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Table 1 Variables and parameters of the mathematical model.

From: Rational design of modular circuits for gene transcription: A test of the bottom-up approach

 

Description

Value

Units

I

IPTG concentration

 

mM

G

Concentration of GFP protein

 

molecules per cell

L F

Free LacI molecules, i.e. not bound to operator sites or IPTG molecule

 

molecules per cell

L I

LacI molecules bound to IPTG

 

molecules per cell

M G

mRNA molecules of GFP

 

molecules per cell

M L

mRNA molecules of LacI

 

molecules per cell

D G / L F

Free Repressor/Reporter plasmids

 

plasmids per cell

D G / L L

Repressor/Reporter plasmids bound to LacI molecules

 

plasmids per cell

D G / L I

Repressor/Reporter plasmids bound to induced LacI molecules

 

plasmids per cell

D G 0

Number of Reporter plasmids per cell

80

plasmids per cell

D L 0

Number of Repressor plasmids per cell

D G 0 / 3.75 § = 21.33

plasmids per cell

λ G/L

Protein degradation rate

0.0214§

min-1

λ G / L M

mRNA degradation rate

0.271[39]

min-1

α G

GFP rate of synthesis

540λ G = 11.54[40]

min-1

Α L

LacI rate of synthesis

α G /4 = 2.88

min-1

α G M

GFP transcription rate

0.56†

min-1

α L M

LacI transcription rate

α G M / 1.23 § = 0.45

min-1

K x L

Equilibrium binding constant of the complex LacI-Ox

K 1 L

0.13[41]

molecules per cell

  

K 2 L

1.63[41]

molecules per cell

  

K s L

0.0394†

molecules per cell

K x I

Equilibrium binding constant for the binding of induced LacI molecule to the operator sequence Ox

K 1 I

25336†

molecules per cell

  

K 2 I

∞

molecules per cell

  

K s I

313†

molecules per cell

K LI

Equilibrium binding constant for the binding IPTG-LacI

0.2890†

mM

n

Cooperativity of the binding LacI-IPTG

1.8688†

 

Ï„ LI

Time constant of LacI binding to the operator sequences

0.02[43]

min

Ï„ DI

Time constant of induced-LacI binding to the operator sequences

*

min

Ï„ DL

Time constant of the binding LacI-IPTG

*

min

  1. * Only the steady-state behaviors of the gene circuits are analyzed, thus arbitrary values can be used for these time constants. †Values defined through the fitting procedure. §Values obtained by experimental measurements. References are included for the values retrieved from the literature.