Difference between revisions of "Binding of R2 to C"
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When deciding how to describe the uncertainty for each parameter there are a few points to be taken into consideration. Firstly, the values reported in literature are spread in a relatively large range and correspond to TetR and TetR mutant proteins. Additionally, most of the values were acquired by ''in vitro'' testing. 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 distributions. | When deciding how to describe the uncertainty for each parameter there are a few points to be taken into consideration. Firstly, the values reported in literature are spread in a relatively large range and correspond to TetR and TetR mutant proteins. Additionally, most of the values were acquired by ''in vitro'' testing. 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 distributions. | ||
− | With regards to the <math>K_{d4}</math> the value that is mostly reported in different publications is <math> 1 nM </math>, therefore we will put the weight of the distribution in the range <math> 1-10 nM </math> and consider as least likely the larger values. Therefore, the mode of the log-normal distribution is set to <math> 5 nM </math> and the confidence interval factor is <math> | + | With regards to the <math>K_{d4}</math> the value that is mostly reported in different publications is <math> 1 nM </math>, therefore we will put the weight of the distribution in the range <math> 1-10 nM </math> and consider as least likely the larger values. Therefore, the mode of the log-normal distribution is set to <math> 5 nM </math> and the confidence interval factor is <math> 1000 </math>. Thus the range where 95% of the values are found is between <math> 5 \cdot 10^{-3}</math> and <math> 5 \cdot 10^{3} nM</math>. |
− | + | Since the mode chosen for <math>K_{d4}</math> is set in the <math> 10^{-9} M</math> range and the two parameters are interconnected, the smaller values reported by Schubert et al. (<math> 10^{-4} min^{-1}</math>) are considered least likely for <math>k^{-}_{4}</math>. Therefore, the mode of the log-normal distribution for <math>k^{-}_{4}</math> is set to <math>1.3 min^{-1}</math> and the confidence interval factor is <math>100</math>. In this way the range where 95% of the values are found is between 0.013 and 130 <math>min^{-1}</math>. | |
The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following: | The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following: | ||
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|- | |- | ||
|<math>k^{-}_{4}</math> | |<math>k^{-}_{4}</math> | ||
− | |<math> | + | |<math>2.4401</math> |
− | |<math> | + | |<math>1.4757</math> |
|} | |} | ||
==References== | ==References== | ||
<references/> | <references/> |
Revision as of 05:37, 13 October 2015
SCBs (C2) bind to ScbR homo-dimer (R2) and inactivate its repressing activity.
Contents
Chemical equation
The exact mechanism is still unclear, however in our model we assumed that two SCBs bind to the ScbR homo-dimer.
Rate equation
Parameters
The parameters of this reaction are the dissociation constant for binding of SCB to ScbR () and the dissociation rate for binding of SCB to ScbR (). ScbR is a member of the TetR family of repressors, named after the member of this group which is the most completely characterized, the TetR repressor protein. TetR binds to the operator tetO, repressing its own expression and that of the efflux determinant tetA. However, [MgTc]+ binds to TetR and thus the affinity of the later for the operator tetO is 9-fold reduced. This procedure is similar to ScbR binding to OR and OA and repressing its own expression and the expression of ScbA, while binding to SCBs reduces its affinity for the two operators. Therefore parameter values were derived from published data on the TetR-[MgTc]+ and TetR-Tc (without Mg+) interactions.
Name | Value | Units | Value in previous GBL models [1] [2] | Remarks-Reference |
---|---|---|---|---|
[3] [4] [5] [6] [7] |
(Range tested: ) (Bistability range: [1] and [2]) |
According to Hillen et al. and Orth et al. the association constant for TetR-Tc binding is in the ~ range in presence of Mg2+, therefore a Kd= ~
On the other hand, Kedracka-Krok et al. reported an association constant Ka= in absence of Mg2+ (therefore a Kd=) and an association constant Ka= for binding of TetR to [Tc-Mg]+ (therefore a Kd=). Finally, Schubert et al. reported Mg2+ independent KAs in the ~ range and Mg2+ dependent KAs in the ~ range. | ||
[3] [7] |
(Range tested: ) (Bistability range: [1] and [2]) |
According to Kedracka-Krok et al. the unbinding rate for the TetR-Tc complex is in absence of Mg2+ and in presence of Mg2+ (see figure above).
However, Schubert et al. reported a dissociation rate of (see table above). |
Name | Value | Units | Origin | Remarks |
---|---|---|---|---|
TetR-like Rv3066 from M. tuberculosis
TetR in complex with the inducer tetracycline-Mg2+ |
Repressor protein TetR binds to [MgTc]+ and its affinity for the operator tetO is 9-fold reduced. Similar structure and activity as SCB binding to ScbR. | |||
[3] | SPR of a TetR-like protein (RolR) on a Gram and GC content ~ 50-60% from Corynebacterium glutamicum |
Parameters with uncertainty
When deciding how to describe the uncertainty for each parameter there are a few points to be taken into consideration. Firstly, the values reported in literature are spread in a relatively large range and correspond to TetR and TetR mutant proteins. Additionally, most of the values were acquired by in vitro testing. 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 distributions.
With regards to the the value that is mostly reported in different publications is , therefore we will put the weight of the distribution in the range and consider as least likely the larger values. Therefore, the mode of the log-normal distribution is set to and the confidence interval factor is . Thus the range where 95% of the values are found is between and .
Since the mode chosen for is set in the range and the two parameters are interconnected, the smaller values reported by Schubert et al. () are considered least likely for . Therefore, the mode of the log-normal distribution for is set to and the confidence interval factor is . In this way the range where 95% of the values are found is between 0.013 and 130 .
The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following:
The location and scale parameters of the distributions are:
Parameter | μ | σ |
---|---|---|
Failed to parse (Cannot store math image on filesystem.): 5.3401 | Failed to parse (Cannot store math image on filesystem.): 1.9315 | |
Failed to parse (Cannot store math image on filesystem.): 2.4401 |
References
- ↑ 1.0 1.1 1.2 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.
- ↑ 2.0 2.1 2.2 A. Chatterjee, L. Drews, S. Mehra, E. Takano, Y.N. Kaznessis, and W.-S. Hu. Convergent transcription in the butyrolactone regulon in streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis. PLoS ONE, 6(7), 2011.
- ↑ 3.0 3.1 3.2 3.3 3.4 Sylwia Kedracka-Krok, Andrzej Gorecki, Piotr Bonarek, and Zygmunt Wasylewski. Kinetic and Thermodynamic Studies of Tet Repressor−Tetracycline Interaction. Biochemistry 2005 44 (3), 1037-1046
- ↑ Kamionka A, Bogdanska-Urbaniak J, Scholz O, Hillen W. Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Research. 2004;32(2):842-847.
- ↑ 5.0 5.1 Orth P., Schnappinger D, Hillen W, Saenger W, Hinrichs W. Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nature Structural & Molecular Biology, 2000;7(3):215-9.
- ↑ 6.0 6.1 Hillen W., Berens C. Mechanisms underlying expression of Tn10 encoded tetracycline resistance. Annu Rev Microbiol. 1994;48:345-69.
- ↑ 7.0 7.1 7.2 Schubert P., Pfleiderer K., Hillen W. Tet repressor residues indirectly recognizing anhydrotetracycline. Eur J Biochem. 2004 Jun;271(11):2144-52.