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BIOMD0000000192 - Görlich2003_RanGTP_gradient

 

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Reference Publication
Publication ID: 12606574
Görlich D, Seewald MJ, Ribbeck K.
Characterization of Ran-driven cargo transport and the RanGTPase system by kinetic measurements and computer simulation.
EMBO J. 2003 Mar; 22(5): 1088-1100
ZMBH, INF 282, 69120 Heidelberg, Germany. dg@zmbh.uni-heidelberg.de  [more]
Model
Original Model: DOQCS logo
Submitter: Sharat Vayttaden
Submission ID: MODEL4969417017
Submission Date: 11 Sep 2008 21:34:57 UTC
Last Modification Date: 02 Dec 2010 06:10:54 UTC
Creation Date: 09 Sep 2008 22:04:34 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Dirk Gorlich
set #1
bqbiol:isPartOf Reactome REACT_9507
set #2
bqbiol:occursIn Taxonomy Homo sapiens
set #3
bqbiol:isVersionOf Gene Ontology Ran GTPase binding
Notes
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.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2008 The BioModels Team.
For more information see the terms of use .

Model
Publication ID: 12606574 Submission Date: 11 Sep 2008 21:34:57 UTC Last Modification Date: 02 Dec 2010 06:10:54 UTC Creation Date: 09 Sep 2008 22:04:34 UTC
Mathematical expressions
Reactions
RCC1_binding GDP_dissociation GTP_binding RanGTP_release
Cytoplasmic_transfer Nucleoplasmic_transfer RanGTP_binding RanBP1_RanGDP
RanGAP_RanGDP      
Physical entities
Compartments Species
nucleus RanGDP_nuc RCC1_RanGDP GDP
RCC1 RCC1_RanGTP RCC1_Ran
GTP RanGTP_nuc  
cytoplasm RanGAP RanBP1 RanGTP_cy
RanGTP_RanBP1 RanGDP_cy  
Reactions (9)
 
 RCC1_binding [RanGDP_nuc] + [RCC1] ↔ [RCC1_RanGDP];  
 
 GDP_dissociation [RCC1_RanGDP] ↔ [RCC1_Ran] + [GDP];  
 
 GTP_binding [RCC1_Ran] + [GTP] ↔ [RCC1_RanGTP];  
 
 RanGTP_release [RCC1_RanGTP] ↔ [RanGTP_nuc] + [RCC1];  
 
 Cytoplasmic_transfer [RanGTP_nuc] ↔ [RanGTP_cy];  
 
 Nucleoplasmic_transfer [RanGDP_nuc] ↔ [RanGDP_cy];  
 
 RanGTP_binding [RanGTP_cy] + [RanBP1] ↔ [RanGTP_RanBP1];  
 
 RanBP1_RanGDP [RanGTP_RanBP1] ↔ [RanGDP_cy] + [RanBP1];   {RanGAP}
 
 RanGAP_RanGDP [RanGTP_cy] ↔ [RanGDP_cy];   {RanGAP}
 
  Spatial dimensions: 3.0  Compartment size: 1.2E-11
 
 RanGDP_nuc
Compartment: nucleus
Initial concentration: 0.0
 
 RCC1_RanGDP
Compartment: nucleus
Initial concentration: 0.0
 
 GDP
Compartment: nucleus
Initial concentration: 1.6
 
 RCC1
Compartment: nucleus
Initial concentration: 0.7
 
 RCC1_RanGTP
Compartment: nucleus
Initial concentration: 0.0
 
 RCC1_Ran
Compartment: nucleus
Initial concentration: 0.0
 
 GTP
Compartment: nucleus
Initial concentration: 500.0
 
 RanGTP_nuc
Compartment: nucleus
Initial concentration: 0.0
 
  Spatial dimensions: 3.0  Compartment size: 1.8E-11
 
 RanGAP
Compartment: cytoplasm
Initial concentration: 0.7
 
 RanBP1
Compartment: cytoplasm
Initial concentration: 2.0
 
 RanGTP_cy
Compartment: cytoplasm
Initial concentration: 0.0
 
 RanGTP_RanBP1
Compartment: cytoplasm
Initial concentration: 0.0
 
 RanGDP_cy
Compartment: cytoplasm
Initial concentration: 5.0
 
RCC1_binding (2)
 
   r1
Value: 74.0   (Units: pmicroMpsec)
Constant
 
   r8
Value: 55.0   (Units: psec)
Constant
 
GDP_dissociation (2)
 
   r2
Value: 21.0   (Units: psec)
Constant
 
   r7
Value: 11.0   (Units: pmicroMpsec)
Constant
 
GTP_binding (2)
 
   r3
Value: 0.6   (Units: pmicroMpsec)
Constant
 
   r6
Value: 19.0   (Units: psec)
Constant
 
RanGTP_release (2)
 
   r4
Value: 55.0   (Units: psec)
Constant
 
   r5
Value: 100.0   (Units: pmicroMpsec)
Constant
 
Cytoplasmic_transfer (1)
 
   kpermRanGTP
Value: 0.03   (Units: psec)
Constant
 
Nucleoplasmic_transfer (1)
 
   kpermRanGDP
Value: 0.12   (Units: psec)
Constant
 
RanGTP_binding (2)
 
   kon
Value: 0.3   (Units: pmicroMpsec)
Constant
 
   koff
Value: 4.0E-4   (Units: psec)
Constant
 
RanBP1_RanGDP (2)
 
   kcat
Value: 10.8   (Units: psec)
Constant
 
   Km
Value: 0.1   (Units: microM)
Constant
 
RanGAP_RanGDP (2)
 
   kcat
Value: 10.6   (Units: psec)
Constant
 
   Km
Value: 0.7   (Units: microM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000192

Curator's comment: (updated: 11 Sep 2008 14:29:39 PDT)

The model is simulated and integrated using SBML OdeSolver with options (-n --printstep 500). Figure 4 (Simulated time course for generation of the RanGTP gradient) of the original paper (Gorlich et al., 2003) is reproduced in here.

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