//genesis
// kkit Version 11 flat dumpfile
 
// Saved on Mon Feb 13 12:38:55 2006
 
include kkit {argv 1}
 
FASTDT = 0.0001
SIMDT = 0.01
CONTROLDT = 5
PLOTDT = 10
MAXTIME = 28800
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 1
DEFAULT_VOL = 1.6667e-21
VERSION = 11.0
setfield /file/modpath value /home2/bhalla/scripts/modules
kparms
 
//genesis

initdump -version 3 -ignoreorphans 1
simobjdump doqcsinfo filename accessname accesstype transcriber developer \
  citation species tissue cellcompartment methodology sources \
  model_implementation model_validation x y z
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 geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
  z
simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
  geomname 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 text str
simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black \
  795 225 0
simundump kpool /kinetics/R 0 0 0.01 0.01 0.01 0.01 0 0 1 0 \
  /kinetics/geometry blue black 751 188 0
simundump kreac /kinetics/JAK_binding 0 100 0.05 "" white black 755 148 0
simundump kpool /kinetics/JAK 0 0 0.02 0.02 0.02 0.02 0 0 1 0 \
  /kinetics/geometry 0 black 762 184 0
simundump kpool /kinetics/RJ 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 26 black \
  748 95 0
simundump kpool /kinetics/IFNRJ 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 48 \
  black 720 -20 0
simundump kpool /kinetics/IFN 0 0 0.01 0.01 0.01 0.01 0 0 1 4 \
  /kinetics/geometry 35 black 738 84 0
simundump kreac /kinetics/IFN_binding 0 20 0.02 "" white black 730 37 0
simundump kpool /kinetics/IFNRJ2 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 52 \
  black 658 -15 0
simundump kreac /kinetics/IFNRJ_dimerisation 0 40 0.2 "" white black 709 33 0
simundump kreac /kinetics/IFNRJ_activation 0 0.005 0 "" white black 760 45 0
simundump kpool /kinetics/IFNRJ2* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 62 \
  black 752 79 0
simundump kpool /kinetics/STAT1c 0 0 1 1 1 1 0 0 1 0 /kinetics/geometry 24 \
  black 616 -17 0
simundump kpool /kinetics/IFNRJ2*-STAT1c 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 12 black 691 87 0
simundump kreac /kinetics/STAT1c_activation 0 0.4 0 "" white black 685 38 0
simundump kpool /kinetics/STAT1c* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 0 \
  black 703 -19 0
simundump kreac /kinetics/STAT1c*_binding 0 5 0.5 "" white black 782 38 0
simundump kpool /kinetics/IFNRJ2*-STAT1c* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 22 black 779 82 0
simundump kreac /kinetics/STAT1c*_dimerisation 0 20 0.1 "" white black 730 \
  -68 0
simundump kpool /kinetics/STAT1c*-STAT1c* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 52 black 747 -15 0
simundump kpool /kinetics/SHP-2 0 0 0.1 0.1 0.1 0.1 0 0 1 0 \
  /kinetics/geometry 45 black 612 88 0
simundump kpool /kinetics/IFNRJ2*-SHP-2 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 7 black 586 91 0
simundump kpool /kinetics/PPX 0 0 0.05 0.05 0.05 0.05 0 0 1 0 \
  /kinetics/geometry 45 black 637 -14 0
simundump kpool /kinetics/PPX-STAT1c* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
  61 black 586 -11 0
simundump kpool /kinetics/PPX-STAT1c*-STAT1c* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 6 black 678 -21 0
simundump kreac /kinetics/STAT1c*_dephosphorylation[1] 0 0.003 0 "" white \
  black 663 -65 0
simundump kpool /kinetics/STAT1n*-STAT1n* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 62 black 731 -123 0
simundump kpool /kinetics/STAT1n* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 0 \
  black 666 -121 0
simundump kreac /kinetics/STAT1n*_dimerisation 0 20 0.1 "" white black 715 \
  -147 0
simundump kpool /kinetics/PPN 0 0 0.06 0.06 0.06 0.06 0 0 1 0 \
  /kinetics/geometry 45 black 627 -119 0
simundump kreac /kinetics/PPN_binding 0 1 0.2 "" white black 639 -142 0
simundump kpool /kinetics/PPN-STAT1n* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
  54 black 605 -118 0
simundump kreac /kinetics/STAT1n*_dephosphorylation 0 0.005 0 "" white black \
  601 -83 0
simundump kpool /kinetics/STAT1n 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 10 \
  black 578 -114 0
simundump kreac /kinetics/PPN_binding[1] 0 1 0.2 "" white black 698 -74 0
simundump kpool /kinetics/PPN-STAT1n*-STAT1n* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 54 black 697 -119 0
simundump kreac /kinetics/STAT1n*_dephosphorylation[1] 0 0.005 0 "" white \
  black 655 -77 0
simundump kpool /kinetics/Transcription_complex 0 0 0.001 0.001 0.001 0.001 0 \
  0 1 4 /kinetics/geometry white black 813 -133 0
simundump kenz /kinetics/Transcription_complex/DNA 0 0 0 0 0 1 0.125 0.04 \
  0.01 0 1 "" red white "" 810 -143 0
simundump kpool /kinetics/SOCS1 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 12 \
  black 700 201 0
simundump kpool /kinetics/SOCS1-IFNRJ2* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 27 black 762 202 0
simundump kpool /kinetics/SOCS1-IFNRJ2*-STAT1c 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 27 black 717 97 0
simundump kreac /kinetics/SHP-2_binding[1] 0 1 0.2 "" white black 619 173 0
simundump kpool /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry 27 black 659 202 0
simundump kreac /kinetics/degradation 0 0.0005 0 "" white black 807 132 0
simundump kreac /kinetics/mRNA_deg 0 0.0005 0 "" white black 818 36 0
simundump kpool /kinetics/SOCS1_Deg 0 0 0 0 0 0 0 0 1 4 /kinetics/geometry \
  blue black 804 81 0
simundump kpool /kinetics/mRNA_remain 0 0 0 0 0 0 0 0 1 4 /kinetics/geometry \
  blue black 804 -4 0
simundump kpool /kinetics/dup_STAT1n*-STAT1n* 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry blue black 772 -138 0
simundump kreac /kinetics/SOCS1_synthesis 0 0.01 0 "" white black 824 49 0
simundump kreac /kinetics/IFN-R_bind 0 20 0.02 "" white black 735 128 0
simundump kpool /kinetics/IFNR 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \
  black 731 196 0
simundump kreac /kinetics/IFNR-JAK_bind 0 100 0.05 "" white black 768 136 0
simundump kpool /kinetics/IFNRJ_ 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \
  black 719 78 0
simundump kreac /kinetics/IFNRJ2*-STAT1c_bind_SHP2 0 1 0.2 "" white black 611 \
  37 0
simundump kpool /kinetics/IFNRJ2*-STAT1c-SHP2 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry blue black 644 90 0
simundump kreac /kinetics/dephospo_IFNRJ2* 0 0.003 0 "" white black 653 33 0
simundump kpool /kinetics/Transcription_comp2 0 0 0.001 0.001 0.001 0.001 0 0 \
  1 4 /kinetics/geometry blue black 778 -111 0
simundump kenz /kinetics/Transcription_comp2/DNA 0 0 0 0 0 1 0.125 0.04 0.01 \
  0 1 "" red blue "" 777 -105 0
simundump kpool /kinetics/mRNAVn 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \
  black 802 -106 0
simundump kreac /kinetics/cyto_trans2 0 0.001 0 "" white black 799 -67 0
simundump kpool /kinetics/mRNAVc 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \
  black 797 -20 0
simundump kpool /kinetics/mRNAVc_dupli 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
  blue black 774 -14 0
simundump kreac /kinetics/AV_formation 0 0.002 0 "" white black 801 27 0
simundump kpool /kinetics/AV 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry blue \
  black 822 196 0
simundump kreac /kinetics/AV_degdra 0 1e-05 0 "" white black 824 149 0
simundump kpool /kinetics/AV_degraded 0 0 0 0 0 0 0 0 1 4 /kinetics/geometry \
  blue black 824 81 0
simundump kreac /kinetics/mRNAVc_deg 0 0.002 0 "" white black 782 -73 0
simundump kpool /kinetics/mRNAVc_remain 0 0 0 0 0 0 0 0 1 4 \
  /kinetics/geometry blue black 773 -29 0
simundump kreac /kinetics/SOCS1_unbind 0 0.0005 0 "" white black 725 142 0
simundump kreac /kinetics/SOCS1_unbind[1] 0 0.0005 0 "" white black 582 128 0
simundump kreac /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 0 0.003 0 "" white black \
  654 165 0
simundump kreac /kinetics/STAT1c_binding[2] 0 8 0.8 "" white black 707 156 0
simundump kreac /kinetics/STAT1c_binding[1] 0 8 0.8 "" white black 752 29 0
simundump kreac /kinetics/unbind_SOCS1[2] 0 0.0005 0 "" white black 630 126 0
simundump kreac /kinetics/IFNRJ2*_dephospo 0 0.003 0 "" white black 680 142 0
simundump kreac /kinetics/PPX_binding[2] 0 1 0.2 "" white black 696 -63 0
simundump kreac /kinetics/PPX_binding[1] 0 1 0.2 "" white black 617 -70 0
simundump kpool /kinetics/mRNASn 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry white \
  black 825 -110 0
simundump kpool /kinetics/mRNASc 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 34 \
  black 815 -43 0
simundump kpool /kinetics/dup_mRNASc 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
  blue black 825 -12 0
simundump kreac /kinetics/unbind_SOCS1[1] 0 0.0005 0 "" white black 800 160 0
simundump kreac /kinetics/SOCS1c_binding[2] 0 20 0.1 "" white black 703 128 0
simundump kreac /kinetics/SOCS1_binding[1] 0 20 0.1 "" white black 791 123 0
simundump kreac /kinetics/SOCS1_binding[3] 0 20 0.1 "" white black 600 148 0
simundump kreac /kinetics/SHP2_binding[2] 0 1 0.2 "" white black 620 140 0
simundump kreac /kinetics/SOCS1c_binding[4] 0 20 0.1 "" white black 652 133 0
simundump kreac /kinetics/STAT1c_binding[3] 0 8 0.8 "" white black 597 114 0
simundump kreac /kinetics/SHP-2_binding[3] 0 1 0.2 "" white black 631 50 0
simundump kpool /kinetics/SOCS1-IFNRJ2*-SHP2 0 0 0 0 0 0 0 0 1 0 \
  /kinetics/geometry blue black 588 203 0
simundump kreac /kinetics/mRNAn_cyto_tran1 0 0.001 0 "" white black 817 -81 0
simundump kreac /kinetics/STAT1c_nuclear_trans 0 0.005 0 "" white black 756 \
  -79 0
simundump kreac /kinetics/STAT1n_cyto_trans 0 0.05 0 "" white black 590 -53 0
simundump kreac /kinetics/IFNRJ2*_dephosp 0 0.003 0 "" white black 589 46 0
simundump kreac /kinetics/STAT1c*_dephosp 0 0.003 0 "" white black 595 18 0
simundump doqcsinfo /kinetics/doqcsinfo 0 \
  jak.g "Jak-Stat_Pathway" \
  pathway "Sharat J. Vayttaden and Prasoon Agarwal, NCBS" "Yamada S, Shiono S, Joo A, Yoshimura A. " \
  "FEBS Letters, (2003) 534:190-196" mouse Liver "Cytosol, Nucleus" \
  "Quantitative match to experiments" \
  "<a href =http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12527385&query_hl=3&itool=pubm?cmded_DocSum>Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6</a>" \
  "Exact GENESIS implementation" "Replicates original data " 748 220 0
simundump xgraph /graphs/conc1 0 0 28800 0 0.1 0
simundump xgraph /graphs/conc2 0 0 28800 0 0.008 0
simundump xplot /graphs/conc1/SOCS1.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 12 0 0 1
simundump xplot /graphs/conc2/IFNRJ2*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 62 0 0 1
simundump xplot /graphs/conc2/mRNASc.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 34 0 0 1
simundump xgraph /moregraphs/conc3 0 0 28800 0 0.05 0
simundump xgraph /moregraphs/conc4 0 0 28800 0 1 0
simundump xplot /moregraphs/conc3/STAT1c*-STAT1c*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 52 0 0 1
simundump xplot /moregraphs/conc3/STAT1n.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 10 0 0 1
simundump xplot /moregraphs/conc4/STAT1c.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 24 0 0 1
simundump xplot /moregraphs/conc4/STAT1n*-STAT1n*.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 62 0 0 1
simundump xcoredraw /edit/draw 0 576 827 -149 227
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 \
"From Fig.15-63 of Molecular Biology of Cell by Alberts et al 4th ed." \
"Shows Jak-STAT pathway activated by alpha-Interferon." \
"" \
"Based on I Swameye et al PNAS, USA 2003, 100(3):1028-1033" \
""
addmsg /kinetics/JAK_binding /kinetics/R REAC A B 
addmsg /kinetics/IFN-R_bind /kinetics/R REAC A B 
addmsg /kinetics/R /kinetics/JAK_binding SUBSTRATE n 
addmsg /kinetics/JAK /kinetics/JAK_binding SUBSTRATE n 
addmsg /kinetics/RJ /kinetics/JAK_binding PRODUCT n 
addmsg /kinetics/JAK_binding /kinetics/JAK REAC A B 
addmsg /kinetics/IFNR-JAK_bind /kinetics/JAK REAC A B 
addmsg /kinetics/JAK_binding /kinetics/RJ REAC B A 
addmsg /kinetics/IFN_binding /kinetics/RJ REAC A B 
addmsg /kinetics/IFN_binding /kinetics/IFNRJ REAC B A 
addmsg /kinetics/IFNRJ_dimerisation /kinetics/IFNRJ REAC A B 
addmsg /kinetics/IFN_binding /kinetics/IFN REAC A B 
addmsg /kinetics/IFN-R_bind /kinetics/IFN REAC A B 
addmsg /kinetics/RJ /kinetics/IFN_binding SUBSTRATE n 
addmsg /kinetics/IFNRJ /kinetics/IFN_binding PRODUCT n 
addmsg /kinetics/IFN /kinetics/IFN_binding SUBSTRATE n 
addmsg /kinetics/IFNRJ_activation /kinetics/IFNRJ2 REAC A B 
addmsg /kinetics/IFNRJ2*_dephosp /kinetics/IFNRJ2 REAC B A 
addmsg /kinetics/IFNRJ2*_dephospo /kinetics/IFNRJ2 REAC B A 
addmsg /kinetics/dephospo_IFNRJ2* /kinetics/IFNRJ2 REAC B A 
addmsg /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 /kinetics/IFNRJ2 REAC B A 
addmsg /kinetics/IFNRJ_dimerisation /kinetics/IFNRJ2 REAC B A 
addmsg /kinetics/IFNRJ /kinetics/IFNRJ_dimerisation SUBSTRATE n 
addmsg /kinetics/IFNRJ_ /kinetics/IFNRJ_dimerisation SUBSTRATE n 
addmsg /kinetics/IFNRJ2 /kinetics/IFNRJ_dimerisation PRODUCT n 
addmsg /kinetics/IFNRJ2 /kinetics/IFNRJ_activation SUBSTRATE n 
addmsg /kinetics/IFNRJ2* /kinetics/IFNRJ_activation PRODUCT n 
addmsg /kinetics/IFNRJ_activation /kinetics/IFNRJ2* REAC B A 
addmsg /kinetics/STAT1c_binding[1] /kinetics/IFNRJ2* REAC A B 
addmsg /kinetics/STAT1c_activation /kinetics/IFNRJ2* REAC B A 
addmsg /kinetics/STAT1c*_binding /kinetics/IFNRJ2* REAC A B 
addmsg /kinetics/SHP-2_binding[3] /kinetics/IFNRJ2* REAC A B 
addmsg /kinetics/SOCS1_binding[1] /kinetics/IFNRJ2* REAC A B 
addmsg /kinetics/unbind_SOCS1[1] /kinetics/IFNRJ2* REAC B A 
addmsg /kinetics/STAT1c_binding[1] /kinetics/STAT1c REAC A B 
addmsg /kinetics/STAT1c*_dephosp /kinetics/STAT1c REAC B A 
addmsg /kinetics/STAT1n_cyto_trans /kinetics/STAT1c REAC B A 
addmsg /kinetics/STAT1c_binding[2] /kinetics/STAT1c REAC A B 
addmsg /kinetics/IFNRJ2*_dephospo /kinetics/STAT1c REAC B A 
addmsg /kinetics/dephospo_IFNRJ2* /kinetics/STAT1c REAC B A 
addmsg /kinetics/STAT1c_binding[3] /kinetics/STAT1c REAC A B 
addmsg /kinetics/STAT1c*_dephosphorylation[1] /kinetics/STAT1c REAC B A 
addmsg /kinetics/STAT1c_binding[1] /kinetics/IFNRJ2*-STAT1c REAC B A 
addmsg /kinetics/STAT1c_activation /kinetics/IFNRJ2*-STAT1c REAC A B 
addmsg /kinetics/IFNRJ2*-STAT1c_bind_SHP2 /kinetics/IFNRJ2*-STAT1c REAC A B 
addmsg /kinetics/SOCS1c_binding[2] /kinetics/IFNRJ2*-STAT1c REAC A B 
addmsg /kinetics/SOCS1_unbind /kinetics/IFNRJ2*-STAT1c REAC B A 
addmsg /kinetics/IFNRJ2*-STAT1c /kinetics/STAT1c_activation SUBSTRATE n 
addmsg /kinetics/IFNRJ2* /kinetics/STAT1c_activation PRODUCT n 
addmsg /kinetics/STAT1c* /kinetics/STAT1c_activation PRODUCT n 
addmsg /kinetics/STAT1c_activation /kinetics/STAT1c* REAC B A 
addmsg /kinetics/STAT1c*_binding /kinetics/STAT1c* REAC A B 
addmsg /kinetics/STAT1c*_dimerisation /kinetics/STAT1c* REAC A B 
addmsg /kinetics/STAT1c*_dimerisation /kinetics/STAT1c* REAC A B 
addmsg /kinetics/PPX_binding[1] /kinetics/STAT1c* REAC A B 
addmsg /kinetics/STAT1c*_dephosphorylation[1] /kinetics/STAT1c* REAC B A 
addmsg /kinetics/STAT1c* /kinetics/STAT1c*_binding SUBSTRATE n 
addmsg /kinetics/IFNRJ2* /kinetics/STAT1c*_binding SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c* /kinetics/STAT1c*_binding PRODUCT n 
addmsg /kinetics/STAT1c*_binding /kinetics/IFNRJ2*-STAT1c* REAC B A 
addmsg /kinetics/STAT1c* /kinetics/STAT1c*_dimerisation SUBSTRATE n 
addmsg /kinetics/STAT1c*-STAT1c* /kinetics/STAT1c*_dimerisation PRODUCT n 
addmsg /kinetics/STAT1c* /kinetics/STAT1c*_dimerisation SUBSTRATE n 
addmsg /kinetics/STAT1c*_dimerisation /kinetics/STAT1c*-STAT1c* REAC B A 
addmsg /kinetics/PPX_binding[2] /kinetics/STAT1c*-STAT1c* REAC A B 
addmsg /kinetics/STAT1c_nuclear_trans /kinetics/STAT1c*-STAT1c* REAC A B 
addmsg /kinetics/SHP-2_binding[3] /kinetics/SHP-2 REAC A B 
addmsg /kinetics/IFNRJ2*_dephosp /kinetics/SHP-2 REAC B A 
addmsg /kinetics/SHP-2_binding[1] /kinetics/SHP-2 REAC A B 
addmsg /kinetics/IFNRJ2*_dephospo /kinetics/SHP-2 REAC B A 
addmsg /kinetics/IFNRJ2*-STAT1c_bind_SHP2 /kinetics/SHP-2 REAC A B 
addmsg /kinetics/dephospo_IFNRJ2* /kinetics/SHP-2 REAC B A 
addmsg /kinetics/SHP2_binding[2] /kinetics/SHP-2 REAC A B 
addmsg /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 /kinetics/SHP-2 REAC B A 
addmsg /kinetics/SHP-2_binding[3] /kinetics/IFNRJ2*-SHP-2 REAC B A 
addmsg /kinetics/IFNRJ2*_dephosp /kinetics/IFNRJ2*-SHP-2 REAC A B 
addmsg /kinetics/SOCS1_binding[3] /kinetics/IFNRJ2*-SHP-2 REAC A B 
addmsg /kinetics/SOCS1_unbind[1] /kinetics/IFNRJ2*-SHP-2 REAC B A 
addmsg /kinetics/PPX_binding[1] /kinetics/PPX REAC A B 
addmsg /kinetics/STAT1c*_dephosp /kinetics/PPX REAC B A 
addmsg /kinetics/PPX_binding[2] /kinetics/PPX REAC A B 
addmsg /kinetics/STAT1c*_dephosphorylation[1] /kinetics/PPX REAC B A 
addmsg /kinetics/PPX_binding[1] /kinetics/PPX-STAT1c* REAC B A 
addmsg /kinetics/STAT1c*_dephosp /kinetics/PPX-STAT1c* REAC A B 
addmsg /kinetics/PPX_binding[2] /kinetics/PPX-STAT1c*-STAT1c* REAC B A 
addmsg /kinetics/STAT1c*_dephosphorylation[1] /kinetics/PPX-STAT1c*-STAT1c* REAC A B 
addmsg /kinetics/PPX-STAT1c*-STAT1c* /kinetics/STAT1c*_dephosphorylation[1] SUBSTRATE n 
addmsg /kinetics/PPX /kinetics/STAT1c*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/STAT1c /kinetics/STAT1c*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/STAT1c* /kinetics/STAT1c*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/STAT1c_nuclear_trans /kinetics/STAT1n*-STAT1n* REAC B A 
addmsg /kinetics/STAT1n*_dimerisation /kinetics/STAT1n*-STAT1n* REAC B A 
addmsg /kinetics/PPN_binding[1] /kinetics/STAT1n*-STAT1n* REAC A B 
addmsg /kinetics/STAT1n*_dimerisation /kinetics/STAT1n* REAC A B 
addmsg /kinetics/STAT1n*_dimerisation /kinetics/STAT1n* REAC A B 
addmsg /kinetics/PPN_binding /kinetics/STAT1n* REAC A B 
addmsg /kinetics/STAT1n*_dephosphorylation[1] /kinetics/STAT1n* REAC B A 
addmsg /kinetics/STAT1n* /kinetics/STAT1n*_dimerisation SUBSTRATE n 
addmsg /kinetics/STAT1n*-STAT1n* /kinetics/STAT1n*_dimerisation PRODUCT n 
addmsg /kinetics/STAT1n* /kinetics/STAT1n*_dimerisation SUBSTRATE n 
addmsg /kinetics/PPN_binding /kinetics/PPN REAC A B 
addmsg /kinetics/STAT1n*_dephosphorylation /kinetics/PPN REAC B A 
addmsg /kinetics/PPN_binding[1] /kinetics/PPN REAC A B 
addmsg /kinetics/STAT1n*_dephosphorylation[1] /kinetics/PPN REAC B A 
addmsg /kinetics/STAT1n* /kinetics/PPN_binding SUBSTRATE n 
addmsg /kinetics/PPN /kinetics/PPN_binding SUBSTRATE n 
addmsg /kinetics/PPN-STAT1n* /kinetics/PPN_binding PRODUCT n 
addmsg /kinetics/PPN_binding /kinetics/PPN-STAT1n* REAC B A 
addmsg /kinetics/STAT1n*_dephosphorylation /kinetics/PPN-STAT1n* REAC A B 
addmsg /kinetics/PPN-STAT1n* /kinetics/STAT1n*_dephosphorylation SUBSTRATE n 
addmsg /kinetics/PPN /kinetics/STAT1n*_dephosphorylation PRODUCT n 
addmsg /kinetics/STAT1n /kinetics/STAT1n*_dephosphorylation PRODUCT n 
addmsg /kinetics/STAT1n*_dephosphorylation /kinetics/STAT1n REAC B A 
addmsg /kinetics/STAT1n_cyto_trans /kinetics/STAT1n REAC A B 
addmsg /kinetics/STAT1n*_dephosphorylation[1] /kinetics/STAT1n REAC B A 
addmsg /kinetics/PPN /kinetics/PPN_binding[1] SUBSTRATE n 
addmsg /kinetics/STAT1n*-STAT1n* /kinetics/PPN_binding[1] SUBSTRATE n 
addmsg /kinetics/PPN-STAT1n*-STAT1n* /kinetics/PPN_binding[1] PRODUCT n 
addmsg /kinetics/PPN_binding[1] /kinetics/PPN-STAT1n*-STAT1n* REAC B A 
addmsg /kinetics/STAT1n*_dephosphorylation[1] /kinetics/PPN-STAT1n*-STAT1n* REAC A B 
addmsg /kinetics/PPN-STAT1n*-STAT1n* /kinetics/STAT1n*_dephosphorylation[1] SUBSTRATE n 
addmsg /kinetics/PPN /kinetics/STAT1n*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/STAT1n /kinetics/STAT1n*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/STAT1n* /kinetics/STAT1n*_dephosphorylation[1] PRODUCT n 
addmsg /kinetics/Transcription_complex /kinetics/Transcription_complex/DNA ENZYME n 
addmsg /kinetics/dup_STAT1n*-STAT1n* /kinetics/Transcription_complex/DNA SUBSTRATE n 
addmsg /kinetics/SOCS1_binding[1] /kinetics/SOCS1 REAC A B 
addmsg /kinetics/IFNRJ2*_dephospo /kinetics/SOCS1 REAC B A 
addmsg /kinetics/degradation /kinetics/SOCS1 REAC A B 
addmsg /kinetics/SOCS1_synthesis /kinetics/SOCS1 REAC B A 
addmsg /kinetics/SOCS1c_binding[2] /kinetics/SOCS1 REAC A B 
addmsg /kinetics/SOCS1_binding[3] /kinetics/SOCS1 REAC A B 
addmsg /kinetics/SOCS1c_binding[4] /kinetics/SOCS1 REAC A B 
addmsg /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 /kinetics/SOCS1 REAC B A 
addmsg /kinetics/SOCS1_binding[1] /kinetics/SOCS1-IFNRJ2* REAC B A 
addmsg /kinetics/STAT1c_binding[2] /kinetics/SOCS1-IFNRJ2* REAC A B 
addmsg /kinetics/unbind_SOCS1[1] /kinetics/SOCS1-IFNRJ2* REAC A B 
addmsg /kinetics/SHP2_binding[2] /kinetics/SOCS1-IFNRJ2* REAC A B 
addmsg /kinetics/STAT1c_binding[2] /kinetics/SOCS1-IFNRJ2*-STAT1c REAC B A 
addmsg /kinetics/SHP-2_binding[1] /kinetics/SOCS1-IFNRJ2*-STAT1c REAC A B 
addmsg /kinetics/SOCS1c_binding[2] /kinetics/SOCS1-IFNRJ2*-STAT1c REAC B A 
addmsg /kinetics/SOCS1_unbind /kinetics/SOCS1-IFNRJ2*-STAT1c REAC A B 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c /kinetics/SHP-2_binding[1] SUBSTRATE n 
addmsg /kinetics/SHP-2 /kinetics/SHP-2_binding[1] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 /kinetics/SHP-2_binding[1] PRODUCT n 
addmsg /kinetics/SHP-2_binding[1] /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 REAC B A 
addmsg /kinetics/IFNRJ2*_dephospo /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 REAC A B 
addmsg /kinetics/unbind_SOCS1[2] /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 REAC A B 
addmsg /kinetics/SOCS1c_binding[4] /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 REAC B A 
addmsg /kinetics/STAT1c_binding[3] /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 REAC B A 
addmsg /kinetics/SOCS1 /kinetics/degradation SUBSTRATE n 
addmsg /kinetics/SOCS1_Deg /kinetics/degradation PRODUCT n 
addmsg /kinetics/mRNASc /kinetics/mRNA_deg SUBSTRATE n 
addmsg /kinetics/mRNA_remain /kinetics/mRNA_deg PRODUCT n 
addmsg /kinetics/degradation /kinetics/SOCS1_Deg REAC B A 
addmsg /kinetics/mRNA_remain /kinetics/mRNA_remain SUMTOTAL n nInit 
addmsg /kinetics/mRNA_deg /kinetics/mRNA_remain REAC B A 
addmsg /kinetics/Transcription_complex/DNA /kinetics/dup_STAT1n*-STAT1n* REAC sA B 
addmsg /kinetics/STAT1n*-STAT1n* /kinetics/dup_STAT1n*-STAT1n* SUMTOTAL n nInit 
addmsg /kinetics/Transcription_comp2/DNA /kinetics/dup_STAT1n*-STAT1n* REAC sA B 
addmsg /kinetics/dup_mRNASc /kinetics/SOCS1_synthesis SUBSTRATE n 
addmsg /kinetics/SOCS1 /kinetics/SOCS1_synthesis PRODUCT n 
addmsg /kinetics/IFN /kinetics/IFN-R_bind SUBSTRATE n 
addmsg /kinetics/R /kinetics/IFN-R_bind SUBSTRATE n 
addmsg /kinetics/IFNR /kinetics/IFN-R_bind PRODUCT n 
addmsg /kinetics/IFN-R_bind /kinetics/IFNR REAC B A 
addmsg /kinetics/IFNR-JAK_bind /kinetics/IFNR REAC A B 
addmsg /kinetics/IFNR /kinetics/IFNR-JAK_bind SUBSTRATE n 
addmsg /kinetics/JAK /kinetics/IFNR-JAK_bind SUBSTRATE n 
addmsg /kinetics/IFNRJ_ /kinetics/IFNR-JAK_bind PRODUCT n 
addmsg /kinetics/IFNR-JAK_bind /kinetics/IFNRJ_ REAC B A 
addmsg /kinetics/IFNRJ_dimerisation /kinetics/IFNRJ_ REAC A B 
addmsg /kinetics/SHP-2 /kinetics/IFNRJ2*-STAT1c_bind_SHP2 SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c /kinetics/IFNRJ2*-STAT1c_bind_SHP2 SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c-SHP2 /kinetics/IFNRJ2*-STAT1c_bind_SHP2 PRODUCT n 
addmsg /kinetics/IFNRJ2*-STAT1c_bind_SHP2 /kinetics/IFNRJ2*-STAT1c-SHP2 REAC B A 
addmsg /kinetics/dephospo_IFNRJ2* /kinetics/IFNRJ2*-STAT1c-SHP2 REAC A B 
addmsg /kinetics/unbind_SOCS1[2] /kinetics/IFNRJ2*-STAT1c-SHP2 REAC B A 
addmsg /kinetics/SOCS1c_binding[4] /kinetics/IFNRJ2*-STAT1c-SHP2 REAC A B 
addmsg /kinetics/IFNRJ2*-STAT1c-SHP2 /kinetics/dephospo_IFNRJ2* SUBSTRATE n 
addmsg /kinetics/IFNRJ2 /kinetics/dephospo_IFNRJ2* PRODUCT n 
addmsg /kinetics/STAT1c /kinetics/dephospo_IFNRJ2* PRODUCT n 
addmsg /kinetics/SHP-2 /kinetics/dephospo_IFNRJ2* PRODUCT n 
addmsg /kinetics/Transcription_comp2 /kinetics/Transcription_comp2/DNA ENZYME n 
addmsg /kinetics/dup_STAT1n*-STAT1n* /kinetics/Transcription_comp2/DNA SUBSTRATE n 
addmsg /kinetics/Transcription_comp2/DNA /kinetics/mRNAVn MM_PRD pA 
addmsg /kinetics/cyto_trans2 /kinetics/mRNAVn REAC A B 
addmsg /kinetics/mRNAVn /kinetics/cyto_trans2 SUBSTRATE n 
addmsg /kinetics/mRNAVc /kinetics/cyto_trans2 PRODUCT n 
addmsg /kinetics/cyto_trans2 /kinetics/mRNAVc REAC B A 
addmsg /kinetics/mRNAVc_deg /kinetics/mRNAVc REAC A B 
addmsg /kinetics/mRNAVc /kinetics/mRNAVc_dupli SUMTOTAL n nInit 
addmsg /kinetics/AV_formation /kinetics/mRNAVc_dupli REAC A B 
addmsg /kinetics/mRNAVc_dupli /kinetics/AV_formation SUBSTRATE n 
addmsg /kinetics/AV /kinetics/AV_formation PRODUCT n 
addmsg /kinetics/AV_formation /kinetics/AV REAC B A 
addmsg /kinetics/AV_degdra /kinetics/AV REAC A B 
addmsg /kinetics/AV /kinetics/AV_degdra SUBSTRATE n 
addmsg /kinetics/AV_degraded /kinetics/AV_degdra PRODUCT n 
addmsg /kinetics/AV_degdra /kinetics/AV_degraded REAC B A 
addmsg /kinetics/mRNAVc /kinetics/mRNAVc_deg SUBSTRATE n 
addmsg /kinetics/mRNAVc_remain /kinetics/mRNAVc_deg PRODUCT n 
addmsg /kinetics/mRNAVc_deg /kinetics/mRNAVc_remain REAC B A 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c /kinetics/SOCS1_unbind SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c /kinetics/SOCS1_unbind PRODUCT n 
addmsg /kinetics/SOCS1-IFNRJ2*-SHP2 /kinetics/SOCS1_unbind[1] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-SHP-2 /kinetics/SOCS1_unbind[1] PRODUCT n 
addmsg /kinetics/SOCS1-IFNRJ2*-SHP2 /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 SUBSTRATE n 
addmsg /kinetics/SOCS1 /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 PRODUCT n 
addmsg /kinetics/IFNRJ2 /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 PRODUCT n 
addmsg /kinetics/SHP-2 /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 PRODUCT n 
addmsg /kinetics/STAT1c /kinetics/STAT1c_binding[2] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2* /kinetics/STAT1c_binding[2] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c /kinetics/STAT1c_binding[2] PRODUCT n 
addmsg /kinetics/IFNRJ2* /kinetics/STAT1c_binding[1] SUBSTRATE n 
addmsg /kinetics/STAT1c /kinetics/STAT1c_binding[1] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c /kinetics/STAT1c_binding[1] PRODUCT n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 /kinetics/unbind_SOCS1[2] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c-SHP2 /kinetics/unbind_SOCS1[2] PRODUCT n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 /kinetics/IFNRJ2*_dephospo SUBSTRATE n 
addmsg /kinetics/SOCS1 /kinetics/IFNRJ2*_dephospo PRODUCT n 
addmsg /kinetics/IFNRJ2 /kinetics/IFNRJ2*_dephospo PRODUCT n 
addmsg /kinetics/SHP-2 /kinetics/IFNRJ2*_dephospo PRODUCT n 
addmsg /kinetics/STAT1c /kinetics/IFNRJ2*_dephospo PRODUCT n 
addmsg /kinetics/PPX /kinetics/PPX_binding[2] SUBSTRATE n 
addmsg /kinetics/STAT1c*-STAT1c* /kinetics/PPX_binding[2] SUBSTRATE n 
addmsg /kinetics/PPX-STAT1c*-STAT1c* /kinetics/PPX_binding[2] PRODUCT n 
addmsg /kinetics/STAT1c* /kinetics/PPX_binding[1] SUBSTRATE n 
addmsg /kinetics/PPX /kinetics/PPX_binding[1] SUBSTRATE n 
addmsg /kinetics/PPX-STAT1c* /kinetics/PPX_binding[1] PRODUCT n 
addmsg /kinetics/mRNAn_cyto_tran1 /kinetics/mRNASn REAC A B 
addmsg /kinetics/Transcription_complex/DNA /kinetics/mRNASn MM_PRD pA 
addmsg /kinetics/mRNAn_cyto_tran1 /kinetics/mRNASc REAC B A 
addmsg /kinetics/mRNA_deg /kinetics/mRNASc REAC A B 
addmsg /kinetics/SOCS1_synthesis /kinetics/dup_mRNASc REAC A B 
addmsg /kinetics/mRNASc /kinetics/dup_mRNASc SUMTOTAL n nInit 
addmsg /kinetics/SOCS1-IFNRJ2* /kinetics/unbind_SOCS1[1] SUBSTRATE n 
addmsg /kinetics/IFNRJ2* /kinetics/unbind_SOCS1[1] PRODUCT n 
addmsg /kinetics/SOCS1 /kinetics/SOCS1c_binding[2] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-STAT1c /kinetics/SOCS1c_binding[2] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c /kinetics/SOCS1c_binding[2] PRODUCT n 
addmsg /kinetics/IFNRJ2* /kinetics/SOCS1_binding[1] SUBSTRATE n 
addmsg /kinetics/SOCS1 /kinetics/SOCS1_binding[1] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2* /kinetics/SOCS1_binding[1] PRODUCT n 
addmsg /kinetics/SOCS1 /kinetics/SOCS1_binding[3] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-SHP-2 /kinetics/SOCS1_binding[3] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-SHP2 /kinetics/SOCS1_binding[3] PRODUCT n 
addmsg /kinetics/SHP-2 /kinetics/SHP2_binding[2] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2* /kinetics/SHP2_binding[2] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-SHP2 /kinetics/SHP2_binding[2] PRODUCT n 
addmsg /kinetics/SOCS1 /kinetics/SOCS1c_binding[4] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 /kinetics/SOCS1c_binding[4] PRODUCT n 
addmsg /kinetics/IFNRJ2*-STAT1c-SHP2 /kinetics/SOCS1c_binding[4] SUBSTRATE n 
addmsg /kinetics/STAT1c /kinetics/STAT1c_binding[3] SUBSTRATE n 
addmsg /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2 /kinetics/STAT1c_binding[3] PRODUCT n 
addmsg /kinetics/SOCS1-IFNRJ2*-SHP2 /kinetics/STAT1c_binding[3] SUBSTRATE n 
addmsg /kinetics/IFNRJ2* /kinetics/SHP-2_binding[3] SUBSTRATE n 
addmsg /kinetics/SHP-2 /kinetics/SHP-2_binding[3] SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-SHP-2 /kinetics/SHP-2_binding[3] PRODUCT n 
addmsg /kinetics/SOCS1_binding[3] /kinetics/SOCS1-IFNRJ2*-SHP2 REAC B A 
addmsg /kinetics/SHP2_binding[2] /kinetics/SOCS1-IFNRJ2*-SHP2 REAC B A 
addmsg /kinetics/SOCS1_unbind[1] /kinetics/SOCS1-IFNRJ2*-SHP2 REAC A B 
addmsg /kinetics/Disso_SOCS1-IFNRJ2*-SHP2 /kinetics/SOCS1-IFNRJ2*-SHP2 REAC A B 
addmsg /kinetics/STAT1c_binding[3] /kinetics/SOCS1-IFNRJ2*-SHP2 REAC A B 
addmsg /kinetics/mRNASn /kinetics/mRNAn_cyto_tran1 SUBSTRATE n 
addmsg /kinetics/mRNASc /kinetics/mRNAn_cyto_tran1 PRODUCT n 
addmsg /kinetics/STAT1c*-STAT1c* /kinetics/STAT1c_nuclear_trans SUBSTRATE n 
addmsg /kinetics/STAT1n*-STAT1n* /kinetics/STAT1c_nuclear_trans PRODUCT n 
addmsg /kinetics/STAT1c /kinetics/STAT1n_cyto_trans PRODUCT n 
addmsg /kinetics/STAT1n /kinetics/STAT1n_cyto_trans SUBSTRATE n 
addmsg /kinetics/IFNRJ2*-SHP-2 /kinetics/IFNRJ2*_dephosp SUBSTRATE n 
addmsg /kinetics/SHP-2 /kinetics/IFNRJ2*_dephosp PRODUCT n 
addmsg /kinetics/IFNRJ2 /kinetics/IFNRJ2*_dephosp PRODUCT n 
addmsg /kinetics/PPX-STAT1c* /kinetics/STAT1c*_dephosp SUBSTRATE n 
addmsg /kinetics/STAT1c /kinetics/STAT1c*_dephosp PRODUCT n 
addmsg /kinetics/PPX /kinetics/STAT1c*_dephosp PRODUCT n 
addmsg /kinetics/SOCS1 /graphs/conc1/SOCS1.Co PLOT Co *SOCS1.Co *12 
addmsg /kinetics/IFNRJ2* /graphs/conc2/IFNRJ2*.Co PLOT Co *IFNRJ2*.Co *62 
addmsg /kinetics/mRNASc /graphs/conc2/mRNASc.Co PLOT Co *mRNASc.Co *34 
addmsg /kinetics/STAT1c*-STAT1c* /moregraphs/conc3/STAT1c*-STAT1c*.Co PLOT Co *STAT1c*-STAT1c*.Co *52 
addmsg /kinetics/STAT1n /moregraphs/conc3/STAT1n.Co PLOT Co *STAT1n.Co *10 
addmsg /kinetics/STAT1c /moregraphs/conc4/STAT1c.Co PLOT Co *STAT1c.Co *24 
addmsg /kinetics/STAT1n*-STAT1n* /moregraphs/conc4/STAT1n*-STAT1n*.Co PLOT Co *STAT1n*-STAT1n*.Co *62 
enddump
// End of dump

call /kinetics/R/notes LOAD \
"JAK binds to the intracellular domain of the" \
"IFN gamma receptor" \
"" \
"R = 10 nM = 0.01 uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/JAK_binding/notes LOAD \
"Binding of JAK to the intracellular domain of the" \
"IFN gamma receptor" \
"" \
"Kf = 100*10e+06 /M/sec = 100/uM/sec" \
"Kb = 0.05 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/JAK/notes LOAD \
"JAK: Janus Kinase" \
"" \
"JAK = 20 nM = 0.02 uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/RJ/notes LOAD \
"JAK bound to the intracellular domain of the" \
"IFN gamma receptor" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ/notes LOAD \
"IFN gamma liganding to the IFN gamma receptor that has" \
"JAK bound to its intracellular domain" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFN/notes LOAD \
"IFN gamma liganding to the IFN gamma receptor that has" \
"JAK bound to its intracellular domain." \
"" \
"IFN = 10nM = 0.01uM" \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFN_binding/notes LOAD \
"Binding of JAK to the intracellular domain of the" \
"IFN gamma receptor" \
"" \
"Kf = 20*10e+06 /M/sec = 20/uM/sec" \
"Kb = 0.02 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2/notes LOAD \
"Dimer of IFN gamma liganding to the IFN gamma receptor " \
"that has JAK bound to its intracellular domain" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ_dimerisation/notes LOAD \
"Dimerisation of the RJ complex" \
"" \
"Kf = 40*10e+06 /M/sec = 40/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ_activation/notes LOAD \
"Dimerisation of the RJ complex leads to the phosphorylation " \
"of several tyrosine residues by JAK" \
"" \
"Kf = 0.005*10e+06 /M/sec = 0.005/uM/sec" \
"Kb = 0 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2*/notes LOAD \
"Phosphorylated dimer of IFN gamma liganding to the " \
"IFN gamma receptor that has JAK bound to its " \
"intracellular domain" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c/notes LOAD \
"STAT: Signal Transducer and Activator of Transcription" \
"STAT1c binds to IFNRJ2* and is phosphorylated by JAK." \
"The phosphorylated STAT1 forms a homodimer which is" \
"translocated to the nucleus and works as " \
"transcription factors." \
"" \
"STAT1c = 1000nM = 1uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2*-STAT1c/notes LOAD \
"STAT1c complexed with phosphorylated IFNRJ dimer" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c_activation/notes LOAD \
"Dimerisation of the RJ complex leads to the phosphorylation " \
"of several tyrosine residues by JAK" \
"" \
"Kf = 0.4 /sec" \
"Kb = 0 /M/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*/notes LOAD \
"STAT: Signal Transducer and Activator of Transcription" \
"Cytoplasmic fraction of phosphorylated STAT1" \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*_binding/notes LOAD \
"Binding of phosphorylated STAT1c to " \
"JAK-IFNR phosphorylated dimer" \
"" \
"Kf = 5*10e+06 /M/sec = 5/uM/sec" \
"Kb = 0.5 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2*-STAT1c*/notes LOAD \
"Phosphorylated STAT1c complexed with " \
"phosphorylated IFNRJ dimer" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*_dimerisation/notes LOAD \
"Dimerisation of phosphorylated STAT1c" \
"" \
"Kf = 20*10e+06 /M/sec = 20/uM/sec" \
"Kb = 0.1 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*-STAT1c*/notes LOAD \
"Cytoplasmic fraction of phosphorylated STAT1 dimers" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SHP-2/notes LOAD \
"SHP-2: SH2 domain-containing tyrosine phosphatase 2" \
"" \
"SHP-2 = 100nM = 0.1uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2*-SHP-2/notes LOAD \
"Phosphorylated IFNRJ dimer bound to SH2 domain containing" \
"tyrosine phosphatase 2" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPX/notes LOAD \
"PPX: Unidentified phosphatase in the cytoplasm" \
"" \
"PPX = 50nM = 0.05uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPX-STAT1c*/notes LOAD \
"Phosphorylated STAT1c bound to cytoplasmic phosphatase" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPX-STAT1c*-STAT1c*/notes LOAD \
"Phosphorylated STAT1c dimer bound to cytoplasmic phosphatase" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*_dephosphorylation[1]/notes LOAD \
"Cytoplasmic phosphatase (PPX) dephosphorylates STAT1c dimer" \
"" \
"Kf = 0.003/sec" \
"Kb = 0/sec/uM^2" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n*-STAT1n*/notes LOAD \
"Nucleoplasmic fraction of phosphorylated STAT1 dimers" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n*/notes LOAD \
"STAT: Signal Transducer and Activator of Transcription" \
"Nucleoplasmic fraction of phosphorylated STAT1" \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n*_dimerisation/notes LOAD \
"Dimerisation of phosphorylated STAT1n" \
"" \
"Kf = 20/sec/uM" \
"Kb = 0.1/sec" \
"" \
"Notes : These values of kf and kb are put according to the data" \
"sheet provided by the authour." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPN/notes LOAD \
"PPX: Unidentified phosphatase in the nucleus" \
"" \
"PPX = 60nM = 0.06uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPN_binding/notes LOAD \
"Binding of PPN to phosphorylated STAT1n" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPN-STAT1n*/notes LOAD \
"Phosphorylated STAT1n bound to nucleoplasmic phosphatase" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n*_dephosphorylation/notes LOAD \
"Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n" \
"" \
"Kf = 0.005 /sec" \
"Kb = 0 /uM/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n/notes LOAD \
"STAT: Signal Transducer and Activator of Transcription" \
"Nucleoplasmic fraction of STAT1" \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPN_binding[1]/notes LOAD \
"Binding of PPN to phosphorylated STAT1n dimer" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPN-STAT1n*-STAT1n*/notes LOAD \
"Phosphorylated STAT1n dimer " \
"bound to nucleoplasmic phosphatase" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n*_dephosphorylation[1]/notes LOAD \
"Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n" \
"" \
"Kf = 0.005 /sec" \
"Kb = 0 /uM/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/Transcription_complex/notes LOAD \
"DNA to which STAT1 is bound " \
"along with other transcription factors" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/Transcription_complex/DNA/notes LOAD \
"Km = 400nM = 0.4uM" \
"Vmax = 0.01 nM/sec. " \
"Assume [enz] = 1 nM, then kcat = 0.01/sec." \
" " \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1/notes LOAD \
"SOCS1: Suppressor of cytokine signaling-1" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1-IFNRJ2*/notes LOAD \
"SOCS1 complexed with phosphorylated IFNRJ dimer." \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1-IFNRJ2*-STAT1c/notes LOAD \
"STAT1 bound to SOCS1 complexed with " \
"phosphorylated IFNRJ dimer" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SHP-2_binding[1]/notes LOAD \
"Binding of SHP-2 to JAK-IFNR phosphorylated dimer complexed" \
"with SOCS1 and STAT1c" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2/notes LOAD \
"SHP-2 bound to phosphorylated IFNRJ dimer " \
"complexed with SOCS1 and STAT1" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/degradation/notes LOAD \
"Degdration of SOCS1" \
"" \
"kf = 0.0005/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/mRNA_deg/notes LOAD \
"Degradation of mRNAc in the cytoplasm." \
"" \
"kf = 0.0005/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1_Deg/notes LOAD \
"Degraded SOCS1" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/mRNA_remain/notes LOAD \
"mRNAc degraded in cytoplasm" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/dup_STAT1n*-STAT1n*/notes LOAD \
"Duplicate of the STAT1c dimer" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1_synthesis/notes LOAD \
"SOCS1 synthesis from duplicate mRNAc" \
"" \
"kf = 0.01/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada" \
"FEBS Letters 534:190-196"
call /kinetics/IFN-R_bind/notes LOAD \
"Binding reaction of IFN + R." \
"" \
"kf = 20/sec/uM" \
"kb = 0.02/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/IFNR/notes LOAD \
"Formation of IFNR." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
" "
call /kinetics/IFNRJ_/notes LOAD \
"Formation of IFNRJ_ by the combining of iFNR+ JAK." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/IFNRJ2*-STAT1c_bind_SHP2/notes LOAD \
"Binding of IFNRJ2*-STAT1c to SHP2" \
"" \
"kf = 1/sec/uM" \
"kb = 0.2/sec" \
"" \
"Appendix, Satoshi Yamada 2003" \
"FEBS Letters 534:190-196."
call /kinetics/IFNRJ2*-STAT1c-SHP2/notes LOAD \
"IFNRJ2*-STAT1c-SHP2" \
"" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters, 534:190-196."
call /kinetics/Transcription_comp2/notes LOAD \
"DNA to which STAT1*D and other transcription factors bound." \
"" \
"Appendix, Sattoshi Yamada et al 2003" \
"FEBS Letters 534;190-196." \
""
call /kinetics/Transcription_comp2/DNA/notes LOAD \
"Translation of mRNAVn" \
"" \
"Km = 400nM = 0.4uM" \
"kcat = 0.01/sec " \
"" \
"Appendix, Satoshi Yamada 2003" \
"FEBS Letters 534:190-196."
call /kinetics/mRNAVn/notes LOAD \
"Nuclear fraction of the mRNAVn after transcription." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196."
call /kinetics/cyto_trans2/notes LOAD \
"cytoplasmic transport of the mRNAV from nucleus to cytoplasm." \
"" \
"kf = 0.001/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/mRNAVc/notes LOAD \
"Cytoplasmic fraction of the mRNAV." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/mRNAVc_dupli/notes LOAD \
"Duplicate of the mRNAVc." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/AV_formation/notes LOAD \
"Fromation of AV" \
"" \
"kf = 0.002/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/AV/notes LOAD \
"AV fromed after translation." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/AV_degdra/notes LOAD \
"Degaradation reaction of AV" \
" " \
"kf = 0.00001/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
"" \
""
call /kinetics/AV_degraded/notes LOAD \
"AV after degradation." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/mRNAVc_deg/notes LOAD \
"mRNAVc degradation reaction." \
"" \
"kf = 0.002/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
"" \
""
call /kinetics/mRNAVc_remain/notes LOAD \
"mRNA remains after degradation." \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534;190-196." \
""
call /kinetics/SOCS1_unbind/notes LOAD \
"Unbinding reaction of the SOCS1 from SOCS1-IFNRJ2*-STAT1c" \
"" \
"kf = 0.0005/sec" \
"kb =0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/SOCS1_unbind[1]/notes LOAD \
"Unbinding reaction of SOCS1 from SOCS1-IFNRJ2*-SHP2" \
"" \
"kf = 0.0005/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/Disso_SOCS1-IFNRJ2*-SHP2/notes LOAD \
"Dissociation reaction of SOCS1-IFNRJ2*-SHP2." \
"" \
"kf = 0.003/sec" \
"kb = 0/sec/uM^2" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
"" \
""
call /kinetics/STAT1c_binding[2]/notes LOAD \
"Binding of STAT1c to JAK-IFNR phosphorylated dimer" \
"complexed with SOCS1" \
"" \
"Kf = 8*10e+06 /M/sec = 8/uM/sec" \
"Kb = 0.8 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c_binding[1]/notes LOAD \
"Binding of STAT1c to JAK-IFNR phosphorylated dimer" \
"" \
"Kf = 8*10e+06 /M/sec = 8/uM/sec" \
"Kb = 0.8 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/unbind_SOCS1[2]/notes LOAD \
"IFNRJ2*-STAT1c-SHP2 formation reaction" \
"" \
"kf = 0.0005/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196."
call /kinetics/IFNRJ2*_dephospo/notes LOAD \
"SHP-2 dephosphorylates JAK-IFNR dimer " \
"complexed with SOCS1 and STAT1c" \
"" \
"Kf = 0.003 /sec" \
"Kb = 0 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPX_binding[2]/notes LOAD \
"Binding of PPX to phosphorylated STAT1c dimer" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/PPX_binding[1]/notes LOAD \
"Binding of PPX to phosphorylated STAT1c" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/mRNASn/notes LOAD \
"Nuclear fraction of mRNA transcribed from DNA " \
"by STAT1 activation factors" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/mRNASc/notes LOAD \
"Cytoplasmic fraction of mRNA transcribed from DNA " \
"by STAT1 activation factors" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/dup_mRNASc/notes LOAD \
"Duplicate of the mRNAc" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/unbind_SOCS1[1]/notes LOAD \
"The unbinding reactoion of SOCS1 from SOCS1-IFNRJ2*" \
"" \
"kf = 0.0005/sec" \
"kb = 0/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/SOCS1c_binding[2]/notes LOAD \
"Binding reaction of SOCS1+IFNRJ2*-STAT1c" \
"" \
"kf = 20/sec/uM" \
"kb = 0.1/sec" \
"" \
"Appendix,Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/SOCS1_binding[1]/notes LOAD \
"Binding of SOCS1 to phosphorylated dimer of IFN gamma" \
"liganding to the IFN gamma receptor that has JAK bound " \
"to its intracellular domain" \
"" \
"Kf = 20*10e+06 /M/sec = 20/uM/sec" \
"Kb = 0.1 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1_binding[3]/notes LOAD \
"SOCS1 binding reaction of SOCS1+IFNRJ2*-SHP2" \
"" \
"kf = 20/sec/uM" \
"kb = 0.1/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/SHP2_binding[2]/notes LOAD \
"SHP2 binding reaction to SOCS1-IFNRJ2*" \
"" \
"kf = 1/sec/uM" \
"kb = 0.2/sec" \
"" \
"Appendix,Satoshi Yamada et al 2003" \
"FEBS LEtters 534:190-196." \
""
call /kinetics/SOCS1c_binding[4]/notes LOAD \
"SOCS1 binding to IFNRJ2*-STAT1c-SHP2" \
"" \
"kf = 20/sec/uM" \
"kb = 0.1/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c_binding[3]/notes LOAD \
"Binding reaction of STAT1c + SOCS1-IFNRJ2*-SHP2." \
"" \
"kf = 8/sec/uM" \
"kb = 0.8/sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/SHP-2_binding[3]/notes LOAD \
"Binding of SHP-2 to JAK-IFNR phosphorylated dimer" \
"" \
"Kf = 1*10e+06 /M/sec = 1/uM/sec" \
"Kb = 0.2 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/SOCS1-IFNRJ2*-SHP2/notes LOAD \
"Formation of SOCS1-IFNRJ2*-SHP2" \
"" \
"Appenndix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196." \
""
call /kinetics/mRNAn_cyto_tran1/notes LOAD \
"Transport of nucleoplasmic mRNA to the cytoplasm" \
"" \
"Kf = 0.001 /sec" \
"Kb = 0 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c_nuclear_trans/notes LOAD \
"Transport of cytoplasmic, phosphorylated STAT1 dimers to" \
"the nucleus" \
"" \
"Kf = 0.005 /sec" \
"Kb = 0 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1n_cyto_trans/notes LOAD \
"Transport of nucleoplasmic STAT1 to the cytoplasm" \
"" \
"Kf = 0.05 /sec" \
"Kb = 0 /sec" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/IFNRJ2*_dephosp/notes LOAD \
"SHP-2 dephosphorylates JAK-IFNR dimer" \
"" \
"Kf = 0.003 /sec" \
"Kb = 0 /sec/uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/STAT1c*_dephosp/notes LOAD \
"Cytoplasmic phosphatase (PPX) dephosphorylates STAT1c" \
"" \
"Kf = 0.003/sec" \
"Kb = 0/sec/uM" \
"" \
"Appendix, Satoshi Yamada et al 2003" \
"FEBS Letters 534:190-196"
call /kinetics/doqcsinfo/notes LOAD \
"This model was taken from the <a href =http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12527385&query_hl=3&itool=pubm?cmded_DocSum>Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6</a>" \
"This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. " \
"Note: There are a few ambiguities in the paper like initial concentration of IFN and some reactions were missing in the paper that were employed for obtaining the results. The graphs are almost similar to the graphs as shown in the paper but still some ambiguities regarding the concentration are there." \
"Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in the simulations."
complete_loading