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Team:NTU-Singapore/Modelling/Parameter
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==Lactose controlled production of E7 + Imm== | ==Lactose controlled production of E7 + Imm== | ||
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#LacI = A | #LacI = A | ||
#Lactose =B | #Lactose =B | ||
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==Iron and Ai2 controlled production of Lysis== | ==Iron and Ai2 controlled production of Lysis== | ||
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#Ai-2 : A | #Ai-2 : A | ||
#ai-2-phos : B | #ai-2-phos : B | ||
Revision as of 02:04, 26 June 2008
|
Contents |
Variables
Lactose controlled production of E7 + Imm
- LacI = A
- Lactose =B
- E7 = C
Iron and Ai2 controlled production of Lysis
- Ai-2 : A
- ai-2-phos : B
- LsrR : C
- SupD derivatives : D
- T7ptag : E
- Lysis : F
Parameter Estimation
Estimation of different parameters
- Transcription : 70nt/s
- Translation : 40aa/s
- Number of Essential Genes : 297
- Number of mRNA per cell : 4000
- Average mRNA half life : 5min
- Average mRNA length : 1100
Assumptions
- Rate of transcription is dependent on length of gene
- Number of amino acids is 1/3 of the number of nucleotides in a gene
- Rate of Translation is dependent on number of nucleotides
- For each gene mRNA = 10 at steady state
- Rate of degradation of average mRNA = 1100/ 5 min
- Rate of degradation of protein is equivalent to time for cell division i.e. 40 min
E7 production system
| Type | Parameter | Values | Comments |
| Transcription Rate of Lac I gene | k1A | 21 | Made using Earlier assumptions |
| Transcription Rate of E7 + Imm gene | k1C | 2.470588 | Made using Earlier assumptions |
| Degradation Rate of Lac I mRNA | d1A | 0.76246 | Made using Earlier assumptions |
| Transcription Rate of E7 + Imm mRNA | d1C | 0.0897 | Made using Earlier assumptions |
| Translation Rate of Lac I mRNA | k2A | 36 | Made using Earlier assumptions |
| Translation Rate of E7 + Imm mRNA | k2C | 4.23539 | Made using Earlier assumptions |
| Protein Degradation Rate | d2A,d2C | 0.03465 | Made using Earlier assumptions |
| Hill coefficeint for E7 + Imm | nC | 1 | This is obtained on the assumption that one Repressor Protein binds to one Lactose molecule complex |
| Dissociation Constant for E7 + Imm | KC | 0.8 | [3] |
| Constitutive Portion for E7 + Imm | aC | 0.5 | Estimate since a is between 0 and 1 Implication that Lactose may not be a very strongly Regulated Promoter |
| Complex Formation Rate Between Lac I Repressor and Lactose | k3AB | 1 | Estimate |
E7 production system
| Type | Parameter | Values | Comments |
| Phosphorylation Rate of Ai-2 | kPF | 1 | Estimate |
| Dephosphorylation Rate of Ai-2 | kPB | 1 | Estimate |
| Transcription Rate of LsrR gene | k1C | 4.402517 | Made using Earlier assumptions |
| Transcription Rate of SupD gene | k1D | 46.667 | Made using Earlier assumptions |
| Transcription Rate of t7pTag gene | k1E | 1.5556 | Made using Earlier assumptions |
| Transcription Rate of Lysis gene | k1F | 28 | Made using Earlier assumptions |
| Degradation Rate of LsrR mRNA | d1C | 0.159845 | Made using Earlier assumptions |
| Degradation Rate of SupD mRNA | d1D | 1.694359 | Made using Earlier assumptions |
| Degradation Rate of t7pTag mRNA | d1E | 0.056478 | Made using Earlier assumptions |
| Degradation Rate of Lysis mRNA | d1F | 1.0166 | Made using Earlier assumptions |
| Translation Rate of LsrR Protein | k2C | 7.54716 | Made using Earlier assumptions |
| Translation Rate of t7 pTag Protein | k2E | 2.6667 | Made using Earlier assumptions |
| Translation Rate of Lysis Protein | k2F | 48 | Made using Earlier assumptions |
| Protein Degradation Rate | d2C,d2E,d2F | 0.03465 | Made using Earlier assumptions |
| Hill coefficeint for SupD | nD | 50 | Trial And Error |
| Hill coefficeint for t7 pTag | nE | 1 | Trial And Error |
| Hill coefficeint for Lysis | nF | 1 | Estimate |
| Dissociation Constant for SupD | KD | 15 | [5] |
| Dissociation Constant for t7 pTag | KE | 1 | Estimate |
| Dissociation Constant for Lysis | KF | 0.8 | Estimate |
| Constitutive Portion for SupD | aD | 0.01 | Estimate |
| Constitutive Portion for t7 pTag | aE | 0.01 | Estimate |
| Constitutive Portion for Lysis | aF | 0.0001 | Estimate |
| Complex Formation Rate Between LsrR Repressor and Ai-2-Phosphorylated | k3BC | 0.01 | Estimate |
| Complex Formation Rate Between SupD tRNA and t7 pTag mRNA | k3DE | 0.000000001 | Estimate |
| Amount of Protein Kinase | S | 28.747 | From Earlier Assumptions |
