Degradation of C2-R2

The SCB-ScbR protein complex (C₂-R₂) degrades.

Chemical equation

$C_{2}-R_{2}\rightarrow \varnothing$

Rate equation

$r= d_{CR}\cdot[C_{2}-R_{2}]$

Parameters

The parameter of this reaction is the degradation rate of C₂-R₂ ($d_{CR}$). The parameter values were derived from proteomics studies on different proteins of S. coelicolor.

Name	Value	Units	Value in previous GBL models	Remarks-Reference
$d_{CR}$	$5.02 \cdot 10^{-4}- 0.00578 min^{-1}$	$min^{-1}$	$0.062 s^{-1} (3.72 min^{-1})$ $0.0031 s^{-1} (0.186 min^{-1})$ Range tested: $10^{-7}-10^{-1} s^{-1}$ ($6 \cdot 10^{-6}-6 min^{-1}$) Bistability range: $0.061-0.17 s^{-1}$ ($3.66-10.2 min^{-1}$) and $0.0031-0.068 s^{-1}$ ($0.186-4.08 min^{-1}$)	In a quantitative proteomics study on protein turnover rates in dynamic systems, Jayapal et al. reported the degradation rates of 115 proteins in S. coelicolor cultures undergoing transition from exponential growth to stationary phase. The values were in the range $0.05 \pm 0.014 h^{-1} -0.223 \pm 0.031 h^{-1} (8.3 \pm 2.3 \cdot 10^{-4}-0.0037 \pm 0.00052 min^{-1})$ with a median of $0.097 h^{-1} (0.00162 min^{-1})$. Jayapal et al. 2012 The full list of the proteins studied and their turnover rate constants can be found here. Additionally, an in vivo study examining the stability of 184 proteins in growing and non-growing E. coli reported 47 proteins that degraded within 24 hours, while the rest were either modified (27) or were found to be stable (114). The values measured were in the range $5.02 \cdot 10^{-4} - 0.00578 min^{-1}$ Mosteller et al. 2012

Parameters with uncertainty

When deciding how to describe the uncertainty for this parameter we must take into consideration that the reported values are estimated or calculated from proteomics experiments, using methods which were prone to measurement errors (i.e. optical density of fragmented mycelia to estimate the growth rate (μ)) and extrapolations from cell density to total cellular protein without taking into account the dilution due to cell division. Additionally, the study did not include measurements on protein complexes, although it was conducted on a wide range of S. coelicolor proteins which enables a rough estimation of the range of values of protein degradation in this species. These facts influence the quantification of the parameter uncertainty and therefore the shape of the corresponding distribution. By assigning the appropriate weights to the parameter values and using the method described here, the appropriate probability distribution was designed.

The mode of the log-normal distribution of the $d_{R}$ to $0.0016 min^{-1}$. In order to explore the full range of published values and even sample a percentage of values outside the reported range, the confidence interval factor is set to $2.5$, so that the range where 95.45% of the values are found is between $6.18\cdot 10^{-4}$ and $0.004 min^{-1}$.

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 the reported experimental error (green lines) or a default value of 10% error (orange lines).

The location and scale parameters of the distribution are:

Parameter	μ	σ
$d_{CR}$	$-6.2752$	$0.4285$