Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

Structures

Name
Type
Electrical
PM Membrane (+)   (-)
EC Compartment (+)   (-)
cytoplasm Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
L_EC EC Oxo_EC(). EC
R PM M1R(L!-,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,). PM
RL PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,). PM
Arrestin cytoplasm Arrestin(RLP!-,MEK!-,PP2A!-,). cytoplasm
RLPP_A PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!-,PP2A!-,). PM
RLPPA_M PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!-,). PM
ERK cytoplasm ERK(MEK!-,s~u!-,PP2A!-,PP1!-,). cytoplasm
MEK cytoplasm MEK(Arr!-,ERK!-,). cytoplasm
PP2A cytoplasm PP2A(Arrestin!-,ERK!-,). cytoplasm
pERK cytoplasm pERK(MEK!-,s~p!-,PP2A!-,PP1!-,). cytoplasm
RLppA_ME PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).ERK(MEK!4,s~u!-,PP2A!-,PP1!-,). PM
RLppA_MpE PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).pERK(MEK!4,s~p!-,PP2A!-,PP1!-,). PM
RL_A PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!-,PP2A!-,). PM
RL_A_PP2A PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!-,). PM
ERK_KTR_probe cytoplasm probe(site~u!-,). cytoplasm
phos_ERK_KTR_probe cytoplasm phos_probe(Site0~p!-,). cytoplasm
GRK PM GRK(R!-,). PM
RLGRK PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!2,PP1!-,).GRK(R!2,). PM
RLGRKpp PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!2,PP1!-,).GRK(R!2,). PM
RLpp PM Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,). PM
RL_A_PP2A_pERK PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).pERK(MEK!-,s~p!-,PP2A!4,PP1!-,). PM
RL_A_PP2A_ERK PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).ERK(MEK!-,s~u!-,PP2A!4,PP1!-,). PM
RL_PP1_pool PM Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!2,).PP1(RL!2,). PM
PP1 cytoplasm PP1(RL!-,). cytoplasm

Molecules

Name
BioNetGen Definition
DEPICTION
M1R M1R(L,S228~u~p,S273~u~p,Arr,GRK,PP1,)
Oxo Oxo(R,)
Arrestin Arrestin(RLP,MEK,PP2A,)
MEK MEK(Arr,ERK,)
ERK ERK(MEK,s~u,PP2A,PP1,)
pERK pERK(MEK,s~p,PP2A,PP1,)
Oxo_EC Oxo_EC()
PP2A PP2A(Arrestin,ERK,)
probe probe(site~u,)
phos_probe phos_probe(Site0~p,)
GRK GRK(R,)
PP1 PP1(RL,)

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_M1R_tot PM Molecules M1R(L!-,S228!-,S273!-,Arr!-,GRK!?,PP1!?,). Multimolecular
O0_Oxo_EC EC Molecules Oxo(R!-,). Multimolecular
O0_Arrestin cytoplasm Molecules Arrestin(RLP!-,MEK!-,PP2A!?,). Multimolecular
O0_RLPPA PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!-,PP2A!?,). Multimolecular
O0_MEK cytoplasm Molecules MEK(Arr!-,ERK!-,). Multimolecular
O0_ERK cytoplasm Molecules ERK(MEK!-,s~u!?,PP2A!?,PP1!?,). Multimolecular
O0_pERK cytoplasm Molecules pERK(MEK!-,s~p!-,PP2A!?,PP1!?,). Multimolecular
O0_RLPPA_M PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!3,PP2A!?,). MEK(Arr!3,ERK!-,). Multimolecular
O0_RLP1 PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~u!-,Arr!-,GRK!?,PP1!?,). Multimolecular
O0_RLP2 PM Molecules Oxo(R!1,). M1R(L!1,S228~u!-,S273~p!-,Arr!-,GRK!?,PP1!?,). Multimolecular
O0_RLPP PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!?,PP1!?,). Multimolecular
O0_RLA PM Molecules Oxo(R!1,). M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!-,PP2A!?,). Multimolecular
O0_Oxo_EC_tot cytoplasm Molecules Oxo_EC(). Multimolecular
O0_PP2A_tot cytoplasm Molecules PP2A(Arrestin!-,ERK!?,). Multimolecular
O0_RLAPP2A PM Molecules Oxo(R!1,). M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!-,PP2A!3,). PP2A(Arrestin!3,ERK!?,). Multimolecular
O0_RLppAME PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!3,PP2A!-,). MEK(Arr!3,ERK!4,). ERK(MEK!4,s~u!-,PP2A!?,PP1!?,). Multimolecular
O0_RLppAMpE PM Molecules Oxo(R!1,). M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!?,PP1!?,). Arrestin(RLP!2,MEK!3,PP2A!-,). MEK(Arr!3,ERK!4,). pERK(MEK!4,s~p!-,PP2A!?,PP1!?,). Multimolecular
O0_probe_tot cytoplasm Molecules probe(site!?,). Multimolecular
O0_phos_probe_tot cytoplasm Molecules phos_probe(Site0!?,). Multimolecular
O0_GRK_tot EC Molecules GRK(R!?,). Multimolecular
O0_PP1_tot cytoplasm Molecules PP1(RL!?,). Multimolecular

Applications

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

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
L_EC 100.0 [uM] 0.0 [um2/s] EC
Arrestin 15.0 [uM] 0.0 [um2/s] cytoplasm
ERK 1.0 [uM] 0.0 [um2/s] cytoplasm
MEK 1.0 [uM] 0.0 [um2/s] cytoplasm
PP2A 5.0 [uM] 0.0 [um2/s] cytoplasm
pERK 0.1 [uM] 0.0 [um2/s] cytoplasm
ERK_KTR_probe 5.0 [uM] 0.0 [um2/s] cytoplasm
phos_ERK_KTR_probe 5.0 [uM] 0.0 [um2/s] cytoplasm
PP1 1.0 [uM] 0.0 [um2/s] cytoplasm
R 3500.0 [uM] 0.0 [um2/s] PM
RL 0.0 [uM] 0.0 [um2/s] PM
RLPP_A 0.0 [uM] 0.0 [um2/s] PM
RLPPA_M 0.0 [uM] 0.0 [um2/s] PM
RLppA_ME 0.0 [uM] 0.0 [um2/s] PM
RLppA_MpE 0.0 [uM] 0.0 [um2/s] PM
RL_A 0.0 [uM] 0.0 [um2/s] PM
RL_A_PP2A 0.0 [uM] 0.0 [um2/s] PM
GRK 1000.0 [uM] 0.0 [um2/s] PM
RLGRK 0.0 [uM] 0.0 [um2/s] PM
RLGRKpp 0.0 [uM] 0.0 [um2/s] PM
RLpp 0.0 [uM] 0.0 [um2/s] PM
RL_A_PP2A_pERK 0.0 [uM] 0.0 [um2/s] PM
RL_A_PP2A_ERK 0.0 [uM] 0.0 [um2/s] PM
RL_PP1_pool 0.0 [uM] 0.0 [um2/s] PM

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 900.0

KeepEvery 1

KeepAtMost 1000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial334277079

(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 PM

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
start 60.0[s]
end 540.0[s]
time 60.0[s-1]
washing_agonist ((1.0 * (t > 60.0)) && (t < 540.0))[s-1.uM-1]
on_set 1.0[s-1]
off_set (0.0 * (t > 480.0))[1]
converting_factor 0.0[s-1]
Dephos_factor 0.1[s-1.uM-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 Deterministic.bngl
SBML Deterministic.sbml
Matlab Deterministic.m
NFSim XML Deterministic.xml