Binding of R2 to C

SCBs (C₂) bind to ScbR homo-dimer (R₂) and inactivate 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 SCB1 to ScbR ($K_{d4}$) and the dissociation rate for binding of SCB1 to ScbR ($k^{-}_{4}$).

Name	Value	Units	Origin	Remarks
$K_{d4}$	$0.1 - 6$	$nM$	TetR-like Rv3066 from M. tuberculosis TetR in complex with the inducer tetracycline-Mg2+	Repressor protein TetR binds to [MgTc]+ and its affinity for the operator tetO is 9-fold reduced Similar structure and activity as Scb1 binding to ScbR.
$k^{-}_{4}$	$0.6-1.2$	$min^{-1}$	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 value for the $K_{d4}$ is decided to be $3 nM$ and the confidence interval $2$. This means that the mode of the PDF is 3 and the range where 95% of the values are found is between 1.5 and 6 nM.

In a similar way, the most plausible value for $k^{-}_{4}$ is $0.9 min^{-1}$ and the confidence interval $1.3$. This means that the mode of the PDF is 0.9 and the range where 95% of the values are found is between 0.6923 and 1.17 $min^{-1}$.

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

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The location and scale parameters of the distributions are:

Parameter	μ	σ
$K_{d4}$	$1.2112$	$0.3356$
$k^{-}_{4}$	$-0.0878$	$0.1327$