Diagnostic plots

DynaFit has the ability to produce two classic diagnostic plots frequently used in traditional enzyme kinetic research, namely, the Lineweaver-Burk plot and the Dixon plot.

Lineweaver-Burk plot

In a Lineweaver-Burk plot, both the independent variable (substrate concentration) and the dependent variable (initial reaction velocity) are reciprocally tranformed. The program can be instructed to produce a Lineweaver-Burk diagnostic plot by inserting the line plot Lineweaver-Burk into the [velocity] section of the script file. The plot command must be placed before the first data file is named.

Example 1

In this extended example the program will produce five different Lineweaver-Burk plots, corresponding to the concentration of substrate A = 1, 2, 4, 8, and 16. The reaction mechanism follows a rapid equilibrium random Bi-Bi enzyme system as defined in ref. [6] (p. 643). Note that for the same global data set we produce five separate plots because the system at hand involves three varied concentrations (of substrates A, P, and Q). Note that the different graphs required in this example are identified by the keyword graph, followed by a short descriptive title (e.g., A = 4). A sample output file produced by DynaFit is shown in Figure 8.1.

[task]

   task = simulate
   data = velocities

[mechanism]

   E + A <==> EA        :   Ka     dissoc.
   E + B <==> EB        :   Kb     dissoc.
   E + A + B <==> EAB   :   Kab    dissoc.

   EAB ---> E + P + Q   :   kp

   E + P <==> EP        :   Kp     dissoc.
   E + Q <==> EQ        :   Kq     dissoc.
   E + P + Q <==> EPQ   :   Kpq    dissoc.

   EPQ ---> E + A + B   :   k-p

[constants]

   Ka = 1 ?, Kb = 2 ?, Kab = 3 ?
   kp  = 2 ?

   Kp = 5 ?, Kq = 6 ?, Kpq = 7 ?
   k-p = 1 ?

[concentrations]

   E = 0.001

[responses]

   P = 1

[progress]

   rapid equilibrium

[velocity]

   directory  ./examples/segel/Ch9/N/data
   extension  txt
   mesh       from 1 to 32 step 2 logarithmic
   error      linear 0.000001, 0.0001
   variable   B
   plot       Lineweaver-Burk

   graph A = 1

   file p0a1 | conc P = 0 , Q = 0 , A = 1
   file p1a1 | conc P = 2 , Q = 2 , A = 1
   file p2a1 | conc P = 4 , Q = 4 , A = 1
   file p3a1 | conc P = 8 , Q = 8 , A = 1
   file p4a1 | conc P = 16, Q = 16, A = 1

   graph A = 2

   file p0a2 | conc P = 0 , Q = 0 , A = 2
   file p1a2 | conc P = 2 , Q = 2 , A = 2
   file p2a2 | conc P = 4 , Q = 4 , A = 2
   file p3a2 | conc P = 8 , Q = 8 , A = 2
   file p4a2 | conc P = 16, Q = 16, A = 2

   graph A = 4

   file p0a3 | conc P = 0 , Q = 0 , A = 4
   file p1a3 | conc P = 2 , Q = 2 , A = 4
   file p2a3 | conc P = 4 , Q = 4 , A = 4
   file p3a3 | conc P = 8 , Q = 8 , A = 4
   file p4a3 | conc P = 16, Q = 16 , A = 4

   graph A = 8

   file p0a4 | conc P = 0 , Q = 0 , A = 8
   file p1a4 | conc P = 2 , Q = 2 , A = 8
   file p2a4 | conc P = 4 , Q = 4 , A = 8
   file p3a4 | conc P = 8 , Q = 8 , A = 8
   file p4a4 | conc P = 16, Q = 16, A = 8

   graph A = 16

   file p0a5 | conc P = 0 , Q = 0 , A = 16
   file p1a5 | conc P = 2 , Q = 2 , A = 16
   file p2a5 | conc P = 4 , Q = 4 , A = 16
   file p3a5 | conc P = 8 , Q = 8 , A = 16
   file p4a5 | conc P = 16, Q = 16, A = 16

[output]

   directory  ./examples/segel/Ch9/N/output

[end]

**Figure 8.1:** Postscript graphics generated by program DynaFit, showing one of five Lineweaver-Burk plots defined in Example 1.
$\includegraphics[scale=0.8]{eps/liburk.eps}$

Dixon plot

In a Dixon plot, both the independent variable (concentration of an inhibitor) plotted directly against the reciprocal initial reaction velocity. The program can be instructed to produce a Dixon diagnostic plot by inserting the line plot Dixon into the [velocity] section of the script file. The plot command must be placed before the first data file is named.

Next: Equilibria Up: Velocities Previous: Experimental error Index

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Petr Kuzmic | Jul 12 2005