Mapping behavioral specifications to model parameters in synthetic biology

BMC Bioinformatics

Table 1 Nominal values and meaning of the kinetic parameters for the model of the synthetic sensor construct.

Basal transcription rate	k ₁	0.02 sec⁻¹
Active-promoter transcription rate	k ₂	0.4 sec⁻¹
mRNA degradation rate	k ₃	0.3 sec⁻¹
Protein translation rate	k ₄	3 (nMsec) ⁻¹
Dimerization rate	k ₅	0.1 (nMsec) ⁻¹
Dimer dissociation rate	k ₆	0.001 sec⁻¹
Inhibitor binding rate	k ₇	0.011 (nMsec)⁻¹
Inhibitor unbinding rate	k ₈	0.2 sec⁻¹
Dimer-promoter binding rate	k ₉	0.21 (nMsec)⁻¹
Dimer-promoter unbinding rate	k ₁₀	0.2 sec⁻¹
Protein degradation rate	k ₁₁	0.2 sec⁻¹

Values are based on [19] and slightly adapted to obtain a desired threshold behavior.

ISSN: 1471-2105