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Table 2 Model parameters for which all results are calculated unless otherwise stated

From: Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli

Parameter

Value

Description

k d

10-14.9 M

the Zn(II) dissociation constant for ZnZntR when pH = 8.0 [31]

k d 1

10-15.2 M

the Zn(II) dissociation constant for the ZnZntR-DNA complex when pH = 8.0 [31]

K Z n − T P E N ' MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaem4saS0aa0baaSqaaiabdQfaAjabd6gaUjabgkHiTiabdsfaujabdcfaqjabdweafjabd6eaobqaaiabcEcaNaaaaaa@3618@

1.99*1015 M-1

the apparent association constant for Zn-TPEN at pH = 8.0, 0.1 M ionic strength, calculated from [22]

k 1

0.025 (nM)-1s-1

the forward rate parameter of Reaction (7)

k 1a

1 (nM)-1s-1

the forward rate parameter of Reaction (11)

k 1b

1.253*10-2 (nM)-1s-1

the forward rate parameter of Reaction (4)

k -1

0.9 s-1

the backward rate parameter of Reactions (4,7,11)

k 2

0.02 (nM)-1s-1

the forward rate parameter of Reaction (12)

k 2a

0.00005 (nM)-1s-1

the forward rate parameter of Reaction (2)

k 2b

0.0002 (nM)-1s-1

the forward rate parameter of Reaction (5)

k 2c

0.0037 (nM)-1s-1

the forward rate parameter of Reaction (8)

k -2

0.3 s-1

the backward rate constant of Reactions (2, 5, 8, 12)

k 3

0.011 s-1

the transcription rate parameter

r 1

2.73*102 (nM)-1s-1

the forward rate parameter of Reaction (1)

r 2

3.437*10-4 s-1

the backward rate parameter of Reaction (1)

r 3

4.41*1010 (nM)-2s-1

the forward rate parameter of Reaction (10)

r 4

9*10-3 s-1

the backward rate parameter of Reaction (10)

r 5

3*104 (nM)-1s-1

the forward rate parameter of Reaction (14)

r 6

1.506 *10-2 s-1

the backward rate parameter of Reaction (14)

t d 0

30 min

the time duration for preliminary equilibrium of reactants before NTPs (i.e., nucleoside triphosphates)were added in run-off transcription experiments [22, 29, 37]

t d

15 min

the time duration for run-off transcription after NTPs were added in transcription experiments [22, 29, 37]

t d 1

30 min

the time duration for Zur-DNA interaction assay [22]

Px tot

25 nM

the total concentration of ZntR dimer which is half of the concentration of ZntR monomer denoted as [ZntR] total [22]

Py tot

25 nM

the total concentration of Zur dimer [22]

R 0

50 nM

the total concentration of RNAP [22]

D 0

4 nM

the total concentration of DNA [22]

Zn tot

vary in different assays

the total concentration of Zn(II), also denoted as [Zn] total

TPEN tot

vary in different assays

the total concentration of TPEN

  1. Note: k2b= 4*k2a. Moreover, according to the equilibrium theory of chemical reactions, r2 = k d r1, r6 = r5/ K Z n − T P E N ' MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaem4saS0aa0baaSqaaiabdQfaAjabd6gaUjabgkHiTiabdsfaujabdcfaqjabdweafjabd6eaobqaaiabcEcaNaaaaaa@3618@ and k1b= k1k d /kd 1. The values of four parameters (k1, k-1, k2, k-2) are taken from Hayot's model [43]. These parameters origin from measured rate constants of the λ repressor gene cI in E. coli and are also quoted as physiologically reasonable values by Ingram et al [15, 43, 44]. K Z n − T P E N ' MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaem4saS0aa0baaSqaaiabdQfaAjabd6gaUjabgkHiTiabdsfaujabdcfaqjabdweafjabd6eaobqaaiabcEcaNaaaaaa@3618@ is calculated in the same way as shown in [22] (please note the pH value difference).