Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
B2R_p+arrestinarrestin_bound_receptor arrestin binding cyto_mem MassAction
Ligand+GRK+B2RB2R_p receptor ligand binding cyto_mem MassAction

arrestin binding Universal ID's

arrestin binding Text Annotations

receptor ligand binding Universal ID's

receptor ligand binding Text Annotations

Expressions for arrestin binding

reaction rate

J

(((Kf * B2R_p) * arrestin) - (Kr * arrestin_bound_receptor)) [molecules.um-2.s-1]

global

n

350.0 [molecules.um-2.uM-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]

Expressions for receptor ligand binding

reaction rate

J

((((Kf * Ligand) * GRK) * B2R) - (Kr * B2R_p)) [molecules.um-2.s-1]

global

n

350.0 [molecules.um-2.uM-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

Name
Type
Electrical
cyto_mem Membrane cyto(+)   extra(-)
extra Compartment (+)   (-)
cyto Compartment (+)   (-)

cyto_mem Universal ID's

cyto_mem Text Annotations

extra Universal ID's

extra Text Annotations

cyto Universal ID's

cyto Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
B2R cyto_mem cyto_mem
GRK cyto cyto
B2R_p cyto_mem cyto_mem
Ligand extra extra
arrestin cyto cyto
arrestin_bound_receptor cyto_mem cyto_mem

B2R Universal ID's

B2R Text Annotations

GRK Universal ID's

GRK Text Annotations

B2R_p Universal ID's

B2R_p Text Annotations

Ligand Universal ID's

Ligand Text Annotations

arrestin Universal ID's

arrestin Text Annotations

arrestin_bound_receptor Universal ID's

arrestin_bound_receptor Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
ellipse_099_nucleus5_1 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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)

ellipse_099_nucleus5_1 Universal ID's

ellipse_099_nucleus5_1 Text Annotations

spatially varying receptor Universal ID's

spatially varying receptor Text Annotations

circle Universal ID's

circle Text Annotations

Specifications (Species) - ellipse_099_nucleus5_1 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ligand 1.0 [uM] 1.0 [um2/s] extra
GRK 0.2 [uM] 0.1 [um2/s] cyto
arrestin 1.0 [uM] 1.0 [um2/s] cyto
B2R 100.0 [uM] 0.2 [um2/s] cyto_mem
B2R_p 0.0 [uM] 0.2 [um2/s] cyto_mem
arrestin_bound_receptor 0.0 [uM] 0.002 [um2/s] cyto_mem

Specifications (Reaction) - ellipse_099_nucleus5_1 go to Simulations

Name
Enabled?
arrestin binding included
receptor ligand binding included

Simulations - ellipse_099_nucleus5_1 go to Specifications

Name
End Time
Output Options
Simulation4 60.0

OutputTimeStep 1.0
Copy of Simulation4 60.0

OutputTimeStep 1.0

ellipse_099_nucleus5_1 Universal ID's

ellipse_099_nucleus5_1 Text Annotations

ellipse_099_nucleus5_1 Universal ID's

ellipse_099_nucleus5_1 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry ellipse sep 08 0999 with cyt-n 6:1

(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

Events

Name Variable Rate Expression

Specifications (Species) - spatially varying receptor go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ligand 1.0 [uM] 1.0 [um2/s] extra
GRK 0.2 [uM] 0.1 [um2/s] cyto
arrestin 1.0 [uM] 1.0 [um2/s] cyto
B2R (100.0 * (1.0 + (0.018 * abs(x)))) [uM] 0.2 [um2/s] cyto_mem
B2R_p 0.0 [uM] 0.2 [um2/s] cyto_mem
arrestin_bound_receptor 0.0 [uM] 0.002 [um2/s] cyto_mem

Specifications (Reaction) - spatially varying receptor go to Simulations

Name
Enabled?
arrestin binding included
receptor ligand binding included

Simulations - spatially varying receptor go to Specifications

Name
End Time
Output Options
Simulation0 60.0

OutputTimeStep 1.0
Copy of Simulation0 60.0

OutputTimeStep 1.0

spatially varying receptor Universal ID's

spatially varying receptor Text Annotations

spatially varying receptor Universal ID's

spatially varying receptor Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry ellipse sep 08 0999 with cyt-n 6:1

(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

Events

Name Variable Rate Expression

Specifications (Species) - circle go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ligand 1.0 [uM] 1.0 [um2/s] extra
GRK 0.2 [uM] 0.1 [um2/s] cyto
arrestin 1.0 [uM] 1.0 [um2/s] cyto
B2R (100.0 * (1.0 + (0.018 * abs(x)))) [uM] 0.2 [um2/s] cyto_mem
B2R_p 0.0 [uM] 0.2 [um2/s] cyto_mem
arrestin_bound_receptor 0.0 [uM] 0.002 [um2/s] cyto_mem

Specifications (Reaction) - circle go to Simulations

Name
Enabled?
arrestin binding included
receptor ligand binding included

Simulations - circle go to Specifications

Name
End Time
Output Options
Simulation1 60.0

OutputTimeStep 1.0

circle Universal ID's

circle Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry3

(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

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
n 350.0[molecules.um-2.uM-1]

Universal ID's

Text Annotations