%********************************************************************************** % % CalC version 4.9.8, script "FCT_Fig5.par" % Victor Matveev, January 19, 2004 % % "Facilitation through Buffer Saturation: % Constraints on Endogenous Buffering Properties" % V. Matveev, A. Sherman and R. Zucker % Biophys. J. (2004) 86:2691-2709 % % This script produces the data for the parameter-sweep plots in Fig. 5 and 6A, % and requires a command-line parameter specifying the buffering capacity (kappa0) % For instance, to reproduce Figs. 5A and 6Ab, execute: % % calc FCT_Fig5.par 500 % % the resulting file will be called "FCT_vs_Btotal_and_kon_kappa500", and will consist % of 8 data columns, in the format "Btotal kon P1at1 P5at1 P1at2 P5at2 P1at3 P5at3", % where "P1ati" is the size of the first [Ca2+] transient at site "i", etc. Then % start gnuplot, and type % % splot 'FCT_vs_Btotal_and_kon_kappa500' u 1:2:($6/$5) w lines % % This will make a surface plot of the ratio of the 6th and 5st columns, equal to % the P5/P1 value at site "2". %================================================================================== path = "" % If running under Windows, specify here the path to the % directory containing the script imported below file = path "FCT_main.par" include file % Import the simulation parameters from the main script, % which defines everything but the buffer's parameters: %================================================================================== kappa = $2 % The command-line parameter specifies the total buffering % capacity Buffer.D = 0.2 % Diffusion coefficient is 0.2 um^2/ms kmin = 0.05 % The binding rate will vary from 0.05/(uM ms) kmax = 1.00 % to 1/(uM ms) dK = 0.05 % with steps of 0.05/(uM ms) BTmin = 40 % The buffer concentration will be varied from 40 uM BTmax = 1200 % to 1.2 mM, with steps of 40 uM (30 steps total) dB = 100 for Buffer.total = BTmin to BTmax step dB % Iterations over Btotal concentration % values: this is the outside loop for Buffer.kplus = kmin to kmax step dK % Iterations over binding rate (a.k.a kplus % a.k.a kon): this is the inside loop Buffer.KD = Buffer.total / kappa % Buffer affinity is determined by its % concentration and total capacity %================================================================================== % [Reminder: CalC script is a list of definitions, so all statements can appear in % any order (with some exceptions: see the manual)] P1at1 max Ca1 0 3 % First peak [Ca2+] transient at site "1" (distance=20 nm) P5at1 max Ca1 40 43 % Last peak [Ca2+] transient at the same site P1at2 max Ca2 0 3 % First peak [Ca2+] transient at site "2" (distance=60 nm) P5at2 max Ca2 40 43 % Last peak [Ca2+] transient at the same site P1at3 max Ca3 0 3 % First peak [Ca2+] transient at site "3" (distance=100 nm) P5at3 max Ca3 40 43 % Last peak [Ca2+] transient at the same site % Expression forming the name of the file: outfile = "FCT_vs_Btotal_and_kon_kappa" kappa if (Buffer.kplus == kmin) then if (Buffer.total == BTmin) then print outfile ' ' % Initialize the file at first iteration else append outfile ' ' % Put an empty line after each outside endif % iteration endif % Output the following data into the above file at each iteration: append outfile Buffer.total " " Buffer.kplus " " ... P1at1 " " P5at1 " " P1at2 " " P5at2 " " P1at3 " " P5at3 verbose = 0 % Suppress all simulation status statements %==================================================================================