Team:University of Ottawa/Modeling/Parameters

From 2008.igem.org

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Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555.
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Alon, U. (2007). "Network motifs: theory and experimental approaches." Nature Reviews Genetics 8: 450-461.
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Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369.
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Alon, U. and S. Mangan (2003). "Structure and function of the feed-foward loop network motif." PNAS 100(21): 11980-11985.
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Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104.
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+
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Basu, S., R. Mehreja, et al. (2004). "Spatiotemporal control of gene expression with pulse-generating networks." PNAS 101(17): 6355-6360.
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Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865.
Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865.
-
 
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Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369.
 
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-
Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104.
 
-
 
-
Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555.
 

Revision as of 22:20, 28 October 2008

Values in µM, min, and mL unless specified.

Parameter Value Source
Population and culture
kn 3.85e-3 [1] observed division rate
Nmax 1e8 [1]
V 1e-11 [1]
kdil varied [1]
IP binding to receptor
kassoc 5e-3 [1]
kdissoc 4.55e-3 [1]
Synthesis of CRE1, YPD1, SKN7 species
ks1 6.16e-5 [1]
ks2 6.00e-4 [1]
ks3 2.46e-4 [1]
kdimer 20 [1]
Phosphorylation/Dephosphorylation reactions
kp1 0.1 [1]
kp2 1243 [1]
kp3 56 [1]
kp-3 4.8 [1]
kdp1 5.33e-2 [1]
kdp3 2.89e-3 [1]
kdp3 4.80e-3 [1]
Decay constants
kd1 5.33e-2 [1]
kd2 2.89e-3 [1]
kd3 4.80e-3 [1]
kdip 5e-4 [1]
kdgfp 5.77e-3 [1]
kdtet 3.85e-3 Cell division rate (assumed stable)
kdckx <=3.85e-3 Cell division rate, or lower if diffusion is significant.
Basal expression
kbgfp, kbtet, kbckx 6e-6 adapted from [1]
ktdim 1e3 arbitrary
Induced expression
kgfp 6e-3 adapted from [1]
ktet varied -
kckx varied -
Kg, Kt, Kc varied -
αg, αt αc varied -
Ki 5e-6 Kass = 2e11 M-1 [ ]
β varied -
kipt4 varied -
IPT4 enzyme kinetics -
ksip Varied -
CKX enzyme kinetics
Km 40 µM [ ]
kcat 0.5-1000 s-1 [ ], [ ]

References

Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555.

Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369.

Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104.

Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865.

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