BioModels Database logo

BioModels Database

spacer

BIOMD0000000081 - Suh2004_KCNQ_Regulation

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 15173220
Suh BC, Horowitz LF, Hirdes W, Mackie K, Hille B.
Regulation of KCNQ2/KCNQ3 current by G protein cycling: the kinetics of receptor-mediated signaling by Gq.
J. Gen. Physiol. 2004 Jun; 123(6): 663-683
Department of Physiology and Biophysics, University of Washington School of Medicine, G-424 Health Sciences Building, Box 357290, Seattle, WA 98195-7290, USA.  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL4662889298
Submission Date: 27 Nov 2006 22:15:44 UTC
Last Modification Date: 05 Jul 2012 16:29:50 UTC
Creation Date: 09 Nov 2006 18:25:52 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasPart Gene Ontology phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway
Gene Ontology lipid metabolic process
bqbiol:is KEGG Pathway Calcium signaling pathway
KEGG Pathway Phosphatidylinositol signaling system
bqbiol:occursIn Taxonomy Homo sapiens
Notes

The model reproduces FIG 11A and FIG 11B of the paper. However, please note that FIG 11B is a plot of normalised amounts versus time. The "stoichiometry" field has been used to convert fluxes from membrane species to volume species. The value of 0.0009967 is a product of (Surface to Volume_M*(1/Avagadro's number)*1E21. 0.6 is the surface to volume ratio of the plasma membrane, 1E21 is required for a unit surface to volume ratio and the Avagadro's number is present in the denominator to convert molecules to moles. The model was successfully tested using MathSBML and SBML ODESolver.
All the kinetic laws have the unit items per second , which requires the one reaction taking place in the cytoplasm - IP3Phosphatase - to include an explicit conversion factor both in the kinetic law and the stoichiometry of IP3_C . The kinetic law is multiplied and the stoichiometry divided by the number of molecules per micro-mole. This conversion factor is only required for correct units and can be replaced by 1, if it should lead to numerical problems.


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: 15173220 Submission Date: 27 Nov 2006 22:15:44 UTC Last Modification Date: 05 Jul 2012 16:29:50 UTC Creation Date: 09 Nov 2006 18:25:52 UTC
Mathematical expressions
Reactions
PIP5kinase IP3Phosphatase PIP2binding MgonGGTPgS
GGTPase GTPon GTPgSon GDPbSon
MgGTPon GDPdissoc PIP2_5Pase PLC
AIF4on PI4Kinase MgonGDPAIF4  
Rules
Assignment Rule (variable: MgSat20) Assignment Rule (variable: ATPSat1000) Assignment Rule (variable: MgSat10) Assignment Rule (variable: OxoSat)
Assignment Rule (variable: fGactive) Assignment Rule (variable: Gactive) Assignment Rule (variable: ATPSat300) Assignment Rule (variable: I_KCNQ)
Assignment Rule (variable: GTP_C)      
Events
event_0000001 event_0000002    
Physical entities
Compartments Species
Extracellular oxoM_EX    
Membrane KCNQsites_M PIP2_M GGDPbS_M
GGTPMg_M GGDPAIF4Mg_M G_M
GGTP_M GGDPAIF4_M GGTPgS_M
PI_M PIP_M PIP2xKCNQ_M
GGTPgSMg_M GGDP_M  
Cytoplasm GTPgS_C Mg2_C ATP_C
GDPbS_C GDP_C GTP_C
IP3_C AIF4_C  
Global parameters
MgSat20 ATPSat300 MgSat10 OxoSat
Gactive ATPSat1000 KMgGTPase Koxom
I_KCNQ nHill fGactive NA(micro)
Reactions (15)
 
 PIP5kinase 9.967E-4 × [ATP_C] + [PIP_M] ↔ [PIP2_M];  
 
 IP3Phosphatase 1.666111296E-18 × [IP3_C] ↔ ;  
 
 PIP2binding [KCNQsites_M] + [PIP2_M] ↔ [PIP2xKCNQ_M];  
 
 MgonGGTPgS [GGTPgS_M] ↔ [GGTPgSMg_M];   {Mg2_C}
 
 GGTPase [GGTPMg_M] ↔ [GGDP_M];  
 
 GTPon [G_M] ↔ [GGTP_M];   {GTP_C}
 
 GTPgSon 9.967E-4 × [GTPgS_C] + [G_M] ↔ [GGTPgS_M];  
 
 GDPbSon [G_M] + 9.967E-4 × [GDPbS_C] ↔ [GGDPbS_M];  
 
 MgGTPon [GGTP_M] ↔ [GGTPMg_M];   {Mg2_C}
 
 GDPdissoc [GGDP_M] ↔ 9.967E-4 × [GDP_C] + [G_M];   {oxoM_EX}
 
 PIP2_5Pase [PIP2_M] ↔ [PIP_M];  
 
 PLC [PIP2_M] ↔ 9.967E-4 × [IP3_C];  
 
 AIF4on 9.967E-4 × [AIF4_C] + [GGDP_M] ↔ [GGDPAIF4_M];  
 
 PI4Kinase 9.967E-4 × [ATP_C] + [PI_M] ↔ [PIP_M];  
 
 MgonGDPAIF4 [GGDPAIF4_M] ↔ [GGDPAIF4Mg_M];   {Mg2_C}
 
Rules (9)
 
 Assignment Rule (name: MgSat20) MgSat20 = 1*1/(1+20*1/Mg2_C)
 
 Assignment Rule (name: ATPSat1000) ATPSat1000 = 1*1/(1+1000*1/(0.5+ATP_C))
 
 Assignment Rule (name: MgSat10) MgSat10 = 0.2+0.8*1*1/(1+KMgGTPase*1/Mg2_C)
 
 Assignment Rule (name: OxoSat) OxoSat = 1*1/(1+Koxom*1/(1E-5+oxoM_EX))
 
 Assignment Rule (name: fGactive) fGactive = (GGTPMg_M+GGTPgSMg_M+GGDPAlF4Mg_M)/200
 
 Assignment Rule (name: Gactive) Gactive = GGTPMg_M+GGTPgSMg_M+GGDPAlF4Mg_M
 
 Assignment Rule (name: ATPSat300) ATPSat300 = 1*1/(1+300*1/(0.5+ATP_C))
 
 Assignment Rule (name: I_KCNQ) I_KCNQ = 1.33*(0.025*PIP2xKCNQ_M)^nHill
 
 Assignment Rule (name: GTP_C) GTP_C = 100-50*exp(-0.00833333333333333*(290+t))
 
Events (2)
 
 event_0000001
oxoM_EX = 10
 
 event_0000002
oxoM_EX = 0
 
 Extracellular Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 oxoM_EX
Compartment: Extracellular
Initial concentration: 0.0  (Units: micromole)
 
 Membrane Spatial dimensions: 2.0  Compartment size: 1.0  (Units: um2)
 
 KCNQsites_M
Compartment: Membrane
Initial concentration: 6.7  (Units: molecules)
 
 PIP2_M
Compartment: Membrane
Initial concentration: 5000.0  (Units: molecules)
 
 GGDPbS_M
Compartment: Membrane
Initial concentration: 0.0  (Units: molecules)
 
 GGTPMg_M
Compartment: Membrane
Initial concentration: 0.1  (Units: molecules)
 
 GGDPAIF4Mg_M
Compartment: Membrane
Initial concentration: 0.0  (Units: molecules)
 
 G_M
Compartment: Membrane
Initial concentration: 0.065  (Units: molecules)
 
 GGTP_M
Compartment: Membrane
Initial concentration: 0.048  (Units: molecules)
 
 GGDPAIF4_M
Compartment: Membrane
Initial concentration: 0.0  (Units: molecules)
 
 GGTPgS_M
Compartment: Membrane
Initial concentration: 0.0  (Units: molecules)
 
 PI_M
Compartment: Membrane
Initial concentration: 200000.0  (Units: molecules)
 
 PIP_M
Compartment: Membrane
Initial concentration: 1150.0  (Units: molecules)
 
 PIP2xKCNQ_M
Compartment: Membrane
Initial concentration: 33.3  (Units: molecules)
 
 GGTPgSMg_M
Compartment: Membrane
Initial concentration: 0.0  (Units: molecules)
 
 GGDP_M
Compartment: Membrane
Initial concentration: 200.0  (Units: molecules)
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 GTPgS_C
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: micromole)
 
 Mg2_C
Compartment: Cytoplasm
Initial concentration: 2100.0  (Units: micromole)
 
 ATP_C
Compartment: Cytoplasm
Initial concentration: 3000.0  (Units: micromole)
 
 GDPbS_C
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: micromole)
 
 GDP_C
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: micromole)
 
  GTP_C
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: micromole)
 
 IP3_C
Compartment: Cytoplasm
Initial concentration: 0.48  (Units: micromole)
 
 AIF4_C
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: micromole)
 
Global Parameters (12)
 
   MgSat20
Value: NaN   (Units: dimensionless)
 
   ATPSat300
Value: NaN   (Units: dimensionless)
 
   MgSat10
Value: NaN   (Units: dimensionless)
 
   OxoSat
Value: NaN   (Units: dimensionless)
 
   Gactive
Value: NaN   (Units: molecules_um_2)
 
   ATPSat1000
Value: NaN   (Units: dimensionless)
 
   KMgGTPase
Value: 10.0   (Units: microMolar)
Constant
 
   Koxom
Value: 8.0   (Units: microMolar)
Constant
 
   I_KCNQ
Value: NaN   (Units: dimensionless)
 
   nHill
Value: 1.8   (Units: dimensionless)
Constant
 
   fGactive
Value: NaN   (Units: dimensionless)
 
   NA(micro)
Value: 6.022E17   (Units: items_per_micromole)
Constant
 
PIP5kinase (1)
 
   kPIP5Kinase
Value: 0.06   (Units: s_1)
Constant
 
IP3Phosphatase (1)
 
   kIP3ase
Value: 0.3   (Units: s_1)
Constant
 
PIP2binding (2)
 
   kPIP2on
Value: 2.5E-4   (Units: um2_molecules_1_s_1)
Constant
 
   kPIP2off
Value: 0.25   (Units: s_1)
Constant
 
MgonGGTPgS (1)
 
   kMg2onGTPgS
Value: 0.0020   (Units: uM_1_s_1)
Constant
 
GGTPase (1)
 
   kGGTPase
Value: 1.8   (Units: s_1)
Constant
 
GTPon (2)
 
   kGTPon
Value: 0.45   (Units: uM_1_s_1)
Constant
 
   kGTPoff
Value: 0.08   (Units: s_1)
Constant
 
GTPgSon (2)
 
   kGTPgSon
Value: 0.0060   (Units: uM_1_s_1)
Constant
 
   kGTPgSoff
Value: 0.0050   (Units: s_1)
Constant
 
GDPbSon (2)
 
   kGDPbSon
Value: 0.28   (Units: uM_1_s_1)
Constant
 
   kGGDPbSoff
Value: 0.1   (Units: s_1)
Constant
 
MgGTPon (1)
 
   kMg2onGTP
Value: 0.0030   (Units: uM_1_s_1)
Constant
 
GDPdissoc (3)
 
   kGDPoff
Value: 0.5   (Units: s_1)
Constant
 
   TonicAct
Value: 0.0020   (Units: dimensionless)
Constant
 
   kGDPon
Value: 0.0030   (Units: uM_1_s_1)
Constant
 
PIP2_5Pase (1)
 
   kPIP2Pase
Value: 0.0050   (Units: s_1)
Constant
 
PLC (2)
 
   kPLC
Value: 4.8   (Units: s_1)
Constant
 
   PLCspont
Value: 7.5E-4   (Units: dimensionless)
Constant
 
AIF4on (2)
 
   kAlF4on
Value: 7.0E-6   (Units: uM_1_s_1)
Constant
 
   kAlF4off
Value: 0.0050   (Units: s_1)
Constant
 
PI4Kinase (1)
 
   kPI4Kinase
Value: 1.0E-4   (Units: s_1)
Constant
 
MgonGDPAIF4 (1)
 
   kMgonAlF4
Value: 0.0020   (Units: uM_1_s_1)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000081

Curator's comment: (updated: 29 Sep 2009 16:00:48 BST)

Reproduction of fig 11 A and B from the original publication using SBML ODESolver.

spacer
spacer