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Name - hillelab: JungSR_PAR2_desensitization2015

BioModel ID - 100961371

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
PI4P_MPIP2_M	PIP5K_5Pase M	MassAction	PI4P_MPIP2_M
		reaction rate (J): ((Kf * PI4P_M) - (Kr * PIP2_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (foldPIP2 * (((t < start) * k5K_rest) + ((t >= start) * (t < end) * k5k_Oxo) + ((t >= end) * k5K_recovery)))[s-1] reverse rate constant (Kr): (0.014 * ((k5r_basal * (t < start)) + (k5r_stim * (t >= start) * (t < end)) + (k5r_recovery * (t > end))) * foldPIP2)[s-1] user defined (k5K_rest): 0.02[s-1] user defined (k5k_Oxo): (k5K_rest + ((stim_5k - k5K_rest + k5k_base) * scale5K * (1.0 - exp(((start - t) / tau_stim_onset)))))[s-1] user defined (k5K_recovery): ((exp(((end - t) / tau_stim_recovery)) * scale5K * (stim_5k - k5K_rest + k5k_base)) + k5K_rest)[s-1] user defined (scale5K): 1.0[1] user defined (stim_5k): (stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1] user defined (stim_5K_max): 5.75[s-1] user defined (k5r_basal): 1.0[s-1] user defined (k5r_stim): 3.0[s-1] user defined (k5r_recovery): 1.0[s-1]
PH_YFP_C+PIP2_MPH_YFP_PIP2_M	PH_YFP_PIP2 M	MassAction	PH_YFP_C+PIP2_MPH_YFP_PIP2_M
		reaction rate (J): (((Kf * PH_YFP_C) * PIP2_M) - (Kr * PH_YFP_PIP2_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): speed_PH_PIP2[s-1.uM-1] reverse rate constant (Kr): (KD_PH_PIP2 * speed_PH_PIP2)[s-1]
RLG_GDP_MRLGbeta_M+GaGTP_M	NE_RLG M	GeneralKinetics	RLG_GDP_MRLGbeta_M+GaGTP_M
		reaction rate (J): (Kf * RLG_GDP_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 0.65[s-1]
RL_MRLP_M	reaction 1 for phosphorylation of ligand bound receptor M	GeneralKinetics	RL_MRLP_M
		reaction rate (J): ((kf_RL_M * RL_M * ((weighting_factor_PKC * PKC_DAG_M) + (weighting_factor_GRK * GRK_M))) - (kr_RLP_M * RLP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (GRK_M): ((GRK_M_basal * (t < start)) + (GRK_M_stim * (t >= start) * (t < end)) + (GRK_M_recovery * (t > end)))[molecules.um-2] user defined (weighting_factor_GRK): 0.5[1] user defined (kf_RL_M): ((kf_RL_M_basal * (t < start)) + (kf_RL_M_stim * (t >= start) * (t <= end)) + (kf_RL_M_recovery * (t > end)))[um2.molecules-1.s-1] user defined (kr_RLP_M): ((kr_RLP_M_basal * (t < start)) + (kr_RLP_M_stim * (t >= start) * (t < end)) + (kr_RLP_M_recovery * (t > end)))[s-1] user defined (weighting_factor_PKC): 0.5[1] user defined (GRK_M_basal): 0.0[molecules.um-2] user defined (GRK_M_stim): 600.0[molecules.um-2] user defined (GRK_M_recovery): 0.0[molecules.um-2] user defined (kf_RL_M_basal): 1.0E-4[um2.molecules-1.s-1] user defined (kf_RL_M_stim): 1.0[um2.molecules-1.s-1] user defined (kf_RL_M_recovery): 1.0E-4[um2.molecules-1.s-1] user defined (kr_RLP_M_stim): 0.0125[s-1] user defined (kr_RLP_M_basal): 0.01[s-1] user defined (kr_RLP_M_recovery): 0.01[s-1]
Gbeta_M+Ga_GDP_MG_GDP_M	reconstitution M	GeneralKinetics	Gbeta_M+Ga_GDP_MG_GDP_M
		reaction rate (J): (Kf * Gbeta_M * Ga_GDP_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 1.0[um2.molecules-1.s-1]
RL_M+G_GDP_MRLG_GDP_M	G2 M	MassAction	RL_M+G_GDP_MRLG_GDP_M
		reaction rate (J): (((Kf * RL_M) * G_GDP_M) - (Kr * RLG_GDP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG2[um2.s-1.molecules-1] reverse rate constant (Kr): KrG2[s-1]
DAG_MPA_2AG_M	DAGPase M	GeneralKinetics	DAG_MPA_2AG_M
		reaction rate (J): (Kf * DAG_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 0.1[s-1]
GaGTP_MGa_GDP_M	GTPase_Ga M	GeneralKinetics	GaGTP_MGa_GDP_M
		reaction rate (J): (Kf * GaGTP_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 0.026[s-1]
PLC_M+GaGTP_MGaGTP_PLC_M	PLCassoc M	MassAction	PLC_M+GaGTP_MGaGTP_PLC_M
		reaction rate (J): (((Kf * PLC_M) * GaGTP_M) - (Kr * GaGTP_PLC_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.0[um2.s-1.molecules-1] reverse rate constant (Kr): 0.0[s-1]
IP3_C+PH_YFP_CIP3_PH_YFP_C	PH_YFP_IP3 C	MassAction	IP3_C+PH_YFP_CIP3_PH_YFP_C
		reaction rate (J): (((Kf * IP3_C) * PH_YFP_C) - (Kr * IP3_PH_YFP_C))[uM.s-1] forward rate constant (Kf): speed_PH_IP3[s-1.uM-1] reverse rate constant (Kr): (KD_PH_IP3 * speed_PH_IP3)[s-1]
Palk_C1Palk_C2	r12 C	MassAction	Palk_C1Palk_C2
		reaction rate (J): ((Kf * Palk_C1) - (Kr * Palk_C2))[uM.s-1] forward rate constant (Kf): (q12 * perms2pers)[s-1] reverse rate constant (Kr): (q21 * perms2pers)[s-1] user defined (q12): 0.74[1] user defined (q21): ((VP21 / (1.0 + (kp21 * (IP3_nM ^ 3.0)))) + bp21)[1] user defined (VP21): 0.0949[1] user defined (IP3_nM): (IP3_C * uM2nM)[1] user defined (bp21): 0.11[1] user defined (kp21): 5.0E-10[1]
RG_GDP_M+AP_EXRLG_GDP_M	L2 M	MassAction	RG_GDP_M+AP_EXRLG_GDP_M
		reaction rate (J): (((Kf * RG_GDP_M) * AP_EX) - (Kr * RLG_GDP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1]
dynamin+RLPA2_MRLPAC_M	clathrin formation rate M	GeneralKinetics	dynamin+RLPA2_MRLPAC_M
		reaction rate (J): ((kf_RLPA_M * RLPA2_M * dynamin * (PIP2_M ^ 3.0) / (Kdynamin_binding + dynamin) / ((PIP2_M ^ 3.0) + (K_PIP2_M ^ 3.0))) - kr_RLPAC_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kdynamin_binding): 0.2[uM] user defined (K_PIP2_M): 5000.0[molecules.um-2] user defined (kf_RLPA_M): 0.0[s-1] user defined (kr_RLPAC_M): 0.0[molecules.um-2.s-1]
noninactiveIP3RinactiveIP3R	h_reaction_IP3Rinactivation ERM	GeneralKinetics	noninactiveIP3RinactiveIP3R
		reaction rate (J): - ((KD_inh_Ca_IP3R - ((Ca_C + KD_inh_Ca_IP3R) * h)) * Kon_Ca_IP3R)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (KD_inh_Ca_IP3R): 0.2[uM] user defined (Kon_Ca_IP3R): 2.7[molecules.um-2.uM-1.s-1]
R_M+AP_EXRL_M	L1 M	MassAction	R_M+AP_EXRL_M
		reaction rate (J): (((Kf * R_M) * AP_EX) - (Kr * RL_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL1[s-1.uM-1] reverse rate constant (Kr): KrL1[s-1] user defined (KfL1): (KrL1 / KL1)[uM-1.s-1]
PI4P_MDAG_M	PLC_on_PI4P M	GeneralKinetics	PI4P_MDAG_M
		reaction rate (J): (PI4P_M * PLC_efficiency_PIP * (PLC_basal + (GaGTP_PLC_M * K_plc)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (PLC_efficiency_PIP): 1.0[1]
R_MRP_M	reaction 2 for phosphorylation of receptor M	GeneralKinetics	R_MRP_M
		reaction rate (J): ((kf_R_M * R_M * PKC_DAG_M) - (kr_RP_M * RP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (kr_RP_M): ((kr_RP_M_basal * (t < start)) + (kr_RP_M_stim * (t >= start) * (t <= end)) + (kr_RP_M_recovery * (t > end)))[s-1] user defined (kr_RP_M_stim): 2.0[tbd] user defined (kf_R_M): ((kf_R_M_basal * (t < start)) + (kf_R_M_stim * (t >= start) * (t <= end)) + (kf_R_M_recovery * (t > end)))[s-1] user defined (kf_R_M_stim): 10.0[tbd] user defined (kf_R_M_basal): 1.0E-4[tbd] user defined (kr_RP_M_recovery): 2.0[tbd] user defined (kf_R_M_recovery): 1.0E-4[tbd] user defined (kr_RP_M_basal): 2.0[tbd]
G_GDP_MGaGTP_M+Gbeta_M	NE_G M	MassAction	G_GDP_MGaGTP_M+Gbeta_M
		reaction rate (J): ((Kf * G_GDP_M) - ((Kr * GaGTP_M) * Gbeta_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.5E-5[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1]
RP_M+AP_EXRLP_M	ligand2 M	MassAction	RP_M+AP_EXRLP_M
		reaction rate (J): (((Kf * RP_M) * AP_EX) - (Kr * RLP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): kfL2[s-1.uM-1] reverse rate constant (Kr): krL2[s-1] user defined (kfL2): (krL2 / KL2)[uM-1.s-1] user defined (krL2): 5.55555555555[s-1] user defined (KL2): 60.0[uM]
Palk_C2Palk_O4	r24 C	MassAction	Palk_C2Palk_O4
		reaction rate (J): ((Kf * Palk_C2) - (Kr * Palk_O4))[uM.s-1] forward rate constant (Kf): q24[s-1] reverse rate constant (Kr): q42[s-1] user defined (q24): (7.84 * perms2pers)[s-1] user defined (q42): (3.6 * perms2pers)[s-1]
IP3_C	IP3deg_Palk C	MassAction	IP3_C
		reaction rate (J): (Kf * IP3_C)[uM.s-1] forward rate constant (Kf): (r_Palk_IP3ase * (k5P + (k3K * Ca_C * Ca_C / ((Ca_C * Ca_C) + (kdeg * kdeg)))))[s-1] reverse rate constant (Kr): 0.0[uM.s-1] user defined (k3K): 40.0[s-1] user defined (r_Palk_IP3ase): 0.0[1] user defined (k5P): 0.005[s-1] user defined (kdeg): 0.4[uM]
PI_MPI4P_M	PI4K_4Pase M	MassAction	PI_MPI4P_M
		reaction rate (J): ((Kf * PI_M) - (Kr * PI4P_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (foldPIP2 * ((K4_recover * (t > end)) + (K4_rest * (t < start)) + (K4_Oxo * (t >= start) * (t <= end))))[s-1] reverse rate constant (Kr): (0.03 * ((k4r_basal * (t < start)) + (k4r_stim * (t >= start) * (t <= end)) + (k4r_recovery * (t > end))))[s-1] user defined (K4_Oxo): (K4_rest + ((stim_4k - K4_rest + K4_base) * scale4K * (1.0 - exp(((100.0 - t) / tau_stim_onset)))))[s-1] user defined (K4_rest): 2.6E-4[s-1] user defined (K4_recover): ((exp(((end - t) / tau_stim_recovery)) * scale4K * (stim_4k - K4_rest + K4_base)) + K4_rest)[s-1] user defined (scale4K): 0.75[1] user defined (K4_base): 2.3534E-4[s-1] user defined (stim_4k): (stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1] user defined (stim_4k_max): 0.225[s-1] user defined (k4r_stim): 6.25[s-1] user defined (k4r_basal): 1.0[s-1] user defined (k4r_recovery): 1.0[s-1]
IP3_pipetteIP3_C	IP3_dialysis M	MassAction	IP3_pipetteIP3_C
		reaction rate (J): ((Kf * IP3_pipette) - (Kr * IP3_C))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (0.015 * (t > start) * k_pipette)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): (0.015 * (t > start) * k_pipette)[molecules.um-2.s-1.uM-1] user defined (k_pipette): 0.0[s-1]
LibraVIII_C+IP3_CIP3_LibraVIII_C	IP3_LibraVIII C	MassAction	LibraVIII_C+IP3_CIP3_LibraVIII_C
		reaction rate (J): (((Kf * LibraVIII_C) * IP3_C) - (Kr * IP3_LibraVIII_C))[uM.s-1] forward rate constant (Kf): speed_LibraVIII[s-1.uM-1] reverse rate constant (Kr): (speed_LibraVIII * KD_LibraVIII)[s-1] user defined (speed_LibraVIII): 1.0[uM-1.s-1] user defined (KD_LibraVIII): 0.5[uM]
PIP2_MPI4P_M	VSP M	MassAction	PIP2_MPI4P_M
		reaction rate (J): ((Kf * PIP2_M) - (Kr * PI4P_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kVSP * foldPIP2)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP): (VSPmax / (1.0 + exp((1.5 * qKT * (V - Vhalf)))))[s-1] user defined (Vhalf): 0.1[V] user defined (V): (Vhold + (( - Vhold + Vstep) * (t > VSP_start) * (t < VSP_end)))[V] user defined (VSPmax): 0.0[s-1] user defined (qKT): -40.5898[A.s3.kg-1.m-2] user defined (VSP_end): 150.0[s] user defined (Vstep): 0.1[V] user defined (Vhold): -0.06[V] user defined (VSP_start): 50.0[s]
Gbeta_M+R_MRGbeta_M	G1beta M	MassAction	Gbeta_M+R_MRGbeta_M
		reaction rate (J): (((Kf * Gbeta_M) * R_M) - (Kr * RGbeta_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG1[um2.s-1.molecules-1] reverse rate constant (Kr): KrG1[s-1]
GaGDP_PLC_MGaGTP_PLC_M	NE_GaP M	GeneralKinetics	GaGDP_PLC_MGaGTP_PLC_M
		reaction rate (J): (4.7 * GaGDP_PLC_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
IP3_C	IP3Pase_FDH C	GeneralKinetics	IP3_C
		reaction rate (J): (K_IP3ase * IP3_C)[uM.s-1] user defined (K_IP3ase): (0.08 * r_FDH_IP3ase)[s-1] user defined (r_FDH_IP3ase): 1.0[s-1]
RLP_M+Arrestin2RLPA2_M	arrestin binding M	GeneralKinetics	RLP_M+Arrestin2RLPA2_M
		reaction rate (J): ((kf_RLP_M * RLP_M * Arrestin2) - (kr_RLPA_M * RLPA2_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (kr_RLPA_M): ((kr_RLPA_M_basal * (t < start)) + (kr_RLPA_M_stim * (t >= start) * (t <= end)) + (kr_RLPA_M_recovery * (t > end)))[s-1] user defined (kf_RLP_M): ((kf_RLP_M_basal * (t < start)) + (kf_RLP_M_stim * (t >= start) * (t <= end)) + (kf_RLP_M_recovery * (t > end)))[s-1] user defined (kr_RLPA_M_recovery): 1.0E-6[s-1] user defined (kr_RLPA_M_basal): 1.0E-6[s-1] user defined (kr_RLPA_M_stim): 1.0E-6[s-1] user defined (kf_RLP_M_stim): 0.003[s-1] user defined (kf_RLP_M_recovery): 0.0[s-1] user defined (kf_RLP_M_basal): 0.0[s-1]
Palk_C2Palk_C3	r23 C	MassAction	Palk_C2Palk_C3
		reaction rate (J): ((Kf * Palk_C2) - (Kr * Palk_C3))[uM.s-1] forward rate constant (Kf): (q23 * perms2pers)[s-1] reverse rate constant (Kr): (q32 * perms2pers)[s-1] user defined (q23): (alpha23 * p23 * P23)[1] user defined (q32): (alpha32 * p32 * P32)[1] user defined (p32): (((V32 / ((k32 ^ 3.0) + (Ca_nM ^ 3.0))) + b32) * ((Vm32 * (Ca_nM ^ 7.0) / ((km32 ^ 7.0) + (Ca_nM ^ 7.0))) + bm32))[1] user defined (P32): ((VP32 * (IP3_nM ^ 3.0) / (1.0 + (kp32 * (IP3_nM ^ 3.0)))) + bp32)[1] user defined (alpha32): 50.0[1] user defined (VP32): 3.0E-12[1] user defined (IP3_nM): (ip3_Palk_scale_factor * IP3_C * uM2nM)[1] user defined (bp32): 0.0[1] user defined (kp32): 1.5E-10[1] user defined (b32): 0.005[1] user defined (km32): 150.0[1] user defined (V32): 7000000.0[1] user defined (bm32): 0.03[1] user defined (k32): 520.0[1] user defined (Ca_nM): (Ca_C * uM2nM)[1] user defined (Vm32): 1.06[1] user defined (p23): (a23 - (((V23 / ((k23 ^ 2.0) + (Ca_nM ^ 2.0))) + b23) * ((Vm23 * (Ca_nM ^ 5.0) / ((km23 ^ 5.0) + (Ca_nM ^ 5.0))) + bm23)))[1] user defined (P23): ((VP23 / (1.0 + (kp23 * (IP3_nM ^ 3.0)))) + bp23)[1] user defined (alpha23): 1000.0[1] user defined (bp23): 0.001[1] user defined (VP23): 0.162[1] user defined (kp23): 5.0E-9[1] user defined (Vm23): 0.3545[1] user defined (km23): 72.0[1] user defined (b23): 2.2[1] user defined (bm23): 0.042[1] user defined (a23): 0.9775171065493647[1] user defined (V23): 1.08E-6[1] user defined (k23): 2000.0[1] user defined (ip3_Palk_scale_factor): 1.0[1]
KCNQ_M+PIP2_MKCNQ_PIP2_M	PIP2bindKCNQ M	GeneralKinetics	KCNQ_M+PIP2_MKCNQ_PIP2_M
		reaction rate (J): ((Kf * PIP2_M * KCNQ_M) - (Kr * KCNQ_PIP2_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kr): (KD_PIP2_KCNQ * Kf)[s-1] user defined (Kf): speed_PIP2_KCNQ[um2.molecules-1.s-1] user defined (KD_PIP2_KCNQ): KA_PIP2_KCNQ[molecules.um-2] user defined (KA_PIP2_KCNQ): 2000.0[molecules.um-2] user defined (speed_PIP2_KCNQ): 0.05[um2.molecules-1.s-1]
RLPAC_M+dynaminendocytosis	pinching M	GeneralKinetics	RLPAC_M+dynaminendocytosis
		reaction rate (J): (kf_RLPAC_M * RLPAC_M * dynamin / (Kdynamin + dynamin))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kdynamin): 0.2[uM] user defined (kf_RLPAC_M): 0.0[s-1]
Gbeta_M+RL_MRLGbeta_M	G2beta M	MassAction	Gbeta_M+RL_MRLGbeta_M
		reaction rate (J): (((Kf * Gbeta_M) * RL_M) - (Kr * RLGbeta_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG2[um2.s-1.molecules-1] reverse rate constant (Kr): KrG2[s-1]
PIP2_MIP3_C+DAG_M	PIP2hydr M	GeneralKinetics	PIP2_MIP3_C+DAG_M
		reaction rate (J): ((PIP2_M * (PLC_basal + (K_plc * foldPIP2 * GaGTP_PLC_M))) + (PIP2_M * PLC_stim * GaGTP_PLC_M * (Ca_C / (Ca_C + KD_PLC_Ca)) * (t > start) * (t <= end)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (PLC_stim): 7.0[s-1] user defined (KD_PLC_Ca): 1.0[tbd] user defined (K_plc): ((0.2 * (t >= start) * (t < end)) + (0.2 * (t < start)))[um2.molecules-1.s-1]
AP_conc_EXAP_EX	Oxo_appl EX	MassAction	AP_conc_EXAP_EX
		reaction rate (J): ((Kf * AP_conc_EX) - (Kr * AP_EX))[uM.s-1] forward rate constant (Kf): (50.0 * (t > start) * (t < end))[s-1] reverse rate constant (Kr): (50.0 * (t > end))[s-1]
GaGDP_PLC_MGa_GDP_M+PLC_M	PLCdiss M	MassAction	GaGDP_PLC_MGa_GDP_M+PLC_M
		reaction rate (J): ((Kf * GaGDP_PLC_M) - ((Kr * Ga_GDP_M) * PLC_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 0.71[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1]
R_M+G_GDP_MRG_GDP_M	G1 M	MassAction	R_M+G_GDP_MRG_GDP_M
		reaction rate (J): (((Kf * R_M) * G_GDP_M) - (Kr * RG_GDP_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG1[um2.s-1.molecules-1] reverse rate constant (Kr): KrG1[s-1]
GaGTP_PLC_MGaGDP_PLC_M	GTPase_GaP M	GeneralKinetics	GaGTP_PLC_MGaGDP_PLC_M
		reaction rate (J): ((15.0 * GaGTP_PLC_M * (t < start)) + (15.0 * GaGTP_PLC_M * (t >= start) * (t < end)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
DAG_M+PKC_cytoPKC_DAG_M	PKC_DAG binding M	GeneralKinetics	DAG_M+PKC_cytoPKC_DAG_M
		reaction rate (J): ((kf_pkc_DAG * PKC_cyto * DAG_M) - (kr_pkc_DAG * PKC_DAG_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (kr_pkc_DAG): 0.06[s-1] user defined (kf_pkc_DAG): 0.02[uM-1.s-1]
C1_dom_C+DAG_MC1_DAG_M	C1bindDAG M	MassAction	C1_dom_C+DAG_MC1_DAG_M
		reaction rate (J): (((Kf * C1_dom_C) * DAG_M) - (Kr * C1_DAG_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): speed_DAG_C1[s-1.uM-1] reverse rate constant (Kr): (KD_DAG_C1 * speed_DAG_C1)[s-1]
PIP2_MboundPIP2_M	PIP2_buffering M	MassAction	PIP2_MboundPIP2_M
		reaction rate (J): ((Kf * PIP2_M) - (Kr * boundPIP2_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (( - 1.0 + foldPIP2) * speed_buffering)[s-1] reverse rate constant (Kr): speed_buffering[s-1] user defined (speed_buffering): 1000.0[s-1]
RG_GDP_MGaGTP_M+RGbeta_M	NE_RG M	MassAction	RG_GDP_MGaGTP_M+RGbeta_M
		reaction rate (J): ((Kf * RG_GDP_M) - ((Kr * GaGTP_M) * RGbeta_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.5E-5[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1]
Fura4F_C+Ca_CCa_Fura4F_C	Cabind_Fura4F C	MassAction	Fura4F_C+Ca_CCa_Fura4F_C
		reaction rate (J): (((Kf * Fura4F_C) * Ca_C) - (Kr * Ca_Fura4F_C))[uM.s-1] forward rate constant (Kf): speed_Ca_Fura4F[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Fura4F * kd_Fura4F)[s-1] user defined (speed_Ca_Fura4F): 10.0[uM-1.s-1] user defined (kd_Fura4F): 0.14[uM]
RGbeta_M+AP_EXRLGbeta_M	L2beta M	MassAction	RGbeta_M+AP_EXRLGbeta_M
		reaction rate (J): (((Kf * RGbeta_M) * AP_EX) - (Kr * RLGbeta_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1]
RLP_M+Arrestin1RLPA1	Arrestin 1 M	MassAction	RLP_M+Arrestin1RLPA1
		reaction rate (J): (((Kf * RLP_M) * Arrestin1) - (Kr * RLPA1))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 0.006[s-1.uM-1] reverse rate constant (Kr): 1.0E-6[s-1]
RLPA1RLPAC_M	RLPA1 to clathrin M	MassAction	RLPA1RLPAC_M
		reaction rate (J): ((Kf * RLPA1) - (Kr * RLPAC_M))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 0.0[s-1] reverse rate constant (Kr): 0.0[s-1]

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

C	Compartment (+) (-)

Ca_store	Compartment (+) (-)

M	Membrane N/A

ERM	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
RLPAC_M	M

dynamin	C

endocytosis	M

PI_M	M

KCNQ_M	M

G_GDP_M	M

C1_dom_C	C

PH_YFP_PIP2_M	M

RLPA2_M	M

PA_2AG_M	M

IP3_C	C

RLGbeta_M	M

KCNQ_PIP2_M	M

PLC_M	M

Ca_Fura4F_C	C

GaGTP_M	M

GaGDP_PLC_M	M

K_C	C

RLP_M	M

Gbeta_M	M

Fura4F_C	C

RGbeta_M	M

R_M	M

Ga_GDP_M	M

RG_GDP_M	M

Arrestin2	C

IP3_LibraVIII_C	C

IP3_PH_YFP_C	C

PIP2_M	M

Ca_Ca_store	Ca_store

boundPIP2_M	M

LibraVIII_C	C

DAG_M	M

AP_EX	EX

Palk_C1	C

PH_YFP_C	C

RL_M	M

GaGTP_PLC_M	M

noninactiveIP3R	ERM

RLG_GDP_M	M

K_EX	EX

PKC_cyto	C

Palk_C2	C

Ca_C	C

PKC_DAG_M	M

RP_M	M

Palk_O4	C

IP3_pipette	EX

C1_DAG_M	M

AP_conc_EX	EX

PI4P_M	M

inactiveIP3R	ERM

Palk_C3	C

RLPA1	M

Arrestin1	C

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
modelinOct2010	Deterministic (ODE) Compartmental	cloned from 'modelinOct2010' owned by user bfalken cloned from 'modelinOct2010' owned by user hillelab cloned from 'modelinOct2010' owned by user bfalken (copied from PBio519 talk) (copied from M1R activation, manuscript 1) (copied from M1R activation) (copied from PipDecay) cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab

Application - modelinOct2010

Specifications(Species) - modelinOct2010 See in Dashboard
Species	Initial Condition	Diffusion Constant
AP_EX	0.0 [uM]	0.0 [um2/s]
K_EX	0.0 [uM]	0.0 [um2/s]
IP3_pipette	0.0 [uM]	0.0 [um2/s]
AP_conc_EX	100.0 [uM]	0.0 [um2/s]
dynamin	10.0 [uM]	0.0 [um2/s]
C1_dom_C	0.0 [uM]	0.0 [um2/s]
IP3_C	0.015 [uM]	0.0 [um2/s]
Ca_Fura4F_C	0.0 [uM]	0.0 [um2/s]
K_C	100000.0 [uM]	0.0 [um2/s]
Fura4F_C	0.0 [uM]	0.0 [um2/s]
Arrestin2	7.5 [uM]	0.0 [um2/s]
IP3_LibraVIII_C	0.0 [uM]	0.0 [um2/s]
IP3_PH_YFP_C	0.0 [uM]	0.0 [um2/s]
LibraVIII_C	0.0 [uM]	0.0 [um2/s]
Palk_C1	1.0 [uM]	0.0 [um2/s]
PH_YFP_C	0.0 [uM]	0.0 [um2/s]
PKC_cyto	1.0 [uM]	0.0 [um2/s]
Palk_C2	0.0 [uM]	0.0 [um2/s]
Ca_C	0.13 [uM]	0.0 [um2/s]
Palk_O4	0.0 [uM]	0.0 [um2/s]
Palk_C3	0.0 [uM]	0.0 [um2/s]
Arrestin1	7.5 [uM]	0.0 [um2/s]
Ca_Ca_store	400.0 [uM]	0.0 [um2/s]
RLPAC_M	0.0 [uM]	0.0 [um2/s]
endocytosis	0.0 [uM]	0.0 [um2/s]
PI_M	140000.0 [uM]	0.0 [um2/s]
KCNQ_M	0.0 [uM]	0.0 [um2/s]
G_GDP_M	40.0 [uM]	0.0 [um2/s]
PH_YFP_PIP2_M	0.0 [uM]	0.0 [um2/s]
RLPA2_M	0.0 [uM]	0.0 [um2/s]
PA_2AG_M	0.0 [uM]	0.0 [um2/s]
RLGbeta_M	0.0 [uM]	0.0 [um2/s]
KCNQ_PIP2_M	0.0 [uM]	0.0 [um2/s]
PLC_M	10.0 [uM]	0.0 [um2/s]
GaGTP_M	0.0 [uM]	0.0 [um2/s]
GaGDP_PLC_M	0.0 [uM]	0.0 [um2/s]
RLP_M	0.0 [uM]	0.0 [um2/s]
Gbeta_M	0.0 [uM]	0.0 [um2/s]
RGbeta_M	0.0 [uM]	0.0 [um2/s]
R_M	5000.0 [uM]	0.0 [um2/s]
Ga_GDP_M	0.0 [uM]	0.0 [um2/s]
RG_GDP_M	0.0 [uM]	0.0 [um2/s]
PIP2_M	5000.0 [uM]	0.0 [um2/s]
boundPIP2_M	(( - 1.0 + foldPIP2) * PIP2_M) [uM]	0.0 [um2/s]
DAG_M	13.0 [uM]	0.0 [um2/s]
RL_M	0.0 [uM]	0.0 [um2/s]
GaGTP_PLC_M	0.0 [uM]	0.0 [um2/s]
RLG_GDP_M	0.0 [uM]	0.0 [um2/s]
PKC_DAG_M	0.0 [uM]	0.0 [um2/s]
RP_M	0.0 [uM]	0.0 [um2/s]
C1_DAG_M	0.0 [uM]	0.0 [um2/s]
PI4P_M	3600.0 [uM]	0.0 [um2/s]
RLPA1	0.0 [uM]	0.0 [um2/s]
noninactiveIP3R	1.0 [uM]	0.0 [um2/s]
inactiveIP3R	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - modelinOct2010 See in Dashboard
Name	Reaction Mapping
PIP5K_5Pase	included
PH_YFP_PIP2	included
NE_RLG	included
reaction 1 for phosphorylation of ligand bound receptor	included
reconstitution	included
G2	included
DAGPase	included
GTPase_Ga	included
PLCassoc	included
PH_YFP_IP3	included
r12	excluded
L2	included
clathrin formation rate	included
h_reaction_IP3Rinactivation	included
L1	included
PLC_on_PI4P	included
reaction 2 for phosphorylation of receptor	included
NE_G	included
ligand2	included
r24	excluded
IP3deg_Palk	excluded
PI4K_4Pase	included
IP3_dialysis	included
IP3_LibraVIII	included
VSP	included
G1beta	included
NE_GaP	included
IP3Pase_FDH	included
arrestin binding	included
r23	excluded
PIP2bindKCNQ	included
pinching	included
G2beta	included
PIP2hydr	included
Oxo_appl	included
PLCdiss	included
G1	included
GTPase_GaP	included
PKC_DAG binding	included
C1bindDAG	included
PIP2_buffering	included
NE_RG	included
Cabind_Fura4F	included
L2beta	included
Arrestin 1	included
RLPA1 to clathrin	included
SERCA_flux_FDH	included
KCNQ2/3	included
SERCA_Palk	excluded
leak_Palk	excluded
IP3R_flux_FDH	included
RyR_Palk	excluded
IP3R_Palk	excluded
ER_leak_flux_FDH	included

Simulations - modelinOct2010 See in Dashboard
Name	End Time	Output Options
Figure 7	1000.0 [s]	KeepEvery 10 KeepAtMost 1000

Geometry non-spatial754981975 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			ERM

Global Parameters

Global Parameters See in Dashboard
Name	Expression
KfL1	(KrL1 / KL1)[uM-1.s-1]

KrL1	5.555555555555555[s-1]

KfG1	(0.1 * KfG2)[um2.molecules-1.s-1]

KfG2	0.0026666[um2.molecules-1.s-1]

KrG2	0.68[s-1]

KfL2	KfL1[uM-1.s-1]

KrL2	(KL2 * KfL2) [s-1]

allRL	(RL_M + RLG_GDP_M + RLGbeta_M)[molecules.um-2]

KrG1	(KfG1 * KG1) [s-1]

alpha	100.0 [1]

KL1	40.0 [uM]

KL2	2.0 [uM]

KG1	(KG2 * alpha) [molecules.um-2]

KG2	(KrG2 / KfG2) [molecules.um-2]

allRGbeta	(RG_GDP_M + RLG_GDP_M + RLGbeta_M + RGbeta_M)[molecules.um-2]

allGabg	(G_GDP_M + RG_GDP_M + RLG_GDP_M)[molecules.um-2]

allGaPLC	(GaGTP_PLC_M + GaGDP_PLC_M)[molecules.um-2]

allPIP2M	(PIP2_M + KCNQ_PIP2_M + PH_YFP_PIP2_M + boundPIP2_M)[molecules.um-2]

allPH_cytoplasm	(PH_YFP_C + IP3_PH_YFP_C)[uM]

speed_PH_PIP2	1.0[uM-1.s-1]

KD_PH_PIP2	0.1[uM]

speed_PH_IP3	10.0[uM-1.s-1]

KD_PH_IP3	0.1[uM]

K_plc	0.2[um2.molecules-1.s-1]

PLC_basal	1.0E-4[s-1]

start	100.0[s]

end	1000.0[s]

foldPIP2	3.0 [1]

KD_act_Ca_IP3R	0.2[uM]

KD_IP3_IP3R	0.1[uM]

IP3R	pow((h * IP3_C * Ca_C / (IP3_C + KD_IP3_IP3R) / (Ca_C + KD_act_Ca_IP3R)),3.0)[1]

KD_DAG_C1	2.0[uM]

speed_DAG_C1	10.0[uM-1.s-1]

activePKC	(DAG_M * PIP2_M / ((DAG_M + (1000.0 * KD_DAG_C1)) * (PIP2_M + (1000.0 * KD_PH_PIP2))))[1]

h	(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R))[1]

stim_4k	(stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) [s-1]

stim_4k_max	0.15 [s-1]

stim_5K_max	5.75 [s-1]

stim_5k	(stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) [s-1]

tau_stim_onset	1.0[s]

tau_stim_recovery	5.0[s]

k5k_base	0.0181[s-1]

OxoMforKinases	0.0 [uM]

all_IP3	(IP3_C + IP3_LibraVIII_C + IP3_PH_YFP_C)[uM]

r_FDH	1.0[1]

r_Palk	0.0[1]

perms2pers	1000.0[s-1]

uM2nM	1000.0[uM-1]

removeuM	1.0[uM-1]

kf_R_M	1.0E-4[s-1]

kr_RP_M	2.0[s-1]

Kp2	0.2[molecules.um-2]

kf_R_M_stim	0.01[tbd]