Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Gs_a_PM+AC_PMAC_Gsa_PM 04: Gs-AC binding PM GeneralKinetics
ATP_cellcAMP_cell 05b: cAMP production PM HMMIrreversible
R2C2_cell+cAMP_cellcAMP_R2C2_cell cAMP bind R2C2 cell MassAction
MAPK_active_nucleusMAPK_thr_nucleus MKP2 deact MAPKact nucleus HMMIrreversible
Rap1GAP_cell+Rap1_GTP_GMRap1_RGII_GM 10a: Rap1-RGII binding GM MassAction
cAMP_R2C2_cell+cAMP_cellcAMP2_R2C2_cell cAMP_binds_cAMPR2C2 cell MassAction
Gs_a_PMGsa_GDP_PM Gs GTPase PM GeneralKinetics
Rap1_RGII_GMRap1_GDP_GM+Rap1GAP_cell 10: Rap1 GTPase GM GeneralKinetics
MAPKK_Ser_cellMAPKK_cell PP2A_inact_MAPKKSer cell HMMIrreversible
MAPK_cellMAPK_Thr_cell MAPKK_act_MAPK cell HMMIrreversible
MKP1_RNA_cellMKP1_cell MKP_translation cell MassAction
MAPKK_Ser_cellMAPKK_active_cell reaction1 cell GeneralKinetics
PDE_star_cellPDE_cell PP2A_dephos_PDEstar cell HMMIrreversible
GRK_Gbg_PMGRK_PM+G_bg_PM GRK PM recruitment PM MassAction
PKI_nucleus+PKA_nucleusinhibitedPKA_nucleus PKA inhibition by PKI nucleus MassAction
cAMP_cell+cAMP2_R2C2_cellcAMP3_R2C2_cell cAMP_bind_cAMP2R2C2 cell MassAction
CREB_Ser_nucleusCREB_nucleus Pp2A_deact_CREB nucleus HMMIrreversible
beta_isop_PM+Gs_trimer_PMbetaAR_Gs_PM 2: ARbeta-Gs binding PM MassAction
MKP1gene_nucleusMKP1_RNA_nucleus MAPK_act_MKPtranscription nucleus HMMIrreversible
cAMP_cellAMP_cell PDEstar_deact_cAMP cell HMMIrreversible
beta_isop_PMbeta_P_PM 03: GRK activity PM GeneralKinetics
cAMP4_R2C_cellcAMP4_R2_cell+PKA_cell Release of C2 cell MassAction
MKP1gene_nucleusMKP1_RNA_nucleus MKP1 basal transcription nucleus MassAction
MAPK_Thr_cellMAPK_cell reaction0 cell HMMIrreversible
MAPK_active_cellMAPK_Thr_cell reaction3 cell HMMIrreversible
MAPK_Thr_cellMAPK_cell MKP_decat_MAPKtyr cell HMMIrreversible
MAPKK_Ser_cellMAPKK_active_cell RapRaf_act_MAPKKSer GM HMMIrreversible
MKP1p_cell MKP1p turnover cell MassAction
MKP1p_cellMKP1_cell MKP1 dephosph cell MassAction
MAPK_active_cellMAPK_Thr_cell MKP1p_deact_MAPKactive cell HMMIrreversible
betaAR_Gs_PMbeta_isop_PM+Gs_a_PM+G_bg_PM 02b: Gs activation PM MassAction
BRaf_cell+Rap1_GTP_GMRap1_BRaf_GM Rap1_binds_BRaf GM MassAction
MAPKK_cellMAPKK_Ser_cell BRaf_act_MAPKK cell HMMIrreversible
BRaf_star_cellBRaf_cell PP_deact_BRaf cell HMMIrreversible
BRaf_cellBRaf_star_cell PKA_act_BRaf cell GeneralKinetics
cAMP3_R2C2_cell+cAMP_cellcAMP4_R2C2_cell cAMP_binds_A2 cell MassAction
GRK_PMGRK_cell GRK to cytosol PM MassAction
Rap1_Epac_GMEpac_cAMP_cell+Rap1_GTP_GM 08: Epac exchange GM GeneralKinetics
cAMP4_R2C2_cellcAMP4_R2C_cell+PKA_cell Release of C1 cell MassAction
MAPKK_cellMAPKK_Ser_cell Rap1raf_act_MAPKK GM GeneralKinetics
MKP1_cellMKP1p_cell MKP1 phospho by MAPKactive cell HMMIrreversible
MKP1p_nucleus MKP1p turnover nucleus nucleus MassAction
cAMP_cellAMP_cell 07: PDE cell HMMIrreversible
MAPK_active_nucleusMAPK_thr_nucleus MKP1p deact MAPKact nucleus HMMIrreversible
MKP1_nucleus MKP1 turnover in nucleus nucleus MassAction
isoprenaline_ec+beta_PMbeta_isop_PM 01b: isoprenaline binding PM MassAction
PTPSL_star_cellPTPSL_cell PTPSL_dephos cell HMMIrreversible
MAPK_Thr_cellMAPK_active_cell MAPKK_act_MAPK_thr cell HMMIrreversible
beta_P_PMbeta_PM Receptor recycling PM MassAction
PDE_cellPDE_star_cell PKA_act_PDE cell HMMIrreversible
MAPKK_active_cellMAPKK_Ser_cell PP2A_inact_MAPKK_active cell HMMIrreversible
MAPK_active_cellMAPK_Thr_cell MAPK dephosph by PTP cell HMMIrreversible
G_bg_PM+GRK_cellGRK_Gbg_PM GRK-Gbg binding PM MassAction
MAPK_Thr_cellMAPK_cell MKPp_decat_MAPKtyr cell HMMIrreversible
inhibitedPKA_cellPKI_cell+PKA_cell PKA release by PKI cell MassAction
Rap1_GDP_GM+Epac_cAMP_cellRap1_Epac_GM 8a: Rap1-Epac binding GM MassAction
cAMP_cell+Epac_cellEpac_cAMP_cell Epac-cAMP binding cell MassAction
CREB_nucleusCREB_Ser_nucleus PKA_act_CREB nucleus HMMIrreversible
PTPSL_cellPTPSL_star_cell PKA_deact_PTPSL cell HMMIrreversible
CREB_nucleusCREB_Ser_nucleus MSK_act_CREB nucleus HMMIrreversible
cAMP_cellAMP_cell PDE_highKm deact cAMP cell HMMIrreversible
MSK_active_nucleusMSK_nucleus MSK_dephos nucleus MassAction
Rap1_GDP_GMRap1_GTP_GM constit exch+hydrolysis GM MassAction
MAPK_thr_nucleusMAPK_nucleus MKP1p deact MAPKtyr nucleus HMMIrreversible
CREB_Ser_nucleusCREB_nucleus PP1A_dephos_CREB nucleus HMMIrreversible
MAPK_active_nucleusMAPK_thr_nucleus MKP1 deact MAPKact nucleus HMMIrreversible
Gsa_GDP_PM+G_bg_PMGs_trimer_PM 14b: Gs trimerization PM MassAction
MAPK_thr_nucleusMAPK_nucleus MKP1 deact MAPKtyr nucleus HMMIrreversible
MSK_nucleusMSK_active_nucleus reaction2 nucleus HMMIrreversible
MKP1_cell MKP1 turnover cell MassAction
MAPK_thr_nucleusMAPK_nucleus MKP2 deact MAPK tyr nucleus HMMIrreversible
MKP1_nucleusMKP1p_nucleus MKP1 phosph by MAPKactive_nucleus nucleus HMMIrreversible
MKP1p_nucleusMKP1_nucleus MKP1 dephosph in nucleus nucleus MassAction
MAPK_active_cellMAPK_Thr_cell MKP1_deact_MAPKactive cell HMMIrreversible

Structures

Name
Type
Electrical
GM Membrane golgi(+)   cell(-)
PM Membrane cell(+)   ec(-)
nuclear membrane Membrane nucleus(+)   cell(-)
golgi Compartment (+)   (-)
cell Compartment (+)   (-)
ec Compartment (+)   (-)
nucleus Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
MSK_active_nucleus nucleus nucleus
AMP_cell cell cell
BRaf_cell cell cell
MAPK_act_cell cell cell
cAMP4_R2C2_cell cell cell
cAMP4_R2C_cell cell cell
cAMP4_R2_cell cell cell
MAPK_nucleus nucleus nucleus
MKP1_nucleus nucleus nucleus
MKP2_nucleus nucleus nucleus
MAPK_thr_nucleus nucleus nucleus
MKP1p_cell cell cell
MKP1p_nucleus nucleus nucleus
MKP2_cell cell cell
G_bg_PM PM PM
Rap1_RGII_GM GM GM
Gsa_GDP_PM PM PM
beta_isop_PM PM PM
PDE_star_cell cell cell
isoprenaline_ec ec ec
MKP1gene_nucleus nucleus nucleus
MSK_nucleus nucleus nucleus
R2C2_cell cell cell
PP2A_cell cell cell
MAPK_active_nucleus nucleus nucleus
cAMP_R2C2_cell cell cell
Rap1_GDP_GM GM GM
beta_PM PM PM
Epac_cAMP_cell cell cell
beta_P_PM PM PM
Rap1_Epac_GM GM GM
MKP1_RNA_nucleus nucleus nucleus
cAMP2_R2C2_cell cell cell
PKA_cell cell cell
MAPKK_Ser_cell cell cell
PKI_cell cell cell
inhibitedPKA_nucleus nucleus nucleus
inhibitedPKA_cell cell cell
Gs_trimer_PM PM PM
GRK_Gbg_PM PM PM
Gs_a_PM PM PM
MAPK_active_cell cell cell
Rap1GAP_cell cell cell
MAPKK_cell cell cell
cAMP3_R2C2_cell cell cell
cAMP_cell cell cell
PP1_cell cell cell
PP1A_nucleus nucleus nucleus
CREB_Ser_nucleus nucleus nucleus
PTPSL_star_cell cell cell
Epac_cell cell cell
MKP1_RNA_cell cell cell
Rap1_BRaf_GM GM GM
MAPKK_active_cell cell cell
PKI_nucleus nucleus nucleus
GRK_cell cell cell
AC_PM PM PM
AC_Gsa_PM PM PM
PDE_cell cell cell
Rap1_GTP_GM GM GM
pp2a_nucleus nucleus nucleus
CREB_nucleus nucleus nucleus
PTPSL_cell cell cell
MAPK_Thr_cell cell cell
PDE_PP_cell cell cell
PDE_highKm_cell cell cell
GRK_PM PM PM
betaAR_Gs_PM PM PM
BRaf_star_cell cell cell
PKA_nucleus nucleus nucleus
MAPK_cell cell cell
ATP_cell cell cell
MKP1_cell cell cell

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Compart Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Compartmental cloned from 'Compart' owned by user eungdamr cloned from 'Compart' owned by user argh

Specifications (Species) - Compart go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
AMP_cell 1.0E-6 [uM] 0.0 [um2/s] cell
BRaf_cell 0.2 [uM] 0.0 [um2/s] cell
MAPK_act_cell 0.0 [uM] 0.0 [um2/s] cell
cAMP4_R2C2_cell 0.0 [uM] 0.0 [um2/s] cell
cAMP4_R2C_cell 0.0 [uM] 0.0 [um2/s] cell
cAMP4_R2_cell 0.0 [uM] 0.0 [um2/s] cell
MKP1p_cell 0.0 [uM] 0.0 [um2/s] cell
MKP2_cell 0.001 [uM] 0.0 [um2/s] cell
PDE_star_cell 0.0 [uM] 0.0 [um2/s] cell
R2C2_cell 0.2 [uM] 0.0 [um2/s] cell
PP2A_cell 0.075 [uM] 0.0 [um2/s] cell
cAMP_R2C2_cell 0.0 [uM] 0.0 [um2/s] cell
Epac_cAMP_cell 1.0E-6 [uM] 0.0 [um2/s] cell
cAMP2_R2C2_cell 0.0 [uM] 0.0 [um2/s] cell
PKA_cell 0.0 [uM] 0.0 [um2/s] cell
MAPKK_Ser_cell 1.0E-6 [uM] 0.0 [um2/s] cell
PKI_cell 0.4 [uM] 0.0 [um2/s] cell
inhibitedPKA_cell 0.0 [uM] 0.0 [um2/s] cell
MAPK_active_cell 0.0 [uM] 0.0 [um2/s] cell
Rap1GAP_cell 0.15 [uM] 0.0 [um2/s] cell
MAPKK_cell 0.18 [uM] 0.0 [um2/s] cell
cAMP3_R2C2_cell 0.0 [uM] 0.0 [um2/s] cell
cAMP_cell 1.0E-4 [uM] 0.0 [um2/s] cell
PP1_cell 0.04 [uM] 0.0 [um2/s] cell
PTPSL_star_cell 0.0 [uM] 0.0 [um2/s] cell
Epac_cell 0.16 [uM] 0.0 [um2/s] cell
MKP1_RNA_cell 4.0E-5 [uM] 0.0 [um2/s] cell
MAPKK_active_cell 1.0E-6 [uM] 0.0 [um2/s] cell
GRK_cell 0.045 [uM] 0.0 [um2/s] cell
PDE_cell 0.4 [uM] 0.0 [um2/s] cell
PTPSL_cell 0.01 [uM] 0.0 [um2/s] cell
MAPK_Thr_cell 0.0 [uM] 0.0 [um2/s] cell
PDE_PP_cell 0.2 [uM] 0.0 [um2/s] cell
PDE_highKm_cell 0.5 [uM] 0.0 [um2/s] cell
BRaf_star_cell 0.0 [uM] 0.0 [um2/s] cell
MAPK_cell 0.263 [uM] 0.0 [um2/s] cell
ATP_cell 4000.0 [uM] 0.0 [um2/s] cell
MKP1_cell 3.6E-4 [uM] 0.0 [um2/s] cell
isoprenaline_ec 10.0 [uM] 0.0 [um2/s] ec
MSK_active_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
MAPK_nucleus 0.233 [uM] 0.0 [um2/s] nucleus
MKP1_nucleus 2.2E-4 [uM] 0.0 [um2/s] nucleus
MKP2_nucleus 1.0E-4 [uM] 0.0 [um2/s] nucleus
MAPK_thr_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
MKP1p_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
MKP1gene_nucleus 0.2 [uM] 0.0 [um2/s] nucleus
MSK_nucleus 0.1 [uM] 0.0 [um2/s] nucleus
MAPK_active_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
MKP1_RNA_nucleus 6.5E-7 [uM] 0.0 [um2/s] nucleus
inhibitedPKA_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
PP1A_nucleus 0.04 [uM] 0.0 [um2/s] nucleus
CREB_Ser_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
PKI_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
pp2a_nucleus 0.05 [uM] 0.0 [um2/s] nucleus
CREB_nucleus 0.3 [uM] 0.0 [um2/s] nucleus
PKA_nucleus 0.0 [uM] 0.0 [um2/s] nucleus
Rap1_RGII_GM 0.0 [uM] 0.0 [um2/s] GM
Rap1_GDP_GM 100.0 [uM] 0.0 [um2/s] GM
Rap1_Epac_GM 0.0 [uM] 0.0 [um2/s] GM
Rap1_BRaf_GM 0.0 [uM] 0.0 [um2/s] GM
Rap1_GTP_GM 0.0 [uM] 0.0 [um2/s] GM
G_bg_PM 0.0 [uM] 0.0 [um2/s] PM
Gsa_GDP_PM 1.0E-6 [uM] 0.0 [um2/s] PM
beta_isop_PM 1.0E-6 [uM] 0.0 [um2/s] PM
beta_PM 33.0 [uM] 0.0 [um2/s] PM
beta_P_PM 1.0E-6 [uM] 0.0 [um2/s] PM
Gs_trimer_PM 100.0 [uM] 0.0 [um2/s] PM
GRK_Gbg_PM 0.0 [uM] 0.0 [um2/s] PM
Gs_a_PM 1.0E-6 [uM] 0.0 [um2/s] PM
AC_PM 100.0 [uM] 0.0 [um2/s] PM
AC_Gsa_PM 1.0E-6 [uM] 0.0 [um2/s] PM
GRK_PM 1.0E-6 [uM] 0.0 [um2/s] PM
betaAR_Gs_PM 0.0 [uM] 0.0 [um2/s] PM

Specifications (Reaction) - Compart go to Simulations

Name
Enabled?
04: Gs-AC binding included
05b: cAMP production included
cAMP bind R2C2 included
MKP2 deact MAPKact included
10a: Rap1-RGII binding included
cAMP_binds_cAMPR2C2 included
Gs GTPase included
10: Rap1 GTPase included
PP2A_inact_MAPKKSer included
MAPKK_act_MAPK included
MKP_translation included
reaction1 included
PP2A_dephos_PDEstar included
GRK PM recruitment included
PKA inhibition by PKI included
cAMP_bind_cAMP2R2C2 included
Pp2A_deact_CREB included
2: ARbeta-Gs binding included
MAPK_act_MKPtranscription included
PDEstar_deact_cAMP included
03: GRK activity included
Release of C2 included
MKP1 basal transcription included
reaction0 included
reaction3 included
MKP_decat_MAPKtyr included
RapRaf_act_MAPKKSer included
MKP1p turnover included
MKP1 dephosph included
MKP1p_deact_MAPKactive included
02b: Gs activation included
Rap1_binds_BRaf included
BRaf_act_MAPKK included
PP_deact_BRaf included
PKA_act_BRaf included
cAMP_binds_A2 included
GRK to cytosol included
08: Epac exchange included
Release of C1 included
Rap1raf_act_MAPKK included
MKP1 phospho by MAPKactive included
MKP1p turnover nucleus included
07: PDE included
MKP1p deact MAPKact included
MKP1 turnover in nucleus included
01b: isoprenaline binding included
PTPSL_dephos included
MAPKK_act_MAPK_thr included
Receptor recycling included
PKA_act_PDE included
PP2A_inact_MAPKK_active included
MAPK dephosph by PTP included
GRK-Gbg binding included
MKPp_decat_MAPKtyr included
PKA release by PKI included
8a: Rap1-Epac binding included
Epac-cAMP binding included
PKA_act_CREB included
PKA_deact_PTPSL included
MSK_act_CREB included
PDE_highKm deact cAMP included
MSK_dephos included
constit exch+hydrolysis included
MKP1p deact MAPKtyr included
PP1A_dephos_CREB included
MKP1 deact MAPKact included
14b: Gs trimerization included
MKP1 deact MAPKtyr included
reaction2 included
MKP1 turnover included
MKP2 deact MAPK tyr included
MKP1 phosph by MAPKactive_nucleus included
MKP1 dephosph in nucleus included
MKP1_deact_MAPKactive included
PKI translocation included
MKP1p translocation included
MAPK translocation included
MKP1 translocation included
MAPKactive_translocation included
PKA_translocation included
inhibited PKA export included
MKPRNA_export included

Simulations - Compart go to Specifications

Name
End Time
Output Options
1) MAPK phospho MSK Km 3000.0

KeepEvery 1

KeepAtMost 1000

1) MAPK phospho MSK kcat 3000.0

KeepEvery 1

KeepAtMost 1000

2) MSK dephospho 3000.0

KeepEvery 1

KeepAtMost 1000

3) PKA phospho CREB Km 3000.0

KeepEvery 1

KeepAtMost 1000

3) PKA phospho CREB kcat 3000.0

KeepEvery 1

KeepAtMost 1000

4) MSK phospho CREB Km 3000.0

KeepEvery 1

KeepAtMost 1000

4) MSK phospho CREB kcat 3000.0

KeepEvery 1

KeepAtMost 1000

5) PP2A dephosho CREB Km 3000.0

KeepEvery 1

KeepAtMost 1000

5) PP2A dephosho CREB kcat 3000.0

KeepEvery 1

KeepAtMost 1000

6) PP1A dephospho CREB Km 3000.0

KeepEvery 1

KeepAtMost 1000

6) PP1A dephospho CREB kcat 3000.0

KeepEvery 1

KeepAtMost 1000

7) MKP1 gene activation Km 3000.0

KeepEvery 1

KeepAtMost 1000

7) MKP1 gene activation kcat 3000.0

KeepEvery 1

KeepAtMost 1000

8) MKP1 basal transcription 3000.0

KeepEvery 1

KeepAtMost 1000

9) MAPK_act dephospho by MKP2 Km 3000.0

KeepEvery 1

KeepAtMost 1000

9) MAPK_act dephospho by MKP2 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

10) MAPK_act dephospho by MKP1 Km 3000.0

KeepEvery 1

KeepAtMost 1000

10) MAPK_act dephospho by MKP1 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

11) MAPK_act dephospho by MKP1* Km 3000.0

KeepEvery 1

KeepAtMost 1000

11) MAPK_act dephospho by MKP1* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

12) MAPK_tyr dephospho by MKP2 Km 3000.0

KeepEvery 1

KeepAtMost 1000

12) MAPK_tyr dephospho by MKP2 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

13) MAPK_tyr dephospho by MKP Km 3000.0

KeepEvery 1

KeepAtMost 1000

13) MAPK_tyr dephospho by MKP kcat 3000.0

KeepEvery 1

KeepAtMost 1000

14) MAPK_tyr dephospho by MKP1* Km 3000.0

KeepEvery 1

KeepAtMost 1000

14) MAPK_tyr dephospho by MKP1* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

15) MKP1 phospho by MAPK Km 3000.0

KeepEvery 1

KeepAtMost 1000

15) MKP1 phospho by MAPK kcat 3000.0

KeepEvery 1

KeepAtMost 1000

16) MKP1* dephospho kf 3000.0

KeepEvery 1

KeepAtMost 1000

17) MKP1 turnover kf 3000.0

KeepEvery 1

KeepAtMost 1000

18) MKP1* turnover kf 3000.0

KeepEvery 1

KeepAtMost 1000

19) PKI + PKA kf 3000.0

KeepEvery 1

KeepAtMost 1000

19) PKI + PKA kr 3000.0

KeepEvery 1

KeepAtMost 1000

20) MKP1 translation kf 3000.0

KeepEvery 1

KeepAtMost 1000

21) MEK phospho by Braf* Km 3000.0

KeepEvery 1

KeepAtMost 1000

21) MEK phospho by Braf* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

22) MEK_ser phospho by Braf* Km 3000.0

KeepEvery 1

KeepAtMost 1000

22) MEK_ser phospho by Braf* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

23) MAPK phospho by MEK* Km 3000.0

KeepEvery 1

KeepAtMost 1000

23) MAPK phospho by MEK* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

24) MAPK_tyr phospho by MEK* Km 3000.0

KeepEvery 1

KeepAtMost 1000

24) MAPK_tyr phospho by MEK* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

25) cAMP degradation by PDE Km 3000.0

KeepEvery 1

KeepAtMost 1000

25) cAMP degradation by PDE kcat 3000.0

KeepEvery 1

KeepAtMost 1000

26) cAMP degradation by PDE* Km 3000.0

KeepEvery 1

KeepAtMost 1000

26) cAMP degradation by PDE* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

27) cAMP degradation by PDE_high Km 3000.0

KeepEvery 1

KeepAtMost 1000

27) cAMP degradation by PDE_high kcat 3000.0

KeepEvery 1

KeepAtMost 1000

28) Braf phospho by PKA Km 3000.0

KeepEvery 1

KeepAtMost 1000

28) Braf phospho by PKA kcat 3000.0

KeepEvery 1

KeepAtMost 1000

29) Braf dephospho by PP2A Km 3000.0

KeepEvery 1

KeepAtMost 1000

29) Braf dephospho by PP2A kcat 3000.0

KeepEvery 1

KeepAtMost 1000

30) PTP phospho by PKA Km 3000.0

KeepEvery 1

KeepAtMost 1000

30) PTP phospho by PKA kcat 3000.0

KeepEvery 1

KeepAtMost 1000

31) PTP dephospho by PP1 Km 3000.0

KeepEvery 1

KeepAtMost 1000

31) PTP dephospho by PP1 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

32) MEK* dephospho by PP2A Km 3000.0

KeepEvery 1

KeepAtMost 1000

32) MEK* dephospho by PP2A kcat 3000.0

KeepEvery 1

KeepAtMost 1000

33) MEK_ser dephospho by PP2A Km 3000.0

KeepEvery 1

KeepAtMost 1000

33) MEK_ser dephospho by PP2A kcat 3000.0

KeepEvery 1

KeepAtMost 1000

34) MAPK* dephospho by MKP1 Km 3000.0

KeepEvery 1

KeepAtMost 1000

34) MAPK* dephospho by MKP1 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

35) MAPK_tyr dephospho by MKP1 Km 3000.0

KeepEvery 1

KeepAtMost 1000

35) MAPK_tyr dephospho by MKP1 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

36) MAPK* dephospho by MKP1* Km 3000.0

KeepEvery 1

KeepAtMost 1000

36) MAPK* dephospho by MKP1* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

37) MAPK_tyr dephospho by MKP1* Km 3000.0

KeepEvery 1

KeepAtMost 1000

37) MAPK_tyr dephospho by MKP1* kcat 3000.0

KeepEvery 1

KeepAtMost 1000

38) MAPK* dephospho by MKP2 Km 3000.0

KeepEvery 1

KeepAtMost 1000

38) MAPK* dephospho by MKP2 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

39) MAPK_tyr dephospho by MKP2 Km 3000.0

KeepEvery 1

KeepAtMost 1000

39) MAPK_tyr dephospho by MKP2 kcat 3000.0

KeepEvery 1

KeepAtMost 1000

40) MAPK* dephospho by PTP Km 3000.0

KeepEvery 1

KeepAtMost 1000

40) MAPK* dephospho by PTP kcat 3000.0

KeepEvery 1

KeepAtMost 1000

41) MKP1 phospho by MAPK* cyto Km 3000.0

KeepEvery 1

KeepAtMost 1000

41) MKP1 phospho by MAPK* cyto kcat 3000.0

KeepEvery 1

KeepAtMost 1000

42) MKP1* dephospho cyto kf 3000.0

KeepEvery 1

KeepAtMost 1000

43) MKP1 degradation kf 3000.0

KeepEvery 1

KeepAtMost 1000

44) MKP1* degradation kf 3000.0

KeepEvery 1

KeepAtMost 1000

45) PDE phospho by PKA Km 3000.0

KeepEvery 1

KeepAtMost 1000

45) PDE phospho by PKA kcat 3000.0

KeepEvery 1

KeepAtMost 1000

46) PDE* dephospho Km 3000.0

KeepEvery 1

KeepAtMost 1000

46) PDE* dephospho kcat 3000.0

KeepEvery 1

KeepAtMost 1000

47) R2C2 1 kf 3000.0

KeepEvery 1

KeepAtMost 1000

47) R2C2 1 kr 3000.0

KeepEvery 1

KeepAtMost 1000

48) R2C2 2 kf 3000.0

KeepEvery 1

KeepAtMost 1000

48) R2C2 2 kr 3000.0

KeepEvery 1

KeepAtMost 1000

49) R2C2 3 kf 3000.0

KeepEvery 1

KeepAtMost 1000

49) R2C2 3 kr 3000.0

KeepEvery 1

KeepAtMost 1000

50) R2C2 4 kf 3000.0

KeepEvery 1

KeepAtMost 1000

50) R2C2 4 kr 3000.0

KeepEvery 1

KeepAtMost 1000

51) PKA release 1 kf 3000.0

KeepEvery 1

KeepAtMost 1000

51) PKA release 1 kr 3000.0

KeepEvery 1

KeepAtMost 1000

52) PKA release 2 kf 3000.0

KeepEvery 1

KeepAtMost 1000

52) PKA release 2 kr 3000.0

KeepEvery 1

KeepAtMost 1000

53) PKA release by PKI kf 3000.0

KeepEvery 1

KeepAtMost 1000

54) EPAC activated by cAMP kf 3000.0

KeepEvery 1

KeepAtMost 1000

54) EPAC activated by cAMP kr 3000.0

KeepEvery 1

KeepAtMost 1000

55) MEK phospho by RapRaf Km 3000.0

KeepEvery 1

KeepAtMost 1000

55) MEK phospho by RapRaf kcat 3000.0

KeepEvery 1

KeepAtMost 1000

56) MEK_ser phospho by RapRaf Km 3000.0

KeepEvery 1

KeepAtMost 1000

56) MEK_ser phospho by RapRaf kcat 3000.0

KeepEvery 1

KeepAtMost 1000

57) Braf activation by Rap kf 3000.0

KeepEvery 1

KeepAtMost 1000

57) Braf activation by Rap kr 3000.0

KeepEvery 1

KeepAtMost 1000

58) RapGDP - RapGTP kf 3000.0

KeepEvery 1

KeepAtMost 1000

58) RapGDP - RapGTP kr 3000.0

KeepEvery 1

KeepAtMost 1000

59) Rap1 activation by EPAC step 1 3000.0

KeepEvery 1

KeepAtMost 1000

59) Rap1 activation by EPAC step 2 3000.0

KeepEvery 1

KeepAtMost 1000

60) Rap1 activation by EPAC step 3 3000.0

KeepEvery 1

KeepAtMost 1000

61) Rap1 deactivation step 1 3000.0

KeepEvery 1

KeepAtMost 1000

61) Rap1 deactivation step 2 3000.0

KeepEvery 1

KeepAtMost 1000

62) Rap1 deactivation step 3 3000.0

KeepEvery 1

KeepAtMost 1000

63) cAMP production Km 3000.0

KeepEvery 1

KeepAtMost 1000

63) cAMP production kcat 3000.0

KeepEvery 1

KeepAtMost 1000

64) BAR phosphorylation Km 3000.0

KeepEvery 1

KeepAtMost 1000

64) BAR phosphorylation kcat 3000.0

KeepEvery 1

KeepAtMost 1000

65) BAR activation by ISO kf 3000.0

KeepEvery 1

KeepAtMost 1000

65) BAR activation by ISO kr 3000.0

KeepEvery 1

KeepAtMost 1000

66) Gtrimer binds to BAR kf 3000.0

KeepEvery 1

KeepAtMost 1000

66) Gtrimer binds to BAR kr 3000.0

KeepEvery 1

KeepAtMost 1000

67) Gprotein activation kf 3000.0

KeepEvery 1

KeepAtMost 1000

67) Gprotein activation kr 3000.0

KeepEvery 1

KeepAtMost 1000

68) GRK recruitment by Gbg kf 3000.0

KeepEvery 1

KeepAtMost 1000

68) GRK recruitment by Gbg kr 3000.0

KeepEvery 1

KeepAtMost 1000

69) GRK on membrane kf 3000.0

KeepEvery 1

KeepAtMost 1000

69) GRK on membrane kr 3000.0

KeepEvery 1

KeepAtMost 1000

70) GRK to cytosol kf 3000.0

KeepEvery 1

KeepAtMost 1000

71) AC activation kf 3000.0

KeepEvery 1

KeepAtMost 1000

71) AC activation kr 3000.0

KeepEvery 1

KeepAtMost 1000

72) Gs deactivation kf 3000.0

KeepEvery 1

KeepAtMost 1000

73) G trimerization kf 3000.0

KeepEvery 1

KeepAtMost 1000

74) BAR recycling kf 3000.0

KeepEvery 1

KeepAtMost 1000

MAPK* import 3000.0

KeepEvery 1

KeepAtMost 1000

MAPK* export 3000.0

KeepEvery 1

KeepAtMost 1000

MAPK import 3000.0

KeepEvery 1

KeepAtMost 1000

MAPK export 3000.0

KeepEvery 1

KeepAtMost 1000

PKA import 3000.0

KeepEvery 1

KeepAtMost 1000

PKA export 3000.0

KeepEvery 1

KeepAtMost 1000

PKI.PKA export 3000.0

KeepEvery 1

KeepAtMost 1000

PKI import 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1 mRNA export 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1 import 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1 export 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1* import 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1* export 3000.0

KeepEvery 1

KeepAtMost 1000

Iso 3000.0

KeepEvery 1

KeepAtMost 1000

BAR 3000.0

KeepEvery 1

KeepAtMost 1000

Gs trimer 3000.0

KeepEvery 1

KeepAtMost 1000

AC 3000.0

KeepEvery 1

KeepAtMost 1000

MAPK 3000.0

KeepEvery 1

KeepAtMost 1000

R2C2 3000.0

KeepEvery 1

KeepAtMost 1000

ATP 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1 3000.0

KeepEvery 1

KeepAtMost 1000

bRaf 3000.0

KeepEvery 1

KeepAtMost 1000

Rap1GAP 3000.0

KeepEvery 1

KeepAtMost 1000

MEK 3000.0

KeepEvery 1

KeepAtMost 1000

EPAC 3000.0

KeepEvery 1

KeepAtMost 1000

PTP 3000.0

KeepEvery 1

KeepAtMost 1000

PP2A 3000.0

KeepEvery 1

KeepAtMost 1000

GRK 3000.0

KeepEvery 1

KeepAtMost 1000

PDE 3000.0

KeepEvery 1

KeepAtMost 1000

MKP2 3000.0

KeepEvery 1

KeepAtMost 1000

Rap1GDP 3000.0

KeepEvery 1

KeepAtMost 1000

MSK 3000.0

KeepEvery 1

KeepAtMost 1000

PP1A 3000.0

KeepEvery 1

KeepAtMost 1000

MKP1 DNA 3000.0

KeepEvery 1

KeepAtMost 1000

PP2A nucleus 3000.0

KeepEvery 1

KeepAtMost 1000

CREB 3000.0

KeepEvery 1

KeepAtMost 1000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1212631236

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment nuclear membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kimportPKI 0.001[um.s-1]
Km_Rap1BRaf 0.5[uM]
kcat_Rap1Braf 0.105[s-1]

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Compart.bngl
SBML Compart.sbml
Matlab Compart.m
NFSim XML Compart.xml