//Created by libAntimony v2.4 // Warnings from automatic translation: // Unable to use the formula "(L_iso * R) / K_L" to set the assignment rule for LR: Loop detected: LR's definition ((L_iso * R) / K_L) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_iso * R * G) / (K_H * K_C)" to set the assignment rule for LRG: Loop detected: LRG's definition ((L_iso * R * G) / (K_H * K_C)) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(R * G) / K_C" to set the assignment rule for RG: Loop detected: RG's definition ((R * G) / K_C) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_ach * R) / K_L" to set the assignment rule for LR: Loop detected: LR's definition ((L_ach * R) / K_L) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_ach * R * G) / (K_H * K_C)" to set the assignment rule for LRG: Loop detected: LRG's definition ((L_ach * R * G) / (K_H * K_C)) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(R * G) / K_C" to set the assignment rule for RG: Loop detected: RG's definition ((R * G) / K_C) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_iso * R) / K_L" to set the assignment rule for LR: Loop detected: LR's definition ((L_iso * R) / K_L) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_iso * R * G) / (K_H * K_C)" to set the assignment rule for LRG: Loop detected: LRG's definition ((L_iso * R * G) / (K_H * K_C)) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(R * G) / K_C" to set the assignment rule for RG: Loop detected: RG's definition ((R * G) / K_C) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_ach * R) / K_L" to set the assignment rule for LR: Loop detected: LR's definition ((L_ach * R) / K_L) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(L_ach * R * G) / (K_H * K_C)" to set the assignment rule for LRG: Loop detected: LRG's definition ((L_ach * R * G) / (K_H * K_C)) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). // Unable to use the formula "(R * G) / K_C" to set the assignment rule for RG: Loop detected: RG's definition ((R * G) / K_C) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5'). model iancu_jones_harvey_2007__environment(time_) // Variable initializations: time_ = ; end model iancu_jones_harvey_2007__beta_1_adrenergic_parameters(L_iso, K_H, K_L, K_C, time_) // Assignment Rules: L_iso := piecewise( 1 , ( time_ > 120) && (time_ <= 720 ), 1 ); // Variable initializations: K_H = 0.035; K_L = 0.386; K_C = 8.809; time_ = ; end model iancu_jones_harvey_2007__muscarinic_parameters(L_ach, K_H, K_L, K_C, time_) // Assignment Rules: L_ach := piecewise( 0 , ( time_ > 240) && (time_ <= 540 ), 0 ); // Variable initializations: K_H = 0.16; K_L = 11; K_C = 30; time_ = ; end model iancu_jones_harvey_2007__PDE_parameters(k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4) // Variable initializations: k_PDE2 = 20; Km_PDE2 = 50; k_PDE3 = 1.25; Km_PDE3 = 0.08; k_PDE4 = 2.5; Km_PDE4 = 2.2; end model iancu_jones_harvey_2007__G_s_parameters(k_act1, k_act2, k_hydr, k_reas) // Variable initializations: k_act1 = 5; k_act2 = 0.1; k_hydr = 0.8; k_reas = 1.21e3; end model iancu_jones_harvey_2007__G_i_parameters(k_act1, k_act2, k_hydr, k_reas) // Variable initializations: k_act1 = 2.5; k_act2 = 0.05; k_hydr = 0.8; k_reas = 1.21e3; end model iancu_jones_harvey_2007__caveolar_beta_1_adrenergic_receptor_module(LRG, RG, G, L_iso, K_H, K_L, K_C) // Assignment Rules: R := ((R_Total - LR) - LRG) - RG; // Variable initializations: LR = ; LRG = ; RG = ; R_Total = 0.633; G = ; L_iso = ; K_H = ; K_L = ; K_C = ; end model iancu_jones_harvey_2007__caveolar_muscarinic_receptor_module(LRG, RG, G, L_ach, K_H, K_L, K_C) // Assignment Rules: R := ((R_Total - LR) - LRG) - RG; // Variable initializations: LR = ; LRG = ; RG = ; R_Total = 0.633; G = ; L_ach = ; K_H = ; K_L = ; K_C = ; end model iancu_jones_harvey_2007__caveolar_G_s_protein_activation_module(Gs_alpha_GTP, Gs_beta_gamma, Gs_alpha_GDP, Gs_alpha_beta_gamma, Gs_Total, time_, RG, LRG, k_act1, k_act2, k_hydr, k_reas) // Assignment Rules: Gs_alpha_beta_gamma := (Gs_Total - Gs_alpha_GTP) - Gs_alpha_GDP; // Rate Rules: Gs_alpha_GTP' = (RG * k_act2 + LRG * k_act1) - Gs_alpha_GTP * k_hydr; Gs_beta_gamma' = (RG * k_act2 + LRG * k_act1) - Gs_alpha_GDP * Gs_beta_gamma * k_reas; Gs_alpha_GDP' = Gs_alpha_GTP * k_hydr - Gs_alpha_GDP * Gs_beta_gamma * k_reas; // Variable initializations: Gs_alpha_GTP = 0.041983438; Gs_beta_gamma = 0.042634499; Gs_alpha_GDP = 0.000651061; Gs_Total = 10; time_ = ; RG = ; LRG = ; k_act1 = ; k_act2 = ; k_hydr = ; k_reas = ; end model iancu_jones_harvey_2007__caveolar_G_i_protein_activation_module(Gi_alpha_GTP, Gi_beta_gamma, Gi_alpha_GDP, Gi_alpha_beta_gamma, Gi_Total, time_, RG, LRG, k_act1, k_act2, k_hydr, k_reas) // Assignment Rules: Gi_alpha_beta_gamma := (Gi_Total - Gi_alpha_GTP) - Gi_alpha_GDP; // Rate Rules: Gi_alpha_GTP' = (RG * k_act2 + LRG * k_act1) - Gi_alpha_GTP * k_hydr; Gi_beta_gamma' = (RG * k_act2 + LRG * k_act1) - Gi_alpha_GDP * Gi_beta_gamma * k_reas; Gi_alpha_GDP' = Gi_alpha_GTP * k_hydr - Gi_alpha_GDP * Gi_beta_gamma * k_reas; // Variable initializations: Gi_alpha_GTP = 0.012644961; Gi_beta_gamma = 0.013274751; Gi_alpha_GDP = 0.00062979; Gi_Total = 20; time_ = ; RG = ; LRG = ; k_act1 = ; k_act2 = ; k_hydr = ; k_reas = ; end model iancu_jones_harvey_2007__extracaveolar_beta_1_adrenergic_receptor_module(LRG, RG, G, L_iso, K_H, K_L, K_C) // Assignment Rules: R := ((R_Total - LR) - LRG) - RG; // Variable initializations: LR = ; LRG = ; RG = ; R_Total = 0.633; G = ; L_iso = ; K_H = ; K_L = ; K_C = ; end model iancu_jones_harvey_2007__extracaveolar_muscarinic_receptor_module(LRG, RG, G, L_ach, K_H, K_L, K_C) // Assignment Rules: R := ((R_Total - LR) - LRG) - RG; // Variable initializations: LR = ; LRG = ; RG = ; R_Total = 0.633; G = ; L_ach = ; K_H = ; K_L = ; K_C = ; end model iancu_jones_harvey_2007__extracaveolar_G_s_protein_activation_module(Gs_alpha_GTP, Gs_beta_gamma, Gs_alpha_GDP, Gs_alpha_beta_gamma, Gs_Total, time_, RG, LRG, k_act1, k_act2, k_hydr, k_reas) // Assignment Rules: Gs_alpha_beta_gamma := (Gs_Total - Gs_alpha_GTP) - Gs_alpha_GDP; // Rate Rules: Gs_alpha_GTP' = (RG * k_act2 + LRG * k_act1) - Gs_alpha_GTP * k_hydr; Gs_beta_gamma' = (RG * k_act2 + LRG * k_act1) - Gs_alpha_GDP * Gs_beta_gamma * k_reas; Gs_alpha_GDP' = Gs_alpha_GTP * k_hydr - Gs_alpha_GDP * Gs_beta_gamma * k_reas; // Variable initializations: Gs_alpha_GTP = 0.083866891; Gs_beta_gamma = 0.084522918; Gs_alpha_GDP = 0.000656025; Gs_Total = 10; time_ = ; RG = ; LRG = ; k_act1 = ; k_act2 = ; k_hydr = ; k_reas = ; end model iancu_jones_harvey_2007__extracaveolar_G_i_protein_activation_module(Gi_alpha_GTP, Gi_beta_gamma, Gi_alpha_GDP, Gi_alpha_beta_gamma, Gi_Total, time_, RG, LRG, k_act1, k_act2, k_hydr, k_reas) // Assignment Rules: Gi_alpha_beta_gamma := (Gi_Total - Gi_alpha_GTP) - Gi_alpha_GDP; // Rate Rules: Gi_alpha_GTP' = (RG * k_act2 + LRG * k_act1) - Gi_alpha_GTP * k_hydr; Gi_beta_gamma' = (RG * k_act2 + LRG * k_act1) - Gi_alpha_GDP * Gi_beta_gamma * k_reas; Gi_alpha_GDP' = Gi_alpha_GTP * k_hydr - Gi_alpha_GDP * Gi_beta_gamma * k_reas; // Variable initializations: Gi_alpha_GTP = 0.001018705; Gi_beta_gamma = 0.001475253; Gi_alpha_GDP = 0.000456548; Gi_Total = 1; time_ = ; RG = ; LRG = ; k_act1 = ; k_act2 = ; k_hydr = ; k_reas = ; end model iancu_jones_harvey_2007__AC56_module(dcAMP_AC_56_dt, Gs_alpha_GTP, Gi_alpha_GTP) // Assignment Rules: dcAMP_AC_56_dt := (k_AC56 * AC_56 * AF56 * ATP) / (Km_ATP + ATP); k_AC56 := (((0.7 + (3.8234 * power(Gs_alpha_GTP / 1, 0.9787)) / (0.1986 + power(Gs_alpha_GTP / 1, 0.9787))) * (1 + ((1 / 1.4432) * -(1.0061) * power(Gi_alpha_GTP / 1, 0.8356)) / (0.1918 + power(Gi_alpha_GTP / 1, 0.8356))) * MW_AC56) / 60) * 0.001; // Variable initializations: Gs_alpha_GTP = ; Gi_alpha_GTP = ; AC_56 = 3.379; AF56 = 500; MW_AC56 = 130; ATP = 5000; Km_ATP = 315; end model iancu_jones_harvey_2007__AC47_ecav_module(dcAMP_AC_47_ecav_dt, Gs_alpha_GTP, Gi_beta_gamma) // Assignment Rules: dcAMP_AC_47_ecav_dt := (k_AC47_ecav * AC_47_ecav * AF47 * ATP) / (Km_ATP + ATP); k_AC47_ecav := (((0.063 + (2.01 * power(Gs_alpha_GTP * 1000, 1.0043)) / (31.544 + power(Gs_alpha_GTP * 1000, 1.0043))) * (1 + ((1 / 3.01) * 49.1 * power(Gi_beta_gamma * 1000, 0.8921)) / (25.44 + power(Gi_beta_gamma * 1000, 0.8921))) * MW_AC47) / 60) * 0.001; // Variable initializations: Gs_alpha_GTP = ; Gi_beta_gamma = ; AC_47_ecav = 0.2; AF47 = 130; MW_AC47 = 130; ATP = 5000; Km_ATP = 315; end model iancu_jones_harvey_2007__AC47_cyt_module(dcAMP_AC_47_cyt_dt) // Assignment Rules: dcAMP_AC_47_cyt_dt := (k_AC47_cyt * AC_47_cyt * AF47 * ATP) / (Km_ATP + ATP); // Variable initializations: k_AC47_cyt = 1.08e-3; AC_47_cyt = 0.136; AF47 = 130; ATP = 5000; Km_ATP = 315; end model iancu_jones_harvey_2007__caveolar_PDE_module(dcAMP_cav_PDE2_dt, dcAMP_cav_PDE3_dt, dcAMP_cav_PDE4_dt, cAMP_cav, k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4) // Assignment Rules: dcAMP_cav_PDE2_dt := (k_PDE2 * PDE2 * cAMP_cav) / (Km_PDE2 + cAMP_cav); dcAMP_cav_PDE3_dt := (k_PDE3 * PDE3 * cAMP_cav) / (Km_PDE3 + cAMP_cav); dcAMP_cav_PDE4_dt := (k_PDE4 * PDE4 * cAMP_cav) / (Km_PDE4 + cAMP_cav); // Variable initializations: cAMP_cav = ; PDE2 = 4.5; k_PDE2 = ; Km_PDE2 = ; PDE3 = 5.6; k_PDE3 = ; Km_PDE3 = ; PDE4 = 2; k_PDE4 = ; Km_PDE4 = ; end model iancu_jones_harvey_2007__extracaveolar_PDE_module(dcAMP_ecav_PDE2_dt, dcAMP_ecav_PDE4_dt, cAMP_ecav, k_PDE2, Km_PDE2, k_PDE4, Km_PDE4) // Assignment Rules: dcAMP_ecav_PDE2_dt := (k_PDE2 * PDE2 * cAMP_ecav) / (Km_PDE2 + cAMP_ecav); dcAMP_ecav_PDE4_dt := (k_PDE4 * PDE4 * cAMP_ecav) / (Km_PDE4 + cAMP_ecav); // Variable initializations: cAMP_ecav = ; PDE2 = 0.02; k_PDE2 = ; Km_PDE2 = ; PDE4 = 0.16; k_PDE4 = ; Km_PDE4 = ; end model iancu_jones_harvey_2007__bulk_cytoplasmic_PDE_module(dcAMP_cyt_PDE2_dt, dcAMP_cyt_PDE3_dt, dcAMP_cyt_PDE4_dt, cAMP_cyt, k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4) // Assignment Rules: dcAMP_cyt_PDE2_dt := (k_PDE2 * PDE2 * cAMP_cyt) / (Km_PDE2 + cAMP_cyt); dcAMP_cyt_PDE3_dt := (k_PDE3 * PDE3 * cAMP_cyt) / (Km_PDE3 + cAMP_cyt); dcAMP_cyt_PDE4_dt := (k_PDE4 * PDE4 * cAMP_cyt) / (Km_PDE4 + cAMP_cyt); // Variable initializations: cAMP_cyt = ; PDE2 = 5e-3; k_PDE2 = ; Km_PDE2 = ; PDE3 = 7.5e-3; k_PDE3 = ; Km_PDE3 = ; PDE4 = 5e-3; k_PDE4 = ; Km_PDE4 = ; end model iancu_jones_harvey_2007__cAMP_flux_module(cAMP_cav, cAMP_ecav, cAMP_cyt, time_, dcAMP_AC_56_dt, dcAMP_AC_47_ecav_dt, dcAMP_AC_47_cyt_dt, dcAMP_cav_PDE2_dt, dcAMP_cav_PDE3_dt, dcAMP_cav_PDE4_dt, dcAMP_ecav_PDE2_dt, dcAMP_ecav_PDE4_dt, dcAMP_cyt_PDE2_dt, dcAMP_cyt_PDE3_dt, dcAMP_cyt_PDE4_dt) // Assignment Rules: V_cav := 0.01 * V_cell; V_ecav := 0.02 * V_cell; V_cyt := 0.5 * V_cell; // Rate Rules: cAMP_cav' = ((dcAMP_AC_56_dt - (dcAMP_cav_PDE2_dt + dcAMP_cav_PDE3_dt + dcAMP_cav_PDE4_dt)) - (J_cav_ecav * (cAMP_cav - cAMP_ecav)) / V_cav) - (J_cav_cyt * (cAMP_cav - cAMP_cyt)) / V_cav; cAMP_ecav' = ((dcAMP_AC_47_ecav_dt - (dcAMP_ecav_PDE2_dt + dcAMP_ecav_PDE4_dt)) + (J_cav_ecav * (cAMP_cav - cAMP_ecav)) / V_ecav) - (J_ecav_cyt * (cAMP_ecav - cAMP_cyt)) / V_ecav; cAMP_cyt' = (dcAMP_AC_47_cyt_dt - (dcAMP_cyt_PDE2_dt + dcAMP_cyt_PDE3_dt + dcAMP_cyt_PDE4_dt)) + (J_cav_cyt * (cAMP_cav - cAMP_cyt)) / V_cyt + (J_ecav_cyt * (cAMP_ecav - cAMP_cyt)) / V_cyt; // Variable initializations: cAMP_cav = 0.11750433; cAMP_ecav = 1.092200547; cAMP_cyt = 0.992583576; time_ = ; V_cell = 38e-12; J_cav_ecav = 7.5e-15; J_cav_cyt = 7.5e-14; J_ecav_cyt = 1.5e-17; dcAMP_AC_56_dt = ; dcAMP_AC_47_ecav_dt = ; dcAMP_AC_47_cyt_dt = ; dcAMP_cav_PDE2_dt = ; dcAMP_cav_PDE3_dt = ; dcAMP_cav_PDE4_dt = ; dcAMP_ecav_PDE2_dt = ; dcAMP_ecav_PDE4_dt = ; dcAMP_cyt_PDE2_dt = ; dcAMP_cyt_PDE3_dt = ; dcAMP_cyt_PDE4_dt = ; end model *iancu_jones_harvey_2007____main() // Sub-modules, and any changes to those submodules: environment: iancu_jones_harvey_2007__environment(time_); beta_1_adrenergic_parameters: iancu_jones_harvey_2007__beta_1_adrenergic_parameters(L_iso, K_H, K_L, K_C, time_); muscarinic_parameters: iancu_jones_harvey_2007__muscarinic_parameters(L_ach, K_H0, K_L0, K_C0, time_); PDE_parameters: iancu_jones_harvey_2007__PDE_parameters(k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4); G_s_parameters: iancu_jones_harvey_2007__G_s_parameters(k_act1, k_act2, k_hydr, k_reas); G_i_parameters: iancu_jones_harvey_2007__G_i_parameters(k_act10, k_act20, k_hydr0, k_reas0); caveolar_beta_1_adrenergic_receptor_module: iancu_jones_harvey_2007__caveolar_beta_1_adrenergic_receptor_module(LRG, RG, Gs_alpha_beta_gamma, L_iso, K_H, K_L, K_C); caveolar_muscarinic_receptor_module: iancu_jones_harvey_2007__caveolar_muscarinic_receptor_module(LRG0, RG0, Gi_alpha_beta_gamma, L_ach, K_H0, K_L0, K_C0); caveolar_G_s_protein_activation_module: iancu_jones_harvey_2007__caveolar_G_s_protein_activation_module(Gs_alpha_GTP, Gs_beta_gamma, Gs_alpha_GDP, Gs_alpha_beta_gamma, Gs_Total, time_, RG, LRG, k_act1, k_act2, k_hydr, k_reas); caveolar_G_i_protein_activation_module: iancu_jones_harvey_2007__caveolar_G_i_protein_activation_module(Gi_alpha_GTP, Gi_beta_gamma0, Gi_alpha_GDP, Gi_alpha_beta_gamma, Gi_Total, time_, RG0, LRG0, k_act10, k_act20, k_hydr0, k_reas0); extracaveolar_beta_1_adrenergic_receptor_module: iancu_jones_harvey_2007__extracaveolar_beta_1_adrenergic_receptor_module(LRG1, RG1, Gs_alpha_beta_gamma0, L_iso, K_H, K_L, K_C); extracaveolar_muscarinic_receptor_module: iancu_jones_harvey_2007__extracaveolar_muscarinic_receptor_module(LRG2, RG2, Gi_alpha_beta_gamma0, L_ach, K_H0, K_L0, K_C0); extracaveolar_G_s_protein_activation_module: iancu_jones_harvey_2007__extracaveolar_G_s_protein_activation_module(Gs_alpha_GTP0, Gs_beta_gamma0, Gs_alpha_GDP0, Gs_alpha_beta_gamma0, Gs_Total0, time_, RG1, LRG1, k_act1, k_act2, k_hydr, k_reas); extracaveolar_G_i_protein_activation_module: iancu_jones_harvey_2007__extracaveolar_G_i_protein_activation_module(Gi_alpha_GTP0, Gi_beta_gamma, Gi_alpha_GDP0, Gi_alpha_beta_gamma0, Gi_Total0, time_, RG2, LRG2, k_act10, k_act20, k_hydr0, k_reas0); AC56_module: iancu_jones_harvey_2007__AC56_module(dcAMP_AC_56_dt, Gs_alpha_GTP, Gi_alpha_GTP); AC47_ecav_module: iancu_jones_harvey_2007__AC47_ecav_module(dcAMP_AC_47_ecav_dt, Gs_alpha_GTP0, Gi_beta_gamma); AC47_cyt_module: iancu_jones_harvey_2007__AC47_cyt_module(dcAMP_AC_47_cyt_dt); caveolar_PDE_module: iancu_jones_harvey_2007__caveolar_PDE_module(dcAMP_cav_PDE2_dt, dcAMP_cav_PDE3_dt, dcAMP_cav_PDE4_dt, cAMP_cav, k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4); extracaveolar_PDE_module: iancu_jones_harvey_2007__extracaveolar_PDE_module(dcAMP_ecav_PDE2_dt, dcAMP_ecav_PDE4_dt, cAMP_ecav, k_PDE2, Km_PDE2, k_PDE4, Km_PDE4); bulk_cytoplasmic_PDE_module: iancu_jones_harvey_2007__bulk_cytoplasmic_PDE_module(dcAMP_cyt_PDE2_dt, dcAMP_cyt_PDE3_dt, dcAMP_cyt_PDE4_dt, cAMP_cyt, k_PDE2, Km_PDE2, k_PDE3, Km_PDE3, k_PDE4, Km_PDE4); cAMP_flux_module: iancu_jones_harvey_2007__cAMP_flux_module(cAMP_cav, cAMP_ecav, cAMP_cyt, time_, dcAMP_AC_56_dt, dcAMP_AC_47_ecav_dt, dcAMP_AC_47_cyt_dt, dcAMP_cav_PDE2_dt, dcAMP_cav_PDE3_dt, dcAMP_cav_PDE4_dt, dcAMP_ecav_PDE2_dt, dcAMP_ecav_PDE4_dt, dcAMP_cyt_PDE2_dt, dcAMP_cyt_PDE3_dt, dcAMP_cyt_PDE4_dt); end