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Table 1 A Chemical kinetics representation of Network III

From: Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

# Reaction k Ref. # Reaction k Ref.
1 TcEx --> Tc 3.3E-4 [31] 48 TetOFF2 + OP2 --> TetOFF2:OP2 2.86E+06 [34]
2 2 TetR --> TetR2 1.00E+09 [32] 49 TetOFF2:OP2 --> TetOFF2 + OP2 5.11E-04 [34]
3 TetR2 --> 2 TetR 10 [32] 50 TetR2 + OP2 --> TetR2:OP2 2.86E+06 [34]
4 2 TetOFF --> TetOFF2 1.00E+09 [32] 51 TetR2:OP2 --> TetR2 + OP2 5.11E-04 [34]
5 TetOFF2 --> 2 TetOFF 10 [32] 52 TetOFF2:OP2 + Tc --> Tc:2TetOFF:OP2 2.0E+6 [4]
6 Tc + TetR2 -->Tc:2TetR 2.00E+06 [4] 53 Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP2 1.0E+15 §
7 Tc + Tc:2TetR --> Tc:TetR2 1.0E+15 § 54 Tc:TetOFF2:OP2 --> Tc:TetOFF2 + OP2 5.8E-3 [35]
8 Tc:TetR2 --> TetR2 + 2Tc 0.001 [4] 55 TetR2:OP2 + Tc --> Tc:2TetR:OP2 2.0E+6 [4]
9 Tc + TetOFF2 --> Tc:2TetOFF 2.00E+06 [4] 56 Tc:2TetR:OP2 + Tc --> Tc:TetR2:OP2 1.0E+15 §
10 Tc + Tc:2TetOFF --> Tc:TetOFF2 1.0E+15 § 57 Tc:TetR2:OP2 --> Tc:TetR2 + OP2 5.8E-3 [35]
11 Tc:TetOFF2 --> TetOFF2 + 2Tc 0.001 [4] 58 RNAp + P2 + OP2 --> RNAp:P2:OP2 8.60E+6 [38]
12 TetOFF --> 0.0012 * 59 RNAp:P2:OP2 --> RNAp + P2 + OP2 0.01 [38]
13 TetOFF2 --> 0.0012 * 60 RNAp:P2:OP2 --> RNAp*:P2:OP2 0.013 [38]
14 TetR --> 0.0012 * 61 RNAp*:P2:OP2 --> RNAp*:DNA21 + P2 + OP2 30 [40]
15 TetR2 --> 0.0012 * 62 RNAp + P2 + OP2:TetR2 --> RNAp:P2:OP2:TetR2 8.60E+6 [38]
16 Tc:TetOFF2 --> Tc 0.0012 * 63 RNAp:P2:OP2:TetR2 --> RNAp + P2 + OP2:TetR2 0.01 [38]
17 Tc:TetR2 --> Tc 0.0012 * 64 RNAp:P2:OP2:TetR2 --> RNAp*:P2:OP2:TetR2 0.013 [38]
18 GFP-LAA --> 2.88E-04 [36] 65 RNAp*:P2:OP2:TetR2 --> RNAp*:DNA21 + P2 + OP2:TetR2 30 [40]
19 Tc --> 2.67E-06 [37] 66 RNAp + P2 + OP2:TetOFF2 --> RNAp:P2:OP2:TetOFF2 8.60E+6 [38]
20 TcEx --> 2.67E-06 [37] 67 RNAp:P2:OP2:TetOFF2 --> RNAp + P2 + OP2:TetOFF2 0.01 [38]
21 TetOFF2 + OP1 --> TetOFF2:OP1 2.86E+06 [34] 68 RNAp:P2:OP2:TetOFF2 --> RNAp*:P2:OP2:TetOFF2 0.13
22 TetOFF2:OP1 --> TetOFF2 + OP1 5.11E-04 [34] 69 RNAp*:P2:OP2:TetOFF2 --> RNAp*:DNA21 + P2 + OP2:TetOFF2 30 [40]
23 TetR2 + OP1 --> TetR2:OP1 2.86E+06 [34] 70 RNAp*:DNA21 --> RNAp + mRNA2 30, 621 [40]
24 TetR2:OP1 --> TetR2 + OP1 5.11E-04 [34] 71 mRNA2 --> 0.002 $
25 TetOFF2:OP1 + Tc --> Tc:2TetOFF:OP1 2.0E+6 [4] 72 mRNA2 + Ribosome --> Rib:mRNA2 1.00E+05 $
26 Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP1 1.0E+15 § 73 Rib:mRNA2 --> Rib:mRNA21 + mRNA2 100 [41]
27 Tc:TetOFF2:OP1 --> Tc:TetOFF2 + OP1 5.8E-3 [35] 74 Rib:mRNA21 --> Ribosome + TetR 100, 207 [41]
28 TetR2:OP1 + Tc --> Tc:2TetR:OP1 2.0E+6 [4] 75 TetOFF2 + OP3 --> TetOFF2:OP3 2.86E+06 [34]
29 Tc:2TetR:OP1 + Tc --> Tc:TetR2:OP1 1.0E+15 § 76 TetOFF2:OP3 --> TetOFF2 + OP3 5.11E-04 [34]
30 Tc:TetR2:OP1 --> Tc:TetR2 + OP1 5.8E-3 [35] 77 TetR2 + OP3 --> TetR2:OP3 2.86E+06 [34]
31 RNAp + P1 + OP1 --> RNAp:P1:OP1 8.60E+06 [38] 78 TetR2:OP3 --> TetR2 + OP3 5.11E-04 [34]
32 RNAp:P1:OP1 --> RNAp + P1 + OP1 0.01 [38] 79 TetOFF2:OP3 + Tc --> Tc:2TetOFF:OP3 2.0E+6 [4]
33 RNAp:P1:OP1 --> RNAp*:P1:OP1 0.013 [38] 80 Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP3 1.0E+15 §
34 RNAp*:P1:OP1 --> RNAp*:DNA11 + P1 + OP1 30 [40] 81 Tc:TetOFF2:OP3 --> Tc:TetOFF2 + OP3 5.8E-3 [35]
35 RNAp + P1 + OP1:TetR2 --> RNAp:P1:OP1:TetR2 8.60E+6 [38] 82 TetR2:OP3 + Tc --> Tc:2TetR:OP3 2.0E+6 [4]
36 RNAp:P1:OP1:TetR2 --> RNAp + P1 + OP1:TetR2 0.01 [38] 83 Tc:2TetR:OP3 + Tc --> Tc:TetR2:OP3 1.0E+15 §
37 RNAp:P1:OP1:TetR2 --> RNAp*:P1:OP1:TetR2 0.013 [38] 84 Tc:TetR2:OP3 --> Tc:TetR2 + OP3 5.8E-3 [35]
38 RNAp*:P1:OP1:TetR2 --> RNAp*:DNA11 + P1 + OP1:TetR2 30 [40] 85 RNAp + P3 + OP3 --> RNAp:P3:OP3 8.60E+6 [38]
39 RNAp + P1 + OP1:TetOFF2 --> RNAp:P1:OP1:TetOFF2 8.60E+6 [38] 86 RNAp:P3:OP3 --> RNAp + P3 + OP3 0.01 [38]
40 RNAp:P1:OP1:TetOFF2 --> RNAp + P1 + OP1:TetOFF2 0.01 [38] 87 RNAp:P3:OP3 --> RNAp*:P3:OP3 0.013 [38]
41 RNAp:P1:OP1:TetOFF2 --> RNAp*:P1:OP1:TetOFF2 0.13 88 RNAp*:P3:OP3 --> RNAp*:DNA31 + P3 + OP3 30 [40]
42 RNAp*:P1:OP1:TetOFF2 --> RNAp*:DNA11 + P1 + OP1:TetOFF2 30 [40] 89 RNAp*:DNA31 --> RNAp + mRNA3 30, 723 [40]
43 RNAp*:DNA11 --> RNAp + mRNA1 30, 660 [40] 90 mRNA3 --> 0.002 $
44 mRNA1 --> 0.002 $ 91 mRNA3 + Ribosome --> Rib:mRNA3 1.00E+05 $
45 mRNA1 + Ribosome --> Rib:mRNA1 1.00E+05 $ 92 Rib:mRNA3 --> Rib:mRNA31 + mRNA3 100 [41]
46 Rib:mRNA1 --> Rib:mRNA11 + mRNA1 100 [41] 93 Rib:mRNA31 --> Ribosome + GFP-LAA 100, 248 [41]
47 Rib:mRNA11 --> Ribosome + TetOFF 100, 220 [41]     
  1. Reactions and kinetic rates for the chemical kinetics representation of network III. Units on k: 1st order reaction: sec-1, 2nd order: (M sec)-1, power law kinetics M-2 sec-1. Reactions with two kinetic constants are γ - distributed events, where the first number is the rate of each step and the second is the number of steps. References are noted next to each reaction. §: rate adjusted for fast reacting intermediates. *: rates adjusted for 10 min half-life. ¶: rate adjusted from the function of activator. $: rates adjusted to give 20 protein molecules per mRNA transcript. Numbering of the genes starts from top to bottom as they are shown in Figure 1. For example, P1: promoter of gene 1, OP1: operator of gene 1.