Difference between revisions of "Binding of R2 to A"
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(Bistability range: <math>460-630 s^{-1}</math>) | (Bistability range: <math>460-630 s^{-1}</math>) | ||
− | |According to Northrup et al. the <math>K_{ | + | |According to Northrup et al. the <math>K_{on3}</math> of protein-protein bond formations occur in the order of <math>10^{6} M^{-1}s^{-1}</math>. |
[[Image:K3-text.png|center|thumb|350px|Northrup et al. 1992<ref name="Northrup1992"></ref>]] | [[Image:K3-text.png|center|thumb|350px|Northrup et al. 1992<ref name="Northrup1992"></ref>]] | ||
− | These values are also supported by Ozbabacan et al. who claim that association rates are usually in the range <math>10^5-10^6 M^{-1}s^{-1}</math>. | + | These values are also supported by Ozbabacan et al. who claim that association rates are usually in the range <math>10^5-10^6 M^{-1}s^{-1}</math> (<math>0.006-0.06 nM^{-1}min^{-1}</math>). |
[[Image:K3-text2.png|center|thumb|350px|Ozbabacan et al. 2011<ref name="Saliha2011"></ref>]] | [[Image:K3-text2.png|center|thumb|350px|Ozbabacan et al. 2011<ref name="Saliha2011"></ref>]] | ||
− | + | Therefore, these values are used to generate the probability distribution for <math>K_{on3}</math>. | |
+ | |||
+ | Afterwards, the log-normal distribution for the dissociation rate of the ScbR-ScbA binding <math>k^{-}_{3}</math> is derived from the distributions of <math>k^{-}_{3}</math> and <math>K_{d3}</math>. | ||
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Revision as of 00:12, 6 December 2015
The ScbR homo-dimer (R2) forms a complex with ScbA (A).
Contents
Chemical equation
Rate equation
Parameters
The parameters of this reaction are the dissociation constant for binding of ScbR to ScbA () and the dissociation rate for binding of ScbR to ScbA (). Since there is no concrete evidence of the existence of the ScbA-ScbR complex so far, it is possible that the interaction between the two proteins is unstable/ transient and therefore the parameter values reflect this belief. The values of such complexes according to the literature [1] , lie in the millimolar or micromolar scale.
Name | Value | Units | Value in previous GBL model [3] | Remarks-Reference |
---|---|---|---|---|
[1] |
(Range tested: ) (Bistability range: ) |
According to the Ozbabacan et al. association constants for transient protein protein interactions lie in the millimolar or micromolar range. | ||
[4] [5] |
(Range tested: ) (Bistability range: ) |
According to Northrup et al. the of protein-protein bond formations occur in the order of .
These values are also supported by Ozbabacan et al. who claim that association rates are usually in the range (). Therefore, these values are used to generate the probability distribution for . Afterwards, the log-normal distribution for the dissociation rate of the ScbR-ScbA binding is derived from the distributions of and . |
Parameters with uncertainty
Since the values we are using for this parameter correspond to generic association constant values of a wide range of protein-protein interactions and not specifically to GBL or related systems, we wish to explore the whole range of values and investigate the conditions under which the ScbR-ScbA complex formation would be feasible. Therefore, we set the mode of the log-normal distribution for to and the confidence interval factor to . Thus, the range where 95.45% of the values are found is between and .
Similarly, by following the same reasoning, the mode of the log-normal distribution for is set to and the confidence interval factor to . This means that the range where 95.45% of the values are found is between and .
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.): 11.950 | ||
Failed to parse (Cannot store math image on filesystem.): 10.0825 | Failed to parse (Cannot store math image on filesystem.): 0.4231 |
References
- ↑ 1.0 1.1 1.2 1.3 1.4 Saliha Ece Acuner Ozbabacan, Hatice Billur Engin, Attila Gursoy, and Ozlem Keskin. Transient protein–protein interactions. Protein Engineering, Design and Selection first published online June 15, 2011
- ↑ Perkins J. R., Diboun I., Dessailly B. H., Lees J. G., Orengo C. Transient Protein-Protein Interactions: Structural, Functional, and Network Properties. Structure, 2010;18:10, p. 1233-1243
- ↑ 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.
- ↑ Janin, Joel. The kinetics of protein-protein recognition. Proteins-Structure Function and Bioinformatics (1997): 153-161.
- ↑ 5.0 5.1 Northrup S.H. and Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer simulation.PNAS 1992;89(8),3338-3342