View source for Degradation of A-R2

{{DISPLAYTITLE: Degradation of A-R<sub>2</sub>}}
The ScbR-ScbA protein complex  (AR<sub>2</sub>) degrades.
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==Chemical equation==

<center><math>A-R_{2}\rightarrow \varnothing</math></center>

== Rate equation ==

<center><math> r= d_{AR}\cdot[A-R_{2}]</math></center>

== Parameters ==

The parameter of this reaction is the degradation rate of AR<sub>2</sub> (<math>d_{AR}</math>). The parameter values were derived from proteomics studies on different proteins of ''S. coelicolor''.

{|class="wikitable" 
! Name
! Value
! Units
! Value in previous GBL models <ref name="Mehra2008"> [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0002724&representation=PDF S. Mehra, S. Charaniya, E. Takano, and W.-S. Hu. ''A bistable gene switch for antibiotic biosynthesis: The butyrolactone regulon in streptomyces coelicolor.'' PLoS ONE, 3(7), 2008.] </ref>
! Remarks-Reference
|-
|<math>d_{AR}</math>
|<math>8.3 \cdot 10^{-4}-0.0037 min^{-1}</math> <ref name="Trötschel2013"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815937/pdf/mbt0006-0708.pdf Trötschel C, Albaum SP, Poetsch A. ''Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria.'' Microbial biotechnology. 2013;6(6):708-719.]</ref> <ref name="Jayapal2010"> [http://pubs.acs.org/doi/pdf/10.1021/pr9007738 Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS. ''Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems.'' J Proteome Res. 2010 May 7;9(5):2087-97.]</ref>
|<math> min^{-1} </math> 
|<math>0.062 s^{-1}</math><ref name="Mehra2008"></ref>

(Range tested: <math>10^{-7}-10^{-1} s^{-1}</math>)

(Bistability range: <math>0.051-0.069 s^{-1}</math>)
|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 <math>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}) </math> with a median of <math>0.097 h^{-1} (0.00162 min^{-1})</math>. 
[[Image:DR-text.png|center|thumb|350px|Jayapal et al. 2012<ref name="Jayapal2010"></ref>]]

The full list of the proteins studied and their turnover rate constants can be found [http://kirschner.med.harvard.edu/files/bionumbers/List%20of%20Proteins%20Examined%20and%20Their%20Turnover%20Rate%20Constants.pdf here].
|}

==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 [[Quantification of parameter uncertainty#Design of probability distributions|'''here''']], the appropriate probability distribution was designed.

The mode of the log-normal distribution of the <math>d_{R}</math> to <math> 0.0016 min^{-1} </math>. 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 <math> 2.5 </math>, so that the range where 95.45% of the values are found is between <math>6.18\cdot 10^{-4}</math> and <math>0.004 min^{-1}</math>.

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

[[Image:DAR.png|500px]]

The location and scale parameters of the distribution are:
{|class="wikitable"
! Parameter
! μ
! σ
|-
|<math>d_{AR}</math>
|<math>-6.2752</math>
|<math>0.4285</math>
|}

==References==
<references/>