Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
cAMP cAMP_synth cytosol GeneralKinetics
A2RCA2R+PKAC PKA_act cytosol MassAction
cAMP cAMP_deg cytosol HMMIrreversible
RC+cAMPARC PKA_bind1 cytosol MassAction
AKARpAKAR AKAR_dephos cytosol GeneralKinetics
ARC+cAMPA2RC PKA_bind2 cytosol MassAction
ICUE+cAMPICUE_cAMP ICUE_bind cytosol MassAction
AKARAKARp AKAR_phos cytosol HMMIrreversible

cAMP_synth Universal ID's

cAMP_synth Text Annotations

PKA_act Universal ID's

PKA_act Text Annotations

cAMP_deg Universal ID's

cAMP_deg Text Annotations

PKA_bind1 Universal ID's

PKA_bind1 Text Annotations

AKAR_dephos Universal ID's

AKAR_dephos Text Annotations

PKA_bind2 Universal ID's

PKA_bind2 Text Annotations

ICUE_bind Universal ID's

ICUE_bind Text Annotations

AKAR_phos Universal ID's

AKAR_phos Text Annotations

Expressions for cAMP_synth

reaction rate

J

((Vmax * ATP / (Km + ATP)) + (Vmax_Iso * ATP / (Km_Iso + ATP))) [uM.s-1]

local

Km

860.0 [uM]

local

Vmax

(kfsk * AC_fsk) [uM.s-1]

local

ATP

5000.0 [uM]

local

Vmax_Iso

(kcat_iso * AC_iso) [uM.s-1]

local

Km_Iso

315.0 [uM]

local

kcat_iso

0.75 [s-1]

local

AC_iso

(AC * Iso / (Kd_iso + Iso)) [uM]

local

Iso

(Iso_stim * (t > t_iso)) [uM]

local

Kd_iso

0.1 [uM]

local

kfsk

7.3 [s-1]

local

AC_fsk

(AC * Fsk / (Kd_fsk + Fsk)) [uM]

local

Iso_stim

1.0 [uM]

local

t_iso

200.0 [s]

local

Kd_fsk

860.0 [uM]

local

Fsk

(FSK_stim * (t > t_FSK)) [uM]

local

FSK_stim

50.0 [uM]

local

t_FSK

600.0 [s]

Expressions for PKA_act

reaction rate

J

((Kf * A2RC) - ((Kr * A2R) * PKAC)) [uM.s-1]

forward rate constant

Kf

4375.0 [s-1]

reverse rate constant

Kr

1000.0 [s-1.uM-1]

Expressions for cAMP_deg

reaction rate

J

((Vmax * cAMP) / (Km + cAMP)) [uM.s-1]

Km (1/2 max)

Km

1.305 [uM]

max reaction rate

Vmax

(kcat * PDE_avail) [uM.s-1]

local

kcat

5.0 [s-1]

local

PDE_avail

(PDE * Ki / (Ki + IBMX)) [uM]

local

IBMX

(IBMX_stim * (t > t_IBMX)) [uM]

local

Ki

30.0 [uM]

local

t_IBMX

600.0 [s]

local

IBMX_stim

100.0 [uM]

Expressions for PKA_bind1

reaction rate

J

(((Kf * RC) * cAMP) - (Kr * ARC)) [uM.s-1]

forward rate constant

Kf

1000.0 [s-1.uM-1]

reverse rate constant

Kr

9140.0 [s-1]

Expressions for AKAR_dephos

reaction rate

J

(kcat * PPase * AKARp) [uM.s-1]

local

kcat

8.5 [uM-1.s-1]

local

PPase

2.14 [uM]

Expressions for PKA_bind2

reaction rate

J

(((Kf * ARC) * cAMP) - (Kr * A2RC)) [uM.s-1]

forward rate constant

Kf

1000.0 [s-1.uM-1]

reverse rate constant

Kr

1640.0 [s-1]

Expressions for ICUE_bind

reaction rate

J

(((Kf * ICUE) * cAMP) - (Kr * ICUE_cAMP)) [uM.s-1]

forward rate constant

Kf

5.0 [s-1.uM-1]

reverse rate constant

Kr

10.0 [s-1]

Expressions for AKAR_phos

reaction rate

J

((Vmax * AKAR) / (Km + AKAR)) [uM.s-1]

Km (1/2 max)

Km

21.0 [uM]

max reaction rate

Vmax

(kcat * PKAC) [uM.s-1]

local

kcat

54.0 [s-1]

Structures

Name
Type
Electrical
Membrane Membrane cytosol(+)   Extra Cellular(-)
Extra Cellular Compartment (+)   (-)
cytosol Compartment (+)   (-)

Membrane Universal ID's

Membrane Text Annotations

Extra Cellular Universal ID's

Extra Cellular Text Annotations

cytosol Universal ID's

cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
cAMP cytosol cytosol
AKAR cytosol cytosol
AC cytosol cytosol
RC cytosol cytosol
A2R cytosol cytosol
PDE cytosol cytosol
ARC cytosol cytosol
ICUE_cAMP cytosol cytosol
A2RC cytosol cytosol
AKARp cytosol cytosol
ICUE cytosol cytosol
PKAC cytosol cytosol

cAMP Universal ID's

cAMP Text Annotations

AKAR Universal ID's

AKAR Text Annotations

AC Universal ID's

AC Text Annotations

RC Universal ID's

RC Text Annotations

A2R Universal ID's

A2R Text Annotations

PDE Universal ID's

PDE Text Annotations

ARC Universal ID's

ARC Text Annotations

ICUE_cAMP Universal ID's

ICUE_cAMP Text Annotations

A2RC Universal ID's

A2RC Text Annotations

AKARp Universal ID's

AKARp Text Annotations

ICUE Universal ID's

ICUE Text Annotations

PKAC Universal ID's

PKAC Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cAMP 0.0 [uM] 0.0 [um2/s] cytosol
AKAR 1.25 [uM] 0.0 [um2/s] cytosol
AC 0.05 [uM] 0.0 [um2/s] cytosol
RC 1.0 [uM] 0.0 [um2/s] cytosol
A2R 0.0 [uM] 0.0 [um2/s] cytosol
PDE 0.014 [uM] 0.0 [um2/s] cytosol
ARC 0.0 [uM] 0.0 [um2/s] cytosol
ICUE_cAMP 0.0 [uM] 0.0 [um2/s] cytosol
A2RC 0.0 [uM] 0.0 [um2/s] cytosol
AKARp 0.0 [uM] 0.0 [um2/s] cytosol
ICUE 0.15 [uM] 0.0 [um2/s] cytosol
PKAC 0.0 [uM] 0.0 [um2/s] cytosol

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
cAMP_synth included
PKA_act included
cAMP_deg included
PKA_bind1 included
AKAR_dephos included
PKA_bind2 included
ICUE_bind included
AKAR_phos included

Simulations - Application0 go to Specifications

Name
End Time
Output Options

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1306078419

(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 Membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
ICUE_ratio (ICUE_cAMP / (ICUE + ICUE_cAMP))[1]
AKAR_ratio (AKARp / (AKAR + AKARp))[1]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

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 Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml