Team:TUDelft/Modeling Parameters

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=Modeling Parameters=
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Revision as of 20:22, 12 October 2009

Modeling Parameters

Parameter Values Description Ref
cpLac 5e-10 maximum transcription rate (M/min) [1]
cpTet 1.5e-7 maximum transcription rate (M/min) [2]
c 1.5e-7 maximum transcription rate (M/min) estimate
K50IPTG 1.3e-6 dissociation constant (M) [3]
K50LacI 800e-9 dissociation constant (M) [3]
K50TetR 179e-12 dissociation constant (M) [3]
K50CI 8e-12 dissociation constant (M) [3]
nIPTG 2 Hills coefficient [3]
nLacI 2 Hills coefficient [3]
nTetR 3 Hills coefficient [3]
nCI 2 Hills coefficient [3]
dLacI 0.1386 degradation rate (M/min) [3]
dTetR 0.1386 degradation rate (M/min) [3]
dCI 0.042 degradation rate (M/min) [3]
dRFP 6.3e-3 degradation rate (M/min) [3]
dGFP 6.3e-3 degradation rate (M/min) [3]
dmRNA 0.029 degradation rate (M/min) [4]
α 16 - 57 translation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used) [5]
kIPTG 0.92 rate constant for IPTG diffusion into cell [6]

References

1. M. Santillan, M.C. Mackey, E.S. Zeron, Origin of Bistability in the lac Operon, Biophysical Journal, Volume 92, Issue 11, 1 June 2007, Pages 3830-3842, ISSN 0006-3495, DOI: 10.1529/biophysj.106.101717. (http://www.sciencedirect.com/science/article/B94RW-4V9YVV6-8/2/cd4c5ba8d532a314eed932d787f56a35)

2. Thuc T. Le, Calin C. Guet, Philippe Cluzel, Protein expression enhancement in efflux-deleted mutant bacteria, Protein Expression and Purification, Volume 48, Issue 1, July 2006, Pages 28-31, ISSN 1046-5928, DOI: 10.1016/j.pep.2005.11.018. (http://www.sciencedirect.com/science/article/B6WPJ-4HV73GJ-1/2/36f5ff80fe56e2533f1ec0699bf12a7e)

3. http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters

4. Barrio M, Burrage K, Leier A, Tian T. Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. PLoS Comput Biol. 2006 Sep 8; 2(9): e117.

5. Liang, S.-T., Xu, Y.-C., Dennis, P., Bremer, H. mRNA Composition and Control of Bacterial Gene Expression. J. Bacteriol. 2000 182: 3037-3044.

6. Michail Stamatakis, Nikos V. Mantzaris, Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network, Biophysical Journal, Volume 96, Issue 3, 4 February 2009, Pages 887-906, ISSN 0006-3495, DOI: 10.1016/j.bpj.2008.10.028. (http://www.sciencedirect.com/science/article/B94RW-4VGGB7R-D/2/bd642ea418c1213f10259b778907a1ee)