%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % Victor V. Matveev, Richard Bertram and Arthur Sherman (2009) % Ca2+ current vs. Ca2+ channel cooperativity of exocytosis % Journal of Neuroscience, 29(39): 12196-12209. % % This CalC simulation script produces data for Fig. 8 of the manuscript % Victor Matveev, January 8, 2010 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% verbose = 0 %%%% Create file names for data storage: file = $1 ".Dist" r1 ".Imax" Imax "pA." N "x" N "x" M ".dat" tfile = file ".temp" ICfile = file ".IC" %%%%% Geometry parameters: L = 1 % enclosure length is 1 um cube MID = 0.5 % midpoint r1 = 0.02 % Distance from channel to release site (midpoint) = 20nm r2 = r1 volume 0 L 0 L 0 L %%%% Spatial grid definition: N = 80 M = 50 grid N N M stretch x x1 x2 stretch y MID MID stretch z 0 0 stretch.factor = 1.05 x1 = MID - r1 x2 = MID + r2 Ca.source x1 MID 0 ww ww ww %%% Left Ca2+ channel Ca.source x2 MID 0 ww ww ww %%% Right Ca2+ channel ww = 0.004 Ca.D = 0.2 %%% Ca2+ diffusion coefficient (um^2 / ms) Ca.bgr = 0.1 %%% Background Ca2+ concentration %%%%%%%%%% Simulation parameters: Imax = 0.05 %% Single-channel calcium current (pA) T0 = 1 %%% Pre-pulse sumulation duration (ms) T1 = 1 %%% Pulse duration (ms) T2 = 4 %%% Post-pulse simulation duration (ms) TM = T0 + T1 + T2 %%% Total simulation time Run adaptive T0 currents 0 0 Run adaptive T1 currents I1 I2 Run adaptive T2 currents 0 0 I = Imax pA I1 = I ff{1} %%% "ff" is a channel configuration selector array I2 = I ff{2} %%% (defined in inner for-loop) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% buffer B %%% Buffer definitions B.D = 0.05 B.KD = 1 B.kplus = 0.65 uptake = 0.004 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Ca2+ binding scheme: Felmy Neher Schneggenburger (2003) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% C := Ca[MID,MID,0] %% Ca2+ sensor is located at midpoint between two channels dX/dt = - 5 C kon X + koff X1 dX1/dt = 5 kon C X - koff X1 - 4 C kon X1 + 2 koff b X2 dX2/dt = 4 kon C X1 - 2 koff b X2 - 3 C kon X2 + 3 koff b^2 X3 dX3/dt = 3 kon C X2 - 3 koff b^2 X3 - 2 C kon X3 + 4 koff b^3 X4 dX4/dt = 2 kon C X3 - 4 koff b^3 X4 - C kon X4 + 5 koff b^4 X5 dX5/dt = C kon X4 - 5 koff b^4 X5 - gamma X5 R := gamma X5 % Release rate kon = 0.116 % Binding scheme rate constants koff = 8.430 gamma = 6.96 b = 0.25 % cooperativity parameter Tmax Rmax max R 0 TM %%% Rmax = max release rate; Tmax = time at max release rate Cmax max C 0 TM %%% Cmax = max [Ca2+] at release site (at midpoint) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% B0 = 1 % Min total buffer concentration (uM) B1 = 10000 % Max total buffer concentration (uM) dlog = (log(B1) - log(B0)) / 40 % Logarithmic step in concentration for logB = log(B0) to log(B1) step dlog %% Outer loop over buffer concentration B.total = exp(logB) parStr = B.total for iter = 0 to 3 step 1 %%% Second for-loop spans open channel configurations: if iter == 0 then if logB == log(B0) ff = 0 0 %%% Both channels closed (0 0) T2 = 12 X(0) = 1 plot mute R R0.dat print ICfile "X(0)=" X append ICfile "X1(0)=" X1 append ICfile "X2(0)=" X2 append ICfile "X3(0)=" X3 append ICfile "X4(0)=" X4 append ICfile "Rmax0=" Rmax "; Tmax0=" Tmax "; Cmax0=" Cmax else continue endif else include ICfile endif if iter == 1 then %%% Left channel open (1 0) ff = 1 0 print tfile "Rmax1=" Rmax "; Tmax1=" Tmax "; Cmax1=" Cmax endif if iter == 2 then %%% Right channel open (0 1) ff = 0 1 append tfile "Rmax2=" Rmax "; Tmax2=" Tmax "; Cmax2=" Cmax endif if iter == 3 then %%% Both channels open (1 1) include tfile ff = 1 1 append file parStr " " Rmax0 " " Rmax1 " " Rmax2 " " Rmax ... " " Cmax1 " " Cmax2 " " Cmax ... " " Tmax1 " " Tmax2 " " Tmax endif %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%