Table 1 Chemical Reactions for IκBα/NFκB regulatory circuit with NFκB synthetic decoy ODNs. The parameters of the feedback cycle originate from the work of Hoffmann et al. [20] while the ranges of values for specific binding/unbinding rates come from binding microarray data [26] and in vitro kinetic measurements [24, 51]
From: Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs)
Reactions | Rate coeff | Values |
|---|---|---|
D U +N n →D B | k don | 10 μM−1min−1 |
D B →D U +N n | k doff | \(\sim LogNormal (\Delta \hat {G}, \sigma ^{2})\) |
AD U +N n →AD B | k son | 10 μM−1min−1 |
AD B →AD U +N n | k soff | [0.02−1] min−1 |
AD U ⇒∅ | λ s | [0−0.02] min−1 |
AD B ⇒∅ | λ s | [0−0.02] min−1 |
OFF+N n →ON | k on | 10 μM−1min−1 |
ON→OFF+N n | k off | 1 min−1 |
D B +I n ⇒D U +NI n | k s | [0−10] μM−1min−1 |
ON+I n ⇒OFF+NI n | k s | [0−10] μM−1min−1 |
AD B +I n ⇒AD U +NI n | k s | [0−10] μM−1min−1 |
ON⇒ON+mRNA | k tr | 1.03 μMmin−1 |
mRNA⇒mRNA+I c | k tl | 0.2448 min−1 |
mRNA⇒∅ | k d | 0.017 min−1 |
I c →I n | k in | 0.018 min−1 |
I n →I c | k out | 0.012 min−1 |
N c →N n | k Nin | 5.4 min−1 |
N c +I c →NI c | k f | 30 μM−1min−1 |
NI c →N c +I c | k b | 0.03 min−1 |
N n +I n →NI n | k fn | 30 μM−1min−1 |
NI n →N n +I n | k bn | 0.03 min−1 |
NI c ⇒N c | α | [0.10−0.55] min−1 |
NI n ⇒NI c | k NIout | 0.83 min−1 |