Team:NTU-Singapore/Modelling/Parameter

From 2008.igem.org

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|Estimate. It is assuming that <br> one molecule of iron ion is required <br> to activate the production of one t7mRNA
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|Hill coefficeint for Lysis
|Hill coefficeint for Lysis
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|Estimate. It is assumed that <br> one molecule of t7 is required <br> for activation of one Lysis mRNA
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Revision as of 03:47, 4 July 2008

Contents

Variables

Lactose controlled production of E7 + Imm

  1. LacI = A
  2. Lactose =B
  3. E7 = C

Iron and Ai2 controlled production of Lysis

  1. Ai-2 : A
  2. ai-2-phos : B
  3. LsrR : C
  4. SupD derivatives : D
  5. T7ptag : E
  6. Lysis : F

Parameter Estimation

Estimation of different parameters

  1. Transcription  : 70nt/s
  2. Translation : 40aa/s
  3. Number of Essential Genes : 297
  4. Number of mRNA per cell : 4000
  5. Average mRNA half life : 5min
  6. Average mRNA length  : 1100

Assumptions

  1. Rate of transcription is dependent on length of gene
  2. Number of amino acids is 1/3 of the number of nucleotides in a gene
  3. Rate of Translation is dependent on number of nucleotides
  4. For each gene mRNA = 10 at steady state
  5. Rate of degradation of average mRNA = 1100/ 5 min
  6. Rate of degradation of protein is equivalent to time for cell division i.e. 40 min

Results

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

Lysis 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 Estimate. It is assuming that
one molecule of iron ion is required
to activate the production of one t7mRNA
Hill coefficeint for Lysis nF 1 Estimate. It is assumed that
one molecule of t7 is required
for activation of one Lysis mRNA
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 Trial and Error
Constitutive Portion for t7 pTag aE 0.01 Estimate
Constitutive Portion for Lysis aF 0.0001 Trial and Error
Complex Formation Rate Between
LsrR Repressor and Ai-2-Phosphorylated 		k3BC 0.01 Trial and Error
Complex Formation Rate Between
SupD tRNA and t7 pTag mRNA 		k3DE 0.000000001 Trial and Error
Amount of Protein Kinase S 28.747 From Earlier Assumptions
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