ModelBricks - Model Print Page

Name - Kruse_Kohout_Hille_CiVSP

BioModel ID - 145545992

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
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): 0.77[uM]
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]
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]
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]
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]
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): (0.625 * foldPIP2)[s-1] reverse rate constant (Kr): (0.45 * foldPIP2)[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): 1000.0[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]
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]
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 * VSP_conc)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP): (VSPmax / (1.0 + exp((1.4 * qKT * (V - Vhalf)))))[s-1] user defined (Vhalf): 0.095[V] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[V] user defined (VSPmax): (8.0 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (qKT): -40.5898[A.s3.kg-1.m-2] user defined (VSP_end): 52.0[s] 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]
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): 0.05[s-1]
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 * k4K_max)[s-1] reverse rate constant (Kr): 0.003[s-1] user defined (k4K_max): 2.9E-5[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]
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]
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]
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]
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]
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]
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]
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]
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)))[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]
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]
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]
PIP3PI3_4_P2	VSP_PIP3 M	MassAction	PIP3PI3_4_P2
		reaction rate (J): ((Kf * PIP3) - (Kr * PI3_4_P2))[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_PIP3 * VSP_conc)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP_PIP3): (VSP_PIP3max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PIP3)))))[s-1] user defined (VSP_PIP3max): (2.0 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[V] user defined (Vhalf_PIP3): 0.095[V] user defined (VSP_end): 52.0[s] user defined (VSP_start): 50.0[s] user defined (qKT): -40.5898[A.s3.kg-1.m-2]
PIP2_MPIP3	PI3K_PTEN M	MassAction	PIP2_MPIP3
		reaction rate (J): ((Kf * PIP2_M) - (Kr * PIP3))[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): 0.35454545[s-1] reverse rate constant (Kr): (0.45 * foldPIP2)[s-1]
PI3_4_P2+TAPP1_dom_CTAPP1_PI34P2_M	TAPP1_binding M	MassAction	PI3_4_P2+TAPP1_dom_CTAPP1_PI34P2_M
		reaction rate (J): (((Kf * PI3_4_P2) * TAPP1_dom_C) - (Kr * TAPP1_PI34P2_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_TAPP1_PI34P2[s-1.uM-1] reverse rate constant (Kr): (KD_TAPP1_PI34P2 * speed_TAPP1_PI34P2)[s-1] user defined (speed_TAPP1_PI34P2): 1.0[s-1.uM-1] user defined (KD_TAPP1_PI34P2): 0.1[uM]
PH_Btk_dom_C+PIP3PH_Btk_PIP3_M	PH_Btk_binding M	MassAction	PH_Btk_dom_C+PIP3PH_Btk_PIP3_M
		reaction rate (J): (((Kf * PH_Btk_dom_C) * PIP3) - (Kr * PH_Btk_PIP3_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_Btk_PIP3[s-1.uM-1] reverse rate constant (Kr): (KD_PH_Btk * speed_PH_Btk_PIP3)[s-1] user defined (speed_PH_Btk_PIP3): 1.0[s-1.uM-1] user defined (KD_PH_Btk): 0.3[uM]
PI3_4_P2PI4P_M	PI3K_on_PIP4P M	MassAction	PI3_4_P2PI4P_M
		reaction rate (J): ((Kf * PI3_4_P2) - (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): (7.5E-4 * foldPIP2)[s-1] reverse rate constant (Kr): 7.5E-4[s-1]
P4M_dom_C+PI4P_MP4M_PI4P_M	P4M_PI4P_binding 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]
PIP3PIP2_M	VSP_5P_PIP3 M	MassAction	PIP3PIP2_M
		reaction rate (J): ((Kf * PIP3) - (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): (kVSP_5P_PIP3 * VSP_conc)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP_5P_PIP3): (VSP_5P_PIP3max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PIP3)))))[s-1] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[tbd] user defined (Vhalf_PIP3): 0.095[tbd] user defined (VSP_5P_PIP3max): (44.0 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (VSP_end): 52.0[s] user defined (VSP_start): 50.0[s] user defined (Vhold): -0.1[tbd]
PI4P_MPIP2_M	PIPKIgamma_PIP 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): (kPIPKIgamma * foldPIP2)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kPIPKIgamma): (PIPKIgamma_max / (1.0 + exp((1.56 * qKT * (V - Vhalf)))))[s-1] user defined (PIPKIgamma_max): (0.0 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (Vhalf): 0.057[V] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[V] user defined (qKT): -40.5898[A.s3.kg-1.m-2] user defined (VSP_end): 52.0[s] user defined (VSP_start): 50.0[s] user defined (Vhold): -0.1[V]
PI3_4_P2PIP3	PIPKIgamma_PI34P2 M	MassAction	PI3_4_P2PIP3
		reaction rate (J): ((Kf * PI3_4_P2) - (Kr * PIP3))[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): (kPIPKIgamma_PI34P2 * foldPIP2)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kPIPKIgamma_PI34P2): (PIPKIgamma_PI34P2_max / (1.0 + exp((1.56 * qKT * (V - Vhalf)))))[s-1] user defined (Vhalf): 0.057[V] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[V] user defined (PIPKIgamma_PI34P2_max): (0.0 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (VSP_end): 52.0[s] user defined (VSP_start): 50.0[s] user defined (qKT): -40.5898[A.s3.kg-1.m-2]
PI3_4_P2PI4P_VSPbound	VSP_PI34P2 M	MassAction	PI3_4_P2PI4P_VSPbound
		reaction rate (J): ((Kf * PI3_4_P2) - (Kr * PI4P_VSPbound))[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_PI34P2 * VSP_conc)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP_PI34P2): (VSP_PI34P2max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PI34P2)))))[s-1] user defined (Vhalf_PI34P2): 0.095[V] user defined (V): (Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end)))[V] user defined (VSP_PI34P2max): (0.15 * ((t > VSP_start) * (t < VSP_end)))[s-1] user defined (qKT): -40.5898[A.s3.kg-1.m-2] user defined (VSP_end): 52.0[s] user defined (VSP_start): 50.0[s]
PI4P_VSPboundPI4P_M	PI4P_VSPbound_release M	MassAction	PI4P_VSPboundPI4P_M
		reaction rate (J): ((Kf * PI4P_VSPbound) - (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): (5.0 * (t > VSP_end3))[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (VSP_end3): 52.05[s]

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

C	Compartment (+) (-)

EX	Compartment (+) (-)

M	Membrane N/A

ERM	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

PI_M	M

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

PIP3	M

PI3_4_P2	M

TAPP1_dom_C	C

TAPP1_PI34P2_M	M

PH_Btk_dom_C	C

PH_Btk_PIP3_M	M

P4M_dom_C	C

P4M_PI4P_M	M

PI4P_VSPbound	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
modelinOct2010	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 - modelinOct2010

Specifications(Species) - modelinOct2010 See in Dashboard
Species	Initial Condition	Diffusion Constant
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	0.02 [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]
TAPP1_dom_C	0.0 [uM]	0.0 [um2/s]
PH_Btk_dom_C	0.0 [uM]	0.0 [um2/s]
P4M_dom_C	0.0 [uM]	0.0 [um2/s]
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]
PI4P_M	4000.0 [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]
PI_M	140000.0 [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]
PIP3	1338.0 [uM]	0.0 [um2/s]
PI3_4_P2	1200.0 [uM]	0.0 [um2/s]
TAPP1_PI34P2_M	0.0 [uM]	0.0 [um2/s]
PH_Btk_PIP3_M	0.0 [uM]	0.0 [um2/s]
P4M_PI4P_M	0.0 [uM]	0.0 [um2/s]
PI4P_VSPbound	0.0 [uM]	0.0 [um2/s]
inactiveIP3R	0.0 [uM]	0.0 [um2/s]
noninactiveIP3R	1.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - modelinOct2010 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	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
VSP_PIP3	included
PI3K_PTEN	included
TAPP1_binding	included
PH_Btk_binding	included
PI3K_on_PIP4P	included
P4M_PI4P_binding	included
VSP_5P_PIP3	included
PIPKIgamma_PIP	included
PIPKIgamma_PI34P2	included
VSP_PI34P2	included
PI4P_VSPbound_release	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 - modelinOct2010 See in Dashboard
Name	End Time	Output Options
DFH Figures 4C and 5A "Oxo"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figures 4D and 5B "Oxo" and 6F	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 5A "UTP"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 5B "UTP"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 6B "Oxo"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 6B pipette dialysis	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 6E	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 7B	600.0 [s]	KeepEvery 10 KeepAtMost 1000
VSP	60.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 8C	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 8D "4K at resting rate"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
DFH Figure 8D "4K turned off"	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 1E	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 1F	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figures 4G and 4H	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 6B	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figures 6C and 6D	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 8A except Fura, Libra, C1	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 8A Fura	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 8A Libra, C1	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 8B except Fura, Libra, C1	600.0 [s]	KeepEvery 10 KeepAtMost 1000
FDH Figure 8C except Fura, Libra, C1	600.0 [s]	KeepEvery 10 KeepAtMost 1000

Geometry non-spatial61971900 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	0.2[um2.molecules-1.s-1]

PLC_basal	0.0[s-1]

start	0.0[s]

end	0.0[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]

qKT	-40.5898[tbd]

VSP_conc	1.6[1]

Vstep	0.16[V]

Vhold	-0.1[V]

Vcommand	0.16[V]