%********************************************************************************** % % CalC version 4.9.8, script "FCT_Fig3.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. 3, and % requires a command-line parameter specifying the Ca2+ unbinding rate % (Buffer.kminus). For instance, to reproduce Fig. 3A, execute: % % calc FCT_Fig3.par 0.4 % % the resulting file will be called "FCT_vs_Btotal_and_KD_koff0.4", and will % consist of four data columns, in the format "Btotal KD P1 P5". Then start gnuplot, % and type % splot 'FCT_vs_Btotal_and_KD_koff0.4' u 1:2:($4/$3) w lines % % This will make a surface plot of the ratio of the 4th and 1st columns, equal to % the P5/P1 value. %================================================================================== 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: %================================================================================== Buffer.kminus = $2 % The command-line parameter specifies the buffer-Ca2+ % unbinding rate Buffer.D = 0.2 % Diffusion coefficient is 0.2 um^2/ms KDmin = Buffer.kminus % Since KD = kminus / kplus, and the max binding rate is 1 KDmax = KDmin * 6 dK = (KDmax - KDmin) / 20 % Allow 20 steps along the KD (vertical) axis 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 = 40 for Buffer.KD = KDmin to KDmax step dK % Iterations over buffer affinity values % (outside loop) for Buffer.total = BTmin to BTmax step dB % Iterations over Btotal values % (inside loop) %================================================================================== P1 max Ca2 0 3 % First peak [Ca2+] transient at site "2" (distance=60 nm) P5 max Ca2 40 43 % Last peak [Ca2+] transient at the same site % Expression forming the name of the file: outfile = "FCT_vs_Btotal_and_KD_koff" Buffer.kminus if (Buffer.total == BTmin) then if (Buffer.KD == KDmin) 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.KD " " P1 " " P5 verbose = 0 % Suppress all simulation status statements %==================================================================================