Binding of R2 to C

SCB1 (C₂) binds to ScbR homo-dimer (R₂) and inactivates its repressing activity.

Chemical equation

The exact mechanism is still unclear, however in our model we assumed that two molecules of SCB1 bind to the ScbR homo-dimer.

$C_{2} + R_{2} \rightleftharpoons C_{2}-R_{2}$

Rate equation

$r= \frac{k^{-}_{4}}{K_{d4}}\cdot [C_{2}]\cdot [R_{2}] - k^{-}_{4}\cdot [C_{2}-R_{2}]$

Parameters

The parameters of this reaction are the dissociation constant for binding of ScbR to O_R ($K_{d1}$) and the dissociation rate for binding of ScbR to O_R ($k^{-}_{1}$).

Name	Value	Units	Origin	Remarks
$K_{d1}$	$0.1 - 5.6$	$nM$	TetR-tetO interaction and TetR-like Rv3066 from M. tuberculosis	Repressor protein TetR binds to the operator tetO, repressing its own expression and that of the efflux determinant tetA. Similar structure and activity as ScbR binding to OR
$k^{-}_{1}$	$0.6-1.2$	$min^{-1}$	SPR of a TetR-like protein (RolR) on a Gram and GC content ~ 50-60% from Corynebacterium glutamicum

Parameters with uncertainty

The most plausible parameter values and the confidence interval were decided to be:

$K_{d1} = 4.5 \pm 0.9 nM$

$k^{-}_{1}= 0.9 \pm 0.3 min^{-1}$

The probability distributions, adjusted accordingly in order to reflect the above values, are the following: