Difference between revisions of "Binding of R2 to A"
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|<math>K_{d3}</math> | |<math>K_{d3}</math> | ||
|<math>10^{-6} - 10^{-9} </math> <ref name="Stites1997"> Wesley E. Stites. ''Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis.'' Chemical Reviews 1997 97 (5), 1233-1250</ref> | |<math>10^{-6} - 10^{-9} </math> <ref name="Stites1997"> Wesley E. Stites. ''Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis.'' Chemical Reviews 1997 97 (5), 1233-1250</ref> | ||
− | |<math> | + | |<math>M </math> |
| Comparison of strong vs weak protein-protein interactions | | Comparison of strong vs weak protein-protein interactions | ||
| rowspan="2" |The range of values correspond to weak protein interactions. <math>ΔG^{o} </math> interactions of different proteins were investigated <ref name="Stites1997"> Wesley E. Stites. ''Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis.'' Chemical Reviews 1997 97 (5), 1233-1250</ref> by calculating the <math>K_{eq} </math> by using the Van't Hoff equation <math>\ln K_{eq} = - \frac{{\Delta H^\ominus}}{RT}+ \frac{{\Delta S^\ominus }}{R}. </math> | | rowspan="2" |The range of values correspond to weak protein interactions. <math>ΔG^{o} </math> interactions of different proteins were investigated <ref name="Stites1997"> Wesley E. Stites. ''Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis.'' Chemical Reviews 1997 97 (5), 1233-1250</ref> by calculating the <math>K_{eq} </math> by using the Van't Hoff equation <math>\ln K_{eq} = - \frac{{\Delta H^\ominus}}{RT}+ \frac{{\Delta S^\ominus }}{R}. </math> |
Revision as of 15:47, 2 October 2015
The ScbR homo-dimer (R2) forms a complex with ScbA (A).
Contents
Chemical equation
![A + R_{2} \rightleftharpoons A-R_{2}](/wiki/images/math/e/9/9/e993e240dd775a57df66034766e95a55.png)
Rate equation
![r= \frac{k^{-}_{3}}{K_{d3}}\cdot [A]\cdot [R_{2}] - k^{-}_{3}\cdot [A-R_{2}]](/wiki/images/math/0/c/d/0cd085b3802a4baeb63922cb1279a5da.png)
Parameters
[NOTE TO MARC: I think the parameter values for the k3 are too arbitrary (see explanation below). Is there any way to choose more reliable ones?]
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 no evidence of the existence of the ScbA-ScbR complex has been found so far, our belief is that the interaction between the two proteins should be an unstable/ transient. The values of such complexes according to the literature [1] , lie in the millimolar or micromolar scale.
![](/wiki/images/thumb/f/fd/Protein_Interaction-2011.png/400px-Protein_Interaction-2011.png)
Parameter | Value | Units | Origin | Remarks |
---|---|---|---|---|
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Comparison of strong vs weak protein-protein interactions | The range of values correspond to weak protein interactions. ![]() ![]() ![]() |
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From various mechanisms of protein-protein interaction it was deduced that the ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Parameters with uncertainty
The probability distributions, adjusted accordingly in order to reflect the above values, are the following:
The most plausible parameter value for the is decided to be
and the confidence interval
. This means that the mode of the PDF is
and the range where 95% of the values are found is between
and
nM.
In a similar way, the most plausible value for is
and the confidence interval 6. This means that the mode of the PDF is
and the range where 95% 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 |
---|---|---|
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References
- ↑ 1.0 1.1 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
- ↑ 2.0 2.1 2.2 Wesley E. Stites. Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis. Chemical Reviews 1997 97 (5), 1233-1250
- ↑ 3.0 3.1 Janin, Joel. The kinetics of protein-protein recognition. Proteins-Structure Function and Bioinformatics (1997): 153-161.