Modelling - Parameters

Parameters

PDF file (detailed explanation on parameters and how we deduced them) for Toggle Switch

kplac	pLac production rate	600 proteins/min	[1]
kpTet	pTet production rate	600 proteins/min	[1]
kpMer	pMer production rate	600 proteins/min	[1]
δLacI	LacI degradation rate	4.6E-2 min−1	PDF file
δTetR	TetR degradation rate	4.6E-2 min−1	PDF file
δMerR	MerR degradation rate	4.6E-2 min−1	PDF file
KpLac - LacI	plac - LacI dissociation constant	5.45E-7 M	Kyoto 10
KpMer - MerR	pMer - MerR dissociation constant	1.00E-8 M	[2]
KpTet - TerR	pTet - TetR dissociation constant	5.00E-8 M	[3]
KLacI - IPTG	LacI - IPTG dissociation constant	2.96E-5 M	[4]
KTetR - aTc	aTc - TetR dissociation constant	1.5E-8 M	[5]
KHg2+ - MerR	Hg2+ - MerR dissociation constant	1E-7 M	[2]
nplac	plac cooperativity number	2,3	[4]
npMer	pMer cooperativity number	2,5	[6]
npTet	pTet cooperativity number	3	[7]

Working with the aTc/TetR parameters, we needed to now if our system could work with mercury. In order to see if it's applicable to mercury, we realized a sensitivity to parameters study.

References

[1] Nature. 2000 Jan 20;403(6767):335-8. A synthetic oscillatory network of transcriptional regulators. Elowitz MB, Leibler S.

[2] Mol Gen Genet. 1999 Aug;262(1):154-62. Purification and characterization of MerR, the regulator of the broad-spectrum mercury resistance genes in Streptomyces lividans 1326. Rother D, Mattes R, Altenbuchner J.

[3] David Braun et al. Parameter estimation for two synthetic gene networks: A case study. IEEE 2005.

[4] Nature 403, 339-342 (20 January 2000) Construction of a genetic toggle switch in Escherichia coli. Timothy S. Gardner Charles R. Cantor & James J. Collins

[5] O. Scholz, P. Schubert, M. Kintrup and W. Hillen, Tet repressor induction without Mg2+, Biochemistry 39 (2000), pp. 10914–10920

[6] Ultrasensitivity and heavy-metal selectivity of the allosterically modulated MerR transcription complex. D M Ralston and T V O'Halloran

[7] Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants. Goryachev AB, Toh DJ, Lee T.

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