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] |
| 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 |