ModelBricks - Model Print Page

Name - hillelab: KruseVivasTraynorKaplanHille_PI-metabolism_SCG_2015

BioModel ID - 98296160

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
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]
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]
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]
oxoM_EX+RGbeta_MRLGbeta_M	L2beta M	MassAction	oxoM_EX+RGbeta_MRLGbeta_M
		reaction rate (J): (((Kf * oxoM_EX) * RGbeta_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): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1]
IP3_C+IP3R_IRBITIP3R_IP3	IP3R_IP3_binding C	MassAction	IP3_C+IP3R_IRBITIP3R_IP3
		reaction rate (J): (((Kf * IP3_C) * IP3R_IRBIT) - (Kr * IP3R_IP3))[uM.s-1] forward rate constant (Kf): (speed_IP3_IRBIT * KD_IP3_IP3R_IRBIT)[s-1.uM-1] reverse rate constant (Kr): (speed_IP3_IRBIT * KD_IP3R_IRBIT)[s-1] user defined (speed_IP3_IRBIT): 1.0[uM-1.s-1] user defined (KD_IP3_IP3R_IRBIT): 0.1[uM] user defined (KD_IP3R_IRBIT): 0.5[uM]
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]
OxoM_conc_EXoxoM_EX	Oxo_appl EX	MassAction	OxoM_conc_EXoxoM_EX
		reaction rate (J): ((Kf * OxoM_conc_EX) - (Kr * oxoM_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]
oxoM_EX+R_MRL_M	L1 M	MassAction	oxoM_EX+R_MRL_M
		reaction rate (J): (((Kf * oxoM_EX) * R_M) - (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]
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): 0.2[s-1]
PIP2_M+PH_YFP_CPH_YFP_PIP2_M	PH_YFP_PIP2 M	MassAction	PIP2_M+PH_YFP_CPH_YFP_PIP2_M
		reaction rate (J): (((Kf * PIP2_M) * PH_YFP_C) - (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]
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	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]
Tubby_C+PIP2_MTubby_PIP2_M	Tubby_PIP2 M	MassAction	Tubby_C+PIP2_MTubby_PIP2_M
		reaction rate (J): (((Kf * Tubby_C) * PIP2_M) - (Kr * Tubby_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_Tubby_PIP2[s-1.uM-1] reverse rate constant (Kr): (KD_Tubby_PIP2 * speed_Tubby_PIP2)[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]
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): 42.0[s] user defined (Vstep): 0.1[V] user defined (Vhold): -0.06[V] user defined (VSP_start): 40.0[s]
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]
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)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
GaGTP_PLC_MGaGDP_PLC_M	GTPase_GaP M	GeneralKinetics	GaGTP_PLC_MGaGDP_PLC_M
		reaction rate (J): (15.0 * GaGTP_PLC_M)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
Ca_C+Fura2_CCa_Fura2_C	Cabind_Fura2 C	MassAction	Ca_C+Fura2_CCa_Fura2_C
		reaction rate (J): (((Kf * Ca_C) * Fura2_C) - (Kr * Ca_Fura2_C))[uM.s-1] forward rate constant (Kf): speed_Ca_Fura2[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Fura2 * kd_Fura2)[s-1] user defined (speed_Ca_Fura2): 10.0[uM-1.s-1] user defined (kd_Fura2): 0.145[uM]
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.s-1.um-2.uM-1]
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 * k5K_rest)[s-1] reverse rate constant (Kr): (0.028 * foldPIP2)[s-1] user defined (k5K_rest): 0.02[s-1]
IP3_C+LibraVIII_CIP3_LibraVIII_C	IP3_LibraVIII C	MassAction	IP3_C+LibraVIII_CIP3_LibraVIII_C
		reaction rate (J): (((Kf * IP3_C) * LibraVIII_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]
DAG_M+C1_dom_CC1_DAG_M	C1bindDAG M	MassAction	DAG_M+C1_dom_CC1_DAG_M
		reaction rate (J): (((Kf * DAG_M) * C1_dom_C) - (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]
IP3_C	IP3Pase_KVH C	GeneralKinetics	IP3_C
		reaction rate (J): (K_IP3ase * IP3_C)[uM.s-1] user defined (K_IP3ase): (0.13 * r_FDH_IP3ase)[s-1] user defined (r_FDH_IP3ase): 1.0[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]
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]
oxoM_EX+RG_GDP_MRLG_GDP_M	L2 M	MassAction	oxoM_EX+RG_GDP_MRLG_GDP_M
		reaction rate (J): (((Kf * oxoM_EX) * RG_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): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1]
PI_MPI4P_M	PI4K 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_rest)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (K4_rest): 8.0E-4[s-1]
Ca_Buffer_low_aff+Ca_CCa_Buffer_low_aff_Ca	Ca_Buffering_low_aff C	MassAction	Ca_Buffer_low_aff+Ca_CCa_Buffer_low_aff_Ca
		reaction rate (J): (((Kf * Ca_Buffer_low_aff) * Ca_C) - (Kr * Ca_Buffer_low_aff_Ca))[uM.s-1] forward rate constant (Kf): speed_Ca_Buffer_low_aff[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Buffer_low_aff * KD_Ca_Buffer_low_aff)[s-1] user defined (speed_Ca_Buffer_low_aff): 10.0[s-1.uM-1] user defined (KD_Ca_Buffer_low_aff): 1.0[uM]
G_GDP_M+R_MRG_GDP_M	G1 M	MassAction	G_GDP_M+R_MRG_GDP_M
		reaction rate (J): (((Kf * G_GDP_M) * R_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]
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]
G_GDP_MGbeta_M+GaGTP_M	NE_G M	MassAction	G_GDP_MGbeta_M+GaGTP_M
		reaction rate (J): ((Kf * G_GDP_M) - ((Kr * Gbeta_M) * GaGTP_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]
PI4P_MPI_M	PI4Pase M	MassAction	PI4P_MPI_M
		reaction rate (J): ((Kf * PI4P_M) - (Kr * PI_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): 0.12[s-1] reverse rate constant (Kr): 0.0[s-1]
P4M_dom_C+PI4P_MP4M_PI4P_M	P4M_bind_PI4P M	MassAction	P4M_dom_C+PI4P_MP4M_PI4P_M
		reaction rate (J): (((Kf * P4M_dom_C) * PI4P_M) - (Kr * P4M_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): speed_P4M_PI4P[s-1.uM-1] reverse rate constant (Kr): (KD_P4M_PI4P * speed_P4M_PI4P)[s-1] user defined (speed_P4M_PI4P): 1.0[s-1.uM-1] user defined (KD_P4M_PI4P): 1.5[uM]
Ca_Buffer_high_aff+Ca_CCa_Buffer_high_aff_Ca	Ca_Buffering_high_aff C	MassAction	Ca_Buffer_high_aff+Ca_CCa_Buffer_high_aff_Ca
		reaction rate (J): (((Kf * Ca_Buffer_high_aff) * Ca_C) - (Kr * Ca_Buffer_high_aff_Ca))[uM.s-1] forward rate constant (Kf): speed_Ca_high_aff[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_high_aff * KD_Ca_high_aff)[s-1] user defined (speed_Ca_high_aff): 10.0[s-1.uM-1] user defined (KD_Ca_high_aff): 0.1[uM]
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]
GaGDP_PLC_MPLC_M+Ga_GDP_M	PLCdiss M	MassAction	GaGDP_PLC_MPLC_M+Ga_GDP_M
		reaction rate (J): ((Kf * GaGDP_PLC_M) - ((Kr * PLC_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] forward rate constant (Kf): 0.71[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-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]
PH_YFP_C+IP3_CIP3_PH_YFP_C	PH_YFP_IP3 C	MassAction	PH_YFP_C+IP3_CIP3_PH_YFP_C
		reaction rate (J): (((Kf * PH_YFP_C) * IP3_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]
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]
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]
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]

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

Ca_store	Compartment (+) (-)

EX	Compartment (+) (-)

M	Membrane N/A

ERM	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
Ca_Buffer_high_aff	C

Ca_Buffer_high_aff_Ca	C

IP3R_IRBIT	C

IP3_PH_YFP_C	C

Ca_Ca_store	Ca_store

R_M	M

RLGbeta_M	M

RL_M	M

PH_YFP_C	C

PH_YFP_PIP2_M	M

K_C	C

KCNQ_M	M

Tubby_PIP2_M	M

KCNQ_PIP2_M	M

K_EX	EX

boundPIP2_M	M

Ca_Buffer_low_aff_Ca	C

P4M_dom_C	C

Ca_Fura2_C	C

IP3_LibraVIII_C	C

GaGDP_PLC_M	M

noninactiveIP3R	ERM

OxoM_conc_EX	EX

GaGTP_M	M

inactiveIP3R	ERM

LibraVIII_C	C

Gbeta_M	M

Fura2_C	C

DAG_M	M

C1_dom_C	C

G_GDP_M	M

RG_GDP_M	M

PI_M	M

PA_2AG_M	M

Ca_C	C

PIP2_M	M

PI4P_M	M

GaGTP_PLC_M	M

Palk_C1	C

RLG_GDP_M	M

Ga_GDP_M	M

PLC_M	M

IP3_C	C

Tubby_C	C

Palk_O4	C

RGbeta_M	M

C1_DAG_M	M

Palk_C2	C

Palk_C3	C

Ca_Buffer_low_aff	C

IP3R_IP3	C

oxoM_EX	EX

P4M_PI4P_M	M

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
simulations	Deterministic (ODE) Compartmental	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 - simulations

Specifications(Species) - simulations See in Dashboard
Species	Initial Condition	Diffusion Constant
Ca_Buffer_high_aff	4.9721916 [uM]	0.0 [um2/s]
Ca_Buffer_high_aff_Ca	5.0278084 [uM]	0.0 [um2/s]
IP3R_IRBIT	0.01 [uM]	0.0 [um2/s]
IP3_PH_YFP_C	0.0 [uM]	0.0 [um2/s]
PH_YFP_C	0.0 [uM]	0.0 [um2/s]
K_C	100000.0 [uM]	0.0 [um2/s]
Ca_Buffer_low_aff_Ca	1.836644 [uM]	0.0 [um2/s]
P4M_dom_C	0.0 [uM]	0.0 [um2/s]
Ca_Fura2_C	0.0 [uM]	0.0 [um2/s]
IP3_LibraVIII_C	0.0 [uM]	0.0 [um2/s]
LibraVIII_C	0.0 [uM]	0.0 [um2/s]
Fura2_C	0.0 [uM]	0.0 [um2/s]
C1_dom_C	0.0 [uM]	0.0 [um2/s]
Ca_C	0.101 [uM]	0.0 [um2/s]
Palk_C1	1.0 [uM]	0.0 [um2/s]
IP3_C	0.02 [uM]	0.0 [um2/s]
Tubby_C	0.0 [uM]	0.0 [um2/s]
Palk_O4	0.0 [uM]	0.0 [um2/s]
Palk_C2	0.0 [uM]	0.0 [um2/s]
Palk_C3	0.0 [uM]	0.0 [um2/s]
Ca_Buffer_low_aff	18.163356 [uM]	0.0 [um2/s]
IP3R_IP3	0.0 [uM]	0.0 [um2/s]
Ca_Ca_store	361.8635 [uM]	0.0 [um2/s]
K_EX	0.0 [uM]	0.0 [um2/s]
OxoM_conc_EX	10.0 [uM]	0.0 [um2/s]
oxoM_EX	0.0 [uM]	0.0 [um2/s]
R_M	15.87 [uM]	0.0 [um2/s]
RLGbeta_M	0.0 [uM]	0.0 [um2/s]
RL_M	0.0 [uM]	0.0 [um2/s]
PH_YFP_PIP2_M	0.0 [uM]	0.0 [um2/s]
KCNQ_M	4.0 [uM]	0.0 [um2/s]
Tubby_PIP2_M	0.0 [uM]	0.0 [um2/s]
KCNQ_PIP2_M	0.0 [uM]	0.0 [um2/s]
boundPIP2_M	(( - 1.0 + foldPIP2) * PIP2_M) [uM]	0.0 [um2/s]
GaGDP_PLC_M	0.0 [uM]	0.0 [um2/s]
GaGTP_M	0.0 [uM]	0.0 [um2/s]
Gbeta_M	0.0 [uM]	0.0 [um2/s]
DAG_M	13.0 [uM]	0.0 [um2/s]
G_GDP_M	40.0 [uM]	0.0 [um2/s]
RG_GDP_M	0.0 [uM]	0.0 [um2/s]
PI_M	226975.0 [uM]	0.0 [um2/s]
PA_2AG_M	0.0 [uM]	0.0 [um2/s]
PIP2_M	3232.0 [uM]	0.0 [um2/s]
PI4P_M	4540.0 [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]
Ga_GDP_M	0.0 [uM]	0.0 [um2/s]
PLC_M	3.12 [uM]	0.0 [um2/s]
RGbeta_M	0.0 [uM]	0.0 [um2/s]
C1_DAG_M	0.0 [uM]	0.0 [um2/s]
P4M_PI4P_M	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) - simulations See in Dashboard
Name	Reaction Mapping
PIP2_buffering	included
G2	included
r24	excluded
L2beta	included
IP3R_IP3_binding	included
NE_RLG	included
Oxo_appl	included
L1	included
DAGPase	included
PH_YFP_PIP2	included
PLCassoc	included
IP3deg_Palk	excluded
Tubby_PIP2	included
reconstitution	included
VSP	included
r12	excluded
PIP2hydr	included
GTPase_GaP	included
Cabind_Fura2	included
h_reaction_IP3Rinactivation	included
PIP5K_5Pase	included
IP3_LibraVIII	included
C1bindDAG	included
IP3Pase_KVH	included
G2beta	included
PLC_on_PI4P	included
L2	included
PI4K	included
Ca_Buffering_low_aff	included
G1	included
NE_RG	included
NE_G	included
PI4Pase	included
P4M_bind_PI4P	included
Ca_Buffering_high_aff	included
r23	excluded
PLCdiss	included
GTPase_Ga	included
PH_YFP_IP3	included
PIP2bindKCNQ	included
NE_GaP	included
G1beta	included
SERCA_Palk	excluded
leak_Palk	excluded
SERCA_flux_KVH	included
IP3R_flux_KVH	included
KCNQ2/3	included
ER_leak_flux_KVH	included
RyR_Palk	excluded
IP3R_Palk	excluded

Simulations - simulations See in Dashboard
Name	End Time	Output Options
Oxo-M	600.0 [s]	KeepEvery 10 KeepAtMost 1000
VSP	600.0 [s]	KeepEvery 10 KeepAtMost 1000
Oxo-M with TubbyR332	600.0 [s]	KeepEvery 10 KeepAtMost 1000
Oxo-M with fura-2	600.0 [s]	KeepEvery 10 KeepAtMost 1000
Oxo-M with PH-PLCd1	600.0 [s]	KeepEvery 10 KeepAtMost 1000
Oxo-M with LIBRAVIII	600.0 [s]	KeepEvery 10 KeepAtMost 1000
Oxo-M with C1-domain	600.0 [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	2.0 [uM]

KL2	(KL1 / alpha) [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	2.0[uM]

speed_PH_IP3	10.0[uM-1.s-1]

KD_PH_IP3	0.1[uM]

K_plc	0.3[um2.molecules-1.s-1]

PLC_basal	0.0[s-1]

start	100.0[s]

end	120.0[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	0.2[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	0.0023647 [s-1]

stim_5K_max	0.1819 [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]

KD_OSBP_PI4P	0.2[uM]

speed_OSBP_PI4P	10.0[uM-1.s-1]

speed_Tubby_PIP2	1.0[uM-1.s-1]

KD_Tubby_PIP2	1.5[uM]

r_KVH	1.0[tbd]