AKG-DH (Doug, Feng)
From BioComputationWiKi
Contents |
Model Authors
Feng Qi, Doug Disabato and Daniel A. Beard
Biotechnology and Bioengineering Center and Department of Physiology
Medical College of Wisconsin
dbeard@mcw.edu
Reaction Mechanism
The reaction proceeds as follows
where it is treated as Ordered Ter-Bi. The production of CO2 is ignored in the model.
Curves Fitted
Model Development
- The curves presented as is are not self-consistent. Therefore, we had to make some scaling adjustments to the data.
- For instance, in Figure 2, the value of activity at 5mM EGTA was 10% (with 0.2mM AKG present). The value of activity in Figure 3 at 0.2mM AKG was 16.9% (with 5mM EGTA present).
- We multiplied these percents by each figure's respective Vmax, then came up with a ratio of these values. This ratio was used to correct all the data, using Figure 3 as a standard.
- We first analyzed the role free Calcium and EGTA play in AKGD activity. We used the most general case of activation and inhibition given in Segel to fit the data. A first optimization of all parameters did not give good fits.
- To improve the fits, we noticed that it was possible that either alpha or a and either beta or b could equal one. Both could not equal one, as this would produce no activation or inhibiton. Therefore, we conducted optimizations where we set two of the four parameters equal to one.
- The results showed that setting a and beta equal to one gave the best fits. However, this also gave b<1, which represented inhibition instead of activation.
- Setting b=0 gave us the same fit. Therefore, we concluded preliminarily that Ca2+ played no activating role in AKGD.
- We then added ADP and ATP data to the fit. We derived the new equation from the mechanism given on page 239 of Segel, which describes an activator and inhibitor that are not mutally exclusive. Our final model describes a mechanism where EGTA and Ca are mutally exclusive, ADP and ATP are mutually exclusive, but EGTA/Ca are not mutually exclusive with respect to ADP/ATP. The fits we got from this model were decent.
Fits To Data
Y-axis label should have units of (units/mg protein) instead of (% of maximum)
References
- McCormack JG and Denton RM. Biochem J. (1979) 180, 533-544.
- Segel IH. "Enzyme Kinetics" (1993)
