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BIOMD0000000164 - SmithAE2002_RanTransport

 

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Reference Publication
Publication ID: 11799242
Smith AE, Slepchenko BM, Schaff JC, Loew LM, Macara IG.
Systems analysis of Ran transport.
Science 2002 Jan; 295(5554): 488-491
Center for Cell Signaling, Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA.  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL1886921294
Submission Date: 25 Feb 2008 00:06:35 UTC
Last Modification Date: 07 Apr 2014 00:12:30 UTC
Creation Date: 31 Jan 2008 20:56:18 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf Gene Ontology Ran protein signal transduction
Gene Ontology nucleocytoplasmic transport
set #2
bqbiol:hasTaxon Taxonomy Mammalia
set #3
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

The model reproduces the compartmental model for Ran transport as depicted in Fig 3 of the paper. Model reproduced using MathSBML.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 11799242 Submission Date: 25 Feb 2008 00:06:35 UTC Last Modification Date: 07 Apr 2014 00:12:30 UTC Creation Date: 31 Jan 2008 20:56:18 UTC
Mathematical expressions
Reactions
Carrier FRanGTP binding FRanGTP dephosphorylation dephosphorylationF FRanGTP Carrier binding
NTF2_FRanGDP Unbinding RanBP1 bindingF NTF2_FRanGDP unbinding Microinj
FRanGDP to FRanGTP RanGTP dephosphorylation RanGTP Carrier binding NTF2_RanGDP Unbinding
dephosphorylation RanGDP to RanGTP NTF2_RAN_Nuc_Exchange NTF2_RanGDP unbinding
Carrier RanGTP binding NTF2_FRAN_Nuc_Exchange RanBP1 binding Carrier_RanGTP flux
NTF2 flux NTF2_RanGDP flux Carrier flux FRanGDP flux
Carrier_FRanGTP flux FNTF2_RanGDP flux FRanGTP flux RanGDP flux
RanGTP flux      
Rules
Assignment Rule (variable: Vmax_RanGTP_dephosphorylation_FRanGTP_dephosphorylation) Assignment Rule (variable: Vmax_dephosphorylation_dephosphorylationF) Assignment Rule (variable: Vmax_RanGTP_dephosphorylation_RanGTP_dephosphorylation) Assignment Rule (variable: Vmax_dephosphorylation_dephosphorylation)
Assignment Rule (variable: ar_for_Microinj)      
Physical entities
Compartments Species
Cytosol Carrier_Cytosol Carrier_RanGTP_Cytosol RanGAP_Cytosol
RanBP1_Cytosol RanBP1_Carrier_RanGTP_Cytosol RanGDP_Cytosol
NTF2_RanGDP_Cytosol FRanGTP_Cytosol FCarrier_RanGTP_Cytosol
FRanGDP_Cytosol FNTF2_RanGDP_Cytosol FRanBP1_Carrier_RanGTP_Cytosol
NTF2_Cytosol Pipet_Cytosol RanGTP_Cytosol
EC      
Nucleus NTF2_Nucleus RanGDP_Nucleus RCC1_Nucleus
RanGTP_Nucleus NTF2_RanGDP_Nucleus Carrier_Nucleus
Carrier_RanGTP_Nucleus FCarrier_RanGTP_Nucleus FRanGDP_Nucleus
FNTF2_RanGDP_Nucleus FRanGTP_Nucleus  
Nuc_membrane      
PM      
Global parameters
RanGAP_Kcat_FRanGTP_dephosphorylation Vmax_RanGTP_dephosphorylation_FRanGTP_dephosphorylation RanGAP_Kcat_dephosphorylationF Vmax_dephosphorylation_dephosphorylationF
RanGAP_Kcat_RanGTP_dephosphorylation Vmax_RanGTP_dephosphorylation_RanGTP_dephosphorylation RanGAP_Kcat_dephosphorylation Vmax_dephosphorylation_dephosphorylation
kinj start tau ar_for_Microinj
Reactions (29)
 
 Carrier FRanGTP binding [Carrier_Cytosol] + [FRanGTP_Cytosol] ↔ [FCarrier_RanGTP_Cytosol];  
 
 FRanGTP dephosphorylation [FRanGTP_Cytosol] ↔ [FRanGDP_Cytosol];   {RanGAP_Cytosol}
 
 dephosphorylationF [FRanBP1_Carrier_RanGTP_Cytosol] ↔ [FRanGDP_Cytosol] + [RanBP1_Cytosol] + [Carrier_Cytosol];   {RanGAP_Cytosol}
 
 FRanGTP Carrier binding [Carrier_Nucleus] + [FRanGTP_Nucleus] ↔ [FCarrier_RanGTP_Nucleus];  
 
 NTF2_FRanGDP Unbinding [NTF2_Cytosol] + [FRanGDP_Cytosol] ↔ [FNTF2_RanGDP_Cytosol];  
 
 RanBP1 bindingF [FCarrier_RanGTP_Cytosol] + [RanBP1_Cytosol] ↔ [FRanBP1_Carrier_RanGTP_Cytosol];  
 
 NTF2_FRanGDP unbinding [FNTF2_RanGDP_Nucleus] ↔ [NTF2_Nucleus] + [FRanGDP_Nucleus];  
 
 Microinj  ↔ [FRanGDP_Cytosol];   {Pipet_Cytosol}
 
 FRanGDP to FRanGTP [FRanGDP_Nucleus] ↔ [FRanGTP_Nucleus];   {RCC1_Nucleus} , {NTF2_RanGDP_Nucleus} , {RanGDP_Nucleus}
 
 RanGTP dephosphorylation [RanGTP_Cytosol] ↔ [RanGDP_Cytosol];   {RanGAP_Cytosol}
 
 RanGTP Carrier binding [RanGTP_Nucleus] + [Carrier_Nucleus] ↔ [Carrier_RanGTP_Nucleus];  
 
 NTF2_RanGDP Unbinding [RanGDP_Cytosol] + [NTF2_Cytosol] ↔ [NTF2_RanGDP_Cytosol];  
 
 dephosphorylation [RanBP1_Carrier_RanGTP_Cytosol] ↔ [RanGDP_Cytosol] + [Carrier_Cytosol] + [RanBP1_Cytosol];   {RanGAP_Cytosol}
 
 RanGDP to RanGTP [RanGDP_Nucleus] ↔ [RanGTP_Nucleus];   {RCC1_Nucleus} , {NTF2_RanGDP_Nucleus}
 
 NTF2_RAN_Nuc_Exchange 4.0 × [NTF2_RanGDP_Nucleus] ↔ 4.0 × [NTF2_Nucleus] + [RanGDP_Nucleus] + 3.0 × [RanGTP_Nucleus];   {RCC1_Nucleus}
 
 NTF2_RanGDP unbinding [NTF2_RanGDP_Nucleus] ↔ [RanGDP_Nucleus] + [NTF2_Nucleus];  
 
 Carrier RanGTP binding [RanGTP_Cytosol] + [Carrier_Cytosol] ↔ [Carrier_RanGTP_Cytosol];  
 
 NTF2_FRAN_Nuc_Exchange 4.0 × [FNTF2_RanGDP_Nucleus] ↔ 4.0 × [NTF2_Nucleus] + 3.0 × [FRanGTP_Nucleus] + [FRanGDP_Nucleus];   {RCC1_Nucleus} , {NTF2_RanGDP_Nucleus} , {RanGDP_Nucleus}
 
 RanBP1 binding [RanBP1_Cytosol] + [Carrier_RanGTP_Cytosol] ↔ [RanBP1_Carrier_RanGTP_Cytosol];  
 
 Carrier_RanGTP flux [Carrier_RanGTP_Cytosol] ↔ [Carrier_RanGTP_Nucleus];  
 
 NTF2 flux [NTF2_Cytosol] ↔ [NTF2_Nucleus];  
 
 NTF2_RanGDP flux [NTF2_RanGDP_Cytosol] ↔ [NTF2_RanGDP_Nucleus];  
 
 Carrier flux [Carrier_Cytosol] ↔ [Carrier_Nucleus];  
 
 FRanGDP flux [FRanGDP_Cytosol] ↔ [FRanGDP_Nucleus];  
 
 Carrier_FRanGTP flux [FCarrier_RanGTP_Cytosol] ↔ [FCarrier_RanGTP_Nucleus];  
 
 FNTF2_RanGDP flux [FNTF2_RanGDP_Cytosol] ↔ [FNTF2_RanGDP_Nucleus];  
 
 FRanGTP flux [FRanGTP_Cytosol] ↔ [FRanGTP_Nucleus];  
 
 RanGDP flux [RanGDP_Cytosol] ↔ [RanGDP_Nucleus];  
 
 RanGTP flux [RanGTP_Cytosol] ↔ [RanGTP_Nucleus];  
 
Rules (5)
 
 Assignment Rule (name: Vmax_RanGTP_dephosphorylation_FRanGTP_dephosphorylation) Vmax_RanGTP_dephosphorylation_FRanGTP_dephosphorylation = RanGAP_Kcat_FRanGTP_dephosphorylation*RanGAP_Cytosol
 
 Assignment Rule (name: Vmax_dephosphorylation_dephosphorylationF) Vmax_dephosphorylation_dephosphorylationF = RanGAP_Cytosol*RanGAP_Kcat_dephosphorylationF
 
 Assignment Rule (name: Vmax_RanGTP_dephosphorylation_RanGTP_dephosphorylation) Vmax_RanGTP_dephosphorylation_RanGTP_dephosphorylation = RanGAP_Kcat_RanGTP_dephosphorylation*RanGAP_Cytosol
 
 Assignment Rule (name: Vmax_dephosphorylation_dephosphorylation) Vmax_dephosphorylation_dephosphorylation = RanGAP_Cytosol*RanGAP_Kcat_dephosphorylation
 
 Assignment Rule (name: ar_for_Microinj) ar_for_Microinj = piecewise(kinj*0.0016611295681*Pipet_Cytosol, (t > start) && (t < (start+tau)), 0)
 
   Cytosol Spatial dimensions: 3.0  Compartment size: 1.0  (Units: um3)
 
 Carrier_Cytosol
Compartment: Cytosol
Initial concentration: 11.8952664327711
 
 Carrier_RanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.00182967434742422
 
 RanGAP_Cytosol
Compartment: Cytosol
Initial concentration: 0.5
 
 RanBP1_Cytosol
Compartment: Cytosol
Initial concentration: 2.91577340630959
 
 RanBP1_Carrier_RanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0842265936904004
 
 RanGDP_Cytosol
Compartment: Cytosol
Initial concentration: 1.75546095870568
 
 NTF2_RanGDP_Cytosol
Compartment: Cytosol
Initial concentration: 1.47617820113791
 
 FRanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
 FCarrier_RanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
 FRanGDP_Cytosol
Compartment: Cytosol
Initial concentration: 1.0
 
 FNTF2_RanGDP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
 FRanBP1_Carrier_RanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
 NTF2_Cytosol
Compartment: Cytosol
Initial concentration: 0.023821798862085
 
 Pipet_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
 RanGTP_Cytosol
Compartment: Cytosol
Initial concentration: 0.0
 
   EC Spatial dimensions: 3.0  Compartment size: 1.40845070422535  (Units: um3)
   Nucleus Spatial dimensions: 3.0  Compartment size: 0.408450704225352  (Units: um3)
 
 NTF2_Nucleus
Compartment: Nucleus
Initial concentration: 0.560888580955963
 
 RanGDP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0466849733424111
 
 RCC1_Nucleus
Compartment: Nucleus
Initial concentration: 0.4
 
 RanGTP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0118032373274648
 
 NTF2_RanGDP_Nucleus
Compartment: Nucleus
Initial concentration: 0.939111419044037
 
 Carrier_Nucleus
Compartment: Nucleus
Initial concentration: 10.8211328580636
 
 Carrier_RanGTP_Nucleus
Compartment: Nucleus
Initial concentration: 11.5694219089212
 
 FCarrier_RanGTP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0
 
 FRanGDP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0
 
 FNTF2_RanGDP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0
 
 FRanGTP_Nucleus
Compartment: Nucleus
Initial concentration: 0.0
 
   Nuc_membrane Spatial dimensions: 2.0  Compartment size: 0.245070422535211  (Units: um2)
   PM Spatial dimensions: 2.0  Compartment size: 1.40845070422535  (Units: um2)
Global Parameters (12)
 
   RanGAP_Kcat_FRanGTP_dephosphorylation
Value: 6.0   (Units: s_1)
Constant
 
   Vmax_RanGTP_dephosphorylation_FRanGTP_dephosphorylation
Value: NaN   (Units: uM_s_1)
 
   RanGAP_Kcat_dephosphorylationF
Value: 6.0   (Units: s_1)
Constant
 
   Vmax_dephosphorylation_dephosphorylationF
Value: NaN   (Units: uM_s_1)
 
   RanGAP_Kcat_RanGTP_dephosphorylation
Value: 6.0   (Units: s_1)
Constant
 
   Vmax_RanGTP_dephosphorylation_RanGTP_dephosphorylation
Value: NaN   (Units: uM_s_1)
 
   RanGAP_Kcat_dephosphorylation
Value: 6.0   (Units: s_1)
Constant
 
   Vmax_dephosphorylation_dephosphorylation
Value: NaN   (Units: uM_s_1)
 
   kinj
Value: 25.0   (Units: s_1)
Constant
 
   start
Value: 1.0   (Units: s)
Constant
 
   tau
Value: 0.4   (Units: s)
Constant
 
   ar_for_Microinj  
 
Carrier FRanGTP binding (2)
 
   Kon_Carrier_RanGTP_binding
Constant
 
   Koff_Carrier_RanGTP_binding
Constant
 
FRanGTP dephosphorylation (1)
 
   Km_RanGTP_dephosphorylation
Value: 0.43   (Units: uM)
Constant
 
dephosphorylationF (1)
 
   Km_dephosphorylation
Value: 0.43   (Units: uM)
Constant
 
FRanGTP Carrier binding (2)
 
   Kon_RanGTP_Carrier_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_RanGTP_Carrier_binding
Value: 1.0   (Units: s_1)
Constant
 
NTF2_FRanGDP Unbinding (2)
 
   Kon_NTF2_RanGDP_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_NTF2_RanGDP_binding
Value: 2.5   (Units: s_1)
Constant
 
RanBP1 bindingF (2)
 
   Kon_RanBP1_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_RanBP1_binding
Value: 0.5   (Units: s_1)
Constant
 
NTF2_FRanGDP unbinding (2)
 
   Koff_NTF2_RanGDP_unbinding
Value: 2.5   (Units: s_1)
Constant
 
   Kon_NTF2_RanGDP_unbinding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
FRanGDP to FRanGTP (2)
 
   RCC1Kcat
Value: 8.5   (Units: s_1)
Constant
 
   RCC1Km
Value: 1.1   (Units: uM)
Constant
 
RanGTP dephosphorylation (1)
 
   Km_RanGTP_dephosphorylation
Value: 0.43   (Units: uM)
Constant
 
RanGTP Carrier binding (2)
 
   Kon_RanGTP_Carrier_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_RanGTP_Carrier_binding
Value: 1.0   (Units: s_1)
Constant
 
NTF2_RanGDP Unbinding (2)
 
   Kon_NTF2_RanGDP_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_NTF2_RanGDP_binding
Value: 2.5   (Units: s_1)
Constant
 
dephosphorylation (1)
 
   Km_dephosphorylation
Value: 0.43   (Units: uM)
Constant
 
RanGDP to RanGTP (2)
 
   RCC1Kcat
Value: 8.5   (Units: s_1)
Constant
 
   RCC1Km
Value: 1.1   (Units: uM)
Constant
 
NTF2_RAN_Nuc_Exchange (2)
 
   RCC1Kcat
Value: 8.5   (Units: s_1)
Constant
 
   RCC1Km
Value: 1.1   (Units: uM)
Constant
 
NTF2_RanGDP unbinding (2)
 
   Koff_NTF2_RanGDP_unbinding
Value: 2.5   (Units: s_1)
Constant
 
   Kon_NTF2_RanGDP_unbinding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
Carrier RanGTP binding (2)
 
   Kon_Carrier_RanGTP_binding
Constant
 
   Koff_Carrier_RanGTP_binding
Constant
 
NTF2_FRAN_Nuc_Exchange (2)
 
   RCC1Kcat
Value: 8.5   (Units: s_1)
Constant
 
   RCC1Km
Value: 1.1   (Units: uM)
Constant
 
RanBP1 binding (2)
 
   Kon_RanBP1_binding
Value: 100.0   (Units: uM_1_s_1)
Constant
 
   Koff_RanBP1_binding
Value: 0.5   (Units: s_1)
Constant
 
Carrier_RanGTP flux (2)
 
   I
Constant
 
   Carrier_RanGTP_Kperm
Value: 0.173333   (Units: um_s_1)
Constant
 
NTF2 flux (2)
 
   I
Constant
 
   NTF2_Kperm
Value: 3.73333   (Units: um_s_1)
Constant
 
NTF2_RanGDP flux (2)
 
   I
Constant
 
   NTF2_RanGDP_Kperm
Value: 3.73333   (Units: um_s_1)
Constant
 
Carrier flux (2)
 
   I
Constant
 
   Carrier_Kperm
Value: 1.86667   (Units: um_s_1)
Constant
 
FRanGDP flux (2)
 
   I
Constant
 
   RanGDP_Kperm
Constant
 
Carrier_FRanGTP flux (2)
 
   I
Constant
 
   Carrier_RanGTP_Kperm
Value: 0.173333   (Units: um_s_1)
Constant
 
FNTF2_RanGDP flux (2)
 
   I
Constant
 
   NTF2_RanGDP_Kperm
Value: 3.73333   (Units: um_s_1)
Constant
 
FRanGTP flux (2)
 
   I
Constant
 
   RanGTP_Kperm
Constant
 
RanGDP flux (2)
 
   I
Constant
 
   RanGDP_Kperm
Constant
 
RanGTP flux (2)
 
   I
Constant
 
   RanGTP_Kperm
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000164

Curator's comment: (updated: 01 Feb 2008 17:48:14 GMT)

Plot corresponds to the transients of a compartmental model as depicted in Fig 3 of the paper. Results obtained using MathSBML.

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