//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