//genesis // kkit Version 11 flat dumpfile // Saved on Fri May 12 21:38:09 2006 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 1e-05 CONTROLDT = 5 PLOTDT = 0.1 MAXTIME = 25 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.8e-14 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/geo_nuc 0 1.2e-14 3 sphere "" white black 9 27 0 simundump geometry /kinetics/geo_cyt 0 1.8e-14 3 sphere "" white black 5 27 0 simundump group /kinetics/Nucleus 0 59 black x 0 0 "" Nucleus defaultfile.g 0 \ db8368a34577fe1aedf7b82361969022 0 -10 7 0 simundump kpool /kinetics/Nucleus/GDP.Ran-nuclear 0 0 0 0 0 0 0 0 7.1999e+06 \ 0 /kinetics/geo_nuc blue 59 -19 -2 0 simundump kpool /kinetics/Nucleus/RCC1-GDP.Ran 0 0 0 0 0 0 0 0 7.1999e+06 0 \ /kinetics/geo_nuc 31 59 -15 3 0 simundump kpool /kinetics/Nucleus/GDP 0 0 0 0 0 0 0 0 7.1999e+06 0 \ /kinetics/geo_nuc white 59 -9 5 0 simundump kpool /kinetics/Nucleus/RCC1 0 0 0.7 0.7 5.0399e+06 5.0399e+06 0 0 \ 7.1999e+06 0 /kinetics/geo_nuc 1 59 -10 -2 0 simundump kpool /kinetics/Nucleus/RCC1-RanGTP 0 0 0 0 0 0 0 0 7.1999e+06 0 \ /kinetics/geo_nuc 44 59 -4 5 0 simundump kpool /kinetics/Nucleus/RCC1-Ran 0 0 0 0 0 0 0 0 7.1999e+06 0 \ /kinetics/geo_nuc 32 59 -4 -2 0 simundump kpool /kinetics/Nucleus/GTP 0 0 500.01 500.01 3.6e+09 3.6e+09 0 0 \ 7.1999e+06 0 /kinetics/geo_nuc white 59 -1 1 0 simundump kpool /kinetics/Nucleus/GTP.Ran-nuclear 0 0 0 0 0 0 0 0 7.1999e+06 \ 0 /kinetics/geo_nuc 62 59 15 -2 0 simundump kpool /kinetics/Nucleus/nuclear-NTF2-GDP.Ran 0 0 0 0 0 0 0 0 \ 7.1999e+06 0 /kinetics/geo_nuc 56 59 -19 9 0 simundump kreac /kinetics/Nucleus/NTF2_dissociation[1] 0 0.48 4.1667e-09 "" \ white 59 -19 5 0 simundump kreac /kinetics/Nucleus/RCC1_binding 0 1.0278e-05 55 "" white 59 \ -15 -1 0 simundump kreac /kinetics/Nucleus/GDP_dissociation 0 21 1.5278e-06 "" white \ 59 -9 1 0 simundump kreac /kinetics/Nucleus/GTP_binding 0 8.3334e-08 19 "" white 59 -4 \ 1 0 simundump kreac /kinetics/Nucleus/GTP.Ran_release 0 55 1.3889e-05 "" white 59 \ 6 0 0 simundump kreac /kinetics/Cytoplasmic_transfer 0 0.08 1.3 "" white black 15 4 \ 0 simundump kreac /kinetics/Nucleoplasmic_transfer 0 10000 0.1 "" white black \ -19 15 0 simundump doqcsinfo /kinetics/doqcsinfo 0 \ /home/pragati/models/RanGTP/14Feb2006/fin/160206/RanGTPase.g RanGTPase \ network "Sharat J. Vayttaden and Pragati Jain, NCBS" \ "D.Gorlich, M.J.Seewald and K.Ribbeck" "citation here" "Eukaryotic system" \ "HeLa Cells" "Cytosol, Nucleus" Qualitative \ "Gorlich D et al EMBO J. 2003 Mar 3;22(5):1088-100. (Peer-reviewed publication)" \ "Exact GENESIS implementation" "Approximates original data " 14 27 0 simundump group /kinetics/Cytoplasm 0 yellow black x 0 0 "" Cytoplasm \ defaultfile.g 0 fd292eaea8dee7d05c340568261003c6 0 -6 26 0 simundump kpool /kinetics/Cytoplasm/RanGAP 0 0 0.7 0.7 7.56e+06 7.56e+06 0 0 \ 1.08e+07 0 /kinetics/geo_cyt 26 yellow 2 23 0 simundump kenz /kinetics/Cytoplasm/RanGAP/RanGAP 0 0 0 0 0 1.08e+07 5e-05 \ 43.2 10.8 0 0 "" red 26 "" 0 22 0 simundump kenz /kinetics/Cytoplasm/RanGAP/RanGAP[1] 0 0 0 0 0 1.08e+07 \ 7.0106e-06 42.4 10.6 0 0 "" red 26 "" 4 22 0 simundump kpool /kinetics/Cytoplasm/RanBP1 0 0 2 2 2.16e+07 2.16e+07 0 0 \ 1.08e+07 0 /kinetics/geo_cyt blue yellow 15 24 0 simundump kpool /kinetics/Cytoplasm/GTP.Ran-cytoplasmic 0 0 0 0 0 0 0 0 \ 1.08e+07 0 /kinetics/geo_cyt 14 yellow 15 15 0 simundump kpool /kinetics/Cytoplasm/RanBP1.RanGTP 0 0 0 0 0 0 0 0 1.08e+07 0 \ /kinetics/geo_cyt 47 yellow 5 15 0 simundump kpool /kinetics/Cytoplasm/NTF2 0 0 0.3 0.3 3.24e+06 3.24e+06 0 0 \ 1.08e+07 4 /kinetics/geo_cyt 3 yellow -9 22 0 simundump kpool /kinetics/Cytoplasm/NTF2-GDP.Ran 0 0 0 0 0 0 0 0 1.08e+07 0 \ /kinetics/geo_cyt 56 yellow -19 22 0 simundump kpool /kinetics/Cytoplasm/GDP.Ran-cytoplasmic 0 0 5 5 5.4e+07 \ 5.4e+07 0 0 1.08e+07 0 /kinetics/geo_cyt 24 yellow -3 17 0 simundump kreac /kinetics/Cytoplasm/NTF2_dissociation 0 0.48 2.7778e-09 "" \ white yellow -12 18 0 simundump kreac /kinetics/Cytoplasm/NTF2_binding 0 9.2593e-08 0.1 "" white \ yellow -5 10 0 simundump kreac /kinetics/Cytoplasm/RanGTP_binding 0 1.6667e-06 0.0004 "" \ white yellow 8 11 0 simundump xgraph /graphs/conc1 0 0 25 0 0.1 0 simundump xgraph /graphs/conc2 0 0 25 0 20 0 simundump xplot /graphs/conc1/GTP.Ran-cytoplasmic.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 14 0 0 1 simundump xplot /graphs/conc2/GTP.Ran-nuclear.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 62 0 0 1 simundump xgraph /moregraphs/conc3 0 0 25 0 1 0 simundump xgraph /moregraphs/conc4 0 0 25 0 1 0 simundump xcoredraw /edit/draw 0 -21 17 -4 29 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 \ "RanGTPase system" \ "Shows the kinetics of the RanGTPase system involved in " \ "receptor-mediated nuclear transport" \ "Adapted from Gorlich D et al" \ "EMBO J. 2003, 22(5):1088-1100" addmsg /kinetics/Nucleus/RCC1_binding /kinetics/Nucleus/GDP.Ran-nuclear REAC A B addmsg /kinetics/Nucleus/NTF2_dissociation[1] /kinetics/Nucleus/GDP.Ran-nuclear REAC B A addmsg /kinetics/Cytoplasm/NTF2_dissociation /kinetics/Nucleus/GDP.Ran-nuclear REAC B A addmsg /kinetics/Nucleus/RCC1_binding /kinetics/Nucleus/RCC1-GDP.Ran REAC B A addmsg /kinetics/Nucleus/GDP_dissociation /kinetics/Nucleus/RCC1-GDP.Ran REAC A B addmsg /kinetics/Nucleus/GDP_dissociation /kinetics/Nucleus/GDP REAC B A addmsg /kinetics/Nucleus/RCC1_binding /kinetics/Nucleus/RCC1 REAC A B addmsg /kinetics/Nucleus/GTP.Ran_release /kinetics/Nucleus/RCC1 REAC B A addmsg /kinetics/Nucleus/GTP_binding /kinetics/Nucleus/RCC1-RanGTP REAC B A addmsg /kinetics/Nucleus/GTP.Ran_release /kinetics/Nucleus/RCC1-RanGTP REAC A B addmsg /kinetics/Nucleus/GDP_dissociation /kinetics/Nucleus/RCC1-Ran REAC B A addmsg /kinetics/Nucleus/GTP_binding /kinetics/Nucleus/RCC1-Ran REAC A B addmsg /kinetics/Nucleus/GTP_binding /kinetics/Nucleus/GTP REAC A B addmsg /kinetics/Nucleus/GTP.Ran_release /kinetics/Nucleus/GTP.Ran-nuclear REAC B A addmsg /kinetics/Cytoplasmic_transfer /kinetics/Nucleus/GTP.Ran-nuclear REAC A B addmsg /kinetics/Nucleoplasmic_transfer /kinetics/Nucleus/nuclear-NTF2-GDP.Ran REAC B A addmsg /kinetics/Nucleus/NTF2_dissociation[1] /kinetics/Nucleus/nuclear-NTF2-GDP.Ran REAC A B addmsg /kinetics/Nucleus/nuclear-NTF2-GDP.Ran /kinetics/Nucleus/NTF2_dissociation[1] SUBSTRATE n addmsg /kinetics/Nucleus/GDP.Ran-nuclear /kinetics/Nucleus/NTF2_dissociation[1] PRODUCT n addmsg /kinetics/Cytoplasm/NTF2 /kinetics/Nucleus/NTF2_dissociation[1] PRODUCT n addmsg /kinetics/Nucleus/GDP.Ran-nuclear /kinetics/Nucleus/RCC1_binding SUBSTRATE n addmsg /kinetics/Nucleus/RCC1 /kinetics/Nucleus/RCC1_binding SUBSTRATE n addmsg /kinetics/Nucleus/RCC1-GDP.Ran /kinetics/Nucleus/RCC1_binding PRODUCT n addmsg /kinetics/Nucleus/RCC1-GDP.Ran /kinetics/Nucleus/GDP_dissociation SUBSTRATE n addmsg /kinetics/Nucleus/RCC1-Ran /kinetics/Nucleus/GDP_dissociation PRODUCT n addmsg /kinetics/Nucleus/GDP /kinetics/Nucleus/GDP_dissociation PRODUCT n addmsg /kinetics/Nucleus/RCC1-Ran /kinetics/Nucleus/GTP_binding SUBSTRATE n addmsg /kinetics/Nucleus/RCC1-RanGTP /kinetics/Nucleus/GTP_binding PRODUCT n addmsg /kinetics/Nucleus/GTP /kinetics/Nucleus/GTP_binding SUBSTRATE n addmsg /kinetics/Nucleus/RCC1-RanGTP /kinetics/Nucleus/GTP.Ran_release SUBSTRATE n addmsg /kinetics/Nucleus/GTP.Ran-nuclear /kinetics/Nucleus/GTP.Ran_release PRODUCT n addmsg /kinetics/Nucleus/RCC1 /kinetics/Nucleus/GTP.Ran_release PRODUCT n addmsg /kinetics/Nucleus/GTP.Ran-nuclear /kinetics/Cytoplasmic_transfer SUBSTRATE n addmsg /kinetics/Cytoplasm/GTP.Ran-cytoplasmic /kinetics/Cytoplasmic_transfer PRODUCT n addmsg /kinetics/Nucleus/nuclear-NTF2-GDP.Ran /kinetics/Nucleoplasmic_transfer PRODUCT n addmsg /kinetics/Cytoplasm/NTF2-GDP.Ran /kinetics/Nucleoplasmic_transfer SUBSTRATE n addmsg /kinetics/Cytoplasm/RanGAP/RanGAP /kinetics/Cytoplasm/RanGAP REAC eA B addmsg /kinetics/Cytoplasm/RanGAP/RanGAP[1] /kinetics/Cytoplasm/RanGAP REAC eA B addmsg /kinetics/Cytoplasm/RanGAP /kinetics/Cytoplasm/RanGAP/RanGAP ENZYME n addmsg /kinetics/Cytoplasm/RanBP1.RanGTP /kinetics/Cytoplasm/RanGAP/RanGAP SUBSTRATE n addmsg /kinetics/Cytoplasm/RanGAP /kinetics/Cytoplasm/RanGAP/RanGAP[1] ENZYME n addmsg /kinetics/Cytoplasm/GTP.Ran-cytoplasmic /kinetics/Cytoplasm/RanGAP/RanGAP[1] SUBSTRATE n addmsg /kinetics/Cytoplasm/RanGTP_binding /kinetics/Cytoplasm/RanBP1 REAC A B addmsg /kinetics/Cytoplasmic_transfer /kinetics/Cytoplasm/GTP.Ran-cytoplasmic REAC B A addmsg /kinetics/Cytoplasm/RanGTP_binding /kinetics/Cytoplasm/GTP.Ran-cytoplasmic REAC A B addmsg /kinetics/Cytoplasm/RanGAP/RanGAP[1] /kinetics/Cytoplasm/GTP.Ran-cytoplasmic REAC sA B addmsg /kinetics/Cytoplasm/RanGAP/RanGAP /kinetics/Cytoplasm/RanBP1.RanGTP REAC sA B addmsg /kinetics/Cytoplasm/RanGTP_binding /kinetics/Cytoplasm/RanBP1.RanGTP REAC B A addmsg /kinetics/Cytoplasm/NTF2_binding /kinetics/Cytoplasm/NTF2 REAC A B addmsg /kinetics/Cytoplasm/NTF2_dissociation /kinetics/Cytoplasm/NTF2 REAC B A addmsg /kinetics/Nucleus/NTF2_dissociation[1] /kinetics/Cytoplasm/NTF2 REAC B A addmsg /kinetics/Cytoplasm/NTF2_dissociation /kinetics/Cytoplasm/NTF2-GDP.Ran REAC A B addmsg /kinetics/Cytoplasm/NTF2_binding /kinetics/Cytoplasm/NTF2-GDP.Ran REAC B A addmsg /kinetics/Nucleoplasmic_transfer /kinetics/Cytoplasm/NTF2-GDP.Ran REAC A B addmsg /kinetics/Cytoplasm/RanGAP/RanGAP /kinetics/Cytoplasm/GDP.Ran-cytoplasmic MM_PRD pA addmsg /kinetics/Cytoplasm/RanGAP/RanGAP[1] /kinetics/Cytoplasm/GDP.Ran-cytoplasmic MM_PRD pA addmsg /kinetics/Cytoplasm/NTF2_binding /kinetics/Cytoplasm/GDP.Ran-cytoplasmic REAC A B addmsg /kinetics/Cytoplasm/NTF2-GDP.Ran /kinetics/Cytoplasm/NTF2_dissociation SUBSTRATE n addmsg /kinetics/Cytoplasm/NTF2 /kinetics/Cytoplasm/NTF2_dissociation PRODUCT n addmsg /kinetics/Nucleus/GDP.Ran-nuclear /kinetics/Cytoplasm/NTF2_dissociation PRODUCT n addmsg /kinetics/Cytoplasm/NTF2 /kinetics/Cytoplasm/NTF2_binding SUBSTRATE n addmsg /kinetics/Cytoplasm/NTF2-GDP.Ran /kinetics/Cytoplasm/NTF2_binding PRODUCT n addmsg /kinetics/Cytoplasm/GDP.Ran-cytoplasmic /kinetics/Cytoplasm/NTF2_binding SUBSTRATE n addmsg /kinetics/Cytoplasm/GTP.Ran-cytoplasmic /kinetics/Cytoplasm/RanGTP_binding SUBSTRATE n addmsg /kinetics/Cytoplasm/RanBP1 /kinetics/Cytoplasm/RanGTP_binding SUBSTRATE n addmsg /kinetics/Cytoplasm/RanBP1.RanGTP /kinetics/Cytoplasm/RanGTP_binding PRODUCT n addmsg /kinetics/Cytoplasm/GTP.Ran-cytoplasmic /graphs/conc1/GTP.Ran-cytoplasmic.Co PLOT Co *GTP.Ran-cytoplasmic.Co *14 addmsg /kinetics/Nucleus/GTP.Ran-nuclear /graphs/conc2/GTP.Ran-nuclear.Co PLOT Co *GTP.Ran-nuclear.Co *62 enddump // End of dump call /kinetics/Nucleus/GDP.Ran-nuclear/notes LOAD \ "nuclear-GDP.Ran" \ "Nuclear fraction of GDP bound Ran" \ "Approximately 71% of RanGDP in the nucleus is bound" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3 " \ "" \ "Gorlich D et al (2003) " \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/RCC1-GDP.Ran/notes LOAD \ "RCC1-GDP.Ran" \ "Ran-GDP complex bound to RCC1" \ "" \ "Catherine Chaillan-Huntington et al (2000) J.Biol.Chem. 275(8):5874-5879. " \ "" \ "Nuclear volume = 1.2pL = 1.2e-15 m^3 " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/GDP/notes LOAD \ "GDP released from RCC1-GDP.Ran complex" \ "" \ "Nuclear Volume = 1.2 pL = 1.2e-15 m^3" \ "" \ "Footnote for Table 2" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/RCC1/notes LOAD \ "RCC1" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3" \ "" \ "Nuclear concentration of RCC1 = 0.7 uM" \ "" \ "Supplementary Table B " \ "Gorlich D et al (2003)" \ "EMBO J 2003, 22(5):1088-1100" call /kinetics/Nucleus/RCC1-RanGTP/notes LOAD \ "RCC1-GTP.Ran" \ "Ran-GTP complex bound to RCC1" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3" \ "" \ "Footnote for Table 2 " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/RCC1-Ran/notes LOAD \ "RCC1-GDP.Ran" \ "Ran-GDP complex bound to RCC1" \ "" \ "Nuclear volume = 1.2pL = 1.2e-15 m^3" \ "Footnote for Table 2 " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/GTP/notes LOAD \ "GTP" \ "" \ "Initial GTP concentration = 500uM" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3" \ "" \ "Table II footnote " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/GTP.Ran-nuclear/notes LOAD \ "nuclear-GTP.Ran" \ "Nuclear fraction of Ran-GTP complex" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3 " \ "" \ "Footnote for Table 2" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/nuclear-NTF2-GDP.Ran/notes LOAD \ "NTF2-GDP.Ran" \ "Cytoplasmic fraction of GDP bound Ran" \ "complexed with NTF2" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3" \ "Footnote for Table 2 " \ "Gorlich D et al (2003) " \ "EMBO J 22(5):1088-1100" \ "" \ "Initial cytoplasmic GDP.Ran concentration = 5 uM" \ "Table II footnote" call /kinetics/Nucleus/NTF2_dissociation[1]/notes LOAD \ "Approximation of reaction rates to match " \ "the kinetics described by " \ "" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/RCC1_binding/notes LOAD \ "Binding of GDP-Ran complex with RCC1" \ "Kf = 7.4e+07 /M/sec = 7.4e+01 /uM/sec" \ "Kb = 55 /sec" \ "Christian Klebe et al (1995) Biochemistry 34:12543-12552 ." \ "" \ "Supplementary Table A " \ "Gorlich D et al (2003) EMBO J" \ "22(5):1088-1100" call /kinetics/Nucleus/GDP_dissociation/notes LOAD \ "Release of GDP from the GDP-Ran complex with RCC1" \ "Kf = 21 /sec" \ "Kb = 1.1e+07 /M/sec = 1.1e+01 /uM/sec" \ "Christian Klebe et al (1995) Biochemistry 34:12543-12552 ." \ "" \ "Supplementary Table A " \ "Gorlich D et al (2003) " \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/GTP_binding/notes LOAD \ "Binding of GTP to GDP free Ran-RCC1 complex" \ "Kf = 0.6e+06 /M/sec = 0.6 /uM/sec" \ "Kb = 19 /sec" \ "Christian Klebe et al (1995) Biochemistry 34:12543-12552 ." \ "" \ "Supplementary Table A " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleus/GTP.Ran_release/notes LOAD \ "Release of GTP.Ran from GTP.Ran-RCC1 complex" \ "Kf = 55 /sec" \ "Kb = 1.0e+08 /M/sec = 1.0e+02 /uM/sec" \ "Christian Klebe et al (1995) Biochemistry 34:12543-12552 ." \ "" \ "Supplementary Table A " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasmic_transfer/notes LOAD \ "Approximation to achieve" \ "Cytoplasmic transfer as per kinetics described by " \ "" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Nucleoplasmic_transfer/notes LOAD \ "Approximation to achieve" \ "Nucleoplasmic transfer as per kinetics described by " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/doqcsinfo/notes LOAD \ " This model represents a concentration gradient of RanGTP across the nuclear envelope. This " \ "gradient is generated by distribution of regulators of RanGTPase. We have taken a log " \ "linear plot of graphs generated by GENESIS and compared with the experimental graphs. " call /kinetics/Cytoplasm/RanGAP/notes LOAD \ "RanGAP: RanGAP in the cytoplasm" \ "" \ "Ran has very low intrinsic GTPase activity and is " \ "stimulated by the Ran GTPase activator RanGAP. This has" \ "an antagonistic regulator to RCC1, converting Ran into " \ "its GDP bound OFF form." \ "F. Ralf Bischoff et al (1994)" \ "PNAS, USA 91:2587-2591" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-15 m^3" \ "Total cytoplasmic concentration of RanGAP = 0.7 uM" \ "Supplementary Table A" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" \ "" call /kinetics/Cytoplasm/RanGAP/RanGAP/notes LOAD \ "RanGAP reaction on RanGTP-RanBP1 complex" \ "kcat = 10.8 /sec" \ "Km = 0.1 uM" \ "at 25C" \ "" \ "Table 1." \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/RanGAP/RanGAP[1]/notes LOAD \ "RanGAP reaction on free RanGTP" \ "kcat = 10.6 /sec" \ "Km = 0.7 uM" \ "at 25C" \ "" \ "Table 1. " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/RanBP1/notes LOAD \ "RanBP1" \ "RanBP1 in the cytoplasm" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-15 m^3" \ "Total cytoplasmic concentration of RanBP1 = 2 uM" \ "Supplementary Table B " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" \ "" call /kinetics/Cytoplasm/GTP.Ran-cytoplasmic/notes LOAD \ "cytoplasmic-GTP.Ran" \ "Cytoplasmic fraction of Ran-GTP complex" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-16m^3 " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/RanBP1.RanGTP/notes LOAD \ "RanBP1.RanGTP" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-15 m^3 " \ "" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/NTF2/notes LOAD \ "NTF2: Nuclear Transport Factor 2 dimers" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-15 m^3" \ "Total cellular concentration of NTF2 dimers = 0.3 uM" \ "Table II footnote " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" \ "" \ "Since it is the total cellular conc. the pool is buffered" call /kinetics/Cytoplasm/NTF2-GDP.Ran/notes LOAD \ "NTF2-GDP.Ran" \ "Cytoplasmic fraction of GDP bound Ran" \ "complexed with NTF2" \ "" \ "Nuclear volume = 1.2 pL = 1.2e-15 m^3" \ "Footnote for Table 2 " \ "Gorlich D et al (2003) " \ "EMBO J 22(5):1088-1100" \ "" \ "Initial cytoplasmic GDP.Ran concentration = 5 uM" \ "Table II footnote" call /kinetics/Cytoplasm/GDP.Ran-cytoplasmic/notes LOAD \ "cytoplasmic-GDP.Ran" \ "Cytoplasmic fraction of GDP bound Ran" \ "" \ "Cytoplasmic volume = 1.8 pL = 1.8e-15 m^3" \ "Initial cytoplasmic GDP.Ran concentration = 5 uM" \ "" \ "Table II footnote" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/NTF2_dissociation/notes LOAD \ "Approximation of rates to match " \ "the kinetics described by " \ "" \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" call /kinetics/Cytoplasm/NTF2_binding/notes LOAD \ "Binding of NTF2 to cytoplasmic fraction of GDP.Ran" \ "Kd = 100 nM" \ "" \ "Catherine Chaillan-Huntington et al (2000) J.Biol.Chem. 275(8):5874-5879. " \ "call" \ "/kinetics/Cytoplasm/RanGTP_binding/notes" \ "LOAD" \ "Binding of cytoplasmic fraction of RanGTP to RanBP1" \ "Kf = 3.0e+05 /M/sec = 0.3 /uM/sec" \ "Kb = 4.0e-04 /sec" \ "Carolina I. Villa Braslavsky et al (2000) Biochemistry 39(38):11629-11639. " \ "" \ "Supplementary Table A " \ "Gorlich D et al (2003)" \ "EMBO J 22(5):1088-1100" complete_loading