Team:NTUSingapore/Modelling/Parameter
From 2008.igem.org

Contents 
Parameters
Lactose controlled production of E7 + Imm
 LacI = A
 Lactose =B
 E7 = C
Iron and Ai2 controlled production of Lysis
 Ai2 : A
 ai2phos : 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  [1] 
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. This is based on the assumption that the complex formation is only dependent on the concentrations of Lac I repressor and Lactose 
Detection & Lysis system
Some of the parameter values were obtained via trial and error as the values could not be found in literature. The values are chosen to produce the desired behaviour of the graph. More work has to be done to actually find out how much lysis protein quantity is really required for lysis of the cell as this is still an unknown. Readers may find some of the parameters unrealistic but the purpose of this exercise is to observe how changing certain parameters may affect the system overall output. We advise the reader to look more into the behaviour of the system rather than be focused upon the numerical values.
Type  Parameter  Values  Comments 
Phosphorylation Rate of Ai2  kPF  1  Estimate 
Dephosphorylation Rate of Ai2  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  [2] 
Dissociation Constant for t7 pTag  KE  1  Trial And Error 
Dissociation Constant for Lysis  KF  1  Trial And Error 
Constitutive Portion for SupD  aD  0.01  Trial and Error 
Constitutive Portion for t7 pTag  aE  0.01  Trial And Error 
Constitutive Portion for Lysis  aF  0.0001  Trial and Error 
Complex Formation Rate Between LsrR Repressor and Ai2Phosphorylated  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 
GFP production system with logistic growth
Type  Parameter  Values  Comments 
Forward Reaction rate of Complex  kf  1.2  Trial And Error 
Reverse Reaction rate of Complex  kr  0.5  Trial And Error 
Rate of Logistic Growth  r  0.01  Trial And Error 
Varying Capacity  A & B  1 & 0.9  Trial And Error 
References
1. https://2007.igem.org/title=ETHZ/Parameters
2. Grass G, Otto M, Fricke B, et al., FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress, ARCHIVES OF MICROBIOLOGY, Volume: 183 Issue: 1 Pages: 918 Published: JAN 2005