//genesis
// kkit Version 8 flat dumpfile
 
// Saved on Fri Feb 21 12:07:49 2003
 
include kkit {argv 1}
 
FASTDT = 0.0001
SIMDT = 0.01
CONTROLDT = 5
PLOTDT = 1
MAXTIME = 5000
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 0
DEFAULT_VOL = 3.9e-16
VERSION = 8.0
setfield /file/modpath value /home2/bhalla/scripts/modules
kparms
 
//genesis

initdump -version 3 -ignoreorphans 1
simobjdump table input output alloced step_mode stepsize x y z
simobjdump xtree path script namemode sizescale
simobjdump xcoredraw xmin xmax ymin ymax
simobjdump xtext editable
simobjdump xgraph xmin xmax ymin ymax overlay
simobjdump xplot pixflags script fg ysquish do_slope wy
simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
  link savename file version md5sum mod_save_flag x y z
simobjdump kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \
  xtree_fg_req xtree_textfg_req x y z
simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
  keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
  trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
simobjdump xtab input output alloced step_mode stepsize notes editfunc \
  xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
  xtree_textfg_req x y z
simobjdump transport input output alloced step_mode stepsize dt delay clock \
  kf xtree_fg_req xtree_textfg_req x y z
simobjdump proto x y z
simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z
simobjdump uplink xtree_fg_req xtree_textfg_req x y z
simobjdump downlink xtree_fg_req xtree_textfg_req x y z
simobjdump mirror notes xtree_fg_req x y z
simundump kpool /kinetics/L 0 0.03 0.03 0.03 7020 7020 7020 0 2.34e+05 4 "" \
  blue black -4 2 0
simundump kpool /kinetics/R 0 0.42735 0.42735 0.42735 1e+05 1e+05 1e+05 0 \
  2.34e+05 0 "" blue black -4 0 0
simundump kreac /kinetics/L-bind-R 0 7.1197e-07 0.005 "" white black -2 1 0
simundump kpool /kinetics/C 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black 0 0 0
simundump kreac /kinetics/C-dimer 0 4.2735e-06 1 "" white black 2 1 0
simundump kpool /kinetics/C* 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black 8 0 0
simundump kpool /kinetics/C2 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black 4 0 0
simundump kreac /kinetics/C2-phos 0 0.833 0.0833 "" white black 6 1 0
simundump kpool /kinetics/A1 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 8 2 0
simundump kreac /kinetics/C*-bind-A1 0 2.1368e-05 0.50001 "" white black 10 1 \
  0
simundump kpool /kinetics/A2 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 8 3 0
simundump kreac /kinetics/C*A1-bind-A2 0 2.1368e-05 0.50001 "" white black 14 \
  1 0
simundump kpool /kinetics/C*A1 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black 12 0 \
  0
simundump kreac /kinetics/A1-bind-A2 0 2.1368e-05 0.50001 "" white black -4 3 \
  0
simundump kpool /kinetics/A1A2 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black -9 1 \
  0
simundump kreac /kinetics/C*-bind-A1A2 0 2.1368e-05 0.50001 "" white black -4 \
  -1 0
simundump kpool /kinetics/E0* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 0 black 17 -1 0
simundump kenz /kinetics/E0*/E1_activ 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 0 \
  0 "" red 0 "" 17 -2 0
simundump kpool /kinetics/E1 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 19 -3 0
simundump kpool /kinetics/E1* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 29 black 12 -3 0
simundump kenz /kinetics/E1*/E2_activ 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 0 \
  0 "" red 29 "" 12 -4 0
simundump kpool /kinetics/P1 0 0.021368 0.021368 0.021368 5000 5000 5000 0 \
  2.34e+05 0 "" blue black 17 -5 0
simundump kenz /kinetics/P1/E1*_deactiv 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 \
  0 0 "" red blue "" 17 -4 0
simundump kpool /kinetics/E2 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 15 -5 0
simundump kpool /kinetics/E2* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 42 black 7 -5 0
simundump kenz /kinetics/E2*/E3_activ 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 0 \
  0 "" red 42 "" 7 -6 0
simundump kpool /kinetics/P2 0 0.021368 0.021368 0.021368 5000 5000 5000 0 \
  2.34e+05 0 "" blue black 12 -7 0
simundump kenz /kinetics/P2/E2*_deactiv 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 \
  0 0 "" red blue "" 12 -6 0
simundump kpool /kinetics/E3 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 10 -7 0
simundump kpool /kinetics/E3* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 48 black 2 -7 0
simundump kenz /kinetics/E3*/E4_activ 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 0 \
  0 "" red 48 "" 2 -8 0
simundump kpool /kinetics/P3 0 0.021368 0.021368 0.021368 5000 5000 5000 0 \
  2.34e+05 0 "" blue black 7 -9 0
simundump kenz /kinetics/P3/E3*_deactiv 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 \
  0 0 "" red blue "" 7 -8 0
simundump kpool /kinetics/E4 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 5 -9 0
simundump kpool /kinetics/E4* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 50 black -3 -9 0
simundump kenz /kinetics/E4*/E5_activ 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 0 \
  0 "" red 50 "" -3 -10 0
simundump kenz /kinetics/E4*/E4*_adpt_fb 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 \
  0.1 0 0 "" red 50 "" -4 -6 0
simundump kpool /kinetics/P4 0 0.021368 0.021368 0.021368 5000 5000 5000 0 \
  2.34e+05 0 "" blue black 2 -11 0
simundump kenz /kinetics/P4/E4*_deactiv 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 \
  0 0 "" red blue "" 2 -10 0
simundump kpool /kinetics/E5 0 0.042735 0.042735 0.042735 10000 10000 10000 0 \
  2.34e+05 0 "" blue black 0 -11 0
simundump kpool /kinetics/P5 0 0.021368 0.021368 0.021368 5000 5000 5000 0 \
  2.34e+05 0 "" blue black -3 -13 0
simundump kenz /kinetics/P5/E5*_deactiv 0 0 0 0 0 2.34e+05 4.2735e-05 0.5 0.1 \
  0 0 "" red blue "" -3 -12 0
simundump kpool /kinetics/E5* 0 0 0 0 0 0 0 0 2.34e+05 0 "" 60 black -8 -11 0
simundump kpool /kinetics/A2- 0 0 0 0 0 0 0 0 2.34e+05 0 "" blue black -8 -4 \
  0
simundump xgraph /graphs/conc1 0 0 5000 0 0.014135 0
simundump xgraph /graphs/conc2 0 0 5000 0 1 0
simundump xplot /graphs/conc1/E1*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 29 0 0 1
simundump xplot /graphs/conc1/E2*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 42 0 0 1
simundump xplot /graphs/conc1/E3*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 48 0 0 1
simundump xplot /graphs/conc1/E4*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 50 0 0 1
simundump xplot /graphs/conc1/E5*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 60 0 0 1
simundump xplot /graphs/conc1/E0*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 0 0 0 1
simundump xgraph /moregraphs/conc3 0 0 5000 0 1 0
simundump xgraph /moregraphs/conc4 0 0 5000 0 1 0
simundump xcoredraw /edit/draw 0 -11 21 -15 5
simundump xtree /edit/draw/tree 0 \
  /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
  "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
simundump xtext /file/notes 0 1
xtextload /file/notes \
"This is GENESIS model based on : " \
"A computational study of feedback effects on signal dynamics in" \
"a mitogen-activated kinase(MAPK) pathway model by" \
"Anand R. Asthagiri* and Douglas A. Lauffenburger" \
"Biotechnol. Prog. 2001, 17, 227-239." \
"" \
"Note: " \
"1. Volume of the pools were set to 3.9e-16." \
"2. L was buffered at the CoInit = 0.03uM." \
"3. All the parameters were obtained from above mentioned literature" \
"" \
"Simulation:" \
"This modle simulates figure 7A of paper which indicates mechanism of adaptation" \
"in the presence of adaptor targeted feedback control." \
"In the presence of adaptor targeted feedback, adaptation of not only the target signal e0* but also" \
"signals downstream of the target, ei* for i=1-5." \
""\
"Note:" \
"Results in figure 7A of paper are total no of active enzyme (ei*)" \
"normalized using total enzyme at each level E^Ti. But actual graphs" \
"ploted in genesis is equivalent concentration uM to that of no of enzymes" \
"actual quantity of enzyme in no. of active enzyme can be obtained" \
"by going to each stage of the enzyme cascade and getting n for each of" \
"active enzyme (ei*) and then dividing that by the total enzyme (E^Ti) at" \
"each stage. " \
"summary : " \
"ei* = (total no. of active enzyme/total no. of enzyme at that level" \
"" \
"Example: " \
"Let kpool e1's n=1666.6 got after running simulation for 1000sec" \
"             & nInit = 10^4 no.cells then normalized value will" \
"               be 0.1666." \
"" \
""
addmsg /kinetics/L-bind-R /kinetics/L REAC A B 
addmsg /kinetics/L-bind-R /kinetics/R REAC A B 
addmsg /kinetics/L /kinetics/L-bind-R SUBSTRATE n 
addmsg /kinetics/R /kinetics/L-bind-R SUBSTRATE n 
addmsg /kinetics/C /kinetics/L-bind-R PRODUCT n 
addmsg /kinetics/L-bind-R /kinetics/C REAC B A 
addmsg /kinetics/C-dimer /kinetics/C REAC A B 
addmsg /kinetics/C-dimer /kinetics/C REAC A B 
addmsg /kinetics/C /kinetics/C-dimer SUBSTRATE n 
addmsg /kinetics/C /kinetics/C-dimer SUBSTRATE n 
addmsg /kinetics/C2 /kinetics/C-dimer PRODUCT n 
addmsg /kinetics/C2-phos /kinetics/C* REAC B A 
addmsg /kinetics/C*-bind-A1 /kinetics/C* REAC A B 
addmsg /kinetics/C*-bind-A1A2 /kinetics/C* REAC A B 
addmsg /kinetics/C-dimer /kinetics/C2 REAC B A 
addmsg /kinetics/C2-phos /kinetics/C2 REAC A B 
addmsg /kinetics/C2 /kinetics/C2-phos SUBSTRATE n 
addmsg /kinetics/C* /kinetics/C2-phos PRODUCT n 
addmsg /kinetics/C*-bind-A1 /kinetics/A1 REAC A B 
addmsg /kinetics/A1-bind-A2 /kinetics/A1 REAC A B 
addmsg /kinetics/C* /kinetics/C*-bind-A1 SUBSTRATE n 
addmsg /kinetics/A1 /kinetics/C*-bind-A1 SUBSTRATE n 
addmsg /kinetics/C*A1 /kinetics/C*-bind-A1 PRODUCT n 
addmsg /kinetics/C*A1-bind-A2 /kinetics/A2 REAC A B 
addmsg /kinetics/A1-bind-A2 /kinetics/A2 REAC A B 
addmsg /kinetics/C*A1 /kinetics/C*A1-bind-A2 SUBSTRATE n 
addmsg /kinetics/A2 /kinetics/C*A1-bind-A2 SUBSTRATE n 
addmsg /kinetics/E0* /kinetics/C*A1-bind-A2 PRODUCT n 
addmsg /kinetics/C*-bind-A1 /kinetics/C*A1 REAC B A 
addmsg /kinetics/C*A1-bind-A2 /kinetics/C*A1 REAC A B 
addmsg /kinetics/A2 /kinetics/A1-bind-A2 SUBSTRATE n 
addmsg /kinetics/A1 /kinetics/A1-bind-A2 SUBSTRATE n 
addmsg /kinetics/A1A2 /kinetics/A1-bind-A2 PRODUCT n 
addmsg /kinetics/A1-bind-A2 /kinetics/A1A2 REAC B A 
addmsg /kinetics/C*-bind-A1A2 /kinetics/A1A2 REAC A B 
addmsg /kinetics/A1A2 /kinetics/C*-bind-A1A2 SUBSTRATE n 
addmsg /kinetics/E0* /kinetics/C*-bind-A1A2 PRODUCT n 
addmsg /kinetics/C* /kinetics/C*-bind-A1A2 SUBSTRATE n 
addmsg /kinetics/C*A1-bind-A2 /kinetics/E0* REAC B A 
addmsg /kinetics/C*-bind-A1A2 /kinetics/E0* REAC B A 
addmsg /kinetics/E0*/E1_activ /kinetics/E0* REAC eA B 
addmsg /kinetics/E4*/E4*_adpt_fb /kinetics/E0* REAC sA B 
addmsg /kinetics/E0* /kinetics/E0*/E1_activ ENZYME n 
addmsg /kinetics/E1 /kinetics/E0*/E1_activ SUBSTRATE n 
addmsg /kinetics/E0*/E1_activ /kinetics/E1 REAC sA B 
addmsg /kinetics/P1/E1*_deactiv /kinetics/E1 MM_PRD pA 
addmsg /kinetics/E0*/E1_activ /kinetics/E1* MM_PRD pA 
addmsg /kinetics/P1/E1*_deactiv /kinetics/E1* REAC sA B 
addmsg /kinetics/E1*/E2_activ /kinetics/E1* REAC eA B 
addmsg /kinetics/E1* /kinetics/E1*/E2_activ ENZYME n 
addmsg /kinetics/E2 /kinetics/E1*/E2_activ SUBSTRATE n 
addmsg /kinetics/P1/E1*_deactiv /kinetics/P1 REAC eA B 
addmsg /kinetics/P1 /kinetics/P1/E1*_deactiv ENZYME n 
addmsg /kinetics/E1* /kinetics/P1/E1*_deactiv SUBSTRATE n 
addmsg /kinetics/E1*/E2_activ /kinetics/E2 REAC sA B 
addmsg /kinetics/P2/E2*_deactiv /kinetics/E2 MM_PRD pA 
addmsg /kinetics/E1*/E2_activ /kinetics/E2* MM_PRD pA 
addmsg /kinetics/P2/E2*_deactiv /kinetics/E2* REAC sA B 
addmsg /kinetics/E2*/E3_activ /kinetics/E2* REAC eA B 
addmsg /kinetics/E2* /kinetics/E2*/E3_activ ENZYME n 
addmsg /kinetics/E3 /kinetics/E2*/E3_activ SUBSTRATE n 
addmsg /kinetics/P2/E2*_deactiv /kinetics/P2 REAC eA B 
addmsg /kinetics/P2 /kinetics/P2/E2*_deactiv ENZYME n 
addmsg /kinetics/E2* /kinetics/P2/E2*_deactiv SUBSTRATE n 
addmsg /kinetics/E2*/E3_activ /kinetics/E3 REAC sA B 
addmsg /kinetics/P3/E3*_deactiv /kinetics/E3 MM_PRD pA 
addmsg /kinetics/E2*/E3_activ /kinetics/E3* MM_PRD pA 
addmsg /kinetics/P3/E3*_deactiv /kinetics/E3* REAC sA B 
addmsg /kinetics/E3*/E4_activ /kinetics/E3* REAC eA B 
addmsg /kinetics/E3* /kinetics/E3*/E4_activ ENZYME n 
addmsg /kinetics/E4 /kinetics/E3*/E4_activ SUBSTRATE n 
addmsg /kinetics/P3/E3*_deactiv /kinetics/P3 REAC eA B 
addmsg /kinetics/P3 /kinetics/P3/E3*_deactiv ENZYME n 
addmsg /kinetics/E3* /kinetics/P3/E3*_deactiv SUBSTRATE n 
addmsg /kinetics/E3*/E4_activ /kinetics/E4 REAC sA B 
addmsg /kinetics/P4/E4*_deactiv /kinetics/E4 MM_PRD pA 
addmsg /kinetics/E3*/E4_activ /kinetics/E4* MM_PRD pA 
addmsg /kinetics/P4/E4*_deactiv /kinetics/E4* REAC sA B 
addmsg /kinetics/E4*/E5_activ /kinetics/E4* REAC eA B 
addmsg /kinetics/E4*/E4*_adpt_fb /kinetics/E4* REAC eA B 
addmsg /kinetics/E4* /kinetics/E4*/E5_activ ENZYME n 
addmsg /kinetics/E5 /kinetics/E4*/E5_activ SUBSTRATE n 
addmsg /kinetics/E4* /kinetics/E4*/E4*_adpt_fb ENZYME n 
addmsg /kinetics/E0* /kinetics/E4*/E4*_adpt_fb SUBSTRATE n 
addmsg /kinetics/P4/E4*_deactiv /kinetics/P4 REAC eA B 
addmsg /kinetics/P4 /kinetics/P4/E4*_deactiv ENZYME n 
addmsg /kinetics/E4* /kinetics/P4/E4*_deactiv SUBSTRATE n 
addmsg /kinetics/E4*/E5_activ /kinetics/E5 REAC sA B 
addmsg /kinetics/P5/E5*_deactiv /kinetics/E5 MM_PRD pA 
addmsg /kinetics/P5/E5*_deactiv /kinetics/P5 REAC eA B 
addmsg /kinetics/P5 /kinetics/P5/E5*_deactiv ENZYME n 
addmsg /kinetics/E5* /kinetics/P5/E5*_deactiv SUBSTRATE n 
addmsg /kinetics/E4*/E5_activ /kinetics/E5* MM_PRD pA 
addmsg /kinetics/P5/E5*_deactiv /kinetics/E5* REAC sA B 
addmsg /kinetics/E4*/E4*_adpt_fb /kinetics/A2- MM_PRD pA 
addmsg /kinetics/E1* /graphs/conc1/E1*.Co PLOT Co *E1*.Co *29 
addmsg /kinetics/E2* /graphs/conc1/E2*.Co PLOT Co *E2*.Co *42 
addmsg /kinetics/E3* /graphs/conc1/E3*.Co PLOT Co *E3*.Co *48 
addmsg /kinetics/E4* /graphs/conc1/E4*.Co PLOT Co *E4*.Co *50 
addmsg /kinetics/E5* /graphs/conc1/E5*.Co PLOT Co *E5*.Co *60 
addmsg /kinetics/E0* /graphs/conc1/E0*.Co PLOT Co *E0*.Co *0 
enddump
// End of dump

call /kinetics/L/notes LOAD \
"L CoInit = buffered at 0.03 uM" \
"from" \
"Asthagiri, A.R and Lauffenburger, D.A " \
"Biotechnol. Prog. 2001, 17, 227-239." \
"" \
""
call /kinetics/R/notes LOAD \
"R nInit = 10^5 no./cell" \
"from" \
"Asthagiri, A.R and Lauffenburger, D.A" \
"Biotechnol. Prog. 2001. 17,227-239. "
call /kinetics/L-bind-R/notes LOAD \
"Kf = 10^7/M-1 min-1 and Kr is 0.3 min-1" \
"from" \
"Asthagiri, A.R and Lauffenburger, D.A" \
"Biotechnol. Prog. 2001, 17, 227-239."
call /kinetics/C/notes LOAD \
"Ligand bound receptor" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/C-dimer/notes LOAD \
"Kc is 6*10^7 M-1 min-1 and Ku is 60 min-1" \
"from" \
"Asthagiri, A.R and Lauffenburger, D.A " \
"Biotechnol. Prog. 2001, 17, 227-239."
call /kinetics/C*/notes LOAD \
"Activated form of receptor" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/C2/notes LOAD \
"Dimer formed by receptor binding" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/C2-phos/notes LOAD \
"Kc+ is 50min-1 and Kc- is 5min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/A1/notes LOAD \
"First adaptor protein. Tot.no. 10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/C*-bind-A1/notes LOAD \
"Kf1 is 3*10^8 M-1 min-1 and Kr1 is 0.5/sec" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/A2/notes LOAD \
"Second adaptor protein. Tot.no. 10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/C*A1-bind-A2/notes LOAD \
"kf2 and kr2 are 3*10^8 M-1 min-1 and 0.5/sec" \
"from " \
"Asthagiri and Lauffenburger , 20001."
call /kinetics/C*A1/notes LOAD \
"Adaptor protein bound activated receptor" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/A1-bind-A2/notes LOAD \
"Kc12 and Kd12 are 3*10^8 M-1 min-1 and 0.5/sec" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/A1A2/notes LOAD \
"Adaptor protein heterodimer" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/C*-bind-A1A2/notes LOAD \
"Kf12 and Kr12 are 3*10^8 M-1 min-1 and 0.5/sec" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E0*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/E0*/E1_activ/notes LOAD \
"k1+ =6*10^8 M-1 min-1, k1- =30 min-1, kcat,1 =6 min-1 and km caluculated to 0.06" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E1/notes LOAD \
"E1^T = 10^4 no./cell" \
"from " \
"Asthagiri and Lauffenburger 2001"
call /kinetics/E1*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/E1*/E2_activ/notes LOAD \
"k2+ =6*10^8 M-1 min-1, k2- =30 min-1, kcat,2 =6 min-1" \
"from" \
"Asthagire and Lauffenburger 2001"
call /kinetics/P1/notes LOAD \
"Deactivating enzyme, P1^T = 5000 no./cell" \
"from" \
"Asthagiri and Lauffenburger, 2001"
call /kinetics/P1/E1*_deactiv/notes LOAD \
"kp1+ =6*10^8 M-1 min-1, kp1- =30 min-1, kpcat,1 =6 min-1" \
"form" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E2/notes LOAD \
"E2^T =10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E2*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/E2*/E3_activ/notes LOAD \
"k3+ =6*10^8 M-1 min-1, k3- =30 min-1, kcat,3 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/P2/notes LOAD \
"Deactivating enzyme P2^T = 5000 no./cell." \
"from" \
"Asthagiri and Lauffenburger, 2001."
call /kinetics/P2/E2*_deactiv/notes LOAD \
"kp2+ =6*10^8 M-1 min-1, kp2- = 30 min-1, kpcat,2 = 6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E3/notes LOAD \
"E3^T =10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E3*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/E3*/E4_activ/notes LOAD \
"k4+ = 6*10^8 M-1 min-1, k4- =30 min-1, kcat,4 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/P3/notes LOAD \
"Deactivating enzyme P3^T = 5000 no./cell" \
"from" \
"Asthagiri and Lauffenburger, 2001"
call /kinetics/P3/E3*_deactiv/notes LOAD \
"kp3+ =6*10^8 M-1 min-1, kp3- =30 min-1, kpcat,3 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E4/notes LOAD \
"E4^T =10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/E4*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/E4*/E5_activ/notes LOAD \
"k5+ =6*10^8 M-1 min-1, k5- =30 min-1, kcat,5 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E4*/E4*_adpt_fb/notes LOAD \
"Implementation of adapter feedback induces adaptation of not" \
"only the target signal e0* but also signals downstream of the" \
"target." \
"" \
"k5+ =6*10^8 M-1 min-1, k5- =30 min-1, kcat,5 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001." \
""
call /kinetics/P4/notes LOAD \
"Deactivating enzyme P4^T = 5000 no./cell." \
"from " \
"Asthagiri and Lauffenburger, 2001"
call /kinetics/P4/E4*_deactiv/notes LOAD \
"kp4+ = 6*10^8 M-1 min-1, kp4- =30 min-1, kpcat,4 =6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E5/notes LOAD \
"E5^T = 10^4 no./cell" \
"from" \
"Asthagiri and Lauffenburger 2001"
call /kinetics/P5/notes LOAD \
"Deactivating enzyme P5^T = 5000 no./cell" \
"from" \
"Asthagiri and Lauffenburger, 2001."
call /kinetics/P5/E5*_deactiv/notes LOAD \
"kp5+ = 6*10^8 M-1 min-1, kp5- = 30 min-1, kpcat,5 = 6 min-1" \
"from" \
"Asthagiri and Lauffenburger 2001."
call /kinetics/E5*/notes LOAD \
"Active form of enzyme" \
"from" \
"Asthagiri and Lauffenburger, 2001" \
""
call /kinetics/A2-/notes LOAD \
"Nonfunctional second adaptor enzyme A2-" \
"from" \
"Asthagiri and Lauffnburger, 2001"
complete_loading