BatchKi Reference Manual

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[Enzyme concentration]

The information contained in this section directs the program to treat the enzyme concentration either as a constant or, under special circumstances, as an optimized parameter. The procedure that is used in this case was recently described in the literature [4].

The default settings are as follows:

[Enzyme Concentration]
  Limits = 5
  Multiple = 1
  Optimize = yes

Parameter Optimize

The Optimize parameter has two possible values: `yes' or `no'. When the Optimize parameter is set to no, the program always treats the enzyme concentration as a fixed constant.

When the Optimize parameter is set to yes, the program initially performs the least-squares fit of initial velocity data while treating the enzyme concentration as a constant. Subsequently the program compares the resulting value of $K_{i}^{\rm app}$ with the nominal value of the enzyme concentration. In this comparison the program makes use of the parameter Multiple defined below.

Depending on the result of the comparison (see the description of Multiple below), the program may decide to repeat the regression analysis while treating the enzyme concentration as an optimized (adjustable) parameter.

Parameter Multiple

The Multiple parameter typically should have its value set to 0.5. The parameter has the following meaning.

The program initially analyzes initial reaction velocities while treating the enzyme concentration as a fixed constant. If the inhibition constant determined in this way is smaller than Multiple times the nominal enzyme concentration, the program repeats the regression analysis while treating the enzyme concentration $[E]$ as an adjustable parameter. The optimization of $[E]$ is performed within limits specified by using the parameter Limits.

Parameter Limits

If the program decides to perform an optimization of the enzyme concentration (based on the rules described above), the optimization is performed within limits defined by the parameter Limits.

In particular, the enzyme concentration is allowed to be adjusted at most by a factor Limits in either direction. That is, the adjusted value of $[E]$ can be at most Limits times smaller or Limits times larger than the nominal concentration.

Example

Assume that the nominal concentration of the enzyme is 1.5 nM and that the parameter Limits is set to Limits = 3. In this case the adjusted enzyme concentration has the largest allowed value of 1.5 $\times$ 3 = 4.5 nM, and the smallest allowed value of 1.5 / 3 = 0.5 nM.

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Petr Kuzmic | Jul 12 2008