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
$T_{R}$	$0.165-5.86$	$min^{-1}$	$0.36 s^{-1}$ (Range tested: $10^{-4}-10 s^{-1}$) (Bistability range: $0.25-0.39 s^{-1}$ and $0.09-0.38 s^{-1}$)	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 Failed to parse (Cannot store math image on filesystem.): T_{R}=\frac{215 aa/gene}{0.59 aa/s}=364.4 s/gene=6.07 min/gene and Failed to parse (Cannot store math image on filesystem.): T_{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

The most plausible parameter value for the $P_{R}$ is decided to be Failed to parse (Cannot store math image on filesystem.): 0.5 min^{-1} and the confidence interval $10$. This means that the mode of the PDF is 0.5 and the range where 95% of the values are found is between 0.05 and 5 $min^{-1}$.

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

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The location and scale parameters of the distribution are:

Parameter	μ	σ
$P_{R}$	Failed to parse (Cannot store math image on filesystem.): 0.1220	$0.9028$