Lecture 3

Supplementary files on enzyme fitting

• Create a directory Enzymes and download the following files into it:

  1. enzfitter.gnu and its data file enz1.dat.

  2. If you have Excel, the spreadsheet EnzFitter.xls, or for the ScrumPy VM or linux, EnzFitter.ods.

  3. rmm.gnu to make a 3D plot of the reversible Micaelis-Menten plot as in the Lecture 2 slides.

  Instructions for use:

  1. Either from a terminal session, change to directory Enzymes and type gnuplot, or , if using Windows gnuplot, open the programme and make Enzymes the working folder.

  2. To plot an enzyme function, enter a function name with a list of variables and then the equation. For example:

     • gnuplot> mm(s) = s*V/(Km + s)
       gnuplot> V = 100
       gnuplot> Km = 2
       gnuplot> set xlabel '[S]'
       gnuplot> set ylabel 'rate'
       gnuplot> plot [s=0:5*Km] mm(s)
       gnuplot> Km = 4
       gnuplot> replot
       gnuplot> 

  3. twoenz.gnu generates the reversible Michaelis-Menten graph shown in the Lecture 2 slides. To plot the graph, open gnuplot and type

     • gnuplot> load 'rmm.gnu' 

     show plot, show fun and show var wil show how the plot has been made.

  4. enzfitter.gnu determines K_m and V for the data in enz1.dat.

     • gnuplot> load 'enzfitter.gnu' 

     Use a text editor to see the gnuplot commands ot achieve this.

  5. EnzFitter.xls is an Excel spreadsheet that fits K_m and V. It contains the same data as enz1.dat; the initial estimates are in cells B3 and D3. Go to cell G14 and then select the 'solver' menu item to minimise this cell by altering cells B3 and D3. (This sheet does not work in other spreadsheet software as they don't have the solver add-in: EnzFitter.ods will open in the ScrumPy VM, and will allow you to manually adjust the fit.)