DynaFit Scripting Manual

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Difference response coefficients

In many cases both the substrate and the product will have nonzero molar response coefficients in the given experiment. For example, in the enzymatic hydrolysis of para-nitrophenylalanine peptides, the absorbance upon cleavage next to para-nitrophenylalanine changes by about 10%. In such cases it is often useful to consider the differential molar response coefficient (i.e., the difference between the response coefficients of the reactants and products) as the only information needed to describe the kinetic assay, while the molar response coefficient of either the reactants or the products can be considered as zero.

Example: UV/VIS Spectrophotometry.

An enzyme reaction converts the substrate S (molar absorption coefficient $\epsilon_{\scriptscriptstyle \rm S}$ = 1,300 M ${\phantom .}^{{\rm -1}}$ $\times$ cm ${\phantom .}^{{\rm -1}}$ at the given wavelength) to the products P ( $\epsilon_{\scriptscriptstyle \rm P}$ = 900 M ${\phantom .}^{{\rm -1}}$ $\times$ cm ${\phantom .}^{{\rm -1}}$) and Q ( $\epsilon_{\scriptscriptstyle \rm P}$ = 0). Let us assume that all concentrations throughout the script file are in micromolar units. The conversion of one micromole per liter of the substrate will cause a decrease of absorbance by 0.0004 absorbance units.

[mechanism]
   E + S <==> ES      :  k   ks
   ES ---> E + P + Q  :  kr
[responses]
   P = -0.0004 ; response S = 0.0 assumed
[progress]
   offset = auto ?

In the example above, the keyword auto standing next the offset in the [progress] section orders the program to construct the simulated progress curve by assuming that it is offset on the signal axis. The magnitude of this offset is given by the first experimental data point. For further explanation of the offset keyword see section 7.6.

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Petr Kuzmic | Jul 12 2005