Team:TU-Delft/Timer-Sumo-KillSwitch

From 2013.igem.org

(Difference between revisions)
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|'''Parameter'''
|'''Parameter'''
|'''Value'''
|'''Value'''
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|'''Reference'''
|'''Reference'''
|-
|-
-
|a
+
| c<sub>a</sub>
|1020
|1020
|Translation rate per amino acid
|Translation rate per amino acid
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|4.16
|4.16
|Maximum transcription rate of T7
|Maximum transcription rate of T7
-
|#m/min
+
|#<sub>m</sub>/min
| [[Team:TUDelft/Modeling_References|[2]]]
| [[Team:TUDelft/Modeling_References|[2]]]
|-
|-
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|2.79
|2.79
|Maximum transcription rate of Ptet
|Maximum transcription rate of Ptet
-
|#m/min
+
|#<sub>m</sub>/min
| [[Team:TUDelft/Modeling_References|[4]]]
| [[Team:TUDelft/Modeling_References|[4]]]
 +
|-
 +
| c<sub>pconst</sub>
 +
|0.5
 +
|Transcription rate of Pconst
 +
|#m/min
 +
| Assumption
|-
|-
| c<sub>ci</sub>
| c<sub>ci</sub>
|1.79
|1.79
|Maximum transcription rate of Pci
|Maximum transcription rate of Pci
-
|#m/min
+
|#<sub>m</sub>/min
| [[Team:TUDelft/Modeling_References|[3]]]
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
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|min<sup>-1</sup>
|min<sup>-1</sup>
| [[Team:TUDelft/Modeling_References|[8]]]
| [[Team:TUDelft/Modeling_References|[8]]]
 +
|-
 +
| d<sub>H</sub>
 +
|0.0348
 +
|Degradation rate of holin / Antiholin
 +
|M/min
 +
|  [[Team:TUDelft/Modeling_References|[17]]]
|-
|-
| d<sub>TET</sub>
| d<sub>TET</sub>
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|min<sup>-1</sup>
|min<sup>-1</sup>
| [[Team:TUDelft/Modeling_References|[9]]]
| [[Team:TUDelft/Modeling_References|[9]]]
 +
|-
 +
| k<sub>b,HAH</sub>
 +
|0.3*10<sup>-4</sup>
 +
|Backward rate
 +
|
 +
| [[Team:TUDelft/Modeling_References|[17]]]
 +
|-
 +
| k<sub>f,HAH</sub>
 +
|11.7*10<sup>-4</sup>
 +
|Forward rate
 +
|
 +
| [[Team:TUDelft/Modeling_References|[17]]]
 +
|-
 +
| d<sub>PEP</sub>
 +
|2.1*10<sup>-3</sup>
 +
|Degradation rate of the peptide
 +
|min<sup>-1</sup>
 +
|Assumed three times slower same as GFP
|-
|-
| d<sub>PSU</sub>
| d<sub>PSU</sub>
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|  -
|  -
|Assumption
|Assumption
 +
|-
 +
|l<sub>ci</sub>
 +
|0.002
 +
|Leakage factor of Pci
 +
|  -
 +
|Assumption
 +
|-
 +
|k<sub>tet</sub>
 +
|6
 +
|Dissociation constant of Ptet
 +
|#m
 +
|[[Team:TUDelft/Modeling_References|[10]]]
|-
|-
|k<sub>ci</sub>
|k<sub>ci</sub>
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|[[Team:TUDelft/Modeling_References|[6]]]
|[[Team:TUDelft/Modeling_References|[6]]]
|-
|-
-
|n<sub>tet</sub>
+
|n<sub>ci</sub>
|3
|3
|Hills coefficient
|Hills coefficient
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|[[Team:TUDelft/Modeling_References|[11]]]
|[[Team:TUDelft/Modeling_References|[11]]]
|-
|-
-
|n<sub>ci</sub>
+
|n<sub>tet</sub>
|3
|3
|Hills coefficient
|Hills coefficient
|  -
|  -
|[[Team:TUDelft/Modeling_References|[11]]]
|[[Team:TUDelft/Modeling_References|[11]]]
 +
|-
 +
|s
 +
|0 or 1
 +
|Activation/Inactivation of T7 promoter
 +
|Binary
 +
|Assumption
|-
|-
|s<sub>ci</sub>
|s<sub>ci</sub>
|228
|228
-
|Length of Ci
+
|Length of CI
-
| amino acids
+
|amino acids
|[[Team:TUDelft/Modeling_References|[12]]]
|[[Team:TUDelft/Modeling_References|[12]]]
|-
|-
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|amino acids
|amino acids
|[[Team:TUDelft/Modeling_References|[13]]]
|[[Team:TUDelft/Modeling_References|[13]]]
 +
|-
 +
|s<sub>H</sub>
 +
|219
 +
|Length of Holin
 +
|amino acids
 +
|
 +
|-
 +
|s<sub>AH</sub>
 +
|103
 +
|Length of Antiholin
 +
|amino acids
 +
|
|-
|-
|}
|}

Revision as of 09:54, 17 September 2013

Timer-SUMO-KillSwitch


The separate modules: Timer plus SUMO and Kill Switch are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter.

Differential Equations

Parameters


Parameter Value Description Units Reference
ca 1020 Translation rate per amino acid min-1#a-1 [7]
cT7 4.16 Maximum transcription rate of T7 #m/min [2]
cptet 2.79 Maximum transcription rate of Ptet #m/min [4]
cpconst 0.5 Transcription rate of Pconst #m/min Assumption
cci 1.79 Maximum transcription rate of Pci #m/min [3]
dmRNA 0.231 Degradation rate of mRNA min-1 [8]
dH 0.0348 Degradation rate of holin / Antiholin M/min [17]
dTET 0.1386 Degradation rate of TET min-1 [9]
dCI 0.042 Degradation rate of CI min-1 [9]
kb,HAH 0.3*10-4 Backward rate [17]
kf,HAH 11.7*10-4 Forward rate [17]
dPEP 2.1*10-3 Degradation rate of the peptide min-1 Assumed three times slower same as GFP
dPSU 6.3*10-3 Degradation rate of the peptide plus SUMO min-1 Assumed the same as GFP
dUlp 1.263*10-2 Degradation rate of Ulp min-1 Assumed twice the rate of GFP
lt7 0.002 Leakage factor of T7 - Assumption
lptet 0.002 Leakage factor of Ptet - Assumption
lci 0.002 Leakage factor of Pci - Assumption
ktet 6 Dissociation constant of Ptet #m [10]
kci 20 Dissociation constant of Pci #m [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
nci 3 Hills coefficient - [11]
ntet 3 Hills coefficient - [11]
s 0 or 1 Activation/Inactivation of T7 promoter Binary Assumption
sci 228 Length of CI amino acids [12]
sPSU 18 + 110 Length of peptide plus SUMO amino acids [12]
sTET 206 Length of TET amino acids [13]
sUlp 233 Length of Ulp1 amino acids [13]
sH 219 Length of Holin amino acids
sAH 103 Length of Antiholin amino acids


Results


Figure 1: Simulation Results


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