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BIOMD0000000165 - Saucerman2006_PKA

 

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Reference Publication
Publication ID: 16905651
Saucerman JJ, Zhang J, Martin JC, Peng LX, Stenbit AE, Tsien RY, McCulloch AD.
Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.
Proc. Natl. Acad. Sci. U.S.A. 2006 Aug; 103(34): 12923-12928
Department of Bioengineering, Whitaker Institute of Biomedical Engineering, University of California at San Diego, La Jolla, CA 92093, USA.  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL8003201958
Submission Date: 25 Feb 2008 00:07:00 UTC
Last Modification Date: 10 Oct 2014 10:06:40 UTC
Creation Date: 03 Oct 2007 10:05:51 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasProperty Human Disease Ontology heart disease
set #2
bqbiol:occursIn Cell Type Ontology fetal cardiomyocyte
set #3
bqmodel:isDerivedFrom BioModels Database Saucerman2003_CardiacMyocyte_BetaAdrenergic
set #4
bqbiol:isVersionOf Gene Ontology activation of protein kinase A activity
Gene Ontology adenylate cyclase-modulating G-protein coupled receptor signaling pathway
bqbiol:hasTaxon Taxonomy Rattus norvegicus
set #5
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

The model reproduces Fig 2B of the paper. Model successfully tested on 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: 16905651 Submission Date: 25 Feb 2008 00:07:00 UTC Last Modification Date: 10 Oct 2014 10:06:40 UTC Creation Date: 03 Oct 2007 10:05:51 UTC
Mathematical expressions
Reactions
cAMP_synthesis_GsAC bind_b1AR_propranolol add_propranolol cAMP_photolysis
LRG_activation bind_Lb1AR_Gs desens_bark bind_cAMP_ARC
bind_b1AR_Gs bind_PDEcAMP Gs_gtp_hydrolysis Gs_reassociation
bind_FskAC bind_AKARp_PP desens_pka bind_L_b1ARGs
bind_L_b1AR bind_A2R_PKAC inhib_PKAC bind_RC_cAMP
cAMP_synthesis_FskAC add_Ligand bind_Gs_AC resens_bark
bind_PKAC_AKAR inhibit_PDE AKARp_dephosph AKAR_phosph
RG_activation cAMP_degradation    
Rules
Assignment Rule (variable: Vmax_cAMP_synthesis_GsAC) Assignment Rule (variable: light_cAMP_photolysis) Assignment Rule (variable: Vmax_cAMP_synthesis_FskAC) Assignment Rule (variable: Kf_inhibit_PDE)
Assignment Rule (variable: Kr_inhibit_PDE) Assignment Rule (variable: ar_for_add_propranolol) Assignment Rule (variable: ar_for_add_Ligand) Assignment Rule (variable: Ratio_AKARp_AKARtot)
Physical entities
Compartments Species
ec      
cell Gsbg L Gsa_gdp
Gsa_gtp b1AR_S464 PDEcAMP
PDE ATP b1AR
Gs A2RC A2R
PKAC ARC PKAC_AKAR
Propranolol b1ARinhib light_spot
AC PKI PKAC_PKI
RC b1AR_Gs cAMP
GsAC IBMX PDE_IBMX
Fsk FskAC b1AR_p
L_b1AR AKAR AKARp
PP PP_AKARp DMNB_cAMP
L_b1AR_Gs    
membrane      
Global parameters
k_ac_gsa_cAMP_synthesis_GsAC Vmax_cAMP_synthesis_GsAC ton_global_light_cAMP_photolysis toff_global_light_cAMP_photolysis
ton_local_light_cAMP_photolysis toff_local_light_cAMP_photolysis light_cAMP_photolysis kfsk_cAMP_synthesis_FskAC
Vmax_cAMP_synthesis_FskAC Kf_inhibit_PDE Kr_inhibit_PDE ar_for_add_propranolol
t_propadd Propranolol_pipette tauPropranolol ar_for_add_Ligand
t_Ladd L_pipette tauL Ratio_AKARp_AKARtot
Reactions (30)
 
 cAMP_synthesis_GsAC [ATP] ↔ [cAMP];   {GsAC}
 
 bind_b1AR_propranolol [Propranolol] + [b1AR] ↔ [b1ARinhib];  
 
 add_propranolol  ↔ [Propranolol];  
 
 cAMP_photolysis [DMNB_cAMP] ↔ [cAMP];   {light_spot}
 
 LRG_activation [L_b1AR_Gs] ↔ [Gsa_gtp] + [Gsbg] + [L_b1AR];  
 
 bind_Lb1AR_Gs [Gs] + [L_b1AR] ↔ [L_b1AR_Gs];  
 
 desens_bark [L_b1AR] ↔ [b1AR_S464];   {L_b1AR_Gs}
 
 bind_cAMP_ARC [ARC] + [cAMP] ↔ [A2RC];  
 
 bind_b1AR_Gs [b1AR] + [Gs] ↔ [b1AR_Gs];  
 
 bind_PDEcAMP [PDE] + [cAMP] ↔ [PDEcAMP];  
 
 Gs_gtp_hydrolysis [Gsa_gtp] ↔ [Gsa_gdp];  
 
 Gs_reassociation [Gsbg] + [Gsa_gdp] ↔ [Gs];  
 
 bind_FskAC [AC] + [Fsk] ↔ [FskAC];  
 
 bind_AKARp_PP [PP] + [AKARp] ↔ [PP_AKARp];  
 
 desens_pka [b1AR] ↔ [b1AR_p];   {PKAC} , {L_b1AR_Gs} , {L_b1AR}
 
 bind_L_b1ARGs [b1AR_Gs] + [L] ↔ [L_b1AR_Gs];  
 
 bind_L_b1AR [L] + [b1AR] ↔ [L_b1AR];  
 
 bind_A2R_PKAC [A2RC] ↔ [A2R] + [PKAC];  
 
 inhib_PKAC [PKAC] + [PKI] ↔ [PKAC_PKI];  
 
 bind_RC_cAMP [RC] + [cAMP] ↔ [ARC];  
 
 cAMP_synthesis_FskAC [ATP] ↔ [cAMP];   {FskAC}
 
 add_Ligand  ↔ [L];  
 
 bind_Gs_AC [Gsa_gtp] + [AC] ↔ [GsAC];  
 
 resens_bark [b1AR_S464] ↔ [L_b1AR];  
 
 bind_PKAC_AKAR [AKAR] + [PKAC] ↔ [PKAC_AKAR];  
 
 inhibit_PDE [PDE] + [IBMX] ↔ [PDE_IBMX];  
 
 AKARp_dephosph [PP_AKARp] ↔ [PP] + [AKAR];  
 
 AKAR_phosph [PKAC_AKAR] ↔ [AKARp] + [PKAC];  
 
 RG_activation [b1AR_Gs] ↔ [Gsa_gtp] + [Gsbg] + [b1AR];  
 
 cAMP_degradation [PDEcAMP] ↔ [PDE];  
 
Rules (8)
 
 Assignment Rule (name: Vmax_cAMP_synthesis_GsAC) Vmax_cAMP_synthesis_GsAC = k_ac_gsa_cAMP_synthesis_GsAC*GsAC_cell
 
 Assignment Rule (name: light_cAMP_photolysis) light_cAMP_photolysis = piecewise(1, (t > ton_global_light_cAMP_photolysis) && (t < toff_global_light_cAMP_photolysis), 0)+piecewise(light_spot_cell, (t > ton_local_light_cAMP_photolysis) && (t < toff_local_light_cAMP_photolysis), 0)
 
 Assignment Rule (name: Vmax_cAMP_synthesis_FskAC) Vmax_cAMP_synthesis_FskAC = kfsk_cAMP_synthesis_FskAC*FskAC_cell
 
 Assignment Rule (name: Kf_inhibit_PDE) Kf_inhibit_PDE = piecewise(1000, t > 1000, 0)
 
 Assignment Rule (name: Kr_inhibit_PDE) Kr_inhibit_PDE = piecewise(30000, t > 1000, 0)
 
 Assignment Rule (name: ar_for_add_propranolol) ar_for_add_propranolol = piecewise((Propranolol_pipette+(-Propranolol_cell))*1/tauPropranolol, t > t_propadd, 0)
 
 Assignment Rule (name: ar_for_add_Ligand) ar_for_add_Ligand = piecewise((L_pipette+(-L_cell))*1/tauL, t > t_Ladd, 0)
 
 Assignment Rule (name: Ratio_AKARp_AKARtot) Ratio_AKARp_AKARtot = AKARp_cell/(AKAR_cell+AKARp_cell+PKAC_AKAR_cell+PP_AKARp_cell)
 
 ec Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 cell Spatial dimensions: 3.0  Compartment size: 0.25  (Units: litre)
 
 Gsbg
Compartment: cell
Initial concentration: 0.0
 
 L
Compartment: cell
Initial concentration: 0.0
 
 Gsa_gdp
Compartment: cell
Initial concentration: 0.0
 
 Gsa_gtp
Compartment: cell
Initial concentration: 0.0
 
 b1AR_S464
Compartment: cell
Initial concentration: 0.0
 
 PDEcAMP
Compartment: cell
Initial concentration: 0.0
 
 PDE
Compartment: cell
Initial concentration: 0.014
 
 ATP
Compartment: cell
Initial concentration: 5000.0
 
 b1AR
Compartment: cell
Initial concentration: 0.0132
 
 Gs
Compartment: cell
Initial concentration: 3.83
 
 A2RC
Compartment: cell
Initial concentration: 0.0
 
 A2R
Compartment: cell
Initial concentration: 0.0
 
 PKAC
Compartment: cell
Initial concentration: 0.0
 
 ARC
Compartment: cell
Initial concentration: 0.0
 
 PKAC_AKAR
Compartment: cell
Initial concentration: 0.0
 
 Propranolol
Compartment: cell
Initial concentration: 0.0
 
 b1ARinhib
Compartment: cell
Initial concentration: 0.0
 
 light_spot
Compartment: cell
Initial concentration: 0.0
 
 AC
Compartment: cell
Initial concentration: 0.0497
 
 PKI
Compartment: cell
Initial concentration: 0.18
 
 PKAC_PKI
Compartment: cell
Initial concentration: 0.0
 
 RC
Compartment: cell
Initial concentration: 1.18
 
 b1AR_Gs
Compartment: cell
Initial concentration: 0.0
 
 cAMP
Compartment: cell
Initial concentration: 0.0
 
 GsAC
Compartment: cell
Initial concentration: 0.0
 
 IBMX
Compartment: cell
Initial concentration: 0.0
 
 PDE_IBMX
Compartment: cell
Initial concentration: 0.0
 
 Fsk
Compartment: cell
Initial concentration: 0.0
 
 FskAC
Compartment: cell
Initial concentration: 0.0
 
 b1AR_p
Compartment: cell
Initial concentration: 0.0
 
 L_b1AR
Compartment: cell
Initial concentration: 0.0
 
 AKAR
Compartment: cell
Initial concentration: 10.0
 
 AKARp
Compartment: cell
Initial concentration: 0.0
 
 PP
Compartment: cell
Initial concentration: 0.67
 
 PP_AKARp
Compartment: cell
Initial concentration: 0.0
 
 DMNB_cAMP
Compartment: cell
Initial concentration: 3.01
 
 L_b1AR_Gs
Compartment: cell
Initial concentration: 0.0
 
 membrane Spatial dimensions: 2.0  Compartment size: 0.25  (Units: um2)
Global Parameters (20)
 
   k_ac_gsa_cAMP_synthesis_GsAC
Value: 2.5   (Units: s_1)
Constant
 
   Vmax_cAMP_synthesis_GsAC
Value: NaN   (Units: uM_s_1)
 
   ton_global_light_cAMP_photolysis
Value: 2160.0   (Units: s)
Constant
 
   toff_global_light_cAMP_photolysis
Value: 2165.0   (Units: s)
Constant
 
   ton_local_light_cAMP_photolysis
Constant
 
   toff_local_light_cAMP_photolysis
Constant
 
   light_cAMP_photolysis
Value: NaN   (Units: uM)
 
   kfsk_cAMP_synthesis_FskAC
Value: 7.3   (Units: s_1)
Constant
 
   Vmax_cAMP_synthesis_FskAC
Value: NaN   (Units: uM_s_1)
 
   Kf_inhibit_PDE
Value: NaN   (Units: uM_1_s_1)
 
   Kr_inhibit_PDE
Value: NaN   (Units: s_1)
 
   ar_for_add_propranolol  
 
   t_propadd
Value: 2420.0
Constant
 
   Propranolol_pipette
Value: 1.0
Constant
 
   tauPropranolol
Value: 1.0
Constant
 
   ar_for_add_Ligand  
 
   t_Ladd
Value: 2160.0
Constant
 
   L_pipette
Value: 0.1
Constant
 
   tauL
Value: 1.0
Constant
 
   Ratio_AKARp_AKARtot  
 
cAMP_synthesis_GsAC (1)
 
   Km
Value: 315.0   (Units: uM)
Constant
 
bind_b1AR_propranolol (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 8.0   (Units: s_1)
Constant
 
cAMP_photolysis (1)
 
   kphot
Value: 0.1   (Units: uM_1_s_1)
Constant
 
LRG_activation (1)
 
   k_gact
Value: 16.0   (Units: s_1)
Constant
 
bind_Lb1AR_Gs (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 62.0   (Units: s_1)
Constant
 
desens_bark (1)
 
   k_barkp
Value: 0.0011   (Units: s_1)
Constant
 
bind_cAMP_ARC (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 1640.0   (Units: s_1)
Constant
 
bind_b1AR_Gs (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 33000.0   (Units: s_1)
Constant
 
bind_PDEcAMP (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 1300.0   (Units: s_1)
Constant
 
Gs_gtp_hydrolysis (1)
 
   khyd
Value: 0.8   (Units: s_1)
Constant
 
Gs_reassociation (1)
 
   k_reassoc
Value: 1210.0   (Units: uM_1_s_1)
Constant
 
bind_FskAC (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 860000.0   (Units: s_1)
Constant
 
bind_AKARp_PP (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 7000.0   (Units: s_1)
Constant
 
desens_pka (2)
 
   kpkap
Value: 0.0036   (Units: uM_1_s_1)
Constant
 
   kpkam
Value: 0.0022   (Units: s_1)
Constant
 
bind_L_b1ARGs (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kd
Value: 0.535714   (Units: s_1)
Constant
 
bind_L_b1AR (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 285.0   (Units: s_1)
Constant
 
bind_A2R_PKAC (2)
 
   Kf
Value: 4375.0   (Units: s_1)
Constant
 
   Kr
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
inhib_PKAC (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.2   (Units: s_1)
Constant
 
bind_RC_cAMP (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 9140.0   (Units: s_1)
Constant
 
cAMP_synthesis_FskAC (1)
 
   Km
Value: 860.0   (Units: uM)
Constant
 
bind_Gs_AC (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 400.0   (Units: s_1)
Constant
 
resens_bark (1)
 
   k_barkm
Value: 0.0022   (Units: s_1)
Constant
 
bind_PKAC_AKAR (2)
 
   Kf
Value: 1000.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 21000.0   (Units: s_1)
Constant
 
AKARp_dephosph (1)
 
   kcat_PP_AKARp
Value: 8.5   (Units: s_1)
Constant
 
AKAR_phosph (1)
 
   kpka_akar
Value: 54.0   (Units: s_1)
Constant
 
RG_activation (1)
 
   k_gact
Value: 16.0   (Units: s_1)
Constant
 
cAMP_degradation (1)
 
   kpde
Value: 5.0   (Units: s_1)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000165

Curator's comment: (updated: 31 Jan 2008 17:12:18 GMT)

The plot corresponds to Fig 2B of the paper. Model reproduced using MathSBML.

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