ModelBricks - Model Print Page

Name - PI cycle Figure 6, 7 & S9

BioModel ID - 189512756

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
Ca_C+Fura4F_CCa_Fura4F_C	Cabind_Fura4F C	MassAction	Ca_C+Fura4F_CCa_Fura4F_C
		reaction rate (J): (((Kf * Ca_C) * Fura4F_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): 0.77[uM]
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]
PI4P_MDAG_M	PLC_on_PI4P M	GeneralKinetics	PI4P_MDAG_M
		reaction rate (J): ((PI4P_M * (PLC_basal + (GaGTP_PLC_M * K_plc))) * ((t <= start) + (((start < t) * (t < end)) * (1.0 - exp(( - (t - start) / tau_PIP2_PLC))))) * 0.5)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[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]
R_M+oxoM_EXRL_M	L1 M	MassAction	R_M+oxoM_EXRL_M
		reaction rate (J): (((Kf * R_M) * oxoM_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]
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]
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)))[s-1] reverse rate constant (Kr): 0.00144[s-1] user defined (k5K_rest): 0.0012[s-1] user defined (k5k_Oxo): (k5K_rest + ((stim_5k - k5K_rest + k5k_base) * (1.0 - exp(((start - t) / tau_stim_onset)))))[s-1] user defined (k5k_base): 0.0117624[s-1] user defined (stim_5k): (stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1] user defined (stim_5K_max): 0.003092299998[s-1]
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]
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]
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]
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]
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]
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]
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): 1.0[s-1]
RGbeta_M+oxoM_EXRLGbeta_M	L2beta M	MassAction	RGbeta_M+oxoM_EXRLGbeta_M
		reaction rate (J): (((Kf * RGbeta_M) * oxoM_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]
RLG_GDP_MGaGTP_M+RLGbeta_M	NE_RLG M	GeneralKinetics	RLG_GDP_MGaGTP_M+RLGbeta_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]
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]
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]
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]
R_M+Gbeta_MRGbeta_M	G1beta M	MassAction	R_M+Gbeta_MRGbeta_M
		reaction rate (J): (((Kf * R_M) * Gbeta_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]
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): 5.0[s-1]
PI_MPI4P_M	PI4K_4Pase_M 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 * (t < (start + tau_stim_onset))) + (K4_Oxo * (t >= (start + tau_stim_onset)) * (t <= end))))[s-1] reverse rate constant (Kr): 8.19E-4[s-1] user defined (K4_Oxo): ((K4_rest + ((stim_4k - K4_rest + K4_base) * (1.0 - exp(((start + tau_stim_onset - t) / tau_stim_onset))))) / 4.0)[s-1] user defined (stim_4k): ((0.0141486 / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * stim_second)[s-1] user defined (K4_rest): 3.9E-4[s-1] user defined (K4_base): 3.62826E-4[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]
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): 50.0[s-1]
RL_M+Gbeta_MRLGbeta_M	G2beta M	MassAction	RL_M+Gbeta_MRLGbeta_M
		reaction rate (J): (((Kf * RL_M) * Gbeta_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]
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]
RG_GDP_M+oxoM_EXRLG_GDP_M	L2 M	MassAction	RG_GDP_M+oxoM_EXRLG_GDP_M
		reaction rate (J): (((Kf * RG_GDP_M) * oxoM_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]
GaGTP_M+PLC_MGaGTP_PLC_M	PLCassoc M	MassAction	GaGTP_M+PLC_MGaGTP_PLC_M
		reaction rate (J): (((Kf * GaGTP_M) * PLC_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]
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]
PIP2_M+KCNQ_MKCNQ_PIP2_M	PIP2bindKCNQ M	GeneralKinetics	PIP2_M+KCNQ_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]
PIP2_MDAG_M+IP3_C	PIP2hydr M	GeneralKinetics	PIP2_MDAG_M+IP3_C
		reaction rate (J): (((PIP2_M * (PLC_basal + (K_plc * foldPIP2 * GaGTP_PLC_M))) * (t <= start)) + ((PIP2_M * (PLC_basal + (K_plc * foldPIP2 * GaGTP_PLC_M))) * ((1.0 - exp(( - (t - start) / tau_PIP2_PLC))) * (start < t) * (t < end))))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[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]
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]
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]
G_GDP_M+RL_MRLG_GDP_M	G2 M	MassAction	G_GDP_M+RL_MRLG_GDP_M
		reaction rate (J): (((Kf * G_GDP_M) * RL_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]
Ga_GDP_M+Gbeta_MG_GDP_M	reconstitution M	GeneralKinetics	Ga_GDP_M+Gbeta_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]
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]
PI_GPI4P_G	PI4K_4Pase_G Golgi_Vesicle_M	MassAction	PI_GPI4P_G
		reaction rate (J): ((Kf * PI_G) - (Kr * PI4P_G))[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 * (t < (start + onset_second))) + (K4_Oxo * (t >= (start + onset_second)) * (t <= end))))[s-1] reverse rate constant (Kr): 0.3276[s-1] user defined (K4_Oxo): (K4_rest + ((stim_4k - K4_rest + K4_base) * (1.0 - exp(((start + onset_second - t) / tau_PI4K)))))[s-1] user defined (stim_4k): (((stim_4k_max + 1.0) / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * 0.00288)[s-1] user defined (K4_base): 0.0030978744[s-1]
PI4P_GPIP2_M	PIP5K_5Pase_G M	MassAction	PI4P_GPIP2_M
		reaction rate (J): ((Kf * PI4P_G) - (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 + onset_second)) * (t <= end) * k5k_Oxo))[s-1] reverse rate constant (Kr): (0.024 * (t >= (start + onset_second)) * (t <= end))[s-1] user defined (k5k_Oxo): (k5k_rest + ((k5k_base + K5K_stim - k5k_rest) * (1.0 - exp(((start + onset_second - t) / tau_second)))))[s-1] user defined (k5k_rest): 0.04[s-1] user defined (K5K_stim): (5.0 / (1.0 + exp( - (277.7777777777778 * ( - 0.0175 + OxoMforKinases)))))[s-1] user defined (k5k_base): 0.0015875[s-1]
PI_EPI_M	PI_EX_M M	MassAction	PI_EPI_M
		reaction rate (J): ((Kf * PI_E) - (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): (((PI_EX_rest * (t <= (start + tau_stim_onset))) + (PI_EX_Oxo * ((start + tau_stim_onset) < t) * (t <= end))) / 4.0)[s-1] reverse rate constant (Kr): (0.18144 / 4.0)[s-1] user defined (PI_EX_rest): 0.018144[s-1] user defined (PI_EX_Oxo): (PI_EX_rest + ((PI_EX_base + PI_EX_stim - PI_EX_rest) * (1.0 - exp(((start + tau_stim_onset - t) / tau_PI_EX)))))[s-1] user defined (PI_EX_base): 0.017927[s-1] user defined (tau_PI_EX): 100.0[s] user defined (PI_EX_stim): (stim_PI_EX_max / (1.0 + exp( - (277.7777777777778 * ( - 0.0175 + OxoMforKinases)))))[s-1] user defined (stim_PI_EX_max): 0.02737[s-1]
PI_EPI_G	PI_EX_G Golgi_Vesicle_M	MassAction	PI_EPI_G
		reaction rate (J): ((Kf * PI_E) - (Kr * PI_G))[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): ((0.16 * 3.0) * a)[s-1] reverse rate constant (Kr): ((0.064 * 3.0) * a)[s-1] user defined (a): 0.5[s-1]
P4M_C+PI4P_GP4M_PI4P_G	PI4P_P4M_G Golgi_Vesicle_M	MassAction	P4M_C+PI4P_GP4M_PI4P_G
		reaction rate (J): (((Kf * P4M_C) * PI4P_G) - (Kr * P4M_PI4P_G))[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]
PI4P_M+P4M_CP4M_PI4P_M	PI4P_P4M_M M	MassAction	PI4P_M+P4M_CP4M_PI4P_M
		reaction rate (J): (((Kf * PI4P_M) * P4M_C) - (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]
PI4P_G+FAPP1_CFAPP1_PI4P_G	PI4P_FAPP1_G Golgi_Vesicle_M	MassAction	PI4P_G+FAPP1_CFAPP1_PI4P_G
		reaction rate (J): (((Kf * PI4P_G) * FAPP1_C) - (Kr * FAPP1_PI4P_G))[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_FAPP1_PI4P[s-1.uM-1] reverse rate constant (Kr): (KD_FAPP1_PI4P * speed_FAPP1_PI4P)[s-1] user defined (speed_FAPP1_PI4P): 1.0[s-1.uM-1] user defined (KD_FAPP1_PI4P): 9.0[molecules.um-2]
PI4P_GPI_G	Sac1_G Golgi_Vesicle_M	MassAction	PI4P_GPI_G
		reaction rate (J): ((Kf * PI4P_G) - (Kr * PI_G))[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): (3.276 * (ratio * (((start - 50.0) < t) * (1.0 - exp(((start - 50.0 - t) / 1000.0))))))[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (ratio): 0.0[s-1]

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

Ca_store	Compartment (+) (-)

C	Compartment (+) (-)

M	Membrane N/A

ERM	Membrane N/A

Golgi_Vesicle_M	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
IP3_pipette	EX

PI4P_M	M

PH_YFP_PIP2_M	M

KCNQ_M	M

inactiveIP3R	ERM

IP3_PH_YFP_C	C

RLG_GDP_M	M

RL_M	M

GaGTP_PLC_M	M

GaGTP_M	M

RLGbeta_M	M

Gbeta_M	M

C1_dom_C	C

K_C	C

Ca_C	C

RGbeta_M	M

R_M	M

noninactiveIP3R	ERM

boundPIP2_M	M

IP3_LIBRAvIII_C	C

LIBRAvIII_C	C

G_GDP_M	M

RG_GDP_M	M

Ga_GDP_M	M

DAG_M	M

oxoM_EX	EX

PA_2AG_M	M

PLC_M	M

PH_YFP_C	C

PIP2_M	M

OxoM_conc_EX	EX

Ca_Fura4F_C	C

Ca_Ca_store	Ca_store

Fura4F_C	C

IP3_C	C

Palk_C1	C

Palk_C2	C

Palk_C3	C

Palk_O4	C

C1_DAG_M	M

GaGDP_PLC_M	M

K_EX	EX

KCNQ_PIP2_M	M

PI4P_G	Golgi_Vesicle_M

PI_E	ERM

PI_M	M

PI_G	Golgi_Vesicle_M

P4M_C	C

P4M_PI4P_M	M

P4M_PI4P_G	Golgi_Vesicle_M

FAPP1_C	C

FAPP1_PI4P_G	Golgi_Vesicle_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
Modeling PI cycle	Deterministic (ODE) Compartmental	cloned from 'Modeling PI cycle' owned by user cherubim0521 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 - Modeling PI cycle

Specifications(Species) - Modeling PI cycle See in Dashboard
Species	Initial Condition	Diffusion Constant
IP3_pipette	0.0 [uM]	0.0 [um2/s]
oxoM_EX	0.0 [uM]	0.0 [um2/s]
OxoM_conc_EX	10.0 [uM]	0.0 [um2/s]
K_EX	0.0 [uM]	0.0 [um2/s]
Ca_Ca_store	400.0 [uM]	0.0 [um2/s]
IP3_PH_YFP_C	0.0 [uM]	0.0 [um2/s]
C1_dom_C	0.0 [uM]	0.0 [um2/s]
K_C	100000.0 [uM]	0.0 [um2/s]
Ca_C	0.13 [uM]	0.0 [um2/s]
IP3_LIBRAvIII_C	0.0 [uM]	0.0 [um2/s]
LIBRAvIII_C	0.0 [uM]	0.0 [um2/s]
PH_YFP_C	0.0 [uM]	0.0 [um2/s]
Ca_Fura4F_C	0.0 [uM]	0.0 [um2/s]
Fura4F_C	0.0 [uM]	0.0 [um2/s]
IP3_C	0.033 [uM]	0.0 [um2/s]
Palk_C1	1.0 [uM]	0.0 [um2/s]
Palk_C2	0.0 [uM]	0.0 [um2/s]
Palk_C3	0.0 [uM]	0.0 [um2/s]
Palk_O4	0.0 [uM]	0.0 [um2/s]
P4M_C	0.0 [uM]	0.0 [um2/s]
FAPP1_C	0.0 [uM]	0.0 [um2/s]
PI4P_M	2000.0 [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]
RLG_GDP_M	0.0 [uM]	0.0 [um2/s]
RL_M	0.0 [uM]	0.0 [um2/s]
GaGTP_PLC_M	0.0 [uM]	0.0 [um2/s]
GaGTP_M	0.0 [uM]	0.0 [um2/s]
RLGbeta_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	500.0 [uM]	0.0 [um2/s]
boundPIP2_M	(( - 1.0 + foldPIP2) * PIP2_M) [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]
Ga_GDP_M	0.0 [uM]	0.0 [um2/s]
DAG_M	13.0 [uM]	0.0 [um2/s]
PA_2AG_M	0.0 [uM]	0.0 [um2/s]
PLC_M	10.0 [uM]	0.0 [um2/s]
PIP2_M	5000.0 [uM]	0.0 [um2/s]
C1_DAG_M	0.0 [uM]	0.0 [um2/s]
GaGDP_PLC_M	0.0 [uM]	0.0 [um2/s]
KCNQ_PIP2_M	0.0 [uM]	0.0 [um2/s]
PI_M	1400.0 [uM]	0.0 [um2/s]
P4M_PI4P_M	0.0 [uM]	0.0 [um2/s]
inactiveIP3R	0.0 [uM]	0.0 [um2/s]
noninactiveIP3R	1.0 [uM]	0.0 [um2/s]
PI_E	14000.0 [uM]	0.0 [um2/s]
PI4P_G	1000.0 [uM]	0.0 [um2/s]
PI_G	35000.0 [uM]	0.0 [um2/s]
P4M_PI4P_G	0.0 [uM]	0.0 [um2/s]
FAPP1_PI4P_G	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - Modeling PI cycle See in Dashboard
Name	Reaction Mapping
Cabind_Fura4F	included
IP3_LibraVIII	included
PLC_on_PI4P	included
NE_RG	included
L1	included
h_reaction_IP3Rinactivation	included
PIP5K_5Pase	included
NE_G	included
GTPase_Ga	included
IP3deg_Palk	excluded
r12	excluded
r23	excluded
r24	excluded
PIP2_buffering	included
L2beta	included
NE_RLG	included
NE_GaP	included
PH_YFP_PIP2	included
VSP	included
G1beta	included
DAGPase	included
PI4K_4Pase_M	included
PH_YFP_IP3	included
IP3Pase_FDH	included
G2beta	included
PLCdiss	included
L2	included
PLCassoc	included
G1	included
PIP2bindKCNQ	included
PIP2hydr	included
IP3_dialysis	included
GTPase_GaP	included
Oxo_appl	included
G2	included
reconstitution	included
C1bindDAG	included
PI4K_4Pase_G	included
PIP5K_5Pase_G	included
PI_EX_M	included
PI_EX_G	included
PI4P_P4M_G	included
PI4P_P4M_M	included
PI4P_FAPP1_G	included
Sac1_G	included
RyR_Palk	excluded
leak_Palk	excluded
SERCA_Palk	excluded
KCNQ2/3	included
ER_leak_flux_FDH	included
IP3R_flux_FDH	included
SERCA_flux_FDH	included
IP3R_Palk	excluded

Simulations - Modeling PI cycle See in Dashboard
Name	End Time	Output Options
S Figure 9A. PtdIns4P_M_P4M	720.0 [s]	OutputTimeStep 1.0
S Figure 9D. InsP3_LIBRA	720.0 [s]	OutputTimeStep 1.0
Backbone Figure 7	720.0 [s]	OutputTimeStep 1.0
S Figure 9E. DAG_C1A	720.0 [s]	OutputTimeStep 1.0
S Figure 9C. PH domain	720.0 [s]	OutputTimeStep 1.0
S Figure 9B. FAPP1	720.0 [s]	OutputTimeStep 1.0
Figure 6G. PtdIns4P_M_P4M Sac1	720.0 [s]	OutputTimeStep 1.0
Figure 6F. PH domain Sac1	720.0 [s]	OutputTimeStep 1.0

Geometry non-spatial1595765197 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			Golgi_Vesicle_M

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	20.0[uM-1.s-1]

KD_PH_PIP2	2.0[uM]

speed_PH_IP3	10.0[uM-1.s-1]

KD_PH_IP3	2.0[uM]

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

PLC_basal	0.0[s-1]

start	120.0[s]

end	720.0[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	0.2[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	((0.0023581 / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * stim_second) [s-1]

stim_4k_max	9.0 [s-1]

stim_5K_max	0.03092299998 [s-1]

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

tau_stim_onset	1.0[s]

k5k_base	0.0117624[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]

onset_second	20.0[s]

K4_base	(2.41884E-4 * 6.0)[s-1]

scale4K	0.75[1]

K4_rest	0.00312[s-1]

K4_Oxo	(K4_rest + ((stim_4k - K4_rest + K4_base) * (1.0 - exp(((start + tau_stim_onset - t) / tau_stim_onset)))))[s-1]

tau_second	300.0[s]

tau_Ga_PI4P_PLC	241.0[tbd]

tau_PM_PI4K	210.0[s]

star	120.0[s]

tau_PI4K	300.0[s]

speed_P4M_PI4P	0.01[um2.s-1.molecules-1]

KD_P4M_PI4P	1.5[uM]

stim_second	(1.0 + ((((stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) - (0.0077419 * stim_4k_max)) * (1.0 - exp(((start + onset_second - t) / tau_second)))) * ((start + onset_second) < t) * (t <= end)))[s-1]

tau_PIP2_PLC	20.0[s]