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BIOMD0000000161 - Eungdamrong2007_Ras_Activation

 

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Reference Publication
Publication ID: 17098795
Eungdamrong NJ, Iyengar R.
Compartment-specific feedback loop and regulated trafficking can result in sustained activation of Ras at the Golgi.
Biophys. J. 2007 Feb; 92(3): 808-815
Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA.  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL1633592197
Submission Date: 30 Jan 2008 23:07:20 UTC
Last Modification Date: 20 Mar 2014 17:03:47 UTC
Creation Date: 29 Jan 2008 10:13:13 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom BioModels Database Xu2003 - Phosphoinositide turnover
BioModels Database Bhalla1999_3d_fold_model
PubMed 10388786
PubMed 10579714
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqbiol:isVersionOf KEGG Pathway MAPK signaling pathway - Homo sapiens (human)
bqbiol:isPartOf Gene Ontology epidermal growth factor receptor signaling pathway
bqbiol:hasPart Gene Ontology Ras protein signal transduction
bqbiol:hasTaxon Taxonomy cellular organisms
Notes

The model reproduces the time profiles of Golgi Ras-GTP and plasma membrane Ras-GTP, subjected to a palmitoylation rate of 0.00015849 second inverse. This is depicted in Fig 5a and 5b for various palmitolylation rates, however the value used in this model is not present in the figure in the paper but corresponds to Fig S2 of the supplement. Model successfully reproduced using MathSBML. Please note that the units of volumetric species in this model are molecules/micrometer cubed, to convert this to microMolar as given in the paper, multiply the simulation result by 1/602.


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: 17098795 Submission Date: 30 Jan 2008 23:07:20 UTC Last Modification Date: 20 Mar 2014 17:03:47 UTC Creation Date: 29 Jan 2008 10:13:13 UTC
Mathematical expressions
Reactions
PIP2 synthesis Shc phosphorylation Ca bind CAPRI IP3 degradation
RasGTP depal translocate ca bind rasGRP RasGRP_DAG GEF rasGTP pal translocation
PLCg dephos basal GAP CAPRI translocation reaction5
RasGDP pal CAPRI GAP RasGDPpal translocation sos grb2 binding
RasGDP depal translocate Ras GTP palm1 RasPal basal GAP basal cyt depal GEF
caPLCe gen DAG CaRasGRP act RasGM PIP2 hydrolysis Sos activation
PIP synthesis EGF_internalization calcium buffer RasGM basal GAP
reaction0 EGFR_binding ca act PLCe ras_act_PLCe
RasGDP depal2 CaRasGRP translocation reaction2 EGF act PLCgamma
Ca_binds_IP3R reaction7 Sos act RasPM flux1
flux0 flux2 Ras PM depal1  
Rules
Assignment Rule (variable: Rate_PIP2Synbasal_PIP2_synthesis) Assignment Rule (variable: Rate_PIP2SynStim_PIP2_synthesis) Assignment Rule (variable: Vmax_Shc_phosphorylation) Assignment Rule (variable: Vmax_RasGRP_DAG_GEF)
Assignment Rule (variable: Vmax_CAPRI_GAP) Assignment Rule (variable: Vmax_CaRasGRP_act_RasGM) Assignment Rule (variable: Ratebasal_PIPsyn_PIP_synthesis) Assignment Rule (variable: Ratestim_PIPsyn_PIP_synthesis)
Assignment Rule (variable: Koff_reaction2) Assignment Rule (variable: Vmax_EGF_act_PLCgamma) Assignment Rule (variable: Kr_Ca_binds_IP3R) Assignment Rule (variable: Vmax_Sos_act_RasPM)
Physical entities
Compartments Species
EC EGF_EC    
cyt CAPRI_cyt RasGTP_pal_cyt Ca
IP3 CaCAPRI_cyt RasGTP_depal_cyt
RasGDP_depal_cyt RasGDP_pal_cyt Ca_PLCe_cyt
Sos_cyt Grb2_cyt PLCe_cyt
buffer_cyt ca_buffer_cyt SosGrb2_cyt
RasGRP_cyt CaRasGRP1_cyt  
er Ca_ER    
Golgi      
PM PIP_PM PI_PM Shc_PM
CaCAPRI_PM_PM Shc_star_PM EGFR_PM
PLC_act_PM PLC_PM PIP2_PM
Activated_EGFR_PM DAG_PM SGS_PM
RasGTP_PM RasGDP_PM  
erMembrane serca RactCa Ract
Rinh RinhCa ER_erMembrane
     
GM RasGTP_Golgi_GM RasGDP_Golgi_GM Ca_RasGRP_GM_GM
DAG_GM_GM RasGRP_DAG_GM Ras_CaPLCe_GM
PIP2_GM_GM    
Global parameters
KMOLE kStimSynPIP2_PIP2_synthesis tauPIP2syn_PIP2_synthesis PIP2syndecay_PIP2_synthesis
PIP2_basal_PIP2_synthesis kBasalSynPIP2_PIP2_synthesis Rate_PIP2Synbasal_PIP2_synthesis Rate_PIP2SynStim_PIP2_synthesis
Vmax_Shc_phosphorylation Vmax_RasGRP_DAG_GEF Vmax_CAPRI_GAP Vmax_CaRasGRP_act_RasGM
PIP_basal_PIP_synthesis kBasalSynPIP_PIP_synthesis kStimSynPIP_PIP_synthesis tauPIPsyn_PIP_synthesis
PIPsyndecay_PIP_synthesis Ratebasal_PIPsyn_PIP_synthesis Ratestim_PIPsyn_PIP_synthesis Kon_reaction2
dinh_reaction2 Koff_reaction2 Vmax_EGF_act_PLCgamma dact_Ca_binds_IP3R
Kr_Ca_binds_IP3R Vmax_Sos_act_RasPM    
Reactions (43)
 
 PIP2 synthesis [PIP_PM] ↔ [PIP2_PM];  
 
 Shc phosphorylation [Shc_PM] ↔ [Shc_star_PM];   {Activated_EGFR_PM}
 
 Ca bind CAPRI [Ca] + [CAPRI_cyt] ↔ [CaCAPRI_cyt];  
 
 IP3 degradation [IP3] ↔ ;  
 
 RasGTP depal translocate [RasGTP_depal_cyt] ↔ [RasGTP_Golgi_GM];  
 
 ca bind rasGRP [Ca] + [RasGRP_cyt] ↔ [CaRasGRP1_cyt];  
 
 RasGRP_DAG GEF [RasGDP_Golgi_GM] ↔ [RasGTP_Golgi_GM];   {RasGRP_DAG_GM}
 
 rasGTP pal translocation [RasGTP_pal_cyt] ↔ [RasGTP_PM];  
 
 PLCg dephos [PLC_act_PM] ↔ [PLC_PM];  
 
 basal GAP [RasGTP_PM] ↔ [RasGDP_PM];  
 
 CAPRI translocation [CaCAPRI_cyt] ↔ [CaCAPRI_PM_PM];  
 
 reaction5 [DAG_GM_GM] + [RasGRP_cyt] ↔ [RasGRP_DAG_GM];  
 
 RasGDP pal [RasGDP_Golgi_GM] ↔ [RasGDP_pal_cyt];  
 
 CAPRI GAP [RasGTP_PM] ↔ [RasGDP_PM];   {CaCAPRI_PM_PM}
 
 RasGDPpal translocation [RasGDP_pal_cyt] ↔ [RasGDP_PM];  
 
 sos grb2 binding [Sos_cyt] + [Grb2_cyt] ↔ [SosGrb2_cyt];  
 
 RasGDP depal translocate [RasGDP_depal_cyt] ↔ [RasGDP_Golgi_GM];  
 
 Ras GTP palm1 [RasGTP_Golgi_GM] ↔ [RasGTP_pal_cyt];  
 
 RasPal basal GAP [RasGTP_pal_cyt] ↔ [RasGDP_pal_cyt];  
 
 basal cyt depal GEF [RasGTP_depal_cyt] ↔ [RasGDP_depal_cyt];  
 
 caPLCe gen DAG [PIP2_GM_GM] ↔ [DAG_GM_GM] + [IP3];   {Ras_CaPLCe_GM}
 
 CaRasGRP act RasGM [RasGDP_Golgi_GM] ↔ [RasGTP_Golgi_GM];   {Ca_RasGRP_GM_GM}
 
 PIP2 hydrolysis [PIP2_PM] ↔ [DAG_PM] + [IP3];   {PLC_act_PM}
 
 Sos activation [SosGrb2_cyt] + [Shc_star_PM] ↔ [SGS_PM];  
 
 PIP synthesis [PI_PM] ↔ [PIP_PM];  
 
 EGF_internalization [Activated_EGFR_PM] ↔ ;  
 
 calcium buffer [buffer_cyt] + [Ca] ↔ [ca_buffer_cyt];  
 
 RasGM basal GAP [RasGTP_Golgi_GM] ↔ [RasGDP_Golgi_GM];  
 
 reaction0 [Shc_star_PM] ↔ [Shc_PM];  
 
 EGFR_binding [EGF_EC] + [EGFR_PM] ↔ [Activated_EGFR_PM];  
 
 ca act PLCe [Ca] + [PLCe_cyt] ↔ [Ca_PLCe_cyt];  
 
 ras_act_PLCe [RasGTP_Golgi_GM] + [Ca_PLCe_cyt] ↔ [Ras_CaPLCe_GM];  
 
 RasGDP depal2 [RasGDP_PM] ↔ [RasGDP_depal_cyt];  
 
 CaRasGRP translocation [CaRasGRP1_cyt] ↔ [Ca_RasGRP_GM_GM];  
 
 reaction2 [Rinh] + [Ca] ↔ [RinhCa];  
 
 EGF act PLCgamma [PLC_PM] ↔ [PLC_act_PM];   {Activated_EGFR_PM}
 
 Ca_binds_IP3R [Ract] + [Ca] ↔ [RactCa];  
 
 reaction7 [DAG_GM_GM] ↔ ;  
 
 Sos act RasPM [RasGDP_PM] ↔ [RasGTP_PM];   {SGS_PM}
 
 flux1 [Ca] ↔ [Ca_ER];   {ER_erMembrane} , {serca}
 
 flux0 [Ca] ↔ [Ca_ER];   {ER_erMembrane} , {RactCa} , {Ract} , {IP3} , {Rinh} , {RinhCa}
 
 flux2 [Ca] ↔ [Ca_ER];   {ER_erMembrane}
 
 Ras PM depal1 [RasGTP_PM] ↔ [RasGTP_depal_cyt];  
 
Rules (12)
 
 Assignment Rule (name: Rate_PIP2Synbasal_PIP2_synthesis) Rate_PIP2Synbasal_PIP2_synthesis = piecewise(0.581*kBasalSynPIP2_PIP2_synthesis*((-1)+exp((PIP2_basal_PIP2_synthesis+(-PIP2_PM))*1/PIP2_basal_PIP2_synthesis)), PIP2_PM < PIP2_basal_PIP2_synthesis, 0)
 
 Assignment Rule (name: Rate_PIP2SynStim_PIP2_synthesis) Rate_PIP2SynStim_PIP2_synthesis = piecewise(kStimSynPIP2_PIP2_synthesis*exp(-(t+(-tauPIP2syn_PIP2_synthesis))*1/PIP2syndecay_PIP2_synthesis), t > tauPIP2syn_PIP2_synthesis, 0)
 
 Assignment Rule (name: Vmax_Shc_phosphorylation) Vmax_Shc_phosphorylation = 0.2*Activated_EGFR_PM
 
 Assignment Rule (name: Vmax_RasGRP_DAG_GEF) Vmax_RasGRP_DAG_GEF = 0.05*RasGRP_DAG_GM
 
 Assignment Rule (name: Vmax_CAPRI_GAP) Vmax_CAPRI_GAP = 10*CaCAPRI_PM_PM
 
 Assignment Rule (name: Vmax_CaRasGRP_act_RasGM) Vmax_CaRasGRP_act_RasGM = 0.01*Ca_RasGRP_GM_GM
 
 Assignment Rule (name: Ratebasal_PIPsyn_PIP_synthesis) Ratebasal_PIPsyn_PIP_synthesis = piecewise(0.581*kBasalSynPIP_PIP_synthesis*((-1)+exp((PIP_basal_PIP_synthesis+(-PIP_PM))*1/PIP_basal_PIP_synthesis)), PIP_PM < PIP_basal_PIP_synthesis, 0)
 
 Assignment Rule (name: Ratestim_PIPsyn_PIP_synthesis) Ratestim_PIPsyn_PIP_synthesis = piecewise(kStimSynPIP_PIP_synthesis*exp(-(t+(-tauPIPsyn_PIP_synthesis))*1/PIPsyndecay_PIP_synthesis), t > tauPIPsyn_PIP_synthesis, 0)
 
 Assignment Rule (name: Koff_reaction2) Koff_reaction2 = dinh_reaction2*Kon_reaction2
 
 Assignment Rule (name: Vmax_EGF_act_PLCgamma) Vmax_EGF_act_PLCgamma = 0.3*Activated_EGFR_PM
 
 Assignment Rule (name: Kr_Ca_binds_IP3R) Kr_Ca_binds_IP3R = 1000*dact_Ca_binds_IP3R
 
 Assignment Rule (name: Vmax_Sos_act_RasPM) Vmax_Sos_act_RasPM = 0.02*SGS_PM
 
 EC Spatial dimensions: 3.0  Compartment size: 1.0
 
 EGF_EC
Compartment: EC
Initial concentration: 4.02136  (Units: molecules)
 
 cyt Spatial dimensions: 3.0  Compartment size: 0.976
 
 CAPRI_cyt
Compartment: cyt
Initial concentration: 30.1  (Units: molecules)
 
 RasGTP_pal_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 Ca
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 IP3
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 CaCAPRI_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 RasGTP_depal_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 RasGDP_depal_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 RasGDP_pal_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 Ca_PLCe_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 Sos_cyt
Compartment: cyt
Initial concentration: 81.27  (Units: molecules)
 
 Grb2_cyt
Compartment: cyt
Initial concentration: 502.67  (Units: molecules)
 
 PLCe_cyt
Compartment: cyt
Initial concentration: 12.04  (Units: molecules)
 
 buffer_cyt
Compartment: cyt
Initial concentration: 120.4  (Units: molecules)
 
 ca_buffer_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 SosGrb2_cyt
Compartment: cyt
Initial concentration: 99.33  (Units: molecules)
 
 RasGRP_cyt
Compartment: cyt
Initial concentration: 30.1  (Units: molecules)
 
 CaRasGRP1_cyt
Compartment: cyt
Initial concentration: 0.0  (Units: molecules)
 
 er Spatial dimensions: 3.0  Compartment size: 0.012
 
 Ca_ER
Compartment: er
Initial concentration: 120400.0  (Units: molecules)
 
 Golgi Spatial dimensions: 3.0  Compartment size: 0.012
 PM Spatial dimensions: 2.0  Compartment size: 0.6  (Units: um2)
 
 PIP_PM
Compartment: PM
Initial concentration: 2857.0  (Units: molecules)
 
 PI_PM
Compartment: PM
Initial concentration: 142857.0  (Units: molecules)
 
 Shc_PM
Compartment: PM
Initial concentration: 186.0  (Units: molecules)
 
 CaCAPRI_PM_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 Shc_star_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 EGFR_PM
Compartment: PM
Initial concentration: 21.0  (Units: molecules)
 
 PLC_act_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 PLC_PM
Compartment: PM
Initial concentration: 100.0  (Units: molecules)
 
 PIP2_PM
Compartment: PM
Initial concentration: 1072.0  (Units: molecules)
 
 Activated_EGFR_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 DAG_PM
Compartment: PM
Initial concentration: 2000.0  (Units: molecules)
 
 SGS_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 RasGTP_PM
Compartment: PM
Initial concentration: 0.0  (Units: molecules)
 
 RasGDP_PM
Compartment: PM
Initial concentration: 400.0  (Units: molecules)
 
 erMembrane Spatial dimensions: 2.0  Compartment size: 0.0456  (Units: um2)
 
 serca
Compartment: erMembrane
Initial concentration: 45.0  (Units: molecules)
 
 RactCa
Compartment: erMembrane
Initial concentration: 2.264  (Units: molecules)
 
 Ract
Compartment: erMembrane
Initial concentration: 9.056  (Units: molecules)
 
 Rinh
Compartment: erMembrane
Initial concentration: 7.7825  (Units: molecules)
 
 RinhCa
Compartment: erMembrane
Initial concentration: 3.5375  (Units: molecules)
 
 ER_erMembrane
Compartment: erMembrane
Initial concentration: 2.0  (Units: molecules)
 
 GM Spatial dimensions: 2.0  Compartment size: 0.048  (Units: um2)
 
 RasGTP_Golgi_GM
Compartment: GM
Initial concentration: 0.0  (Units: molecules)
 
 RasGDP_Golgi_GM
Compartment: GM
Initial concentration: 50.0  (Units: molecules)
 
 Ca_RasGRP_GM_GM
Compartment: GM
Initial concentration: 0.0  (Units: molecules)
 
 DAG_GM_GM
Compartment: GM
Initial concentration: 0.0  (Units: molecules)
 
 RasGRP_DAG_GM
Compartment: GM
Initial concentration: 0.0  (Units: molecules)
 
 Ras_CaPLCe_GM
Compartment: GM
Initial concentration: 0.0  (Units: molecules)
 
 PIP2_GM_GM
Compartment: GM
Initial concentration: 250.0  (Units: molecules)
 
Global Parameters (26)
 
   KMOLE
Value: 0.00166112956810631   (Units: uM_um3_molecules_1)
Constant
 
   kStimSynPIP2_PIP2_synthesis
Value: 0.01   (Units: s_1)
Constant
 
   tauPIP2syn_PIP2_synthesis
Value: 0.05   (Units: s)
Constant
 
   PIP2syndecay_PIP2_synthesis
Value: 10.0   (Units: s)
Constant
 
   PIP2_basal_PIP2_synthesis
Value: 1072.0   (Units: molecules_um_2)
Constant
 
   kBasalSynPIP2_PIP2_synthesis
Value: 0.045   (Units: s_1)
Constant
 
   Rate_PIP2Synbasal_PIP2_synthesis
Value: NaN   (Units: s_1)
 
   Rate_PIP2SynStim_PIP2_synthesis
Value: NaN   (Units: s_1)
 
   Vmax_Shc_phosphorylation
Value: NaN   (Units: molecules_um_2_s_1)
 
   Vmax_RasGRP_DAG_GEF
Value: NaN   (Units: molecules_um_2_s_1)
 
   Vmax_CAPRI_GAP
Value: NaN   (Units: molecules_um_2_s_1)
 
   Vmax_CaRasGRP_act_RasGM
Value: NaN   (Units: molecules_um_2_s_1)
 
   PIP_basal_PIP_synthesis
Value: 2857.0   (Units: molecules_um_2)
Constant
 
   kBasalSynPIP_PIP_synthesis
Value: 0.0015   (Units: s_1)
Constant
 
   kStimSynPIP_PIP_synthesis
Value: 0.01   (Units: s_1)
Constant
 
   tauPIPsyn_PIP_synthesis
Value: 0.05   (Units: s)
Constant
 
   PIPsyndecay_PIP_synthesis
Value: 10.0   (Units: s)
Constant
 
   Ratebasal_PIPsyn_PIP_synthesis
Value: NaN   (Units: s_1)
 
   Ratestim_PIPsyn_PIP_synthesis
Value: NaN   (Units: s_1)
 
   Kon_reaction2
Value: 2.1   (Units: uM_1_s_1)
Constant
 
   dinh_reaction2
Value: 0.11   (Units: uM)
Constant
 
   Koff_reaction2
Value: NaN   (Units: s_1)
 
   Vmax_EGF_act_PLCgamma
Value: NaN   (Units: molecules_um_2_s_1)
 
   dact_Ca_binds_IP3R
Value: 0.2   (Units: s_1)
Constant
 
   Kr_Ca_binds_IP3R
Value: NaN   (Units: s_1)
 
   Vmax_Sos_act_RasPM
Value: NaN   (Units: molecules_um_2_s_1)
 
PIP2 synthesis (1)
 
   I
Constant
 
Shc phosphorylation (2)
 
   I
Constant
 
   Km
Value: 1032.0   (Units: molecules_um_2)
Constant
 
Ca bind CAPRI (2)
 
   Kf
Value: 0.1   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.5   (Units: s_1)
Constant
 
IP3 degradation (2)
 
   kIP3deg
Value: 0.5   (Units: s_1)
Constant
 
   IP3_basal
Constant
 
RasGTP depal translocate (3)
 
   I
Constant
 
   Kf
Value: 120.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 0.01   (Units: s_1)
Constant
 
ca bind rasGRP (2)
 
   Kf
Value: 0.1   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.5   (Units: s_1)
Constant
 
RasGRP_DAG GEF (2)
 
   I
Constant
 
   Km
Value: 600.0   (Units: molecules_um_2)
Constant
 
rasGTP pal translocation (3)
 
   I
Constant
 
   Kf
Value: 120.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 0.01   (Units: s_1)
Constant
 
PLCg dephos (3)
 
   I
Constant
 
   Kf
Value: 0.2   (Units: s_1)
Constant
 
   Kr
Constant
 
basal GAP (3)
 
   I
Constant
 
   Kf
Value: 1.0E-4   (Units: s_1)
Constant
 
   Kr
Constant
 
CAPRI translocation (3)
 
   I
Constant
 
   Kf
Value: 120.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 0.1   (Units: s_1)
Constant
 
reaction5 (3)
 
   I
Constant
 
   Kf
Value: 0.5   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.1   (Units: s_1)
Constant
 
RasGDP pal (3)
 
   I
Constant
 
   Kf
Value: 0.015   (Units: s_1)
Constant
 
   Kr
Value: 1.0E-5   (Units: molecules_um_2_uM_1_s_1)
Constant
 
CAPRI GAP (2)
 
   I
Constant
 
   Km
Value: 1200.0   (Units: molecules_um_2)
Constant
 
RasGDPpal translocation (3)
 
   I
Constant
 
   Kf
Value: 120.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 0.01   (Units: s_1)
Constant
 
sos grb2 binding (2)
 
   Kf
Value: 0.025   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.0168   (Units: s_1)
Constant
 
RasGDP depal translocate (3)
 
   I
Constant
 
   Kf
Value: 120.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 0.01   (Units: s_1)
Constant
 
Ras GTP palm1 (3)
 
   I
Constant
 
   Kf
Value: 1.58489319246111E-4   (Units: s_1)
Constant
 
   Kr
Value: 1.0E-5   (Units: molecules_um_2_uM_1_s_1)
Constant
 
RasPal basal GAP (2)
 
   Kf
Value: 1.0E-4   (Units: s_1)
Constant
 
   Kr
Constant
 
basal cyt depal GEF (2)
 
   Kf
Value: 1.0E-4   (Units: s_1)
Constant
 
   Kr
Constant
 
caPLCe gen DAG (2)
 
   I
Constant
 
   kact
Value: 1.18   (Units: um2_molecules_1_s_1)
Constant
 
CaRasGRP act RasGM (2)
 
   I
Constant
 
   Km
Value: 1200.0   (Units: molecules_um_2)
Constant
 
PIP2 hydrolysis (2)
 
   I
Constant
 
   k_PIP2hyd
Value: 1.188   (Units: um2_molecules_1_s_1)
Constant
 
Sos activation (3)
 
   I
Constant
 
   Kf
Value: 90.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.1   (Units: s_1)
Constant
 
PIP synthesis (1)
 
   I
Constant
 
EGF_internalization (3)
 
   I
Constant
 
   Kf
Value: 0.002   (Units: s_1)
Constant
 
   Kr
Constant
 
calcium buffer (2)
 
   Kf
Value: 50.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 10.0   (Units: s_1)
Constant
 
RasGM basal GAP (3)
 
   I
Constant
 
   Km
Value: 600.0   (Units: molecules_um_2)
Constant
 
   Vmax
Value: 1.0   (Units: molecules_um_2_s_1)
Constant
 
reaction0 (3)
 
   I
Constant
 
   Kf
Value: 0.5   (Units: s_1)
Constant
 
   Kr
Constant
 
EGFR_binding (3)
 
   I
Constant
 
   Kf
Value: 1.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.01   (Units: s_1)
Constant
 
ca act PLCe (2)
 
   Kf
Value: 3.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 1.0   (Units: s_1)
Constant
 
ras_act_PLCe (3)
 
   I
Constant
 
   Kf
Value: 15.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 1.0   (Units: s_1)
Constant
 
RasGDP depal2 (3)
 
   I
Constant
 
   Kf
Value: 1.0E-4   (Units: s_1)
Constant
 
   Kr
Constant
 
CaRasGRP translocation (3)
 
   I
Constant
 
   Kf
Value: 10.0   (Units: molecules_um_2_uM_1_s_1)
Constant
 
   Kr
Value: 5.0   (Units: s_1)
Constant
 
reaction2 (1)
 
   I
Constant
 
EGF act PLCgamma (2)
 
   I
Constant
 
   Km
Value: 410.0   (Units: molecules_um_2)
Constant
 
Ca_binds_IP3R (2)
 
   I
Constant
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
reaction7 (3)
 
   I
Constant
 
   Kf
Value: 0.25   (Units: s_1)
Constant
 
   Kr
Constant
 
Sos act RasPM (2)
 
   I
Constant
 
   Km
Value: 600.0   (Units: molecules_um_2)
Constant
 
flux1 (3)
 
   I
Constant
 
   vP
Value: 0.0664   (Units: _one__0E_33_item_2_m2_mol_s_1)
Constant
 
   kP
Value: 0.27
Constant
 
flux0 (3)
 
   I
Constant
 
   dI
Value: 0.8   (Units: uM)
Constant
 
   singleChanFlux
Value: 4.69   (Units: _one__0E_30_item_2_m5_s_1)
Constant
 
flux2 (2)
 
   I
Constant
 
   vL
Value: 3.16E-5   (Units: um3_molecules_1_s_1)
Constant
 
Ras PM depal1 (3)
 
   I
Constant
 
   Kf
Value: 1.0E-4   (Units: s_1)
Constant
 
   Kr
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000161

Curator's comment: (updated: 29 Jan 2008 19:36:08 GMT)

The simulation result corresponds to Fig 5A and 5B of the paper. The plots in the publication show the time profiles of Ras-GTP in the Golgi and Plasma membrane for various palmitoylation rates. The value used in the model is 0.00015849, which is not shown in Fig 5 but is shown in Fig S2 of the supplement. Results obtained with MathSBML.

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