburg2008_TA_Kdon_0-2.png|thumb|400px'''Figure 3.2:''' TCR activity in time for different dimerization rates rates (k<sub>don</sub>)]]</td> |
</tr> | </tr> | ||
</table> | </table> | ||
- | |||
- | |||
- | |||
Increasing the binding rate gives a little higher active TCR densities than increasing the dimerization rate in the same way. | Increasing the binding rate gives a little higher active TCR densities than increasing the dimerization rate in the same way. | ||
<br><br><br> | <br><br><br> | ||
Line 98: | Line 94: | ||
<td> | <td> | ||
low NIP amount: | low NIP amount: | ||
- | [[image:Freiburg_08_TA_lowNIP.png|thumb|left|400px| | + | [[image:Freiburg_08_TA_lowNIP.png|thumb|left|400px|'''Figure 4:''' Active TCR density in time with low NIP Amount (5% of initial TCR in membrane)]] |
</td> | </td> | ||
<td> | <td> | ||
Line 126: | Line 122: | ||
The TCR activity is low when the NIP amount or concentration is low. With an unsufficient amount of NIP many TCRs remain unbound, thus dimerization is low, so the activity remains lower, too. | The TCR activity is low when the NIP amount or concentration is low. With an unsufficient amount of NIP many TCRs remain unbound, thus dimerization is low, so the activity remains lower, too. | ||
<br><br> | <br><br> | ||
+ | <table> | ||
+ | <tr> | ||
+ | <td> | ||
high NIP amount: <br> | high NIP amount: <br> | ||
- | [[image: | + | [[image:Freiburg2008_TA_highNIP.png|thumb|left|400px|'''Figure 5:'''Active TCR density in time with high NIP Amount (30% of initial TCR in membrane)]] |
+ | </td> | ||
+ | <td> | ||
chosen parameters:<br> | chosen parameters:<br> | ||
<font color="#336600"> | <font color="#336600"> | ||
Line 148: | Line 149: | ||
TA0 = 0; % active TCR density; | TA0 = 0; % active TCR density; | ||
</font> | </font> | ||
- | < | + | </td> |
+ | </tr> | ||
+ | </table> | ||
An addition of a high NIP amount leads to high TCR activity, as more TCR-NIP complexes are build and hence more dimers. | An addition of a high NIP amount leads to high TCR activity, as more TCR-NIP complexes are build and hence more dimers. | ||
<br><br> | <br><br> | ||
TCR activity for different amount of NIP (other parameters as in the previous plot): | TCR activity for different amount of NIP (other parameters as in the previous plot): | ||
- | [[image: | + | <table> |
- | < | + | <tr> |
+ | <td> | ||
+ | [[image:Freiburg2008_TA_NIPs.png|thumb|left|400px|'''Figure 6:'''Active TCR density in time with different NIP amounts]] | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
The higher the amount of NIP is, the higher is the activity. | The higher the amount of NIP is, the higher is the activity. | ||
- | + | <br><br> | |
<h4>TCR activity dependent on exchange between spare and interface pool </h4> | <h4>TCR activity dependent on exchange between spare and interface pool </h4> | ||
<br><br> | <br><br> | ||
The TCR can switch from a non-binding state to a binding state or in other words, the TCRs in the spare pool can become TCRs in the interface pool. This exchange is regulated by the parameters '''λ''' and '''φ'''. '''λ''' is a ratio between the spare and the interface pool and '''φ''' is the exchange rate constant<br><br> | The TCR can switch from a non-binding state to a binding state or in other words, the TCRs in the spare pool can become TCRs in the interface pool. This exchange is regulated by the parameters '''λ''' and '''φ'''. '''λ''' is a ratio between the spare and the interface pool and '''φ''' is the exchange rate constant<br><br> | ||
+ | <table> | ||
+ | <tr> | ||
+ | <td> | ||
low exchange: | low exchange: | ||
- | [[image:Freiburg_08_lowE.png|thumb|left| | + | [[image:Freiburg_08_lowE.png|thumb|left|400px|'''Figure 7:''' Active TCR density in time (low exchange: λ=5 and φ=0.05)]] |
- | chosen parameters: | + | </td> |
+ | <td> | ||
+ | chosen parameters: | ||
<font color="#336600"> | <font color="#336600"> | ||
s = 0.1; % turnover rate | s = 0.1; % turnover rate | ||
Line 182: | Line 195: | ||
TA0 = 0; % active TCR density; | TA0 = 0; % active TCR density; | ||
</font> | </font> | ||
- | < | + | </td> |
+ | </tr> | ||
+ | </table> | ||
For a very high ratio λ and a low exchange rate φ the ratio of the spare pool (non-binding TCR) to the interface pool (binding TCR) is high and the switching of a TCR between the non-binding and the binding state is low. Thus there is a low TCR activity because not enough TCRs are accessible by NIP. This can be compared with TCRs which are surrounded by big sized proteins who avoid a TCR-NIP formation. | For a very high ratio λ and a low exchange rate φ the ratio of the spare pool (non-binding TCR) to the interface pool (binding TCR) is high and the switching of a TCR between the non-binding and the binding state is low. Thus there is a low TCR activity because not enough TCRs are accessible by NIP. This can be compared with TCRs which are surrounded by big sized proteins who avoid a TCR-NIP formation. | ||
- | < | + | <table> |
+ | <tr> | ||
+ | <td> | ||
high exchange: <br> | high exchange: <br> | ||
- | [[image:Freiburg_08_highE.png|thumb|left| | + | [[image:Freiburg_08_highE.png|thumb|left|400px|'''Figure 8:'''Active TCR density in time (high exchange: λ=0.2 and φ=5)]] |
+ | </td> | ||
+ | </tr> | ||
chosen parameters:<br> | chosen parameters:<br> | ||
<font color="#336600"> | <font color="#336600"> | ||
Line 207: | Line 226: | ||
TA0 = 0; % active TCR density; | TA0 = 0; % active TCR density; | ||
</font> | </font> | ||
- | < | + | </td> |
+ | </tr> | ||
+ | </table> | ||
A low ratio λ and a high exchange rate φ leads to a high TCR activity as enough TCRs are available in the interface pool for NIP binding. The fast changing from the non-binding to the binding state assures a sufficient amount of TCRs for TCR-NIP and then dimer formation.<br><br> | A low ratio λ and a high exchange rate φ leads to a high TCR activity as enough TCRs are available in the interface pool for NIP binding. The fast changing from the non-binding to the binding state assures a sufficient amount of TCRs for TCR-NIP and then dimer formation.<br><br> | ||
Revision as of 17:45, 27 October 2008