//genesis // kkit Version 11 flat dumpfile // Saved on Fri Oct 10 15:43:56 2008 include kkit {argv 1} FASTDT = 2e-06 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 10 MAXTIME = 6000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-15 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 1e-15 3 sphere "" white black 0 0 0 simundump geometry /kinetics/geometry[1] 0 1e-15 3 sphere "" white black 11 \ 20 0 simundump geometry /kinetics/geometry[2] 0 1e-15 3 sphere "" white black 6 20 \ 0 simundump geometry /kinetics/geometry[3] 0 1e-15 3 sphere "" white black 5 20 \ 0 simundump geometry /kinetics/geometry[4] 0 1e-15 3 sphere "" white black 7 20 \ 0 simundump geometry /kinetics/geometry[5] 0 1e-15 3 sphere "" white black 9 20 \ 0 simundump geometry /kinetics/geometry[6] 0 1e-15 3 sphere "" white black 10 \ 20 0 simundump geometry /kinetics/geometry[7] 0 1e-15 3 sphere "" white black 8 20 \ 0 simundump geometry /kinetics/geometry[8] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[9] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[10] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[11] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[12] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[13] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[14] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[15] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump geometry /kinetics/geometry[16] 0 1e-15 3 sphere "" white black 0 0 \ 0 simundump kpool /kinetics/BDNF 0 0 5e-05 5e-05 29.999 29.999 0 0 5.9998e+05 4 \ /kinetics/geometry 44 black -14 16 0 simundump kpool /kinetics/PLC_g 0 0 0.1 0.1 60000 60000 0 0 6e+05 0 \ /kinetics/geometry cyan black -3 7 0 simundump kpool /kinetics/PLC_g_star 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry "hot pink" black -1 7 0 simundump kpool /kinetics/PIP3 0 0 0 0 0 0 0 0 5.9998e+05 0 \ /kinetics/geometry 43 black -3 -11 0 simundump kpool /kinetics/PDK1 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry[2] 37 black 3 6 0 simundump kenz /kinetics/PDK1/S6K_phospho 0 0 0 0 0 6e+05 8.3333e-07 4 1 0 0 \ "" red 37 "" 7 -7 0 simundump kpool /kinetics/PP2A 0 0 0.15 0.15 90000 90000 0 0 6e+05 0 \ /kinetics/geometry 4 black 11 1 0 simundump kenz /kinetics/PP2A/dephos_clus_S6K 0 0 0 0 0 5.9998e+05 9.4696e-07 \ 4 1 0 0 "" red 25 "" 3 1 0 simundump kenz /kinetics/PP2A/dephos_S6K 0 0 0 0 0 5.9998e+05 9.4696e-07 4 1 \ 0 0 "" red 25 "" 9 -2 0 simundump kenz /kinetics/PP2A/dephosp_S6K 0 0 0 0 0 5.9998e+05 9.4696e-07 4 1 \ 0 0 "" red 25 "" 13 -2 0 simundump kenz /kinetics/PP2A/Dephos_AKTser473 0 0 0 0 0 6e+05 3.125e-06 7.2 \ 1.8 0 0 "" red 46 "" 3 -8 0 simundump kenz /kinetics/PP2A/Dephosph_AKTthr308 0 0 0 0 0 6e+05 3.1249e-06 \ 7.2 1.8 0 0 "" red 46 "" 0 -8 0 simundump kenz /kinetics/PP2A/eEF2thr-56_dephospho 0 0 0 0 0 6e+05 4.4506e-07 \ 1.88 0.47 0 0 "" red 4 "" 23 8 0 simundump kenz /kinetics/PP2A/PP2A_4E-BP_star_star 0 0 0 0 0 6e+05 9.4697e-07 \ 4 1 0 0 "" red 4 "" -11 -10 0 simundump kenz /kinetics/PP2A/PP2A_4E-BP_star 0 0 0 0 0 6e+05 9.4697e-07 4 1 \ 0 0 "" red 4 "" -9 -17 0 simundump kenz /kinetics/PP2A/PP2A_4E-BP 0 0 0 0 0 6e+05 9.4694e-07 4 1 0 0 \ "" red 62 "" -13 -3 0 simundump kenz /kinetics/PP2A/PP2A_4EBP 0 0 0 0 0 6e+05 9.4694e-07 4 1 0 0 "" \ red 62 "" -13 -7 0 simundump group /kinetics/AKT_mod 0 yellow black x 0 0 "" AKT_mod \ defaultfile.g 0 0 0 5 8 0 simundump kpool /kinetics/AKT_mod/PIP3_AKT 0 0 0 0 0 0 0 0 5.9998e+05 0 \ /kinetics/geometry 53 yellow -8 4 0 simundump kpool /kinetics/AKT_mod/PIP3_PDK1 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 9 yellow -4 10 0 simundump kenz /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 0 0 0 0 0 2999.9 \ 0.00020834 40 10 0 0 "" red 9 "" -4 8 0 simundump kpool /kinetics/AKT_mod/PIP3_PDK2 0 0 0.003 0.003 1800 1800 0 0 \ 6e+05 0 /kinetics/geometry 39 yellow 2 10 0 simundump kenz /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 0 0 0 0 0 6e+05 \ 0.00020833 80 20 0 0 "" red 39 "" 2 13 0 simundump kpool /kinetics/AKT_mod/PIP3_AKT_thr308 0 0 0 0 0 0 0 0 5.9998e+05 \ 0 /kinetics/geometry 60 yellow -4 4 0 simundump kpool /kinetics/AKT_mod/PIP3_AKT-t308_s473 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 25 yellow 4 11 0 simundump kenz /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho 0 0 0 0 0 \ 6e+05 4.8544e-06 24 6 0 0 "" red 25 "" 8 11 0 simundump kpool /kinetics/AKT_mod/AKT 0 0 0.20001 0.20001 1.2e+05 1.2e+05 0 0 \ 5.9998e+05 0 /kinetics/geometry 4 yellow -11 1 0 simundump kpool /kinetics/AKT_mod/TSC1-TSC2_star 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 40 yellow 5 2 0 simundump kreac /kinetics/AKT_mod/PIP3_bind_AKT 0 7.5003e-05 0.089 "" white \ yellow -11 4 0 simundump kreac /kinetics/AKT_mod/PIP3_bind_PDK1 0 1.1667e-06 0.98 "" white \ yellow -8 6 0 simundump kreac /kinetics/AKT_mod/TSC1-2_dephospho 0 0.01 0 "" white yellow \ 10 7 0 simundump group /kinetics/TrKB_mod 0 white black x 0 0 "" TrKB_mod \ defaultfile.g 0 0 0 1 8 0 simundump kpool /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx 0 0 0.25 0.25 \ 1.5e+05 1.5e+05 0 0 6e+05 4 /kinetics/geometry yellow white -9 12 0 simundump kpool /kinetics/TrKB_mod/TrKB 0 0 0.25 0.25 1.4999e+05 1.4999e+05 0 \ 0 5.9996e+05 0 /kinetics/geometry 3 white -7 3 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB2_clx 0 0 0 0 0 0 0 0 5.9998e+05 \ 0 /kinetics/geometry 38 white -5 3 0 simundump kreac /kinetics/TrKB_mod/Autophos_TrKB 0 0.02 0 "" white white -4 \ -2 0 simundump kreac /kinetics/TrKB_mod/Dimeriz_TrKB 0 1.6667e-06 0.02 "" white \ white -7 0 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB_clx 0 0 0 0 0 0 0 0 5.9996e+05 0 \ /kinetics/geometry 45 white -6 -3 0 simundump kreac /kinetics/TrKB_mod/Ligand_binding 0 1.6668e-06 0.05 "" white \ white -9 0 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB2_star_clx 0 0 0 0 0 0 0 0 \ 5.9998e+05 0 /kinetics/geometry red white -3 3 0 simundump kenz /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho 0 0 0 0 0 \ 5.9998e+05 1.3889e-05 2 0.5 0 0 "" red red "" -3 5 0 simundump kenz /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho 0 0 0 0 0 \ 5.9998e+05 3.0002e-06 1.2 0.3 0 0 "" red red "" -3 2 0 simundump kreac /kinetics/TrKB_mod/PLC_g_star_dephospho 0 0.07 0 "" white \ white -1 12 0 simundump kpool /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx 0 0 0 0 0 0 0 \ 0 5.9998e+05 0 /kinetics/geometry brown white 2 -3 0 simundump kenz /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho 0 0 0 0 \ 0 5.9998e+05 8.3336e-06 16 4 0 0 "" red brown "" 2 -4 0 simundump kreac /kinetics/TrKB_mod/LR_Internalize 0 0.01 0 "" white white -5 \ 9 0 simundump kreac /kinetics/TrKB_mod/LR_cycling 0 0.001 0.001 "" white white -9 \ 9 0 simundump group /kinetics/PI3K_mod 0 brown black x 0 0 "" PI3K_mod \ defaultfile.g 0 0 0 -9 -15 0 simundump kpool /kinetics/PI3K_mod/PI3K 0 0 0.1 0.1 59998 59998 0 0 \ 5.9998e+05 0 /kinetics/geometry cyan brown 4 -18 0 simundump kpool /kinetics/PI3K_mod/PI3K_basal 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 10 brown -3 -17 0 simundump kenz /kinetics/PI3K_mod/PI3K_basal/basal_phosp 0 0 0 0 0 6e+05 \ 8.3333e-06 16 4 0 0 "" red 10 "" -3 -16 0 simundump kpool /kinetics/PI3K_mod/PIP2 0 0 7 7 4.2e+06 4.2e+06 0 0 6e+05 4 \ /kinetics/geometry orange brown 1 -11 0 simundump kpool /kinetics/PI3K_mod/Shc 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry 5 brown -3 -6 0 simundump kreac /kinetics/PI3K_mod/Shc_star_dephospho 0 0.2 0 "" white brown \ -2 -9 0 simundump kreac /kinetics/PI3K_mod/Grb2_bind_Shc 0 1.6667e-06 1 "" white \ brown 0 -4 0 simundump kpool /kinetics/PI3K_mod/Shc_star_Grb2_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[2] 42 brown 2 -7 0 simundump kpool /kinetics/PI3K_mod/Gab1 0 0 0.7 0.7 4.2e+05 4.2e+05 0 0 6e+05 \ 0 /kinetics/geometry[1] 44 brown 2 -5 0 simundump kreac /kinetics/PI3K_mod/bind_Gab1 0 5e-07 1 "" white brown 5 -5 0 simundump kpool /kinetics/PI3K_mod/Shc_star_Grb2-Gab1_clx 0 0 0 0 0 0 0 0 \ 6e+05 0 /kinetics/geometry 50 brown 6 -9 0 simundump kreac /kinetics/PI3K_mod/PI3K_act 0 8.3336e-06 0.08 "" white brown \ 4 -13 0 simundump kreac /kinetics/PI3K_mod/basal_PI3K_act 0 0.00068 0.45 "" white \ brown 1 -19 0 simundump kpool /kinetics/PLCg_basal 0 0 0.0007 0.0007 420 420 0 0 6e+05 0 \ /kinetics/geometry[4] 33 black -3 11 0 simundump kenz /kinetics/PLCg_basal/PLC_g_phospho 0 0 0 0 0 6e+05 1.3889e-05 \ 2 0.5 0 0 "" red 33 "" -3 10 0 simundump kpool /kinetics/TSC1-TSC2 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry 51 black 12 9 0 simundump kenz /kinetics/TSC1-TSC2/TSC2phospho 0 0 0 0 0 6e+05 0.00055556 80 \ 20 0 0 "" red 51 "" 12 8 0 simundump kpool /kinetics/eIF4E 0 0 0 0 0 0 0 0 5.9999e+05 0 \ /kinetics/geometry 42 black -15 1 0 simundump kpool /kinetics/Rheb-GTP 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry 28 black 20 10 0 simundump kpool /kinetics/Rheb-GDP 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[6] 39 black 15 4 0 simundump group /kinetics/mTOR_model 0 8 black x 0 0 "" mTOR_model \ defaultfile.g 0 cb4f9df2959ba465dbdd4a6b7a857a4c 0 7 -2 0 simundump kreac /kinetics/mTOR_model/Rheb-GTP_bind_TORclx 0 1e-05 3 "" white \ 8 13 -7 0 simundump kpool /kinetics/mTOR_model/TOR-clx 0 0 0.6 0.6 3.6e+05 3.6e+05 0 0 \ 6e+05 0 /kinetics/geometry 25 8 10 -13 0 simundump kpool /kinetics/TOR_Rheb-GTP_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 44 black 12 -19 0 simundump kenz /kinetics/TOR_Rheb-GTP_clx/S6K_phospho 0 0 0 0 0 6e+05 \ 6.2502e-07 0.24 0.06 0 0 "" red 42 "" 12 -16 0 simundump kenz /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho 0 0 0 0 0 6e+05 \ 4.6296e-06 4 1 0 0 "" red 44 "" -6 -11 0 simundump kenz /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star 0 0 0 0 0 6e+05 \ 4.6296e-06 4 1 0 0 "" red 44 "" -2 -20 0 simundump group /kinetics/S6Kinase 0 6 black x 0 0 "" defaultfile \ defaultfile.g 0 0 0 8 9 0 simundump kpool /kinetics/S6Kinase/S6K_star 0 0 0 0 0 0 0 0 5.9998e+05 0 \ /kinetics/geometry 46 6 3 4 0 simundump kpool /kinetics/S6Kinase/S6K 0 0 1.25 1.25 7.5e+05 7.5e+05 0 0 \ 6e+05 0 /kinetics/geometry Pink 6 0 3 0 simundump kpool /kinetics/S6Kinase/S6K_thr-412 0 0 0 0 0 0 0 0 5.9998e+05 0 \ /kinetics/geometry 48 6 7 -16 0 simundump kenz /kinetics/S6Kinase/S6K_thr-412/S6_phos 0 0 0 0 0 5.9998e+05 \ 3.3334e-07 0.04 0.01 0 0 "" red 48 "" 7 -19 0 simundump kreac /kinetics/S6Kinase/S6_dephosph 0 0.01 0 "" white 6 14 5 0 simundump kpool /kinetics/S6Kinase/40S_inact 0 0 0.02 0.02 12000 12000 0 0 \ 6e+05 4 /kinetics/geometry 3 6 16 12 0 simundump group /kinetics/4E-BP_mod 0 white black x 0 0 "" 4E-BP_mod \ defaultfile.g 0 0 0 4 6 0 simundump kreac /kinetics/4E-BP_mod/eIF4E_bind_BP2 0 8.3333e-05 0.15 "" white \ white -14 -18 0 simundump kreac /kinetics/4E-BP_mod/eIF4E-BP2_disso 0 4 1.6667e-06 "" white \ white -16 -17 0 simundump kpool /kinetics/4E-BP_mod/4E-BP 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 47 white -11 -18 0 simundump kpool /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 0 0 0 0 0 0 0 0 6e+05 \ 0 /kinetics/geometry 59 white -11 -13 0 simundump kpool /kinetics/4E-BP_mod/eIF4E-BP 0 0 0.2 0.2 1.2e+05 1.2e+05 0 0 \ 6e+05 0 /kinetics/geometry 52 white -13 -11 0 simundump kpool /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 56 white -11 -5 0 simundump kpool /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 0 0 0 0 0 0 0 0 \ 6e+05 0 /kinetics/geometry 39 white -11 -1 0 simundump kpool /kinetics/40S 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry 7 \ black -11 15 0 simundump kreac /kinetics/eIF4F_clx 0 5.0001e-05 0.1 "" white black -15 10 0 simundump kpool /kinetics/eIF4G-A_clx 0 0 0 0 0 0 0 0 5.9999e+05 0 \ /kinetics/geometry cyan black -6 4 0 simundump kreac /kinetics/eIF4G_A_clx 0 5.0001e-07 1 "" white black -7 9 0 simundump kpool /kinetics/eIF4A 0 0 0.2 0.2 1.2e+05 1.2e+05 0 0 5.9999e+05 0 \ /kinetics/geometry pink black -1 15 0 simundump kpool /kinetics/eIF4G 0 0 0.040001 0.040001 24000 24000 0 0 \ 5.9999e+05 0 /kinetics/geometry 21 black 0 14 0 simundump kpool /kinetics/eIF4F 0 0 0 0 0 0 0 0 5.9999e+05 0 \ /kinetics/geometry 6 black 2 -2 0 simundump kpool /kinetics/mRNA 0 0 0.08 0.08 47999 47999 0 0 5.9999e+05 0 \ /kinetics/geometry 60 black 7 3 0 simundump kreac /kinetics/eIF4F_mRNA_clx 0 3.3334e-07 0.077 "" white black 9 \ -4 0 simundump kpool /kinetics/eIF4F-mRNA_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 59 black 13 -5 0 simundump group /kinetics/43S_complex 0 yellow black x 0 0 "" 43S_complex \ defaultfile.g 0 0 0 2 14 0 simundump kreac /kinetics/43S_complex/Q_binds_R 0 8e-07 0.5 "" white yellow \ -4 13 0 simundump kpool /kinetics/43S_complex/Q.R 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry blue yellow 5 14 0 simundump kreac /kinetics/43S_complex/QR_binds_M 0 8.1667e-07 0.0045 "" white \ yellow 6 11 0 simundump kreac /kinetics/43S_complex/R_binds_M 0 2.1333e-06 0.719 "" white \ yellow -3 4 0 simundump kpool /kinetics/43S_complex/RM 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink yellow -7 3 0 simundump kreac /kinetics/43S_complex/RM_binds_Q 0 1.6333e-07 0.00169 "" \ white yellow -6 7 0 simundump kpool /kinetics/43S_complex/Quaternary_clx 0 0 0.047 0.047 28200 \ 28200 0 0 6e+05 0 /kinetics/geometry 28 yellow -5 11 0 simundump kpool /kinetics/S6K_thr-252 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 6 black -6 17 0 simundump kenz /kinetics/S6K_thr-252/camkIII_phospho 0 0 0 0 0 6e+05 \ 8.3333e-06 4 1 0 0 "" red 6 "" -6 18 0 simundump kenz /kinetics/S6K_thr-252/S6_phospho 0 0 0 0 0 6e+05 3.3333e-06 \ 0.4 0.1 0 0 "" red 4 "" -6 16 0 simundump kpool /kinetics/CaM-Ca4 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ blue yellow 4 27 0 simundump kpool /kinetics/CaMKIII 0 0 0.06 0.06 36000 36000 0 0 6e+05 0 \ /kinetics/geometry 32 black -2 18 0 simundump kpool /kinetics/CaMKIII_CaM-Ca4 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 58 black 18 22 0 simundump kenz /kinetics/CaMKIII_CaM-Ca4/phospho 0 0 0 0 0 6e+05 4.1667e-05 \ 40 10 0 0 "" red 58 "" 18 21 0 simundump kpool /kinetics/eEF2 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry 27 black 26 18 0 simundump kpool /kinetics/eEFthr-56 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry white black 15 15 0 simundump group /kinetics/CaM 1 blue black x 0 0 "" defaultfile defaultfile.g \ 0 14820c1c1999102487c514837dc6c72c 0 8 31 0 simundump kpool /kinetics/CaM/CaM 1 -1e-12 20 20 1.2e+07 1.2e+07 0 0 6e+05 0 \ /kinetics/geometry pink blue 7 29 0 simundump kreac /kinetics/CaM/CaM-Ca3-bind-Ca 1 7.7501e-07 10 "" white blue \ 10 17 0 simundump kpool /kinetics/CaM/CaM-Ca3 1 -1e-12 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry hotpink blue 21 17 0 simundump kreac /kinetics/CaM/CaM-bind-Ca 1 1.4141e-05 8.4853 "" white blue 7 \ 26 0 simundump kpool /kinetics/CaM/CaM-Ca2 1 -1e-12 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink blue 16 30 0 simundump kreac /kinetics/CaM/CaM-Ca2-bind-Ca 1 6.0001e-06 10 "" white blue \ 13 26 0 simundump kreac /kinetics/CaM/CaM-Ca-bind-Ca 1 1.4141e-05 8.4853 "" white \ blue 19 26 0 simundump kpool /kinetics/CaM/CaM-Ca 1 -1e-12 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink blue 11 29 0 simundump kpool /kinetics/Ca 1 0 0.08 0.08 48000 48000 0 0 6e+05 0 \ /kinetics/geometry red black -7 30 0 simundump kpool /kinetics/CaMKIII_basal 0 0 1e-05 1e-05 6 6 0 0 6e+05 0 \ /kinetics/geometry 45 black 10 11 0 simundump kenz /kinetics/CaMKIII_basal/eEF2thr56_basal 0 0 0 0 0 6e+05 \ 4.1667e-05 40 10 0 0 "" red 45 "" 18 15 0 simundump kpool /kinetics/CaMKIII_star 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 57 black 2 11 0 simundump kpool /kinetics/S6K_basal 0 0 0.001 0.001 600 600 0 0 6e+05 0 \ /kinetics/geometry 45 black 24 21 0 simundump kenz /kinetics/S6K_basal/CaMKIII_basal 0 0 0 0 0 6e+05 8.3342e-05 \ 40 10 0 0 "" red 45 "" 23 19 0 simundump kreac /kinetics/dephosp_CaMKIII 0 0.07 0 "" white black 1 20 0 simundump kpool /kinetics/60S_R 0 0 0.068 0.068 40800 40800 0 0 6e+05 4 \ /kinetics/geometry 46 black 22 15 0 simundump kpool /kinetics/Translation_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 52 black 17 0 0 simundump kenz /kinetics/Translation_clx/pro_syn 0 0 0 0 0 6e+05 3.0304e-06 \ 0.08 0.02 0 0 "" red 52 "" 17 -1 0 simundump kenz /kinetics/Translation_clx/rad_pro_syn 0 0 0 0 0 6e+05 \ 2.7778e-06 0.08 0.02 0 0 "" red 52 "" 17 2 0 simundump kpool /kinetics/AA 0 0 0.1 0.1 60000 60000 0 0 6e+05 4 \ /kinetics/geometry cyan black 22 -1 0 simundump kpool /kinetics/peptide 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ brown black 16 -6 0 simundump kreac /kinetics/elongation 0 6.6667e-05 10 "" white black 25 2 0 simundump kreac /kinetics/activation 0 1.6667e-06 0.9 "" white black 23 10 0 simundump kpool /kinetics/degraded_protein 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry white black 25 -18 0 simundump kpool /kinetics/protein 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ red black 16 -18 0 simundump kpool /kinetics/80S_ribos_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry blue black 19 7 0 simundump kpool /kinetics/Grb2 1 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry orange yellow 15 33 0 simundump kpool /kinetics/Shc_star 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ orange yellow 9 29 0 simundump kpool /kinetics/MAPK_star 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry orange yellow 13 1 0 simundump kenz /kinetics/MAPK_star/cluster_phospho_S6K 0 0 0 0 0 6e+05 \ 4.817e-07 4 1 0 0 "" red red "" 0 6 0 simundump kenz /kinetics/MAPK_star/MAPK_star-feedback 1 0 0 0 0 6e+05 \ 3.25e-06 40 10 0 0 "" red orange "" 10 10 0 simundump kenz /kinetics/MAPK_star/phosph_Sos 1 0 0 0 0 6e+05 3.25e-05 40 10 \ 0 0 "" red orange "" 20 30 0 simundump kenz /kinetics/MAPK_star/MAPK_4E-BP_star_star 0 0 0 0 0 6e+05 \ 7.4488e-08 0.64 0.16 0 0 "" red orange "" -8 -10 0 simundump kenz /kinetics/MAPK_star/MAPK_4E-BP_phospho 0 0 0 0 0 6e+05 \ 7.4488e-08 0.64 0.16 0 0 "" red 47 "" -9 -3 0 simundump kpool /kinetics/PKC-active 0 0 2.1222e-16 2.1222e-16 1.2733e-10 \ 1.2733e-10 0 0 6e+05 2 /kinetics/geometry yellow black 2.1325 8.477 0 simundump kenz /kinetics/PKC-active/PKC-act-raf 1 0 0 0 0 6e+05 1.6666e-06 16 \ 4 0 0 "" red yellow "" 11 12 0 simundump kenz /kinetics/PKC-active/PKC-inact-GAP 1 0 0 0 0 1 1e-05 16 4 0 0 \ "" red yellow "" 9 16 0 simundump kenz /kinetics/PKC-active/PKC-act-GEF 1 0 0 0 0 1 1e-05 16 4 0 0 "" \ red yellow "" 7 19 0 simundump group /kinetics/MAPK 0 brown black x 0 0 "" defaultfile \ defaultfile.g 0 0 0 15 11 0 simundump kpool /kinetics/MAPK/craf-1 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry pink brown 6 9 0 simundump kpool /kinetics/MAPK/craf-1_star 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink brown 9 8 0 simundump kpool /kinetics/MAPK/MAPKK 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry pink brown 6 4 0 simundump kpool /kinetics/MAPK/MAPK 0 0 3.6 3.6 2.16e+06 2.16e+06 0 0 6e+05 0 \ /kinetics/geometry pink brown 6 1 0 simundump kpool /kinetics/MAPK/craf-1_star_star 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry hotpink brown 14 8 0 simundump kpool /kinetics/MAPK/MAPK-tyr 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry orange brown 9 1 0 simundump kpool /kinetics/MAPK/MAPKK_star 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink brown 13 4 0 simundump kenz /kinetics/MAPK/MAPKK_star/MAPKKtyr 0 0 0 0 0 6e+05 5.4e-05 1.2 \ 0.3 0 0 "" red pink "" 8 3 0 simundump kenz /kinetics/MAPK/MAPKK_star/MAPKKthr 1 0 0 0 0 6e+05 5.4e-05 1.2 \ 0.3 0 0 "" red pink "" 13 3 0 simundump kpool /kinetics/MAPK/MAPKK-ser 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink brown 9 4 0 simundump kpool /kinetics/MAPK/Raf_star-GTP-Ras 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry red brown 5 5 0 simundump kenz /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 1 0 0 0 0 1 \ 1.5714e-05 1.2 0.3 0 0 "" red red "" 8 5 0 simundump kenz /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 1 0 0 0 0 1 \ 1.5714e-05 1.2 0.3 0 0 "" red red "" 11 5 0 simundump kpool /kinetics/MKP-1 1 0 0.02 0.02 12000 12000 0 0 6e+05 0 \ /kinetics/geometry hotpink black 4 2 0 simundump kenz /kinetics/MKP-1/MKP1-tyr-deph 1 0 0 0 0 6e+05 4.7619e-06 16 4 \ 0 0 "" red hotpink "" 5 3 0 simundump kenz /kinetics/MKP-1/MKP1-thr-deph 1 0 0 0 0 6e+05 4.7619e-06 16 4 \ 0 0 "" red hotpink "" 10 3 0 simundump kreac /kinetics/Ras-act-craf 1 1.6666e-05 0.5 "" white black 5 11 0 simundump kpool /kinetics/PPhosphatase2A 1 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry hotpink yellow 9 9 0 simundump kenz /kinetics/PPhosphatase2A/craf-deph 1 0 0 0 0 6e+05 3.1935e-06 \ 24 6 0 0 "" red hotpink "" 8 10 0 simundump kenz /kinetics/PPhosphatase2A/MAPKK-deph 1 0 0 0 0 6e+05 3.1935e-06 \ 24 6 0 0 "" red hotpink "" 11 7 0 simundump kenz /kinetics/PPhosphatase2A/MAPKK-deph-ser 1 0 0 0 0 6e+05 \ 3.1935e-06 24 6 0 0 "" red hotpink "" 8 7 0 simundump kenz /kinetics/PPhosphatase2A/craf_star_star-deph 1 0 0 0 0 1 \ 3.1935e-06 24 6 0 0 "" red hotpink "" 12 10 0 simundump group /kinetics/Ras 1 blue black x 0 0 "" defaultfile defaultfile.g \ 0 0 0 14.513 16.351 0 simundump kreac /kinetics/Ras/dephosph-GEF 1 1 0 "" white blue 9.0702 17.881 \ 0 simundump kpool /kinetics/Ras/inact-GEF 1 0 0.1 0.1 60000 60000 0 0 6e+05 0 \ /kinetics/geometry hotpink blue 12 21 0 simundump kenz /kinetics/Ras/inact-GEF/basal_GEF_activity 0 0 0 0 0 6e+05 \ 1.65e-08 0.08 0.02 0 0 "" red hotpink "" 12 20 0 simundump kpool /kinetics/Ras/GEF_star 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry hotpink blue 6.4483 17.246 0 simundump kenz /kinetics/Ras/GEF_star/GEF_star-act-ras 1 0 0 0 0 6e+05 \ 3.3e-07 0.08 0.02 0 0 "" red hotpink "" 7.0855 16.086 0 simundump kpool /kinetics/Ras/GTP-Ras 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry orange blue 14 14 0 simundump kpool /kinetics/Ras/GDP-Ras 1 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry pink blue 6.1309 14.165 0 simundump kreac /kinetics/Ras/Ras-intrinsic-GTPase 1 1e-04 0 "" white blue \ 9.0979 13.5 0 simundump kreac /kinetics/Ras/dephosph-GAP 1 0.1 0 "" white blue 4.0234 \ 15.524 0 simundump kpool /kinetics/Ras/GAP_star 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry red blue 3 13 0 simundump kpool /kinetics/Ras/GAP 1 0 0.01 0.01 6000 6000 0 0 6e+05 0 \ /kinetics/geometry red blue 6.6549 12.338 0 simundump kenz /kinetics/Ras/GAP/GAP-inact-ras 1 0 0 0 0 6e+05 8.2476e-05 40 \ 10 0 0 "" red red "" 9.0121 12.403 0 simundump kreac /kinetics/Ras/CaM-bind-GEF 1 0.00033333 1 "" white blue \ 2.4861 21.679 0 simundump kpool /kinetics/Ras/CaM-GEF 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink blue 5.3451 19.58 0 simundump kenz /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras 1 0 0 0 0 6e+05 3.3e-06 \ 0.8 0.2 0 0 "" red pink "" 5.0223 18.657 0 simundump kpool /kinetics/Shc_star.Sos.Grb2 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry brown yellow 11.263 27.112 0 simundump kenz /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF 1 0 0 0 0 6e+05 \ 3.3e-06 0.8 0.2 0 0 "" red brown "" 11.266 24.47 0 simundump group /kinetics/Sos 1 blue black x 0 0 "" defaultfile defaultfile.g \ 0 0 0 21 24 0 simundump kreac /kinetics/Sos/Shc_bind_Sos.Grb2 1 8.3329e-07 0.1 "" white \ blue 11.683 19.08 0 simundump kpool /kinetics/Sos/Sos_star.Grb2 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry orange blue 13.727 30.85 0 simundump kreac /kinetics/Sos/Grb2_bind_Sos_star 1 4.1667e-08 0.0168 "" white \ blue 11.986 27.424 0 simundump kpool /kinetics/Sos/Sos.Grb2 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry orange blue 15.441 19.286 0 simundump kpool /kinetics/Sos/Sos_star 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry red blue 16.874 29.404 0 simundump kreac /kinetics/Sos/dephosph_Sos 1 0.001 0 "" white blue 14.638 \ 26.342 0 simundump kreac /kinetics/Sos/Grb2_bind_Sos 1 4.1667e-08 0.0168 "" white blue \ 17 24 0 simundump kpool /kinetics/Sos/Sos 1 0 0.1 0.1 60000 60000 0 0 6e+05 0 \ /kinetics/geometry red blue 18.834 25.983 0 simundump kpool /kinetics/43Scomplex 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry hotpink black 18 13 0 simundump kreac /kinetics/CaMKIII_bind_CaM-Ca4 0 0.000165 0.09 "" white black \ -8 20 0 simundump kreac /kinetics/pep_elongation 0 0.1 0.001 "" white black 16 -11 0 simundump kreac /kinetics/protein_deg 0 1 0 "" white black 20 -17 0 simundump kreac /kinetics/GDP_to_GTP 0 0.2 0 "" white black 15 1 0 simundump group /kinetics/PKC 0 blue black x 0 0 "" defaultfile defaultfile.g \ 0 0 0 -3.0493 8.2163 0 simundump kpool /kinetics/PKC/PKC-Ca 0 0 3.7208e-17 3.7208e-17 2.2325e-11 \ 2.2325e-11 0 0 6e+05 0 /kinetics/geometry red black -4.0752 1.5108 0 simundump kreac /kinetics/PKC/PKC-act-by-Ca 0 1e-06 0.5 "" white blue -4.0752 \ -0.12295 0 simundump kreac /kinetics/PKC/PKC-act-by-DAG 0 1.3333e-08 8.6348 "" white \ blue -2.0612 0.69395 0 simundump kreac /kinetics/PKC/PKC-Ca-to-memb 0 1.2705 3.5026 "" white blue \ -3.7974 4.2533 0 simundump kreac /kinetics/PKC/PKC-DAG-to-memb 0 1 0.1 "" white blue -2.6168 \ 2.7362 0 simundump kreac /kinetics/PKC/PKC-act-by-Ca-AA 0 2e-09 0.1 "" white blue \ -0.78797 3.8157 0 simundump kreac /kinetics/PKC/PKC-act-by-DAG-AA 0 2 0.2 "" white blue 1.2492 \ 3.2322 0 simundump kpool /kinetics/PKC/PKC-DAG-AA_star 0 0 4.9137e-18 4.9137e-18 \ 2.9482e-12 2.9482e-12 0 0 6e+05 0 /kinetics/geometry cyan blue 0.60098 \ 5.537 0 simundump kpool /kinetics/PKC/PKC-Ca-AA_star 0 0 1.75e-16 1.75e-16 1.05e-10 \ 1.05e-10 0 0 6e+05 0 /kinetics/geometry orange blue -0.60278 6.2956 0 simundump kpool /kinetics/PKC/PKC-Ca-memb_star 0 0 1.3896e-17 1.3896e-17 \ 8.3376e-12 8.3376e-12 0 0 6e+05 0 /kinetics/geometry pink blue -2.7788 \ 6.529 0 simundump kpool /kinetics/PKC/PKC-DAG-memb_star 0 0 9.4352e-21 9.4352e-21 \ 5.6611e-15 5.6611e-15 0 0 6e+05 0 /kinetics/geometry yellow blue -1.8297 \ 5.5078 0 simundump kpool /kinetics/PKC/PKC-basal_star 0 0 0.02 0.02 12000 12000 0 0 \ 6e+05 0 /kinetics/geometry pink blue -4.7465 5.5662 0 simundump kreac /kinetics/PKC/PKC-basal-act 0 1 50 "" white blue -4.978 \ 3.0571 0 simundump kpool /kinetics/PKC/PKC-AA_star 0 0 1.8133e-17 1.8133e-17 1.088e-11 \ 1.088e-11 0 0 6e+05 0 /kinetics/geometry cyan blue 1.7816 6.8207 0 simundump kreac /kinetics/PKC/PKC-act-by-AA 0 2e-10 0.1 "" white blue -4.9925 \ -1.8654 0 simundump kpool /kinetics/PKC/PKC-Ca-DAG 0 0 8.4632e-23 8.4632e-23 5.0779e-17 \ 5.0779e-17 0 0 6e+05 0 /kinetics/geometry white blue 0.2306 1.8026 0 simundump kreac /kinetics/PKC/PKC-n-DAG 0 1e-09 0.1 "" white blue -3.0103 \ -1.9902 0 simundump kpool /kinetics/PKC/PKC-DAG 0 0 1.161e-16 1.161e-16 6.9661e-11 \ 6.9661e-11 0 0 6e+05 0 /kinetics/geometry white blue -0.99631 -1.0857 0 simundump kreac /kinetics/PKC/PKC-n-DAG-AA 0 3e-08 2 "" white blue -1.2278 \ -2.9529 0 simundump kpool /kinetics/PKC/PKC-DAG-AA 0 0 2.5188e-19 2.5188e-19 1.5113e-13 \ 1.5113e-13 0 0 6e+05 0 /kinetics/geometry white blue 0.62413 0.22715 0 simundump kpool /kinetics/PKC/PKC-cytosolic 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry white blue -6.1315 0.59711 0 simundump kpool /kinetics/DAG 1 0 11 11 6.6e+06 6.6e+06 0 0 6e+05 4 \ /kinetics/geometry green black -3.2051 -4.7168 0 simundump kpool /kinetics/Arachidonic_Acid 0 0 5 5 3e+06 3e+06 0 0 6e+05 4 \ /kinetics/geometry darkgreen black -3.2898 -9.3376 0 simundump kpool /kinetics/Basal_Translation 0 0 0.0002 0.0002 120 120 0 0 \ 6e+05 0 /kinetics/geometry[10] 53 black 22 -7 0 simundump kenz /kinetics/Basal_Translation/basal_syn 0 0 0 0 0 1 3.0303e-06 \ 0.08 0.02 0 0 "" red 53 "" 23 -6 0 simundump kenz /kinetics/Basal_Translation/rad_basal_syn 0 0 0 0 0 6e+05 \ 3.0303e-06 0.08 0.02 0 0 "" red 53 "" 27 -11 0 simundump kreac /kinetics/eIF4E-BP_disso 0 1 1.6667e-07 "" white black -7 -5 \ 0 simundump kreac /kinetics/basal_S6K 0 0.01 0 "" white black 4 -1 0 simundump kpool /kinetics/rad_AA 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[13] 45 black 27 -4 0 simundump kpool /kinetics/rad_peptide 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[13] 1 black 18 -8 0 simundump kreac /kinetics/rad_pep_elongation 0 0.1 0.001 "" white black 22 \ -10 0 simundump kpool /kinetics/rad_protein 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[13] 47 black 19 -14 0 simundump kreac /kinetics/rad_protein_deg 0 1 0 "" white black 23 -14 0 simundump kpool /kinetics/rad_deg_pro 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[13] 2 black 27 -14 0 simundump kreac /kinetics/labelling 0 0 0 "" white black 27 1 0 simundump kpool /kinetics/40S_basal 0 0 0.0001 0.0001 60 60 0 0 6e+05 0 \ /kinetics/geometry[14] 44 black 20 3 0 simundump kenz /kinetics/40S_basal/basal 0 0 0 0 0 6e+05 3.3333e-06 0.4 0.1 0 \ 0 "" red 44 "" 20 4 0 simundump kpool /kinetics/4E-BP_t37_46 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[11] 60 black -7 -14 0 simundump kpool /kinetics/PTEN 0 0 0.27 0.27 1.62e+05 1.62e+05 0 0 6e+05 0 \ /kinetics/geometry[15] 37 black 1 -16 0 simundump kenz /kinetics/PTEN/PIP3_dephosp 0 0 0 0 0 6e+05 0.00057292 22 5.5 \ 0 0 "" red 37 "" 1 -15 0 simundump kpool /kinetics/Ras-GTP_PI3K 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[16] 31 black 5 -24 0 simundump kenz /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP 0 0 0 0 0 6e+05 \ 8.3333e-06 16 4 0 0 "" red 31 "" 5 -23 0 simundump kreac /kinetics/PI3K_bind_Ras-GTP 0 3e-06 5 "" white black 13 -24 0 simundump doqcsinfo /kinetics/doqcsinfo 0 mTOR.g mTOR_pathway Network \ "Pragati Jain and Upinder S. Bhalla, NCBS" \ "Pragati Jain and Upinder S. Bhalla, NCBS" "citation here" \ "General Mammalian" Neuronal Dendritic "Quantitative match to experiments" \ "Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )" "Approximate implementation" \ "Approximates original data " 0 0 0 simundump xgraph /graphs/conc1 0 0 11994 0 0.81887 0 simundump xgraph /graphs/conc2 0 0 11994 0 0.10122 0 simundump xplot /graphs/conc1/40S.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 50 0 0 1 simundump xplot /graphs/conc1/protein.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc1/MAPK_star.Co 3 524288 \ "delete_plot.w ; edit_plot.D " orange 0 0 1 simundump xplot /graphs/conc1/eIF4E.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 42 0 0 1 simundump xplot /graphs/conc1/eIF4F-mRNA_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 59 0 0 1 simundump xplot /graphs/conc1/eIF4F.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 6 0 0 1 simundump xplot /graphs/conc1/S6K_thr-252.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 6 0 0 1 simundump xplot /graphs/conc1/TSC1-TSC2_star.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 40 0 0 1 simundump xplot /graphs/conc2/BDNF_TrkB2_star_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc2/43Scomplex.Co 3 524288 \ "delete_plot.w ; edit_plot.D " hotpink 0 0 1 simundump xplot /graphs/conc2/PIP3_AKT-t308_s473.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 25 0 0 1 simundump xplot /graphs/conc2/degraded_protein.Co 3 524288 \ "delete_plot.w ; edit_plot.D " white 0 0 1 simundump xplot /graphs/conc2/eIF4E-BP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 52 0 0 1 simundump xplot /graphs/conc2/eIF4E_4E-BP_t37_46_s65.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 39 0 0 1 simundump xgraph /moregraphs/conc3 0 0 11994 0 0.015861 0 simundump xgraph /moregraphs/conc4 0 -30778 10785 0.15676 0.43802 0 simundump xcoredraw /edit/draw 0 -18 29 -26 35 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "" \ "" \ " " addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/BDNF REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho /kinetics/PLC_g REAC sA B addmsg /kinetics/TrKB_mod/PLC_g_star_dephospho /kinetics/PLC_g REAC B A addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLC_g REAC sA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho /kinetics/PLC_g_star MM_PRD pA addmsg /kinetics/TrKB_mod/PLC_g_star_dephospho /kinetics/PLC_g_star REAC A B addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLC_g_star MM_PRD pA addmsg /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho /kinetics/PIP3 MM_PRD pA addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PIP3 MM_PRD pA addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/PIP3 REAC A B addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/PIP3 REAC A B addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PIP3 REAC sA B addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/PIP3 MM_PRD pA addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/PDK1 REAC A B addmsg /kinetics/PDK1/S6K_phospho /kinetics/PDK1 REAC eA B addmsg /kinetics/PDK1 /kinetics/PDK1/S6K_phospho ENZYME n addmsg /kinetics/S6Kinase/S6K_thr-412 /kinetics/PDK1/S6K_phospho SUBSTRATE n addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/dephos_S6K /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/dephos_clus_S6K /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/dephosp_S6K /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/PP2A_4EBP /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/PP2A_4E-BP /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/eEF2thr-56_dephospho /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/PP2A_4E-BP_star_star /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/PP2A_4E-BP_star /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A /kinetics/PP2A/dephos_clus_S6K ENZYME n addmsg /kinetics/S6Kinase/S6K_star /kinetics/PP2A/dephos_clus_S6K SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/dephos_S6K ENZYME n addmsg /kinetics/S6Kinase/S6K_thr-412 /kinetics/PP2A/dephos_S6K SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/dephosp_S6K ENZYME n addmsg /kinetics/S6K_thr-252 /kinetics/PP2A/dephosp_S6K SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/Dephos_AKTser473 ENZYME n addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /kinetics/PP2A/Dephos_AKTser473 SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/Dephosph_AKTthr308 ENZYME n addmsg /kinetics/AKT_mod/PIP3_AKT_thr308 /kinetics/PP2A/Dephosph_AKTthr308 SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/eEF2thr-56_dephospho ENZYME n addmsg /kinetics/eEFthr-56 /kinetics/PP2A/eEF2thr-56_dephospho SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/PP2A_4E-BP_star_star ENZYME n addmsg /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 /kinetics/PP2A/PP2A_4E-BP_star_star SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/PP2A_4E-BP_star ENZYME n addmsg /kinetics/4E-BP_t37_46 /kinetics/PP2A/PP2A_4E-BP_star SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/PP2A_4E-BP ENZYME n addmsg /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 /kinetics/PP2A/PP2A_4E-BP SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/PP2A_4EBP ENZYME n addmsg /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 /kinetics/PP2A/PP2A_4EBP SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/AKT_mod/PIP3_AKT REAC B A addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_AKT REAC sA B addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/AKT_mod/PIP3_AKT MM_PRD pA addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/AKT_mod/PIP3_PDK1 REAC B A addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_PDK1 REAC eA B addmsg /kinetics/AKT_mod/PIP3_PDK1 /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 ENZYME n addmsg /kinetics/AKT_mod/PIP3_AKT /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_PDK2 REAC eA B addmsg /kinetics/AKT_mod/PIP3_PDK2 /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 ENZYME n addmsg /kinetics/AKT_mod/PIP3_AKT_thr308 /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_AKT_thr308 MM_PRD pA addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_AKT_thr308 REAC sA B addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/AKT_mod/PIP3_AKT_thr308 MM_PRD pA addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/AKT_mod/PIP3_AKT_thr308 REAC sA B addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_AKT-t308_s473 MM_PRD pA addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/AKT_mod/PIP3_AKT-t308_s473 REAC sA B addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/AKT_mod/PIP3_AKT-t308_s473 REAC eA B addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho ENZYME n addmsg /kinetics/TSC1-TSC2 /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/AKT_mod/AKT REAC A B addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/AKT_mod/TSC1-TSC2_star MM_PRD pA addmsg /kinetics/AKT_mod/TSC1-2_dephospho /kinetics/AKT_mod/TSC1-TSC2_star REAC A B addmsg /kinetics/AKT_mod/AKT /kinetics/AKT_mod/PIP3_bind_AKT SUBSTRATE n addmsg /kinetics/PIP3 /kinetics/AKT_mod/PIP3_bind_AKT SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_AKT /kinetics/AKT_mod/PIP3_bind_AKT PRODUCT n addmsg /kinetics/PDK1 /kinetics/AKT_mod/PIP3_bind_PDK1 SUBSTRATE n addmsg /kinetics/PIP3 /kinetics/AKT_mod/PIP3_bind_PDK1 SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_PDK1 /kinetics/AKT_mod/PIP3_bind_PDK1 PRODUCT n addmsg /kinetics/AKT_mod/TSC1-TSC2_star /kinetics/AKT_mod/TSC1-2_dephospho SUBSTRATE n addmsg /kinetics/TSC1-TSC2 /kinetics/AKT_mod/TSC1-2_dephospho PRODUCT n addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx REAC B A addmsg /kinetics/TrKB_mod/LR_cycling /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx REAC A B addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx REAC B A addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/TrKB_mod/TrKB REAC A B addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/TrKB REAC A B addmsg /kinetics/TrKB_mod/LR_cycling /kinetics/TrKB_mod/TrKB REAC B A addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/BDNF_TrkB2_clx REAC B A addmsg /kinetics/TrKB_mod/Autophos_TrKB /kinetics/TrKB_mod/BDNF_TrkB2_clx REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx /kinetics/TrKB_mod/Autophos_TrKB PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_clx /kinetics/TrKB_mod/Autophos_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_clx /kinetics/TrKB_mod/Dimeriz_TrKB PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB_clx /kinetics/TrKB_mod/Dimeriz_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/Dimeriz_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/TrKB_mod/BDNF_TrkB_clx REAC B A addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/BDNF_TrkB_clx REAC A B addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/Ligand_binding SUBSTRATE n addmsg /kinetics/BDNF /kinetics/TrKB_mod/Ligand_binding SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB_clx /kinetics/TrKB_mod/Ligand_binding PRODUCT n addmsg /kinetics/TrKB_mod/Autophos_TrKB /kinetics/TrKB_mod/BDNF_TrkB2_star_clx REAC B A addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho /kinetics/TrKB_mod/BDNF_TrkB2_star_clx REAC eA B addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/BDNF_TrkB2_star_clx REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho /kinetics/TrKB_mod/BDNF_TrkB2_star_clx REAC eA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho ENZYME n addmsg /kinetics/PLC_g /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/PLC_g_phospho SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho ENZYME n addmsg /kinetics/PI3K_mod/Shc /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho SUBSTRATE n addmsg /kinetics/PLC_g_star /kinetics/TrKB_mod/PLC_g_star_dephospho SUBSTRATE n addmsg /kinetics/PLC_g /kinetics/TrKB_mod/PLC_g_star_dephospho PRODUCT n addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx REAC B A addmsg /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx REAC eA B addmsg /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho SUBSTRATE n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx /kinetics/TrKB_mod/LR_Internalize PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx /kinetics/TrKB_mod/LR_Internalize SUBSTRATE n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx /kinetics/TrKB_mod/LR_Internalize PRODUCT n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2_star_clx /kinetics/TrKB_mod/LR_cycling SUBSTRATE n addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/LR_cycling PRODUCT n addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_mod/basal_PI3K_act /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_bind_Ras-GTP /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PI3K_mod/PI3K_basal REAC eA B addmsg /kinetics/PI3K_mod/basal_PI3K_act /kinetics/PI3K_mod/PI3K_basal REAC B A addmsg /kinetics/PI3K_mod/PI3K_basal /kinetics/PI3K_mod/PI3K_basal/basal_phosp ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/PI3K_mod/PI3K_basal/basal_phosp SUBSTRATE n addmsg /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx/Phospho /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PI3K_mod/PIP2 MM_PRD pA addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho /kinetics/PI3K_mod/Shc REAC sA B addmsg /kinetics/PI3K_mod/Shc_star_dephospho /kinetics/PI3K_mod/Shc REAC B A addmsg /kinetics/Shc_star /kinetics/PI3K_mod/Shc_star_dephospho SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc /kinetics/PI3K_mod/Shc_star_dephospho PRODUCT n addmsg /kinetics/Grb2 /kinetics/PI3K_mod/Grb2_bind_Shc SUBSTRATE n addmsg /kinetics/Shc_star /kinetics/PI3K_mod/Grb2_bind_Shc SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc_star_Grb2_clx /kinetics/PI3K_mod/Grb2_bind_Shc PRODUCT n addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/PI3K_mod/Shc_star_Grb2_clx REAC B A addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Shc_star_Grb2_clx REAC A B addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Gab1 REAC A B addmsg /kinetics/PI3K_mod/Shc_star_Grb2-Gab1_clx /kinetics/PI3K_mod/bind_Gab1 PRODUCT n addmsg /kinetics/PI3K_mod/Gab1 /kinetics/PI3K_mod/bind_Gab1 SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc_star_Grb2_clx /kinetics/PI3K_mod/bind_Gab1 SUBSTRATE n addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Shc_star_Grb2-Gab1_clx REAC B A addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/PI3K_mod/Shc_star_Grb2-Gab1_clx REAC A B addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_mod/PI3K_act SUBSTRATE n addmsg /kinetics/TrKB_mod/Shc_star_Grb2-Gab1_PI3K_clx /kinetics/PI3K_mod/PI3K_act PRODUCT n addmsg /kinetics/PI3K_mod/Shc_star_Grb2-Gab1_clx /kinetics/PI3K_mod/PI3K_act SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_mod/basal_PI3K_act SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K_basal /kinetics/PI3K_mod/basal_PI3K_act PRODUCT n addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLCg_basal REAC eA B addmsg /kinetics/PLCg_basal /kinetics/PLCg_basal/PLC_g_phospho ENZYME n addmsg /kinetics/PLC_g /kinetics/PLCg_basal/PLC_g_phospho SUBSTRATE n addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/TSC1-TSC2 REAC sA B addmsg /kinetics/AKT_mod/TSC1-2_dephospho /kinetics/TSC1-TSC2 REAC B A addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/TSC1-TSC2 REAC eA B addmsg /kinetics/TSC1-TSC2 /kinetics/TSC1-TSC2/TSC2phospho ENZYME n addmsg /kinetics/Rheb-GTP /kinetics/TSC1-TSC2/TSC2phospho SUBSTRATE n addmsg /kinetics/4E-BP_mod/eIF4E-BP2_disso /kinetics/eIF4E REAC B A addmsg /kinetics/eIF4F_clx /kinetics/eIF4E REAC A B addmsg /kinetics/eIF4E-BP_disso /kinetics/eIF4E REAC B A addmsg /kinetics/4E-BP_mod/eIF4E_bind_BP2 /kinetics/eIF4E REAC A B addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/Rheb-GTP REAC sA B addmsg /kinetics/GDP_to_GTP /kinetics/Rheb-GTP REAC B A addmsg /kinetics/mTOR_model/Rheb-GTP_bind_TORclx /kinetics/Rheb-GTP REAC A B addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/Rheb-GDP MM_PRD pA addmsg /kinetics/GDP_to_GTP /kinetics/Rheb-GDP REAC A B addmsg /kinetics/Rheb-GTP /kinetics/mTOR_model/Rheb-GTP_bind_TORclx SUBSTRATE n addmsg /kinetics/mTOR_model/TOR-clx /kinetics/mTOR_model/Rheb-GTP_bind_TORclx SUBSTRATE n addmsg /kinetics/TOR_Rheb-GTP_clx /kinetics/mTOR_model/Rheb-GTP_bind_TORclx PRODUCT n addmsg /kinetics/mTOR_model/Rheb-GTP_bind_TORclx /kinetics/mTOR_model/TOR-clx REAC A B addmsg /kinetics/mTOR_model/Rheb-GTP_bind_TORclx /kinetics/TOR_Rheb-GTP_clx REAC B A addmsg /kinetics/TOR_Rheb-GTP_clx/S6K_phospho /kinetics/TOR_Rheb-GTP_clx REAC eA B addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho /kinetics/TOR_Rheb-GTP_clx REAC eA B addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star /kinetics/TOR_Rheb-GTP_clx REAC eA B addmsg /kinetics/TOR_Rheb-GTP_clx /kinetics/TOR_Rheb-GTP_clx/S6K_phospho ENZYME n addmsg /kinetics/S6Kinase/S6K_star /kinetics/TOR_Rheb-GTP_clx/S6K_phospho SUBSTRATE n addmsg /kinetics/TOR_Rheb-GTP_clx /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho ENZYME n addmsg /kinetics/4E-BP_mod/eIF4E-BP /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho SUBSTRATE n addmsg /kinetics/TOR_Rheb-GTP_clx /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star ENZYME n addmsg /kinetics/4E-BP_mod/4E-BP /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star SUBSTRATE n addmsg /kinetics/MAPK_star/cluster_phospho_S6K /kinetics/S6Kinase/S6K_star MM_PRD pA addmsg /kinetics/TOR_Rheb-GTP_clx/S6K_phospho /kinetics/S6Kinase/S6K_star REAC sA B addmsg /kinetics/PP2A/dephos_S6K /kinetics/S6Kinase/S6K_star MM_PRD pA addmsg /kinetics/PP2A/dephos_clus_S6K /kinetics/S6Kinase/S6K_star REAC sA B addmsg /kinetics/basal_S6K /kinetics/S6Kinase/S6K_star REAC B A addmsg /kinetics/MAPK_star/cluster_phospho_S6K /kinetics/S6Kinase/S6K REAC sA B addmsg /kinetics/PP2A/dephos_clus_S6K /kinetics/S6Kinase/S6K MM_PRD pA addmsg /kinetics/basal_S6K /kinetics/S6Kinase/S6K REAC A B addmsg /kinetics/TOR_Rheb-GTP_clx/S6K_phospho /kinetics/S6Kinase/S6K_thr-412 MM_PRD pA addmsg /kinetics/PDK1/S6K_phospho /kinetics/S6Kinase/S6K_thr-412 REAC sA B addmsg /kinetics/PP2A/dephosp_S6K /kinetics/S6Kinase/S6K_thr-412 MM_PRD pA addmsg /kinetics/PP2A/dephos_S6K /kinetics/S6Kinase/S6K_thr-412 REAC sA B addmsg /kinetics/S6Kinase/S6K_thr-412/S6_phos /kinetics/S6Kinase/S6K_thr-412 REAC eA B addmsg /kinetics/S6Kinase/S6K_thr-412 /kinetics/S6Kinase/S6K_thr-412/S6_phos ENZYME n addmsg /kinetics/S6Kinase/40S_inact /kinetics/S6Kinase/S6K_thr-412/S6_phos SUBSTRATE n addmsg /kinetics/40S /kinetics/S6Kinase/S6_dephosph SUBSTRATE n addmsg /kinetics/S6Kinase/40S_inact /kinetics/S6Kinase/S6_dephosph PRODUCT n addmsg /kinetics/S6Kinase/S6_dephosph /kinetics/S6Kinase/40S_inact REAC B A addmsg /kinetics/S6K_thr-252/S6_phospho /kinetics/S6Kinase/40S_inact REAC sA B addmsg /kinetics/40S_basal/basal /kinetics/S6Kinase/40S_inact REAC sA B addmsg /kinetics/S6Kinase/S6K_thr-412/S6_phos /kinetics/S6Kinase/40S_inact REAC sA B addmsg /kinetics/4E-BP_mod/4E-BP /kinetics/4E-BP_mod/eIF4E_bind_BP2 SUBSTRATE n addmsg /kinetics/eIF4E /kinetics/4E-BP_mod/eIF4E_bind_BP2 SUBSTRATE n addmsg /kinetics/4E-BP_mod/eIF4E-BP /kinetics/4E-BP_mod/eIF4E_bind_BP2 PRODUCT n addmsg /kinetics/eIF4E /kinetics/4E-BP_mod/eIF4E-BP2_disso PRODUCT n addmsg /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 /kinetics/4E-BP_mod/eIF4E-BP2_disso SUBSTRATE n addmsg /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 /kinetics/4E-BP_mod/eIF4E-BP2_disso PRODUCT n addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star /kinetics/4E-BP_mod/4E-BP REAC sA B addmsg /kinetics/PP2A/PP2A_4E-BP_star /kinetics/4E-BP_mod/4E-BP MM_PRD pA addmsg /kinetics/4E-BP_mod/eIF4E_bind_BP2 /kinetics/4E-BP_mod/4E-BP REAC A B addmsg /kinetics/4E-BP_mod/eIF4E-BP2_disso /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 REAC B A addmsg /kinetics/MAPK_star/MAPK_4E-BP_star_star /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 MM_PRD pA addmsg /kinetics/PP2A/PP2A_4E-BP_star_star /kinetics/4E-BP_mod/4E-BP_thr37_46_s65 REAC sA B addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho /kinetics/4E-BP_mod/eIF4E-BP REAC sA B addmsg /kinetics/PP2A/PP2A_4EBP /kinetics/4E-BP_mod/eIF4E-BP MM_PRD pA addmsg /kinetics/4E-BP_mod/eIF4E_bind_BP2 /kinetics/4E-BP_mod/eIF4E-BP REAC B A addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_phospho /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 MM_PRD pA addmsg /kinetics/PP2A/PP2A_4EBP /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 REAC sA B addmsg /kinetics/MAPK_star/MAPK_4E-BP_phospho /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 REAC sA B addmsg /kinetics/PP2A/PP2A_4E-BP /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 MM_PRD pA addmsg /kinetics/eIF4E-BP_disso /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 REAC A B addmsg /kinetics/MAPK_star/MAPK_4E-BP_phospho /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 MM_PRD pA addmsg /kinetics/PP2A/PP2A_4E-BP /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 REAC sA B addmsg /kinetics/4E-BP_mod/eIF4E-BP2_disso /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 REAC A B addmsg /kinetics/S6Kinase/S6_dephosph /kinetics/40S REAC A B addmsg /kinetics/S6K_thr-252/S6_phospho /kinetics/40S MM_PRD pA addmsg /kinetics/43S_complex/Q_binds_R /kinetics/40S REAC A B addmsg /kinetics/43S_complex/R_binds_M /kinetics/40S REAC A B addmsg /kinetics/40S_basal/basal /kinetics/40S MM_PRD pA addmsg /kinetics/S6Kinase/S6K_thr-412/S6_phos /kinetics/40S MM_PRD pA addmsg /kinetics/eIF4G-A_clx /kinetics/eIF4F_clx SUBSTRATE n addmsg /kinetics/eIF4F /kinetics/eIF4F_clx PRODUCT n addmsg /kinetics/eIF4E /kinetics/eIF4F_clx SUBSTRATE n addmsg /kinetics/eIF4F_clx /kinetics/eIF4G-A_clx REAC A B addmsg /kinetics/eIF4G_A_clx /kinetics/eIF4G-A_clx REAC B A addmsg /kinetics/eIF4A /kinetics/eIF4G_A_clx SUBSTRATE n addmsg /kinetics/eIF4G /kinetics/eIF4G_A_clx SUBSTRATE n addmsg /kinetics/eIF4G-A_clx /kinetics/eIF4G_A_clx PRODUCT n addmsg /kinetics/eIF4G_A_clx /kinetics/eIF4A REAC A B addmsg /kinetics/eIF4G_A_clx /kinetics/eIF4G REAC A B addmsg /kinetics/eIF4F_clx /kinetics/eIF4F REAC B A addmsg /kinetics/eIF4F_mRNA_clx /kinetics/eIF4F REAC A B addmsg /kinetics/eIF4F_mRNA_clx /kinetics/mRNA REAC A B addmsg /kinetics/mRNA /kinetics/eIF4F_mRNA_clx SUBSTRATE n addmsg /kinetics/eIF4F-mRNA_clx /kinetics/eIF4F_mRNA_clx PRODUCT n addmsg /kinetics/eIF4F /kinetics/eIF4F_mRNA_clx SUBSTRATE n addmsg /kinetics/eIF4F_mRNA_clx /kinetics/eIF4F-mRNA_clx REAC B A addmsg /kinetics/43S_complex/R_binds_M /kinetics/eIF4F-mRNA_clx REAC A B addmsg /kinetics/43S_complex/QR_binds_M /kinetics/eIF4F-mRNA_clx REAC A B addmsg /kinetics/40S /kinetics/43S_complex/Q_binds_R SUBSTRATE n addmsg /kinetics/43S_complex/Quaternary_clx /kinetics/43S_complex/Q_binds_R SUBSTRATE n addmsg /kinetics/43S_complex/Q.R /kinetics/43S_complex/Q_binds_R PRODUCT n addmsg /kinetics/43S_complex/Q_binds_R /kinetics/43S_complex/Q.R REAC B A addmsg /kinetics/43S_complex/QR_binds_M /kinetics/43S_complex/Q.R REAC A B addmsg /kinetics/43S_complex/Q.R /kinetics/43S_complex/QR_binds_M SUBSTRATE n addmsg /kinetics/eIF4F-mRNA_clx /kinetics/43S_complex/QR_binds_M SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/43S_complex/QR_binds_M PRODUCT n addmsg /kinetics/eIF4F-mRNA_clx /kinetics/43S_complex/R_binds_M SUBSTRATE n addmsg /kinetics/43S_complex/RM /kinetics/43S_complex/R_binds_M PRODUCT n addmsg /kinetics/40S /kinetics/43S_complex/R_binds_M SUBSTRATE n addmsg /kinetics/43S_complex/R_binds_M /kinetics/43S_complex/RM REAC B A addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43S_complex/RM REAC A B addmsg /kinetics/43S_complex/RM /kinetics/43S_complex/RM_binds_Q SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/43S_complex/RM_binds_Q PRODUCT n addmsg /kinetics/43S_complex/Quaternary_clx /kinetics/43S_complex/RM_binds_Q SUBSTRATE n addmsg /kinetics/43S_complex/Q_binds_R /kinetics/43S_complex/Quaternary_clx REAC A B addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43S_complex/Quaternary_clx REAC A B addmsg /kinetics/PDK1/S6K_phospho /kinetics/S6K_thr-252 MM_PRD pA addmsg /kinetics/PP2A/dephosp_S6K /kinetics/S6K_thr-252 REAC sA B addmsg /kinetics/S6K_thr-252/S6_phospho /kinetics/S6K_thr-252 REAC eA B addmsg /kinetics/S6K_thr-252/camkIII_phospho /kinetics/S6K_thr-252 REAC eA B addmsg /kinetics/S6K_thr-252 /kinetics/S6K_thr-252/camkIII_phospho ENZYME n addmsg /kinetics/CaMKIII /kinetics/S6K_thr-252/camkIII_phospho SUBSTRATE n addmsg /kinetics/S6K_thr-252 /kinetics/S6K_thr-252/S6_phospho ENZYME n addmsg /kinetics/S6Kinase/40S_inact /kinetics/S6K_thr-252/S6_phospho SUBSTRATE n addmsg /kinetics/CaMKIII_bind_CaM-Ca4 /kinetics/CaM-Ca4 REAC A B addmsg /kinetics/CaM/CaM-Ca3-bind-Ca /kinetics/CaM-Ca4 REAC B A addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/CaM-Ca4 REAC A B addmsg /kinetics/CaMKIII_bind_CaM-Ca4 /kinetics/CaMKIII REAC A B addmsg /kinetics/S6K_thr-252/camkIII_phospho /kinetics/CaMKIII REAC sA B addmsg /kinetics/dephosp_CaMKIII /kinetics/CaMKIII REAC B A addmsg /kinetics/S6K_basal/CaMKIII_basal /kinetics/CaMKIII REAC sA B addmsg /kinetics/CaMKIII_bind_CaM-Ca4 /kinetics/CaMKIII_CaM-Ca4 REAC B A addmsg /kinetics/CaMKIII_CaM-Ca4/phospho /kinetics/CaMKIII_CaM-Ca4 REAC eA B addmsg /kinetics/CaMKIII_CaM-Ca4 /kinetics/CaMKIII_CaM-Ca4/phospho ENZYME n addmsg /kinetics/eEF2 /kinetics/CaMKIII_CaM-Ca4/phospho SUBSTRATE n addmsg /kinetics/CaMKIII_CaM-Ca4/phospho /kinetics/eEF2 REAC sA B addmsg /kinetics/CaMKIII_basal/eEF2thr56_basal /kinetics/eEF2 REAC sA B addmsg /kinetics/PP2A/eEF2thr-56_dephospho /kinetics/eEF2 MM_PRD pA addmsg /kinetics/elongation /kinetics/eEF2 REAC A B addmsg /kinetics/CaMKIII_CaM-Ca4/phospho /kinetics/eEFthr-56 MM_PRD pA addmsg /kinetics/CaMKIII_basal/eEF2thr56_basal /kinetics/eEFthr-56 MM_PRD pA addmsg /kinetics/PP2A/eEF2thr-56_dephospho /kinetics/eEFthr-56 REAC sA B addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/CaM/CaM REAC A B addmsg /kinetics/CaM/CaM-Ca3 /kinetics/CaM/CaM-Ca3-bind-Ca SUBSTRATE n addmsg /kinetics/Ca /kinetics/CaM/CaM-Ca3-bind-Ca SUBSTRATE n addmsg /kinetics/CaM-Ca4 /kinetics/CaM/CaM-Ca3-bind-Ca PRODUCT n addmsg /kinetics/CaM/CaM-Ca2-bind-Ca /kinetics/CaM/CaM-Ca3 REAC B A addmsg /kinetics/CaM/CaM-Ca3-bind-Ca /kinetics/CaM/CaM-Ca3 REAC A B addmsg /kinetics/CaM/CaM /kinetics/CaM/CaM-bind-Ca SUBSTRATE n addmsg /kinetics/Ca /kinetics/CaM/CaM-bind-Ca SUBSTRATE n addmsg /kinetics/CaM/CaM-Ca /kinetics/CaM/CaM-bind-Ca PRODUCT n addmsg /kinetics/CaM/CaM-Ca2-bind-Ca /kinetics/CaM/CaM-Ca2 REAC A B addmsg /kinetics/CaM/CaM-Ca-bind-Ca /kinetics/CaM/CaM-Ca2 REAC B A addmsg /kinetics/CaM/CaM-Ca2 /kinetics/CaM/CaM-Ca2-bind-Ca SUBSTRATE n addmsg /kinetics/Ca /kinetics/CaM/CaM-Ca2-bind-Ca SUBSTRATE n addmsg /kinetics/CaM/CaM-Ca3 /kinetics/CaM/CaM-Ca2-bind-Ca PRODUCT n addmsg /kinetics/CaM/CaM-Ca /kinetics/CaM/CaM-Ca-bind-Ca SUBSTRATE n addmsg /kinetics/Ca /kinetics/CaM/CaM-Ca-bind-Ca SUBSTRATE n addmsg /kinetics/CaM/CaM-Ca2 /kinetics/CaM/CaM-Ca-bind-Ca PRODUCT n addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/CaM/CaM-Ca REAC B A addmsg /kinetics/CaM/CaM-Ca-bind-Ca /kinetics/CaM/CaM-Ca REAC A B addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaM/CaM-Ca2-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaM/CaM-Ca3-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaM/CaM-Ca-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaMKIII_basal/eEF2thr56_basal /kinetics/CaMKIII_basal REAC eA B addmsg /kinetics/CaMKIII_basal /kinetics/CaMKIII_basal/eEF2thr56_basal ENZYME n addmsg /kinetics/eEF2 /kinetics/CaMKIII_basal/eEF2thr56_basal SUBSTRATE n addmsg /kinetics/S6K_thr-252/camkIII_phospho /kinetics/CaMKIII_star MM_PRD pA addmsg /kinetics/dephosp_CaMKIII /kinetics/CaMKIII_star REAC A B addmsg /kinetics/S6K_basal/CaMKIII_basal /kinetics/CaMKIII_star MM_PRD pA addmsg /kinetics/S6K_basal/CaMKIII_basal /kinetics/S6K_basal REAC eA B addmsg /kinetics/S6K_basal /kinetics/S6K_basal/CaMKIII_basal ENZYME n addmsg /kinetics/CaMKIII /kinetics/S6K_basal/CaMKIII_basal SUBSTRATE n addmsg /kinetics/CaMKIII_star /kinetics/dephosp_CaMKIII SUBSTRATE n addmsg /kinetics/CaMKIII /kinetics/dephosp_CaMKIII PRODUCT n addmsg /kinetics/activation /kinetics/60S_R REAC A B addmsg /kinetics/Translation_clx/pro_syn /kinetics/Translation_clx REAC eA B addmsg /kinetics/elongation /kinetics/Translation_clx REAC B A addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/Translation_clx REAC eA B addmsg /kinetics/Translation_clx /kinetics/Translation_clx/pro_syn ENZYME n addmsg /kinetics/AA /kinetics/Translation_clx/pro_syn SUBSTRATE n addmsg /kinetics/Translation_clx /kinetics/Translation_clx/rad_pro_syn ENZYME n addmsg /kinetics/rad_AA /kinetics/Translation_clx/rad_pro_syn SUBSTRATE n addmsg /kinetics/Translation_clx/pro_syn /kinetics/AA REAC sA B addmsg /kinetics/Basal_Translation/basal_syn /kinetics/AA REAC sA B addmsg /kinetics/labelling /kinetics/AA REAC A B addmsg /kinetics/Translation_clx/pro_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/pep_elongation /kinetics/peptide REAC A B addmsg /kinetics/Basal_Translation/basal_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/eEF2 /kinetics/elongation SUBSTRATE n addmsg /kinetics/80S_ribos_clx /kinetics/elongation SUBSTRATE n addmsg /kinetics/Translation_clx /kinetics/elongation PRODUCT n addmsg /kinetics/60S_R /kinetics/activation SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/activation SUBSTRATE n addmsg /kinetics/80S_ribos_clx /kinetics/activation PRODUCT n addmsg /kinetics/protein_deg /kinetics/degraded_protein REAC B A addmsg /kinetics/pep_elongation /kinetics/protein REAC B A addmsg /kinetics/protein_deg /kinetics/protein REAC A B addmsg /kinetics/activation /kinetics/80S_ribos_clx REAC B A addmsg /kinetics/elongation /kinetics/80S_ribos_clx REAC A B addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/Grb2 REAC A B addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Grb2 REAC A B addmsg /kinetics/Sos/Grb2_bind_Sos_star /kinetics/Grb2 REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx/Shc_phospho /kinetics/Shc_star MM_PRD pA addmsg /kinetics/PI3K_mod/Shc_star_dephospho /kinetics/Shc_star REAC A B addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/Shc_star REAC A B addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/Shc_star REAC A B addmsg /kinetics/MAPK_star/cluster_phospho_S6K /kinetics/MAPK_star REAC eA B addmsg /kinetics/MAPK_star/MAPK_4E-BP_phospho /kinetics/MAPK_star REAC eA B addmsg /kinetics/MAPK_star/MAPK_star-feedback /kinetics/MAPK_star REAC eA B addmsg /kinetics/MAPK/MAPKK_star/MAPKKthr /kinetics/MAPK_star MM_PRD pA addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MAPK_star REAC sA B addmsg /kinetics/MAPK_star/phosph_Sos /kinetics/MAPK_star REAC eA B addmsg /kinetics/MAPK_star/MAPK_4E-BP_star_star /kinetics/MAPK_star REAC eA B addmsg /kinetics/MAPK_star /kinetics/MAPK_star/cluster_phospho_S6K ENZYME n addmsg /kinetics/S6Kinase/S6K /kinetics/MAPK_star/cluster_phospho_S6K SUBSTRATE n addmsg /kinetics/MAPK_star /kinetics/MAPK_star/MAPK_star-feedback ENZYME n addmsg /kinetics/MAPK/craf-1_star /kinetics/MAPK_star/MAPK_star-feedback SUBSTRATE n addmsg /kinetics/MAPK_star /kinetics/MAPK_star/phosph_Sos ENZYME n addmsg /kinetics/Sos/Sos /kinetics/MAPK_star/phosph_Sos SUBSTRATE n addmsg /kinetics/MAPK_star /kinetics/MAPK_star/MAPK_4E-BP_star_star ENZYME n addmsg /kinetics/4E-BP_t37_46 /kinetics/MAPK_star/MAPK_4E-BP_star_star SUBSTRATE n addmsg /kinetics/MAPK_star /kinetics/MAPK_star/MAPK_4E-BP_phospho ENZYME n addmsg /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 /kinetics/MAPK_star/MAPK_4E-BP_phospho SUBSTRATE n addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC/PKC-DAG-AA_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC/PKC-Ca-memb_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC/PKC-Ca-AA_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC/PKC-DAG-memb_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC/PKC-basal_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC/PKC-AA_star /kinetics/PKC-active SUMTOTAL n nInit addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-act-raf ENZYME n addmsg /kinetics/MAPK/craf-1 /kinetics/PKC-active/PKC-act-raf SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-inact-GAP ENZYME n addmsg /kinetics/Ras/GAP /kinetics/PKC-active/PKC-inact-GAP SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-act-GEF ENZYME n addmsg /kinetics/Ras/inact-GEF /kinetics/PKC-active/PKC-act-GEF SUBSTRATE n addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/MAPK/craf-1 REAC sA B addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/MAPK/craf-1 MM_PRD pA addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/MAPK/craf-1_star MM_PRD pA addmsg /kinetics/MAPK_star/MAPK_star-feedback /kinetics/MAPK/craf-1_star REAC sA B addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/MAPK/craf-1_star REAC sA B addmsg /kinetics/PPhosphatase2A/craf_star_star-deph /kinetics/MAPK/craf-1_star MM_PRD pA addmsg /kinetics/Ras-act-craf /kinetics/MAPK/craf-1_star REAC A B addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/MAPK/MAPKK MM_PRD pA addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 /kinetics/MAPK/MAPKK REAC sA B addmsg /kinetics/MAPK/MAPKK_star/MAPKKtyr /kinetics/MAPK/MAPK REAC sA B addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MAPK/MAPK MM_PRD pA addmsg /kinetics/MAPK_star/MAPK_star-feedback /kinetics/MAPK/craf-1_star_star MM_PRD pA addmsg /kinetics/PPhosphatase2A/craf_star_star-deph /kinetics/MAPK/craf-1_star_star REAC sA B addmsg /kinetics/MAPK/MAPKK_star/MAPKKtyr /kinetics/MAPK/MAPK-tyr MM_PRD pA addmsg /kinetics/MAPK/MAPKK_star/MAPKKthr /kinetics/MAPK/MAPK-tyr REAC sA B addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MAPK/MAPK-tyr REAC sA B addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MAPK/MAPK-tyr MM_PRD pA addmsg /kinetics/MAPK/MAPKK_star/MAPKKtyr /kinetics/MAPK/MAPKK_star REAC eA B addmsg /kinetics/MAPK/MAPKK_star/MAPKKthr /kinetics/MAPK/MAPKK_star REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/MAPK/MAPKK_star REAC sA B addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 /kinetics/MAPK/MAPKK_star MM_PRD pA addmsg /kinetics/MAPK/MAPKK_star /kinetics/MAPK/MAPKK_star/MAPKKtyr ENZYME n addmsg /kinetics/MAPK/MAPK /kinetics/MAPK/MAPKK_star/MAPKKtyr SUBSTRATE n addmsg /kinetics/MAPK/MAPKK_star /kinetics/MAPK/MAPKK_star/MAPKKthr ENZYME n addmsg /kinetics/MAPK/MAPK-tyr /kinetics/MAPK/MAPKK_star/MAPKKthr SUBSTRATE n addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/MAPK/MAPKK-ser MM_PRD pA addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/MAPK/MAPKK-ser REAC sA B addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 /kinetics/MAPK/MAPKK-ser MM_PRD pA addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 /kinetics/MAPK/MAPKK-ser REAC sA B addmsg /kinetics/Ras-act-craf /kinetics/MAPK/Raf_star-GTP-Ras REAC B A addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 /kinetics/MAPK/Raf_star-GTP-Ras REAC eA B addmsg /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 /kinetics/MAPK/Raf_star-GTP-Ras REAC eA B addmsg /kinetics/MAPK/Raf_star-GTP-Ras /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 ENZYME n addmsg /kinetics/MAPK/MAPKK /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1 SUBSTRATE n addmsg /kinetics/MAPK/Raf_star-GTP-Ras /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 ENZYME n addmsg /kinetics/MAPK/MAPKK-ser /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2 SUBSTRATE n addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MKP-1 REAC eA B addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MKP-1 REAC eA B addmsg /kinetics/MKP-1 /kinetics/MKP-1/MKP1-tyr-deph ENZYME n addmsg /kinetics/MAPK/MAPK-tyr /kinetics/MKP-1/MKP1-tyr-deph SUBSTRATE n addmsg /kinetics/MKP-1 /kinetics/MKP-1/MKP1-thr-deph ENZYME n addmsg /kinetics/MAPK_star /kinetics/MKP-1/MKP1-thr-deph SUBSTRATE n addmsg /kinetics/MAPK/craf-1_star /kinetics/Ras-act-craf SUBSTRATE n addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras-act-craf SUBSTRATE n addmsg /kinetics/MAPK/Raf_star-GTP-Ras /kinetics/Ras-act-craf PRODUCT n addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/craf_star_star-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/craf-deph ENZYME n addmsg /kinetics/MAPK/craf-1_star /kinetics/PPhosphatase2A/craf-deph SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/MAPKK-deph ENZYME n addmsg /kinetics/MAPK/MAPKK_star /kinetics/PPhosphatase2A/MAPKK-deph SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/MAPKK-deph-ser ENZYME n addmsg /kinetics/MAPK/MAPKK-ser /kinetics/PPhosphatase2A/MAPKK-deph-ser SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/craf_star_star-deph ENZYME n addmsg /kinetics/MAPK/craf-1_star_star /kinetics/PPhosphatase2A/craf_star_star-deph SUBSTRATE n addmsg /kinetics/Ras/GEF_star /kinetics/Ras/dephosph-GEF SUBSTRATE n addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/dephosph-GEF PRODUCT n addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/Ras/inact-GEF REAC sA B addmsg /kinetics/Ras/dephosph-GEF /kinetics/Ras/inact-GEF REAC B A addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/Ras/inact-GEF REAC A B addmsg /kinetics/Ras/inact-GEF/basal_GEF_activity /kinetics/Ras/inact-GEF REAC eA B addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/inact-GEF/basal_GEF_activity ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/inact-GEF/basal_GEF_activity SUBSTRATE n addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/Ras/GEF_star MM_PRD pA addmsg /kinetics/Ras/dephosph-GEF /kinetics/Ras/GEF_star REAC A B addmsg /kinetics/Ras/GEF_star/GEF_star-act-ras /kinetics/Ras/GEF_star REAC eA B addmsg /kinetics/Ras/GEF_star /kinetics/Ras/GEF_star/GEF_star-act-ras ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/GEF_star/GEF_star-act-ras SUBSTRATE n addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GTP-Ras REAC sA B addmsg /kinetics/Ras/Ras-intrinsic-GTPase /kinetics/Ras/GTP-Ras REAC A B addmsg /kinetics/Ras/GEF_star/GEF_star-act-ras /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras-act-craf /kinetics/Ras/GTP-Ras REAC A B addmsg /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras/inact-GEF/basal_GEF_activity /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/PI3K_bind_Ras-GTP /kinetics/Ras/GTP-Ras REAC A B addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GDP-Ras MM_PRD pA addmsg /kinetics/Ras/Ras-intrinsic-GTPase /kinetics/Ras/GDP-Ras REAC B A addmsg /kinetics/Ras/GEF_star/GEF_star-act-ras /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/inact-GEF/basal_GEF_activity /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras/Ras-intrinsic-GTPase SUBSTRATE n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/Ras-intrinsic-GTPase PRODUCT n addmsg /kinetics/Ras/GAP_star /kinetics/Ras/dephosph-GAP SUBSTRATE n addmsg /kinetics/Ras/GAP /kinetics/Ras/dephosph-GAP PRODUCT n addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/Ras/GAP_star MM_PRD pA addmsg /kinetics/Ras/dephosph-GAP /kinetics/Ras/GAP_star REAC A B addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GAP REAC eA B addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/Ras/GAP REAC sA B addmsg /kinetics/Ras/dephosph-GAP /kinetics/Ras/GAP REAC B A addmsg /kinetics/Ras/GAP /kinetics/Ras/GAP/GAP-inact-ras ENZYME n addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras/GAP/GAP-inact-ras SUBSTRATE n addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/CaM-bind-GEF SUBSTRATE n addmsg /kinetics/Ras/CaM-GEF /kinetics/Ras/CaM-bind-GEF PRODUCT n addmsg /kinetics/CaM-Ca4 /kinetics/Ras/CaM-bind-GEF SUBSTRATE n addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/Ras/CaM-GEF REAC B A addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/CaM-GEF REAC eA B addmsg /kinetics/Ras/CaM-GEF /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras SUBSTRATE n addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/Shc_star.Sos.Grb2 REAC B A addmsg /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF /kinetics/Shc_star.Sos.Grb2 REAC eA B addmsg /kinetics/Shc_star.Sos.Grb2 /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Shc_star.Sos.Grb2/Sos.Ras_GEF SUBSTRATE n addmsg /kinetics/Sos/Sos.Grb2 /kinetics/Sos/Shc_bind_Sos.Grb2 SUBSTRATE n addmsg /kinetics/Shc_star /kinetics/Sos/Shc_bind_Sos.Grb2 SUBSTRATE n addmsg /kinetics/Shc_star.Sos.Grb2 /kinetics/Sos/Shc_bind_Sos.Grb2 PRODUCT n addmsg /kinetics/Sos/Grb2_bind_Sos_star /kinetics/Sos/Sos_star.Grb2 REAC B A addmsg /kinetics/Sos/Sos_star /kinetics/Sos/Grb2_bind_Sos_star SUBSTRATE n addmsg /kinetics/Grb2 /kinetics/Sos/Grb2_bind_Sos_star SUBSTRATE n addmsg /kinetics/Sos/Sos_star.Grb2 /kinetics/Sos/Grb2_bind_Sos_star PRODUCT n addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Sos/Sos.Grb2 REAC B A addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/Sos/Sos.Grb2 REAC A B addmsg /kinetics/MAPK_star/phosph_Sos /kinetics/Sos/Sos_star MM_PRD pA addmsg /kinetics/Sos/Grb2_bind_Sos_star /kinetics/Sos/Sos_star REAC A B addmsg /kinetics/Sos/dephosph_Sos /kinetics/Sos/Sos_star REAC A B addmsg /kinetics/Sos/Sos_star /kinetics/Sos/dephosph_Sos SUBSTRATE n addmsg /kinetics/Sos/Sos /kinetics/Sos/dephosph_Sos PRODUCT n addmsg /kinetics/Grb2 /kinetics/Sos/Grb2_bind_Sos SUBSTRATE n addmsg /kinetics/Sos/Sos.Grb2 /kinetics/Sos/Grb2_bind_Sos PRODUCT n addmsg /kinetics/Sos/Sos /kinetics/Sos/Grb2_bind_Sos SUBSTRATE n addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Sos/Sos REAC A B addmsg /kinetics/MAPK_star/phosph_Sos /kinetics/Sos/Sos REAC sA B addmsg /kinetics/Sos/dephosph_Sos /kinetics/Sos/Sos REAC B A addmsg /kinetics/43S_complex/QR_binds_M /kinetics/43Scomplex REAC B A addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43Scomplex REAC B A addmsg /kinetics/activation /kinetics/43Scomplex REAC A B addmsg /kinetics/CaM-Ca4 /kinetics/CaMKIII_bind_CaM-Ca4 SUBSTRATE n addmsg /kinetics/CaMKIII /kinetics/CaMKIII_bind_CaM-Ca4 SUBSTRATE n addmsg /kinetics/CaMKIII_CaM-Ca4 /kinetics/CaMKIII_bind_CaM-Ca4 PRODUCT n addmsg /kinetics/protein /kinetics/pep_elongation PRODUCT n addmsg /kinetics/peptide /kinetics/pep_elongation SUBSTRATE n addmsg /kinetics/degraded_protein /kinetics/protein_deg PRODUCT n addmsg /kinetics/protein /kinetics/protein_deg SUBSTRATE n addmsg /kinetics/Rheb-GDP /kinetics/GDP_to_GTP SUBSTRATE n addmsg /kinetics/Rheb-GTP /kinetics/GDP_to_GTP PRODUCT n addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/PKC/PKC-Ca REAC B A addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/PKC/PKC-Ca REAC A B addmsg /kinetics/PKC/PKC-Ca-to-memb /kinetics/PKC/PKC-Ca REAC A B addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/PKC/PKC-Ca REAC A B addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-act-by-Ca SUBSTRATE n addmsg /kinetics/Ca /kinetics/PKC/PKC-act-by-Ca SUBSTRATE n addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-Ca PRODUCT n addmsg /kinetics/DAG /kinetics/PKC/PKC-act-by-DAG SUBSTRATE n addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-DAG SUBSTRATE n addmsg /kinetics/PKC/PKC-Ca-DAG /kinetics/PKC/PKC-act-by-DAG PRODUCT n addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-Ca-to-memb SUBSTRATE n addmsg /kinetics/PKC/PKC-Ca-memb_star /kinetics/PKC/PKC-Ca-to-memb PRODUCT n addmsg /kinetics/PKC/PKC-Ca-DAG /kinetics/PKC/PKC-DAG-to-memb SUBSTRATE n addmsg /kinetics/PKC/PKC-DAG-memb_star /kinetics/PKC/PKC-DAG-to-memb PRODUCT n addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-Ca-AA SUBSTRATE n addmsg /kinetics/Arachidonic_Acid /kinetics/PKC/PKC-act-by-Ca-AA SUBSTRATE n addmsg /kinetics/PKC/PKC-Ca-AA_star /kinetics/PKC/PKC-act-by-Ca-AA PRODUCT n addmsg /kinetics/PKC/PKC-DAG-AA_star /kinetics/PKC/PKC-act-by-DAG-AA PRODUCT n addmsg /kinetics/PKC/PKC-DAG-AA /kinetics/PKC/PKC-act-by-DAG-AA SUBSTRATE n addmsg /kinetics/PKC/PKC-act-by-DAG-AA /kinetics/PKC/PKC-DAG-AA_star REAC B A addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/PKC/PKC-Ca-AA_star REAC B A addmsg /kinetics/PKC/PKC-Ca-to-memb /kinetics/PKC/PKC-Ca-memb_star REAC B A addmsg /kinetics/PKC/PKC-DAG-to-memb /kinetics/PKC/PKC-DAG-memb_star REAC B A addmsg /kinetics/PKC/PKC-basal-act /kinetics/PKC/PKC-basal_star REAC B A addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-basal-act SUBSTRATE n addmsg /kinetics/PKC/PKC-basal_star /kinetics/PKC/PKC-basal-act PRODUCT n addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/PKC/PKC-AA_star REAC B A addmsg /kinetics/Arachidonic_Acid /kinetics/PKC/PKC-act-by-AA SUBSTRATE n addmsg /kinetics/PKC/PKC-AA_star /kinetics/PKC/PKC-act-by-AA PRODUCT n addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-act-by-AA SUBSTRATE n addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/PKC/PKC-Ca-DAG REAC B A addmsg /kinetics/PKC/PKC-DAG-to-memb /kinetics/PKC/PKC-Ca-DAG REAC A B addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-n-DAG SUBSTRATE n addmsg /kinetics/DAG /kinetics/PKC/PKC-n-DAG SUBSTRATE n addmsg /kinetics/PKC/PKC-DAG /kinetics/PKC/PKC-n-DAG PRODUCT n addmsg /kinetics/PKC/PKC-n-DAG /kinetics/PKC/PKC-DAG REAC B A addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/PKC/PKC-DAG REAC A B addmsg /kinetics/PKC/PKC-DAG /kinetics/PKC/PKC-n-DAG-AA SUBSTRATE n addmsg /kinetics/Arachidonic_Acid /kinetics/PKC/PKC-n-DAG-AA SUBSTRATE n addmsg /kinetics/PKC/PKC-DAG-AA /kinetics/PKC/PKC-n-DAG-AA PRODUCT n addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/PKC/PKC-DAG-AA REAC B A addmsg /kinetics/PKC/PKC-act-by-DAG-AA /kinetics/PKC/PKC-DAG-AA REAC A B addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/PKC/PKC-cytosolic REAC A B addmsg /kinetics/PKC/PKC-basal-act /kinetics/PKC/PKC-cytosolic REAC A B addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/PKC/PKC-cytosolic REAC A B addmsg /kinetics/PKC/PKC-n-DAG /kinetics/PKC/PKC-cytosolic REAC A B addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/DAG REAC A B addmsg /kinetics/PKC/PKC-n-DAG /kinetics/DAG REAC A B addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/Arachidonic_Acid REAC A B addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/Arachidonic_Acid REAC A B addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/Arachidonic_Acid REAC A B addmsg /kinetics/Basal_Translation/basal_syn /kinetics/Basal_Translation REAC eA B addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/Basal_Translation REAC eA B addmsg /kinetics/Basal_Translation /kinetics/Basal_Translation/basal_syn ENZYME n addmsg /kinetics/AA /kinetics/Basal_Translation/basal_syn SUBSTRATE n addmsg /kinetics/Basal_Translation /kinetics/Basal_Translation/rad_basal_syn ENZYME n addmsg /kinetics/rad_AA /kinetics/Basal_Translation/rad_basal_syn SUBSTRATE n addmsg /kinetics/4E-BP_mod/eIF4E-BP_thr37_46 /kinetics/eIF4E-BP_disso SUBSTRATE n addmsg /kinetics/4E-BP_t37_46 /kinetics/eIF4E-BP_disso PRODUCT n addmsg /kinetics/eIF4E /kinetics/eIF4E-BP_disso PRODUCT n addmsg /kinetics/S6Kinase/S6K /kinetics/basal_S6K SUBSTRATE n addmsg /kinetics/S6Kinase/S6K_star /kinetics/basal_S6K PRODUCT n addmsg /kinetics/labelling /kinetics/rad_AA REAC B A addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/rad_AA REAC sA B addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/rad_AA REAC sA B addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/rad_peptide MM_PRD pA addmsg /kinetics/rad_pep_elongation /kinetics/rad_peptide REAC A B addmsg /kinetics/rad_peptide /kinetics/rad_pep_elongation SUBSTRATE n addmsg /kinetics/rad_protein /kinetics/rad_pep_elongation PRODUCT n addmsg /kinetics/rad_pep_elongation /kinetics/rad_protein REAC B A addmsg /kinetics/rad_protein_deg /kinetics/rad_protein REAC A B addmsg /kinetics/rad_protein /kinetics/rad_protein_deg SUBSTRATE n addmsg /kinetics/rad_deg_pro /kinetics/rad_protein_deg PRODUCT n addmsg /kinetics/rad_protein_deg /kinetics/rad_deg_pro REAC B A addmsg /kinetics/AA /kinetics/labelling SUBSTRATE n addmsg /kinetics/rad_AA /kinetics/labelling PRODUCT n addmsg /kinetics/40S_basal/basal /kinetics/40S_basal REAC eA B addmsg /kinetics/40S_basal /kinetics/40S_basal/basal ENZYME n addmsg /kinetics/S6Kinase/40S_inact /kinetics/40S_basal/basal SUBSTRATE n addmsg /kinetics/eIF4E-BP_disso /kinetics/4E-BP_t37_46 REAC B A addmsg /kinetics/MAPK_star/MAPK_4E-BP_star_star /kinetics/4E-BP_t37_46 REAC sA B addmsg /kinetics/PP2A/PP2A_4E-BP_star_star /kinetics/4E-BP_t37_46 MM_PRD pA addmsg /kinetics/TOR_Rheb-GTP_clx/TOR_4E-BP_star /kinetics/4E-BP_t37_46 MM_PRD pA addmsg /kinetics/PP2A/PP2A_4E-BP_star /kinetics/4E-BP_t37_46 REAC sA B addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PTEN REAC eA B addmsg /kinetics/PTEN /kinetics/PTEN/PIP3_dephosp ENZYME n addmsg /kinetics/PIP3 /kinetics/PTEN/PIP3_dephosp SUBSTRATE n addmsg /kinetics/PI3K_bind_Ras-GTP /kinetics/Ras-GTP_PI3K REAC B A addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/Ras-GTP_PI3K REAC eA B addmsg /kinetics/Ras-GTP_PI3K /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP SUBSTRATE n addmsg /kinetics/Ras/GTP-Ras /kinetics/PI3K_bind_Ras-GTP SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_bind_Ras-GTP SUBSTRATE n addmsg /kinetics/Ras-GTP_PI3K /kinetics/PI3K_bind_Ras-GTP PRODUCT n addmsg /kinetics/40S /graphs/conc1/40S.Co PLOT Co *40S.Co *50 addmsg /kinetics/protein /graphs/conc1/protein.Co PLOT Co *protein.Co *red addmsg /kinetics/MAPK_star /graphs/conc1/MAPK_star.Co PLOT Co *MAPK_star.Co *orange addmsg /kinetics/eIF4E /graphs/conc1/eIF4E.Co PLOT Co *eIF4E.Co *42 addmsg /kinetics/eIF4F-mRNA_clx /graphs/conc1/eIF4F-mRNA_clx.Co PLOT Co *eIF4F-mRNA_clx.Co *59 addmsg /kinetics/eIF4F /graphs/conc1/eIF4F.Co PLOT Co *eIF4F.Co *6 addmsg /kinetics/S6K_thr-252 /graphs/conc1/S6K_thr-252.Co PLOT Co *S6K_thr-252.Co *6 addmsg /kinetics/AKT_mod/TSC1-TSC2_star /graphs/conc1/TSC1-TSC2_star.Co PLOT Co *TSC1-TSC2_star.Co *40 addmsg /kinetics/TrKB_mod/BDNF_TrkB2_star_clx /graphs/conc2/BDNF_TrkB2_star_clx.Co PLOT Co *BDNF_TrkB2_star_clx.Co *red addmsg /kinetics/43Scomplex /graphs/conc2/43Scomplex.Co PLOT Co *43Scomplex.Co *hotpink addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /graphs/conc2/PIP3_AKT-t308_s473.Co PLOT Co *PIP3_AKT-t308_s473.Co *25 addmsg /kinetics/degraded_protein /graphs/conc2/degraded_protein.Co PLOT Co *degraded_protein.Co *white addmsg /kinetics/4E-BP_mod/eIF4E-BP /graphs/conc2/eIF4E-BP.Co PLOT Co *eIF4E-BP.Co *52 addmsg /kinetics/4E-BP_mod/eIF4E_4E-BP_t37_46_s65 /graphs/conc2/eIF4E_4E-BP_t37_46_s65.Co PLOT Co *eIF4E_4E-BP_t37_46_s65.Co *39 enddump // End of dump call /kinetics/PP2A/notes LOAD \ "Protein Phosphatase" call /kinetics/AKT_mod/PIP3_AKT-t308_s473/notes LOAD \ "aaa" call /kinetics/S6Kinase/S6K_star/notes LOAD \ "" \ "" \ "" call /kinetics/S6Kinase/40S_inact/notes LOAD \ "Inactivated form of S6K" \ "" call /kinetics/40S/notes LOAD \ "Activated form of S6" \ "" call /kinetics/43S_complex/Q.R/notes LOAD \ "Q.R= Quaternary complex.Ribosome" \ "" call /kinetics/43S_complex/Quaternary_clx/notes LOAD \ "Q= Quaternary complex" \ "" call /kinetics/CaM/CaM/notes LOAD \ "There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al)" \ "Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying" \ "it is comparable to CaMK levels. " \ "" call /kinetics/CaM/CaM-Ca3-bind-Ca/notes LOAD \ "Use K3 = 21.5 uM here from Stemmer and Klee table 3." \ "kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10" call /kinetics/CaM/CaM-bind-Ca/notes LOAD \ "Lets use the fast rate consts here. Since the rates are so different, I am not" \ "sure whether the order is relevant. These correspond to the TR2C fragment." \ "We use the Martin et al rates here, plus the Drabicowski binding consts." \ "All are scaled by 3X to cell temp." \ "kf = 2e-10 kb = 72" \ "Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ "If kb=72, kf = 2e-10 (Exactly the same !)" \ "" \ "19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ "two steps, each binding 1 Ca. This improves numerical" \ "stability and is conceptually better too." \ "" \ "Overall rates are the same, so each kf and kb is the " \ "square root of the earlier ones. So" \ "kf = 1.125e-4, kb = 8.4853" \ "" call /kinetics/CaM/CaM-Ca2/notes LOAD \ "This is the intermediate where the TR2 end (the high-affinity end) has" \ "bound the Ca but the TR1 end has not." call /kinetics/CaM/CaM-Ca2-bind-Ca/notes LOAD \ "K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \ "kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \ "" call /kinetics/CaM/CaM-Ca-bind-Ca/notes LOAD \ "Lets use the fast rate consts here. Since the rates are so different, I am not" \ "sure whether the order is relevant. These correspond to the TR2C fragment." \ "We use the Martin et al rates here, plus the Drabicowski binding consts." \ "All are scaled by 3X to cell temp." \ "kf = 2e-10 kb = 72" \ "Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11." \ "If kb=72, kf = 2e-10 (Exactly the same !)" \ "" \ "19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into" \ "two steps, each binding 1 Ca. This improves numerical" \ "stability and is conceptually better too." \ "" \ "Overall rates are the same, so each kf and kb is the " \ "square root of the earlier ones. So" \ "kf = 1.125e-4, kb = 8.4853" \ "" call /kinetics/CaM/CaM-Ca/notes LOAD \ "This is the intermediate where the TR2 end (the high-affinity end) has" \ "bound the Ca but the TR1 end has not." call /kinetics/Grb2/notes LOAD \ "There is probably a lot of it in the cell: it is also known" \ "as Ash (abundant src homology protein I think). Also " \ "Waters et al JBC 271:30 18224 1996 say that only a small" \ "fraction of cellular Grb is precipitated out when SoS is" \ "precipitated. As most of the Sos seems to be associated" \ "with Grb2, it would seem like there is a lot of the latter." \ "Say 1 uM. I haven't been able to find a decent...." call /kinetics/MAPK_star/MAPK_star-feedback/notes LOAD \ "Ueki et al JBC 269(22):15756-15761 show the presence of" \ "this step, but not the rate consts, which are derived from" \ "Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the" \ "MAPK_star notes." call /kinetics/MAPK_star/phosph_Sos/notes LOAD \ "See Porfiri and McCormick JBC 271:10 pp5871 1996 for the" \ "existence of this step. We'll take the rates from the ones" \ "used for the phosph of Raf by MAPK." \ "Sep 17 1997: The transient activation curve matches better" \ "with k1 up by 10 x." call /kinetics/PKC-active/notes LOAD \ "Conc of PKC in brain is about 1 uM (?)" call /kinetics/PKC-active/PKC-act-raf/notes LOAD \ "Rate consts from Chen et al Biochem 32, 1032 (1993)" \ "k3 = k2 = 4" \ "k1 = 9e-5" \ "recalculated gives 1.666e-5, which is not very different." \ "Looks like k3 is rate-limiting in this case: there is a huge amount" \ "of craf locked up in the enz complex. Let us assume a 10x" \ "higher Km, ie, lower affinity. k1 drops by 10x." \ "Also changed k2 to 4x k3." \ "Lowerd k1 to 1e-6 to balance 10X DAG sensitivity of PKC" call /kinetics/PKC-active/PKC-inact-GAP/notes LOAD \ "Rate consts copied from PCK-act-raf" \ "This reaction inactivates GAP. The idea is from the " \ "Boguski and McCormick review." call /kinetics/PKC-active/PKC-act-GEF/notes LOAD \ "Rate consts from PKC-act-raf." \ "This reaction activates GEF. It can lead to at least 2X stim of ras, and" \ "a 2X stim of MAPK over and above that obtained via direct phosph of" \ "c-raf. Note that it is a push-pull reaction, and there is also a contribution" \ "through the phosphorylation and inactivation of GAPs." \ "The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X" call /kinetics/MAPK/craf-1/notes LOAD \ "Couldn't find any ref to the actual conc of craf-1 but I" \ "should try Strom et al Oncogene 5 pp 345" \ "In line with the other kinases in the cascade, I estimate the conc to be" \ "0.2 uM. To init we use 0.15, which is close to equil" \ "16 May 2003: Changing to synaptic levels. Increasing 2.5 fold to 0.5 uM." \ "See Mihaly et al 1991 Brain Res 547(2):309-14" \ "and " \ "Morice et al 1999 Eur J Neurosci 11(6):1995-2006" call /kinetics/MAPK/MAPKK/notes LOAD \ "Conc is from Seger et al JBC 267:20 pp14373 (1992)" \ "mwt is 45/46 Kd" \ "We assume that phosphorylation on both ser and thr is needed for" \ "activiation. See Kyriakis et al Nature 358 417 1992" \ "Init conc of total is 0.18" \ "Ortiz et al 1995 J Neurosci 15(2):1285-1297 suggest that levels are" \ "higher in hippocampus than other brain regions, and further elevated " \ "in synapses. Estimate 3x higher levels than before, at 0.5 uM." \ "Similar results from Schipper et al 1999 Neuroscience 93(2):585-595" \ "but again lacking in quantitation." call /kinetics/MAPK/MAPK/notes LOAD \ "conc is from Sanghera et al JBC 265 pp 52 (1990)" \ "A second calculation gives 3.1 uM, from same paper." \ "They est MAPK is 1e-4x total protein, and protein is 15% of cell wt," \ "so MAPK is 1.5e-5g/ml = 0.36uM. which is closer to our first estimate." \ "Lets use this." \ "Updated 16 May 2003." \ "Ortiz et al 1995 J Neurosci 15(2):1285-1297 provide estimates of " \ "ERK2 levels in hippocampus: 1009 ng/mg. This comes to about 3.6uM, which" \ "may still be an underestimate of synaptic levels." call /kinetics/MAPK/craf-1_star_star/notes LOAD \ "Negative feedback by MAPK_star by hyperphosphorylating craf-1_star gives" \ "rise to this pool." \ "Ueki et al JBC 269(22):15756-15761, 1994" \ "" call /kinetics/MAPK/MAPK-tyr/notes LOAD \ "Haystead et al FEBS Lett. 306(1) pp 17-22 show that phosphorylation" \ "is strictly sequential, first tyr185 then thr183." call /kinetics/MAPK/MAPKK_star/notes LOAD \ "MAPKK phosphorylates MAPK on both the tyr and thr residues, first" \ "tyr then thr. Refs: Seger et al JBC267:20 pp 14373 1992" \ "The MAPKK itself is phosphorylated on ser as well as thr residues." \ "Let us assume that the ser goes first, and that the sequential phosphorylation" \ "is needed. See Kyriakis et al Nature 358 417-421 1992" call /kinetics/MAPK/MAPKK_star/MAPKKtyr/notes LOAD \ "The actual MAPKK is 2 forms from Seger et al JBC 267:20 14373(1992)" \ "Vmax = 150nmol/min/mg" \ "From Haystead et al FEBS 306(1):17-22 we get Km=46.6nM for at least one" \ "of the phosphs." \ "Putting these together:" \ "k3=0.15/sec, scale to get k2=0.6." \ "k1=0.75/46.6nM=2.7e-5" call /kinetics/MAPK/MAPKK_star/MAPKKthr/notes LOAD \ "Rate consts same as for MAPKKtyr." call /kinetics/MAPK/MAPKK-ser/notes LOAD \ "Intermediately phophorylated, assumed inactive, form of MAPKK" call /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.1/notes LOAD \ "Kinetics are the same as for the craf-1_star activity, ie.," \ "k1=1.1e-6, k2=.42, k3 =0.105" \ "These are based on Force et al PNAS USA 91 1270-1274 1994." \ "These parms cannot reach the observed 4X stim of MAPK. So lets" \ "increase the affinity, ie, raise k1 10X to 1.1e-5" \ "Lets take it back down to where it was." \ "Back up to 5X: 5.5e-6" call /kinetics/MAPK/Raf_star-GTP-Ras/Raf_star-GTP-Ras.2/notes LOAD \ "Same kinetics as other c-raf activated forms. See " \ "Force et al PNAS 91 1270-1274 1994." \ "k1 = 1.1e-6, k2 = .42, k3 = 1.05" \ "raise k1 to 5.5e-6" \ "" call /kinetics/MKP-1/notes LOAD \ "MKP-1 dephosphoryates and inactivates MAPK in vivo: Sun et al Cell 75 " \ "487-493 1993. Levels of MKP-1" \ "are regulated, and rise in 1 hour. " \ "Kinetics from Charles et al PNAS 90:5292-5296 1993. They refer" \ "to Charles et al Oncogene 7 187-190 who show that half-life of MKP1/3CH134" \ "is 40 min. 80% deph of MAPK in 20 min" \ "Sep 17 1997: CoInit now 0.4x to 0.0032. See parm searches" \ "from jun96 on." call /kinetics/MKP-1/MKP1-tyr-deph/notes LOAD \ "The original kinetics have been modified to obey the k2 = 4 * k3 rule," \ "while keeping kcat and Km fixed. As noted in the NOTES, the only constraining" \ "data point is the time course of MAPK dephosphorylation, which this" \ "model satisfies. It would be nice to have more accurate estimates of" \ "rate consts and MKP-1 levels from the literature. " \ "Effective Km : 67 nM" \ "kcat = 1.43 umol/min/mg" call /kinetics/MKP-1/MKP1-thr-deph/notes LOAD \ "See MKP1-tyr-deph" call /kinetics/Ras-act-craf/notes LOAD \ "Assume the binding is fast and limited only by the amount of " \ "Ras_star available. So kf=kb/[craf-1]" \ "If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6" \ "Later: Raise it by 10 X to 4e-5" \ "From Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is" \ "complexed with Ras. So we raise kb 4x to 4" \ "This step needed to memb-anchor and activate Raf: Leevers et al Nature" \ "369 411-414" \ "May 16, 2003" \ "Changed Ras and Raf to synaptic levels, an increase of about 2x for each." \ "To maintain the percentage of complexed Raf, reduced the kf by 2.4 fold" \ "to 10." \ "" call /kinetics/PPhosphatase2A/notes LOAD \ "Refs: Pato et al Biochem J 293:35-41(93);" \ "Takai&Mieskes Biochem J 275:233-239" \ "k1=1.46e-4, k2=1000,k3=250. these use" \ "kcat values for calponin. Also, units of kcat may be in min!" \ "revert to Vmax base:" \ "k3=6, k2=25,k1=3.3e-6 or 6,6,1e-6" \ "CoInit assumed 0.1 uM." \ "See NOTES for MAPK_Ras50.g. CoInit now 0.08" \ "Sep 17 1997: Raise CoInt 1.4x to 0.224, see parm" \ "searches from jun 96 on." \ "" call /kinetics/PPhosphatase2A/craf-deph/notes LOAD \ "See parent PPhosphatase2A for parms" \ "" call /kinetics/PPhosphatase2A/MAPKK-deph/notes LOAD \ "See: Kyriakis et al Nature 358 pp 417-421 1992" \ "Ahn et al Curr Op Cell Biol 4:992-999 1992 for this pathway." \ "See parent PPhosphatase2A for parms." call /kinetics/PPhosphatase2A/craf_star_star-deph/notes LOAD \ "Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of" \ "craf, so this is there to dephosphorylate it. Identity of phosphatase is not" \ "known to me, but it may be PP2A like the rest, so I have made it so." call /kinetics/Ras/notes LOAD \ "Ras has now gotten to be a big enough component of the model to" \ "deserve its own group. The main refs are" \ "Boguski and McCormick Nature 366 643-654 '93 Major review" \ "Eccleston et al JBC 268:36 pp 27012-19" \ "Orita et al JBC 268:34 2554246" call /kinetics/Ras/inact-GEF/notes LOAD \ "Assume that SoS is present only at 50 nM." \ "Revised to 100 nM to get equil to experimentally known levels." call /kinetics/Ras/GEF_star/notes LOAD \ "phosphorylated and thereby activated form of GEF. See, e.g." \ "Orita et al JBC 268:34 25542-25546 1993, Gulbins et al." \ "It is not clear whether there is major specificity for tyr or ser/thr." call /kinetics/Ras/GEF_star/GEF_star-act-ras/notes LOAD \ "Kinetics same as GEF-bg-act-ras" \ "" call /kinetics/Ras/GTP-Ras/notes LOAD \ "Only a very small fraction (7% unstim, 15% stim) of ras is GTP-bound." \ "Gibbs et al JBC 265(33) 20437" \ "" call /kinetics/Ras/GDP-Ras/notes LOAD \ "GDP bound form. See Rosen et al Neuron 12 1207-1221 June 1994." \ "the activation loop is based on Boguski and McCormick Nature 366 643-654 93" \ "Assume Ras is present at about the same level as craf-1, 0.2 uM." \ "Hallberg et al JBC 269:6 3913-3916 1994 estimate upto 5-10% of cellular" \ "Raf is assoc with Ras. Given that only 5-10% of Ras is GTP-bound, we" \ "need similar amounts of Ras as Raf." call /kinetics/Ras/Ras-intrinsic-GTPase/notes LOAD \ "This is extremely slow (1e-4), but it is significant as so little GAP actually" \ "gets complexed with it that the total GTP turnover rises only by" \ "2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and " \ "Eccleston et al JBC 268(36) 27012-27019" \ "kf = 1e-4" \ "" call /kinetics/Ras/dephosph-GAP/notes LOAD \ "Assume a reasonably good rate for dephosphorylating it, 1/sec" call /kinetics/Ras/GAP/notes LOAD \ "GTPase-activating proteins. See Boguski and McCormick." \ "Turn off Ras by helping to hydrolyze bound GTP. " \ "This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids," \ "and expressed in neural cells. p120-GAP is also a possible candidate, but" \ "is less regulated. Both may exist at similar levels." \ "See Eccleston et al JBC 268(36) pp27012-19" \ "Level=.002" \ "16 May 2003: Increased level to 0.0036, in line with other concentration" \ "raises at the synapse." call /kinetics/Ras/GAP/GAP-inact-ras/notes LOAD \ "From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec" \ "From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min" \ "I will go with the Eccleston figures as there are good error bars (10%). In general" \ "the values are reasonably close." \ "k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting)" \ "5 Nov 2002: Changed ratio term to 4 from 100. Now we have" \ "k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting." call /kinetics/Ras/CaM-bind-GEF/notes LOAD \ "We have no numbers for this. It is probably between" \ "the two extremes represented by the CaMKII phosph states," \ "and I have used guesses based on this." \ "kf=1e-4" \ "kb=1" \ "The reaction is based on Farnsworth et al Nature 376 524-527" \ "1995" call /kinetics/Ras/CaM-GEF/notes LOAD \ "See Farnsworth et al Nature 376 524-527 1995" call /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras/notes LOAD \ "Kinetics same as GEF-bg_act-ras" \ "" call /kinetics/Sos/Shc_bind_Sos.Grb2/notes LOAD \ "Sasaoka et al JBC 269:51 pp 32621 1994, table on pg" \ "32623 indicates that this pathway accounts for about " \ "50% of the GEF activation. (88% - 39%). Error is large," \ "about 20%. Fig 1 is most useful in constraining rates." \ "" \ "Chook et al JBC 271:48 pp 30472, 1996 say that the Kd is" \ "0.2 uM for Shc binding to EGFR. The Kd for Grb direct binding" \ "is 0.7, so we'll ignore it." call /kinetics/Sos/Grb2_bind_Sos_star/notes LOAD \ "Same rates as Grb2_bind_Sos: Porfiri and McCormick JBC" \ "271:10 pp 5871 1996 show that the binding is not affected" \ "by the phosph." call /kinetics/Sos/dephosph_Sos/notes LOAD \ "The only clue I have to these rates is from the time" \ "courses of the EGF activation, which is around 1 to 5 min." \ "The dephosph would be expected to be of the same order," \ "perhaps a bit longer. Lets use 0.002 which is about 8 min." \ "Sep 17: The transient activation curve matches better with" \ "kf = 0.001" call /kinetics/Sos/Grb2_bind_Sos/notes LOAD \ "As there are 2 SH3 domains, this reaction could be 2nd order." \ "I have a Kd of 22 uM from peptide binding (Lemmon et al " \ "JBC 269:50 pg 31653). However, Chook et al JBC 271:48 pg30472" \ "say it is 0.4uM with purified proteins, so we believe them." \ "They say it is 1:1 binding." call /kinetics/Sos/Sos/notes LOAD \ "I have tried using low (0.02 uM) initial concs, but these" \ "give a very flat response to EGF stim although the overall" \ "activation of Ras is not too bad. I am reverting to 0.1 " \ "because we expect a sharp initial response, followed by" \ "a decline." \ "Sep 17 1997: The transient activation curve looks better with" \ "[Sos] = 0.05." \ "Apr 26 1998: Some error there, it is better where it was" \ "at 0.1" call /kinetics/43Scomplex/notes LOAD \ "40S_complex consist of Quaternary complex, mRNA complex, " \ "40S Ribosomes." call /kinetics/PKC/PKC-act-by-Ca/notes LOAD \ "Need est of rate of assoc of Ca and PKC. Assume it is fast" \ "The original parameter-searched kf of 439.4 has been" \ "scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085" \ "Raised kf to 1e-6 to match Ca curve, kb to .5" \ "" call /kinetics/PKC/PKC-act-by-DAG/notes LOAD \ "Need est of rate. Assume it is fast" \ "Obtained from param search" \ "kf raised 10 X : see Shinomura et al PNAS 88 5149-5153 1991." \ "kf changed from 3.865e-7 to 2.0e-7 in line with closer analysis of" \ "Shinomura data." \ "26 June 1996: Corrected DAG data: reduce kf 15x from " \ "2e-7 to 1.333e-8" call /kinetics/PKC/PKC-DAG-to-memb/notes LOAD \ "Raise kb from .087 to 0.1 to match data from Shinomura et al." \ "Lower kf from 1.155 to 1.0 to match data from Shinomura et al." call /kinetics/PKC/PKC-act-by-Ca-AA/notes LOAD \ "Schaechter and Benowitz We have to increase Kf for conc scaling" \ "Changed kf to 2e-9 on Sept 19, 94. This gives better match." \ "" call /kinetics/PKC/PKC-act-by-DAG-AA/notes LOAD \ "Assume slowish too. Schaechter and Benowitz" call /kinetics/PKC/PKC-basal-act/notes LOAD \ "Initial basal levels were set by kf = 1, kb = 20. In model, though, the" \ "basal levels of PKC activity are higher." call /kinetics/PKC/PKC-act-by-AA/notes LOAD \ "Raise kf from 1.667e-10 to 2e-10 to get better match to data." call /kinetics/PKC/PKC-n-DAG/notes LOAD \ "kf raised 10 X based on Shinomura et al PNAS 88 5149-5153 1991" \ "closer analysis of Shinomura et al: kf now 1e-8 (was 1.66e-8)." \ "Further tweak. To get sufficient AA synergy, increase kf to 1.5e-8" \ "26 June 1996: Corrected DAG levels: reduce kf by 15x from" \ "1.5e-8 to 1e-9" call /kinetics/PKC/PKC-DAG/notes LOAD \ "CoInit was .0624" \ "" call /kinetics/PKC/PKC-n-DAG-AA/notes LOAD \ "Reduced kf to 0.66X to match Shinomura et al data." \ "Initial: kf = 3.3333e-9" \ "New: 2e-9" \ "Newer: 2e-8" \ "kb was 0.2" \ "now 2." call /kinetics/PKC/PKC-cytosolic/notes LOAD \ "Marquez et al J. Immun 149,2560(92) est 1e6/cell for chromaffin cells" \ "We will use 1 uM as our initial concen" \ "" call /kinetics/DAG/notes LOAD \ "The conc of this has been a problem. Schaecter and Benowitz use 50 uM," \ "but Shinomura et al have < 5. So I have altered the DAG-dependent " \ "rates in the PKC model to reflect this." call /kinetics/Basal_Translation/notes LOAD \ "It will contribute to mTOR independent translation." call /kinetics/doqcsinfo/notes LOAD \ "This model consists of various sub-modules. They are as follows:" \ "1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model" \ "5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model. " complete_loading