ModelBricks - Model Print Page

Name - Greenwald MIMB 2012 - Perturb

BioModel ID - 65183128

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
cAMP	cAMP_synth cytosol	GeneralKinetics	cAMP
		reaction rate (J): ((Vmax * ATP / (Km + ATP)) + (Vmax_Iso * ATP / (Km_Iso + ATP)))[uM.s-1] user defined (Km): 860.0[uM] user defined (Vmax): (kfsk * AC_fsk)[uM.s-1] user defined (ATP): 5000.0[uM] user defined (Vmax_Iso): (kcat_iso * AC_iso)[uM.s-1] user defined (Km_Iso): 315.0[uM] user defined (kcat_iso): 0.200273[s-1] user defined (AC_iso): (AC * Iso / (Kd_iso + Iso))[uM] user defined (Iso): (Iso_stim * (t > t_iso))[uM] user defined (Kd_iso): 0.1[uM] user defined (kfsk): 25.0451[s-1] user defined (AC_fsk): (AC * Fsk / (Kd_fsk + Fsk))[uM] user defined (Iso_stim): 0.0[uM] user defined (t_iso): 0.0[s] user defined (Kd_fsk): 860.0[uM] user defined (Fsk): (FSK_stim * (t > t_FSK))[uM] user defined (FSK_stim): 0.0[uM] user defined (t_FSK): 0.0[s]
A2RCA2R+PKAC	PKA_act cytosol	MassAction	A2RCA2R+PKAC
		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]
cAMP	cAMP_deg cytosol	HMMIrreversible	cAMP
		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] user defined (kcat): 5.0[s-1] user defined (PDE_avail): (PDE * Ki / (Ki + IBMX))[uM] user defined (IBMX): (IBMX_stim * (t > t_IBMX))[uM] user defined (Ki): 30.0[uM] user defined (t_IBMX): 0.0[s] user defined (IBMX_stim): 0.0[uM]
RC+cAMPARC	PKA_bind1 cytosol	MassAction	RC+cAMPARC
		reaction rate (J): (((Kf * RC) * cAMP) - (Kr * ARC))[uM.s-1] forward rate constant (Kf): 107.99[s-1.uM-1] reverse rate constant (Kr): 28939.0[s-1]
AKARpAKAR	AKAR_dephos cytosol	GeneralKinetics	AKARpAKAR
		reaction rate (J): (kcat * PPase * AKARp)[uM.s-1] user defined (kcat): 0.6478[uM-1.s-1] user defined (PPase): 0.15563[uM]
ARC+cAMPA2RC	PKA_bind2 cytosol	MassAction	ARC+cAMPA2RC
		reaction rate (J): (((Kf * ARC) * cAMP) - (Kr * A2RC))[uM.s-1] forward rate constant (Kf): 720.64[s-1.uM-1] reverse rate constant (Kr): 1640.0[s-1]
ICUE+cAMPICUE_cAMP	ICUE_bind cytosol	MassAction	ICUE+cAMPICUE_cAMP
		reaction rate (J): (((Kf * ICUE) * cAMP) - (Kr * ICUE_cAMP))[uM.s-1] forward rate constant (Kf): 34.2093[s-1.uM-1] reverse rate constant (Kr): 10.0[s-1]
AKARAKARp	AKAR_phos cytosol	HMMIrreversible	AKARAKARp
		reaction rate (J): ((Vmax * AKAR) / (Km + AKAR))[uM.s-1] Km (1/2 max) (Km): 0.908288[uM] max reaction rate (Vmax): (kcat * PKAC)[uM.s-1] user defined (kcat): 54.0[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
Extra Cellular	Compartment (+) (-)

cytosol	Compartment (+) (-)

Membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
AC	cytosol

RC	cytosol

A2R	cytosol

PDE	cytosol

ARC	cytosol

ICUE_cAMP	cytosol

A2RC	cytosol

AKARp	cytosol

ICUE	cytosol

PKAC	cytosol

cAMP	cytosol

AKAR	cytosol

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Application0	Deterministic (ODE) Compartmental

Application - Application0

Specifications(Species) - Application0 See in Dashboard
Species	Initial Condition	Diffusion Constant
AC	0.05 [uM]	0.0 [um2/s]
RC	0.581355 [uM]	0.0 [um2/s]
A2R	0.0 [uM]	0.0 [um2/s]
PDE	0.014 [uM]	0.0 [um2/s]
ARC	0.0 [uM]	0.0 [um2/s]
ICUE_cAMP	0.0 [uM]	0.0 [um2/s]
A2RC	0.0 [uM]	0.0 [um2/s]
AKARp	0.0 [uM]	0.0 [um2/s]
ICUE	0.15 [uM]	0.0 [um2/s]
PKAC	0.0 [uM]	0.0 [um2/s]
cAMP	0.0 [uM]	0.0 [um2/s]
AKAR	1.25 [uM]	0.0 [um2/s]

Specifications(Reaction) - Application0 See in Dashboard
Name	Reaction Mapping
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 See in Dashboard
Name	End Time	Output Options

Geometry non-spatial1306078419 See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
Name	Expression
ICUE_ratio	(ICUE_cAMP / (ICUE + ICUE_cAMP))[1]

AKAR_ratio	(AKARp / (AKAR + AKARp))[1]