Timer-SUMO-KillSwitch

From 2013.igem.org

(Difference between revisions)
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|'''Reference'''
|'''Reference'''
|-
|-
-
| c<sub>a</sub>
+
|a
|1020
|1020
|Translation rate per amino acid
|Translation rate per amino acid
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|min<sup>-1</sup>
|min<sup>-1</sup>
| [[Team:TUDelft/Modeling_References|[9]]]
| [[Team:TUDelft/Modeling_References|[9]]]
-
|-
 
-
| d<sub>PEP</sub>
 
-
|6.3*10<sup>-3</sup>
 
-
|Degradation rate of the peptide
 
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|min<sup>-1</sup>
 
-
|Assumed the same as GFP
 
|-
|-
| d<sub>PSU</sub>
| d<sub>PSU</sub>
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|  -
|  -
|Assumption
|Assumption
-
|-
 
-
|l<sub>ci</sub>
 
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|0.002
 
-
|Leakage factor of Pci
 
-
|  -
 
-
|Assumption
 
-
|-
 
-
|k<sub>tet</sub>
 
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|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>ci</sub>
+
|n<sub>tet</sub>
|3
|3
|Hills coefficient
|Hills coefficient
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|[[Team:TUDelft/Modeling_References|[11]]]
|[[Team:TUDelft/Modeling_References|[11]]]
|-
|-
-
|n<sub>tet</sub>
+
|n<sub>ci</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
+
| -
-
|[[Team:TUDelft/Modeling_References|[12]]]
+
|[[Team:TUDelft/Modeling_References|[11]]]
-
|-
+
-
|s<sub>PSU</sub>
+
-
|18 + 110
+
-
|Length of peptide plus SUMO
+
-
|amino acids
+
-
|[[Team:TUDelft/Modeling_References|[12]]]
+
-
|-
+
-
|s<sub>TET</sub>
+
-
|206
+
-
|Length of TET
+
-
|amino acids
+
-
|[[Team:TUDelft/Modeling_References|[13]]]
+
-
|-
+
-
|s<sub>Ulp</sub>
+
-
|233
+
-
|Length of Ulp1
+
-
|amino acids
+
-
|[[Team:TUDelft/Modeling_References|[13]]]
+
|-
|-
|}
|}

Revision as of 13:17, 16 August 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
a 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]
cci 1.79 Maximum transcription rate of Pci #m/min [3]
dmRNA 0.231 Degradation rate of mRNA min-1 [8]
dTET 0.1386 Degradation rate of TET min-1 [9]
dCI 0.042 Degradation rate of CI min-1 [9]
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 the same as GFP
lt7 0.002 Leakage factor of T7 - Assumption
lptet 0.002 Leakage factor of Ptet - Assumption
kci 20 Dissociation constant of Pci #m [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
ntet 3 Hills coefficient - [11]
nci 3 Hills coefficient - [11]
sci 228 Length of Ci - [11]




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