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Name - Jung_PNAS_2017_wildtypeM1R_figure5

BioModel ID - 123465498

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction

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

EC	Compartment (+) (-)

PM	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
L_EC	EC	Oxo_EC().

R	PM	M1R(L!-,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!-,).

RL	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!-,).

Arrestin	cytoplasm	Arrestin(RLP!-,MEK!-,PP2A!-,).

RLPP_A	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,).

RLPPA_M	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!-,).

ERK	cytoplasm	ERK(MEK!-,s~u!-,PP2A!-,PP1!-,).

MEK	cytoplasm	MEK(Arr!-,ERK!-,).

PP2A	cytoplasm	PP2A(Arrestin!-,ERK!-,).

pERK	cytoplasm	pERK(MEK!-,s~p!-,PP2A!-,PP1!-,).

RLppA_ME	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).ERK(MEK!4,s~u!-,PP2A!-,PP1!-,).

RLppA_MpE	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).pERK(MEK!4,s~p!-,PP2A!-,PP1!-,).

RL_A	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,).

RL_A_PP2A	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!-,).

ERK_KTR_probe	cytoplasm	probe(site~u!-,).

phos_ERK_KTR_probe	cytoplasm	phos_probe(Site0~p!-,).

GRK	PM	GRK(RL!-,).

RLGRK	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!2,PP1!-,CK2!-,).GRK(RL!2,).

RLGRKpp	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!2,PP1!-,CK2!-,).GRK(RL!2,).

RLpp	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!-,).

RL_A_PP2A_pERK	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).pERK(MEK!-,s~p!-,PP2A!4,PP1!-,).

RL_A_PP2A_ERK	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).ERK(MEK!-,s~u!-,PP2A!4,PP1!-,).

RL_PP1_pool	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!2,CK2!-,).PP1(RL!2,).

PP1	cytoplasm	PP1(RL!-,).

CK2	cytoplasm	CK2(RL!-,).

RL_CK2	PM	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!2,).CK2(RL!2,).

RLpp_CK2	PM	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!2,).CK2(RL!2,).

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition
M1R	Text Annotations	M1R(L,S228~u~p,S273~u~p,Arr,GRK,PP1,CK2,)

Oxo	Text Annotations	Oxo(R,)

Arrestin	Text Annotations	Arrestin(RLP,MEK,PP2A,)

MEK	Text Annotations	MEK(Arr,ERK,)

ERK	Text Annotations	ERK(MEK,s~u,PP2A,PP1,)

pERK	Text Annotations	pERK(MEK,s~p,PP2A,PP1,)

Oxo_EC	Text Annotations	Oxo_EC()

PP2A	Text Annotations	PP2A(Arrestin,ERK,)

probe	Text Annotations	probe(site~u,)

phos_probe	Text Annotations	phos_probe(Site0~p,)

GRK	Text Annotations	GRK(RL,)

PP1	Text Annotations	PP1(RL,)

CK2	Text Annotations	CK2(RL,)

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_M1R_tot	Molecules Multimolecular	M1R(L!-,S228!-,S273!-,Arr!-,GRK!-,PP1!-,CK2!-,).

O0_Oxo_EC	Molecules Multimolecular	Oxo(R!-,).

O0_Arrestin	Molecules Multimolecular	Arrestin(RLP!-,MEK!-,PP2A!-,).

O0_RLPPA	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,).

O0_MEK	Molecules Multimolecular	MEK(Arr!-,ERK!-,).

O0_ERK	Molecules Multimolecular	ERK(MEK!-,s~u!-,PP2A!-,PP1!-,).

O0_pERK	Molecules Multimolecular	pERK(MEK!-,s~p!-,PP2A!-,PP1!-,).

O0_RLPPA_M	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!-,).

O0_RLPP	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!-,).

O0_RLA	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,).

O0_Oxo_EC_tot	Molecules Multimolecular	Oxo_EC().

O0_PP2A_tot	Molecules Multimolecular	PP2A(Arrestin!-,ERK!-,).

O0_RLAPP2A	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!-,).

O0_RLppAME	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).ERK(MEK!4,s~u!-,PP2A!?,PP1!?,).

O0_RLppAMpE	Molecules Multimolecular	Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).pERK(MEK!4,s~p!-,PP2A!?,PP1!?,).

O0_probe_tot	Molecules Multimolecular	probe(site!?,).

O0_phos_probe_tot	Molecules Multimolecular	phos_probe(Site0!?,).

O0_GRK_tot	Molecules Multimolecular	GRK(RL!?,).

O0_PP1_tot	Molecules Multimolecular	PP1(RL!?,).

O0_CK2_tot	Molecules Multimolecular	CK2(RL!?,).

Applications

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

Application - Deterministic

Specifications(Species) - Deterministic See in Dashboard
Species	Initial Condition	Diffusion Constant
Arrestin	15.0 [uM]	0.0 [um2/s]
ERK	1.0 [uM]	0.0 [um2/s]
MEK	1.0 [uM]	0.0 [um2/s]
PP2A	5.0 [uM]	0.0 [um2/s]
pERK	0.1 [uM]	0.0 [um2/s]
ERK_KTR_probe	5.0 [uM]	0.0 [um2/s]
phos_ERK_KTR_probe	5.0 [uM]	0.0 [um2/s]
PP1	1.0 [uM]	0.0 [um2/s]
CK2	1.0 [uM]	0.0 [um2/s]
L_EC	100.0 [uM]	0.0 [um2/s]
R	3500.0 [uM]	0.0 [um2/s]
RL	0.0 [uM]	0.0 [um2/s]
RLPP_A	0.0 [uM]	0.0 [um2/s]
RLPPA_M	0.0 [uM]	0.0 [um2/s]
RLppA_ME	0.0 [uM]	0.0 [um2/s]
RLppA_MpE	0.0 [uM]	0.0 [um2/s]
RL_A	0.0 [uM]	0.0 [um2/s]
RL_A_PP2A	0.0 [uM]	0.0 [um2/s]
GRK	10.0 [uM]	0.0 [um2/s]
RLGRK	0.0 [uM]	0.0 [um2/s]
RLGRKpp	0.0 [uM]	0.0 [um2/s]
RLpp	0.0 [uM]	0.0 [um2/s]
RL_A_PP2A_pERK	0.0 [uM]	0.0 [um2/s]
RL_A_PP2A_ERK	0.0 [uM]	0.0 [um2/s]
RL_PP1_pool	0.0 [uM]	0.0 [um2/s]
RL_CK2	0.0 [uM]	0.0 [um2/s]
RLpp_CK2	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - Deterministic See in Dashboard
Name	Reaction Mapping

Simulations - Deterministic See in Dashboard
Name	End Time	Output Options
Simulation0	900.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry non-spatial334277079 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			PM

Global Parameters

Global Parameters See in Dashboard
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]