EdinburghModeling

From 2006.igem.org

Contents 1 System Diagram of Arsenic Biosensor 2 Reaction set 3 Initial concentration 4 Methodology 5 Results 5.1 System response 5.2 Parameter sensitivity analysis 5.3 Species sensitivity analysis 6 Conclusion 7 Future work 8 Reference

System Diagram of Arsenic Biosensor

Reaction set

No.	Name	Equation	Rate Law	Parameters
1	ArsD binding to Arsenic (III)	ArsD+2As(III)=ArsD-2As(III)	Mass Action	K1=1000 K-1=0.65
2	ArsD binding to promoter1	2 ArsD+promoter1=2ArsD-promoter1	Mass Action	K2=10000, K-2=0.65
3	ArsD degradation	ArsD->null	Mass Action	K3=0.05
4	ArsD production	promoter1->promoter1+ArsD	Michaelis-Menten	V4m=0.5, K4m=75
5	ArsR binding to Arsenic (III)	ArsR+2As(III)=ArsR-2As(III)	Mass Action	K5=1000, K-5=0.65
6	ArsR binding to promoter2	2ArsR+promoter2=2ArsR-promoter2	Mass Action	K6=10000, K-6=0.65
7	ArsR degradation	ArsR->null	Mass Action	K7=0.05
8	ArsR production	promoter2->promoter2+ArsR	Michaelis-Menten	V8m=10, K8m=25
9	LacI binding to allolactose	LacI+allolactose=LacI-allolactose	Mass Action	K9=10000, K-9=0.1
10	LacI binding to promoter4	LacI+promoter4 = LacI-promoter4	Mass Action	K10=1000, K-10=0.5
11	LacI degradation	LacI->null	Mass Action	K11=0.1
12	LacI production	promoter3->promoter3+LacI	Michaelis-Menten	V12m=0.5, K12m=40
13	lacZ degradation	lacZ->null	Mass Action	K13=0.1
14	lacZ production	promoter1->promoter1+lacZ	Michaelis-Menten	V14m=25, K14m=10
15	LCI binding to promoter 4	LCI+promoter4=LCI-promoter4	Mass Action	K15=10000, K-15=0.5
16	LCI degradation	LCI->null	Mass Action	K16=0.1
17	LCI production	promoter2->promoter2+LCI	Michaelis-Menten	V17m=10, K17m=25
18	Urease degradation	Urease->null	Mass Action	K18=0.1
19	Urease production	promoter4->promoter4+Urease	Michaelis-Menten	V19m=10, K19m=40

Note: The units for first, second and third order rate constants are expressed in units of second^-1, nMol^-1*second^-1 and nMol^-2*second^-1 respectively.

This reaction map is generated from the reaction set above using Simbiology Toolbox.

Initial concentration

No.	Species	Intial Concentration (nMol)
1	ArsD	25
2	As(III)	40
3	2ArsD-promoter1	25
4	promoter1	5
5	ArsR	25
6	2ArsR-promoter2	25
7	promoter2	5
8	LCI	4
9	LacI	0.1
10	LacI-allolactose	0.1
11	allolactose	1000
12	LacI-promoter4	0.1
13	promoter4	25
14	LCI-promoter4	0.1
15	Urease	0.1
16	promoter3	5
17	Other species	0

Methodology

Results

System response

Parameter sensitivity analysis

The most sensitive parameters affecting lacZ

Nanme	Description	Peak value of sensitivity	Normal value
K-1	ArsD-2AS(III) dissociate rate	-2	0.65/s
K-2	2ArsD-promoter1 dissociate rate	4	0.65/s
K3	ArsD degradation rate	90	0.05/s
K7	ArsR degradation rate	12	0.05/s
K13	LacZ degradation rate	-35	0.1/s

The most sensitive parameters affecting Urease

Nanme	Description	Peak value of sensitivity	Normal value
k3	ArsD degradation rate	-30	0.05/s
k-6	2ArsR-promoter2 dissociate rate	-5	0.65/s
k7	ArsR degradation rate	-120	0.05/s
K18	Urease degradation rate	-350	0.1/s
V19m	Urease production maxium rate	3.5	10 nMol/s

Species sensitivity analysis

The most sensitive species affecting lacZ

Name	Initial concentration (nMol)
promoter1	5.0
promoter2	5.0
ArsD-2As(III)	0
ArsD	25
ArsR	25

The most sensitive species affecting Urease

Name	Initial concentration (nMol)
LCI	4
LacI-promoter4	0.1
promoter4	25
promoter2	5
promoter1	5

Conclusion

Future work

Reference