Translation of R

The scbR mRNA (r) is translated into ScbR protein (R).

Chemical equation

$r \rightarrow r + R$

Rate equation

$r= P_{R}\cdot [r]$

Parameters

The parameter of this reaction is the translation rate of ScbR ($P_{R}$). The parameter values were derived from calculations of the protein translation rate based on genomic properties of Streptomyces coelicolor A3(2) and E.coli.

Name	Value	Units	Value in previous GBL models	Remarks-Reference
$P_{R}$	$0.165−5.86$	$min^{-1}$	$0.36 s^{-1}$ $(21.6 min^{-1})$ Range tested: $10^{-4}-10 s^{-1}$ ($0.0001-600 min^{-1}$) Bistability range: $0.25-0.39 s^{-1}$ ($15-23.4 min^{-1}$) and $0.09-0.38 s^{-1}$ ($5.4-22.8 min^{-1}$)	In a recent publication by R.A. Cox, genomic properties and macromolecular compositions of Streptomyces coelicolor A3(2) and E.coli were reported, along with equations that connect these properties. For S. coelicolor, the polypeptide elongation rate $ε_{aa}$ is reported to be in the range between 0.59 and 3.17 amino acids s-1. As ScbR has 215 aa, the transcription rate constant can be calculated as per $P_{R}=\frac{215 aa/gene}{0.59 aa/s}=364.4 s/gene=6.07 min/gene$ and $P_{R}=\frac{215 aa/gene}{3.17 aa/s}=67.82 s/gene=1.13 min/gene$, thus resulting in a final value of $0.165 min^{-1}$ and $0.89 min^{-1}$. Cox et al. 2004 Cox et al. 2004 Additionally, Cox reports translation rates for E. coli between 12 and 21 aa/s. By the same calculations, the corresponding transcription rate constants are in the range $3.35-5.86 min^{-1}$. Cox et al. 2004

Parameters with uncertainty

When deciding how to describe the uncertainty for this parameter we must take into consideration the fact that the reported values are either calculated or derived with approximation from experiments and from other macromolecular properties. Additionally, some of the values correspond to protein translation rates of different bacteria species (E. coli). This means that there might be a notable difference between actual parameter values and the ones reported in literature. These facts influence the quantification of the parameter uncertainty and therefore the shape of the corresponding distribution.

Therefore, although the weight of the distribution is put on the values calculated for S. coelicolor by setting $0.74 min^{-1}$ as the mode of the log-normal distribution for the $P_{R}$, we wish to explore the full range of reported values. Thus, the Spread is set to $3.2$ and the range where 68.27% of the values are found is between $0.23$ and $2.38$ $min^{-1}$.

The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:

The values retrieved from literature and their weights are indicated by the blue dashed lines, and the uncertainty for each value is indicated using a default value of 10% error (orange lines).

The parameter information of the distribution is:

Parameter	Mode	Spread	μ	σ
$P_{R}$	$0.744$	$3.2$	$0.42952$	$0.85176$