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Name - Rangamani Cell 2013 B2R signaling

BioModel ID - 84235320

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
B2R_p+arrestinarrestin_bound_receptor	arrestin binding cyto_mem	MassAction	B2R_p+arrestinarrestin_bound_receptor
		reaction rate (J): (((Kf * B2R_p) * arrestin) - (Kr * arrestin_bound_receptor))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] forward rate constant (Kf): 0.45[s-1.uM-1] reverse rate constant (Kr): 1.0[s-1]
Ligand+GRK+B2RB2R_p	receptor ligand binding cyto_mem	MassAction	Ligand+GRK+B2RB2R_p
		reaction rate (J): ((((Kf * Ligand) * GRK) * B2R) - (Kr * B2R_p))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] forward rate constant (Kf): 20.0[s-1.uM-2] reverse rate constant (Kr): 0.06666666666666667[s-1]

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

cyto	Compartment (+) (-)

cyto_mem	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
B2R	cyto_mem

GRK	cyto

B2R_p	cyto_mem

Ligand	extra

arrestin	cyto

arrestin_bound_receptor	cyto_mem

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
ellipse_099_nucleus5_1	Deterministic (ODE) Spatial (2D)	(copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
spatially varying receptor	Deterministic (ODE) Spatial (2D)	(copied from ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
circle	Deterministic (ODE) Spatial (2D)	(copied from Copy of ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)

Application - ellipse_099_nucleus5_1

Specifications(Species) - ellipse_099_nucleus5_1 See in Dashboard
Species	Initial Condition	Diffusion Constant
Ligand	1.0 [uM]	1.0 [um2/s]
GRK	0.2 [uM]	0.1 [um2/s]
arrestin	1.0 [uM]	1.0 [um2/s]
B2R	100.0 [uM]	0.2 [um2/s]
B2R_p	0.0 [uM]	0.2 [um2/s]
arrestin_bound_receptor	0.0 [uM]	0.002 [um2/s]

Specifications(Reaction) - ellipse_099_nucleus5_1 See in Dashboard
Name	Reaction Mapping
arrestin binding	included
receptor ligand binding	included

Simulations - ellipse_099_nucleus5_1 See in Dashboard
Name	End Time	Output Options
Simulation4	60.0 [s]	OutputTimeStep 1.0
Copy of Simulation4	60.0 [s]	OutputTimeStep 1.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 See in Dashboard
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	Cell		74.97675 [um2]	cyto
Volume	Analytical	ECM		42.52324999999999 [um2]	extra
Surface		Cell_ECM_membrane	Cell \| ECM	93.46482136095845 [um]	cyto_mem

Application - spatially varying receptor

Specifications(Species) - spatially varying receptor See in Dashboard
Species	Initial Condition	Diffusion Constant
Ligand	1.0 [uM]	1.0 [um2/s]
GRK	0.2 [uM]	0.1 [um2/s]
arrestin	1.0 [uM]	1.0 [um2/s]
B2R	(100.0 * (1.0 + (0.018 * abs(x)))) [uM]	0.2 [um2/s]
B2R_p	0.0 [uM]	0.2 [um2/s]
arrestin_bound_receptor	0.0 [uM]	0.002 [um2/s]

Specifications(Reaction) - spatially varying receptor See in Dashboard
Name	Reaction Mapping
arrestin binding	included
receptor ligand binding	included

Simulations - spatially varying receptor See in Dashboard
Name	End Time	Output Options
Simulation0	60.0 [s]	OutputTimeStep 1.0
Copy of Simulation0	60.0 [s]	OutputTimeStep 1.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 See in Dashboard
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	Cell		74.9298128342246 [um2]	cyto
Volume	Analytical	ECM		42.5701871657754 [um2]	extra
Surface		Cell_ECM_membrane	Cell \| ECM	93.03794179617861 [um]	cyto_mem

Application - circle

Specifications(Species) - circle See in Dashboard
Species	Initial Condition	Diffusion Constant
Ligand	1.0 [uM]	1.0 [um2/s]
GRK	0.2 [uM]	0.1 [um2/s]
arrestin	1.0 [uM]	1.0 [um2/s]
B2R	(100.0 * (1.0 + (0.018 * abs(x)))) [uM]	0.2 [um2/s]
B2R_p	0.0 [uM]	0.2 [um2/s]
arrestin_bound_receptor	0.0 [uM]	0.002 [um2/s]

Specifications(Reaction) - circle See in Dashboard
Name	Reaction Mapping
arrestin binding	included
receptor ligand binding	included

Simulations - circle See in Dashboard
Name	End Time	Output Options
Simulation1	60.0 [s]	OutputTimeStep 1.0

Geometry Geometry3 See in Dashboard
(Origin: -10.0, -10.0, 0.0; Extent: 20.0, 20.0, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain1		169.16 [um2]	cyto
Volume	Analytical	subdomain0		230.84 [um2]	extra
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	46.24554814672766 [um]	cyto_mem

Global Parameters

Global Parameters See in Dashboard
Name	Expression
n	350.0[molecules.um-2.uM-1]