DynaFit Scripting Manual

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Analysis of reaction velocities

In the analysis of (initial) reaction velocities, there are several special considerations with regard to molar response coefficients. Occasionally the initial velocity data might be expressed in different time units (e.g., absorbance units per minute) then the rate constants are (reciprocal seconds). In such cases, the response coefficient must reflect the disparity in time units.

Example: UV/VIS Spectrophotometry - initial velocities.

As in the previous example, an enzyme reaction converts the substrate S (molar absorption coefficient $\epsilon_{\scriptscriptstyle \rm S}$ = 1,000 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. However the reaction velocities, listed in the second column of the datafile, are in milli-OD per minute. Therefore, we must first multiply by 1000 and then divide by 60 to obtain the correct nominal value of $\Delta \epsilon$:

[mechanism]
   E + S <==> ES      :  k   ks
   ES ---> E + P + Q  :  kr
[responses]
   P = -0.00666 ; = -0.0004 / 60 * 1000
[velocity]
   file   VEL.TXT  ; second column milli-OD/min

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Petr Kuzmic | Jul 12 2005