Formation of homo-dimer R2

Two ScbR (R) proteins bind together to form an ScbR homo-dimer (R₂).

Chemical equation

$2R \rightleftharpoons R_{2}$

Rate equation

$r= \frac{k^{-}_{6}}{K_{d6}}\cdot [R]^{2} - k^{-}_{6}\cdot [R_{2}]$

Parameters

The parameters of this reaction are the dissociation constant for binding of one ScbR to another ($K_{d6}$) and the dissociation rate for binding of one ScbR to another ($k^{-}_{6}$).

Name	Value	Units	Value in previous GBL models	Remarks-Reference
$K_{d6}$	$35.3-114$	$nM$	N/A	Majka et al. published a study on dimerization of the initiator Protein DnaA of Streptomyces and on its mutants, where they report dissociation constants in the range $35.3-114 nM$. Majka et al. 2001 These values agree with Ozbabacan et al. who state that strong protein-protein interactions such as homodimerization have equilibrium dissociation constants $< 10^{-6} M$ and mostly in the nanomolar range.
$k^{-}_{6}$	$60-6 \cdot 10^{4}$	$min^{-1}$	N/A	According to Northrup et al. the $K_{a}$ of protein-protein bond formations occur in the order of $10^{6} M^{-1}s^{-1}$. Therefore, this value is used to calculate the dissociation rate for the ScbR homo-dimer formation. Therefore the range of the $k^{-}_{3}$ values is calculated as per $k^{-}_{6}=K_{d6} \cdot K_{a}$. Northrup et al. 1992

Parameters with uncertainty

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

The most plausible parameter value for the $K_{d6}$ is decided to be $35 nM$ and the confidence interval $100$. This means that the mode of the PDF is $35$ and the range where 95% of the values are found is between $0.1$ and $10^{3} nM$.

In a similar way, the most plausible value for $k^{-}_{6}$ is $10^{-3} min^{-1}$ and the confidence interval 10. This means that the mode of the PDF is $10^{-3}$ and the range where 95% of the values are found is between $10^{-4}$ and $10^{-2}$ $min^{-1}$.

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
$K_{d6}$	$5.7331$	$1.4757$
$k^{-}_{6}$	$-6.0926$	$0.9028$