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Classic Odes Parameters

Parameter Name	Value	Unit	Source
AraC synthesis rate vmAraC	12*10-8	mol.L-1.min-1	Yes [1] and explanation 1
Ca synthesis rate vmAraC	2*10-9	mol.L-1.min-1	No, explanation 2
AraC threshold KAraC	0.3*10-6	mol.L-1	No, explanation 3
Ca threshold KCa (for (CRP-cAMP) activation)	0.6*10-6	mol.L-1	No, explanation 3
Ca threshold K'Ca (for AraC* activation)	0.6*10-6	mol.L-1	No, explanation 3
Dissociation constant of cAMP and CRP Kc	10-5	mol.L-1	Yes [2]
Dissociation of arabinose with AraC Kc1	2*10-13	mol.L-1	Yes [3]
Degradation rate of AraC αAraC	6*10-3	min-1	Yes [1]
Degradation rate of Ca αCa	6*10-3	min-1	No, explanation 4
Degradation/exports rate of cAMP αcAMP	2.1	min-1	Yes [4]
Arabinose concentration	10-6	mol.L-1	Chosen by the team
CRP concentration	10-6	mol.L-1	Yes [5] and explanation 1
cAMP import constant η	6*10-1	min-1	No, explanation 5
Catalysis constant kcat	6*135	min-1	No, explanation 6
Hill cooperativity n, η1, η2	1.5	/	No, explanation 7
AraC basal value pAraC	12*10-11	mol.L-1.min-1	No, explanation 1
Ca basal value pAraC	2*10-12	mol.L-1.min-1	No, explanation 1

Explanation 1

Arac and Ca:

Once the production of Arac has been activated, we have:

In addition, we assume that p_Arac ≪v_mArac thus, we get:

In addition we know that the maximum number of copies per cell of Arac is 40, thus

where

Avogadro number and

is E. coli volume. Thus, we have

. Then, we get the value of

.

For the adenylate cyclase, but we assumed that there is less adenylate cyclase in the cell than Arac. Indeed, when there is too much cAMP is inhibits the production of the adenylate cyclase (see reference [6]).

CRP:

We have 1000 copies per cell of CRP, and it’s a constant. Then by the same computation, we make the conversion into mol/L, and we get the value of CRP.

Explanation 2

We don’t know the value of the synthesis rate of adenylate cyclase, but we assume that there is less adenylate cyclase, because if there is a huge amont of adenylate cyclase, there will too much cAMP, and then cAMP will repress the adenylate cyclase production (see reference [6]). For the basal production, we make the same assumption as for Arac.

Explanation 3

Activations by (CRP-cAMP):

To set the value of this parameter, we plotted the concentration of (CRP-cAMP) at t=2000 min as we varied the initial concentration of cAMP:

Evolution of (CRP-cAMP) concentration at t=2000 minutes in function of the initial concentration of cAMP.

We could notice that the maximum value of (CRP-cAMP) varied between 0 and 10^-6 mol/L. The value of the threshold had to be in this range of concentration. Not too low, else it would have meant that the proteins are always produced, and not to high, else the genes would never be expressed. In addition we assumed that arac had to be turned on first and without amplification of cAMP, seing that it is only when arac is expressed the adenylate cyclase is produced.

Remark: when we have [cAMP]>> 10^-6 mol/L=[CRP], we have by the same reasoning as for Arac:

and we have

when [cAMP] increases. Thus, in this case we could be sure that the concentration of (CRP-cAMP) wouldn’t exceed 10^-6 mol/L. In addition, when [cAMP]≤10^-6 mol/L, we also know that because of the value of [CRP], [(CRP-cAMP)] wouldn’t exceed this threshold.

Activation by Arac*:

Same reasoning, we give the same type of graph:

We could set the value of K'_Ca.

Explanation 4

Inspired from Arac. By discussing with the biologists we concluded that Ca is also a stable protein.

Explanation 5

By discussing with the biologists, we assumed that there is around 10 times more cAMP out of the cell than inside the cell.

Explanation 6

In the reference [6], we have k_cat=100 min^-1 in vitro. However, by discussing with the biologists, we assumed that in vivo this value was higher.

Quorum sensing parameters

Explanation 1

We assumed that they wouldn’t be glued together, but not too far at the same time.

Explanation 2

We work above the threshold, because we want to know the speed of the diffusion when we have a detection.

References

[1] Bionumbers. http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=arac&org=

[2] Purification of and properties of the cyclic adenosine 2' ,5'-monophosphate receptor which mediates cyclic adenosine 3',5'-monophosphate dependent gene transcription in E. Coli.
W.B. Aderson, A. B. Schneider, M. Emmer, R.L. Perlman, and I. Pasta

[3] AraC protein, regulation of the L-arabinose operon inEscherichiacoli, and the light switch mechanism of AraC action.
Robert Schleif Biology Department, Johns Hopkins University, Baltimore, MD, USA.

[4] Epstein et Hesse 1975.

[5] Transcriptional regulation shapes the organization of genes on bacterial chromosomes.
Sarath Chandra Janga, Heladia Salgado, Augustino Martinez.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699516/

[6] Regulation of adenylate cyclase in E. coli.
Edith Gstrein-Reider and Manfred Schweiger, Institut fur Biochemie (nat. Fak.), UniversitAt Innsbruck, A-6020 Innsbruck, Austria.

[7] Purification and characterization of adenylate cyclase from E. coli K12.
Yang and Epstein 1983.

[8] Solubility and diffusion coefficient of adenosine 3’ :5’ – monophosphate.
Martin Dworkin and Kenneth H. Keller, 1976.

[9] http://ccdb.wishartlab.com/CCDB/cgi-bin/STAT_NEW.cgi

@@ Line 9: / Line 9: @@
 </br>
-<center><img src="https://static.igem.org/mediawiki/2012/4/44/Tab_parameters.png" alt="" /></center>
+<!--<center><img src="https://static.igem.org/mediawiki/2012/4/44/Tab_parameters.png" alt="" /></center>-->
 <table id="param">
@@ Line 25: / Line 25: @@
 		<td class="colonne2">12*10<span class="exposant">-8</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span>.min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">Yes [1] and explanation 1</td>
+		<td class="colonne4">Yes [1] and <a href="#exp1">explanation 1</a></td>
 	</tr>
 	<tr class="impair">
@@ Line 31: / Line 31: @@
 		<td class="colonne2">2*10<span class="exposant">-9</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span>.min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 2</td>
+		<td class="colonne4">No, <a href="#exp2">explanation 2</a></td>
 	</tr>
 	<tr class="pair">
@@ Line 37: / Line 37: @@
 		<td class="colonne2">0.3*10<span class="exposant">-6</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 3</td>
+		<td class="colonne4">No, <a href="#exp3">explanation 3</a></td>
 	</tr>
 	<tr class="impair">
@@ Line 43: / Line 43: @@
 		<td class="colonne2">0.6*10<span class="exposant">-6</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 3</td>
+		<td class="colonne4">No, <a href="#exp3">explanation 3</a></td>
 	</tr>
 	<tr class="pair">
@@ Line 49: / Line 49: @@
 		<td class="colonne2">0.6*10<span class="exposant">-6</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 3</td>
+		<td class="colonne4">No, <a href="#exp3">explanation 3</a></td>
 	</tr>
 	<tr class="impair">
@@ Line 73: / Line 73: @@
 		<td class="colonne2">6*10<span class="exposant">-3</span></td>
 		<td class="colonne3"><i>min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 4</td>
+		<td class="colonne4">No, <a href="#exp4">explanation 4</a></td>
 	</tr>
 	<tr class="impair">
@@ Line 91: / Line 91: @@
 		<td class="colonne2">10<span class="exposant">-6</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i></td>
-		<td class="colonne4">Yes [5] and explanation 1</td>
+		<td class="colonne4">Yes [5] and <a href="#exp1">explanation 1</a></td>
 	</tr>
 	<tr class="pair">
@@ Line 97: / Line 97: @@
 		<td class="colonne2">6*10<span class="exposant">-1</span></td>
 		<td class="colonne3"><i>min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 5</td>
+		<td class="colonne4">No, <a href="#exp5">explanation 5</a></td>
 	</tr>
 	<tr class="impair">
@@ Line 103: / Line 103: @@
 		<td class="colonne2">6*135</td>
 		<td class="colonne3"><i>min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 6</td>
+		<td class="colonne4">No, <a href="#exp6">explanation 6</a></td>
 	</tr>
 	<tr class="pair">
@@ Line 115: / Line 115: @@
 		<td class="colonne2">12*10<span class="exposant">-11</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i>.<i>min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 1</td>
+		<td class="colonne4">No, <a href="#exp1">explanation 1</a></td>
 	</tr>
 	<tr class="pair">
@@ Line 121: / Line 121: @@
 		<td class="colonne2">2*10<span class="exposant">-12</span></td>
 		<td class="colonne3"><i>mol.L<span class="exposant">-1</span></i>.<i>min<span class="exposant">-1</span></i></td>
-		<td class="colonne4">No, explanation 1</td>
+		<td class="colonne4">No, <a href="#exp1">explanation 1</a></td>
 	</tr>
      </tbody>
@@ Line 129: / Line 129: @@
 </br>
-<h2>Explanation 1</h2>
+<h2 id="exp1">Explanation 1</h2>
 </br>
@@ Line 157: / Line 157: @@
 </br>
 </br>
-<h2>Explanation 2</h2>
+<h2 id="exp2">Explanation 2</h2>
 </br>
 We don’t know the value of the synthesis rate of adenylate cyclase, but we assume that there is less adenylate cyclase, because if there is a huge amont of adenylate cyclase, there will too much cAMP, and then cAMP will repress the adenylate cyclase production (see reference [6]). For the basal production, we make the same assumption as for Arac.
 </br>
 </br>
-<h2>Explanation 3</h2>
+<h2 id="exp3">Explanation 3</h2>
 </br>
 <ul><li><u>Activations by (CRP-cAMP):</u></li></ul>
@@ Line 195: / Line 195: @@
 </br>
 </br>
-<h2>Explanation 4</h2>
+<h2 id="exp4">Explanation 4</h2>
 </br>
 Inspired from Arac. By discussing with the biologists we concluded that Ca is also a stable protein.
 </br>
 </br>
-<h2>Explanation 5</h2>
+<h2 id="exp5">Explanation 5</h2>
 </br>
 By discussing with the biologists, we assumed that there is around 10 times more cAMP out of the cell than inside the cell.
 </br>
 </br>
-<h2>Explanation 6</h2>
+<h2 id="exp6">Explanation 6</h2>
 </br>
 In the reference [6], we have k<SUB>cat</SUB>=100 min<SUP>-1</SUP> in vitro. However, by discussing with the biologists, we assumed that in vivo this value was higher.

Team:Grenoble/Modeling/Amplification/Sensitivity

From 2012.igem.org

Revision as of 00:40, 25 September 2012

Classic Odes Parameters

Explanation 1

Explanation 2

Explanation 3

Explanation 4

Explanation 5

Explanation 6

Quorum sensing parameters

Explanation 1

Explanation 2

References