dallepezze1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000581) Biomodels notes: Figure 2 of the reference publication has been reproduced. The model was simulated using Copasi v4.15 (Build 95). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1.0 dimensionless | |
| — | 60.0 second | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| compartment_1 | Membrane | 3.0 | 1.0 | |
| compartment_2 | Cytoplasm | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| species_1 | Sink | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_10 | PRAS40_pT246 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_11 | mTORC1 | 4.3225 | compartment_2 (Cytoplasm) | ✘ | |
| species_12 | PRAS40_pS183 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_13 | PDK2 | 12.1175 | compartment_2 (Cytoplasm) | ✘ | |
| species_14 | PDK2_p | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_15 | IR_beta_refractory | 0.0 | compartment_1 (Membrane) | ✘ | |
| species_16 | PI3K_variant_p | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_17 | p70S6K_pT389 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_18 | PI3K_variant | 2.965 | compartment_2 (Cytoplasm) | ✘ | |
| species_19 | IRS1_pS636_PI3K | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_2 | mTORC1_pS2448 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_20 | IR_beta | 12.1175 | compartment_1 (Membrane) | ✘ | |
| species_21 | IR_beta_pY1146 | 0.0 | compartment_1 (Membrane) | ✘ | |
| species_22 | mTORC2_pS2481 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_23 | PI3K | 2.965 | compartment_2 (Cytoplasm) | ✔ | |
| species_27 | Akt | 144.13 | compartment_2 (Cytoplasm) | ✘ | |
| species_28 | Amino_Acids | 100.0 | compartment_2 (Cytoplasm) | ✔ | |
| species_3 | Akt_pT308 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_4 | Akt_pT308_pS473 | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_41 | Insulin | 100.0 | compartment_1 (Membrane) | ✔ | |
| species_42 | IRS1_PI3K | 2.965 | compartment_2 (Cytoplasm) | ✘ | |
| species_47 | p70S6K | 127.0725 | compartment_2 (Cytoplasm) | ✘ | |
| species_5 | mTORC2 | 6.2175 | compartment_2 (Cytoplasm) | ✘ | |
| species_6 | TSC_clx | 10.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_7 | IRS1_p_PI3K | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_8 | TSC_p_clx | 0.0 | compartment_2 (Cytoplasm) | ✘ | |
| species_9 | PRAS40 | 73.2175 | compartment_2 (Cytoplasm) | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition | |
|---|---|
| species_42 = species_23 | |
| species_18 = species_23 |
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| reaction_1 | mTORC2_pS2481_dephosphorylation | species_22 > species_5 compartment_2 * k1 * species_22 | |||
| reaction_10 | PRAS40_pT246_dephosphorylation | species_10 > species_9 compartment_2 * k1 * species_10 | |||
| reaction_11 | PRAS40_pS183_dephosphorylation | species_12 > species_9 compartment_2 * k1 * species_12 | |||
| reaction_12 | PRAS40_S183_phosphorylation_by_mTORC1_pS2448 | species_9 + species_2 > species_12 + species_2 compartment_2 * k1 * species_9 * species_2 | |||
| reaction_13 | Akt_pT308_S473_phosphorylation_by_PDK2 | species_3 + species_14 > species_4 + species_14 compartment_2 * k1 * species_3 * species_14 | |||
| reaction_14 | PDK2_p_dephosphorylation | species_14 > species_13 compartment_2 * k1 * species_14 | |||
| reaction_15 | PDK2_phosphorylation | species_13 + species_21 > species_14 + species_21 k1 * species_13 * species_21 | |||
| reaction_16 | p70S6K_T389_phosphorylation_by_mTORC1_pS2448 | species_47 + species_2 > species_17 + species_2 compartment_2 * k1 * species_47 * species_2 | |||
| reaction_17 | p70S6K_pT389_dephosphorylation | species_17 > species_47 compartment_2 * k1 * species_17 | |||
| reaction_18 | mTORC2_S2481_phosphorylation_by_PI3K_variant_p | species_5 + species_16 > species_22 + species_16 compartment_2 * k1 * species_5 * species_16 | |||
| reaction_19 | PI3K_variant_phosphorylation_by_IR_beta_pY1146 | species_18 + species_21 > species_16 + species_21 k1 * species_18 * species_21 | |||
| reaction_2 | IR_beta_pY1146_dephosphorylation | species_21 > species_15 compartment_1 * k1 * species_21 | |||
| reaction_20 | PI3K_variant_p_dephosphorylation | species_16 > species_18 compartment_2 * k1 * species_16 | |||
| reaction_22 | IRS1_S636_phosphorylation_by_p70S6K_pT389 | species_42 + species_17 > species_19 + species_17 compartment_2 * k1 * species_42 * species_17 | |||
| reaction_23 | IRS1_PI3K_phosphorylation_by_IR_beta_pY1146 | species_42 + species_21 > species_7 + species_21 k1 * species_42 * species_21 | |||
| reaction_3 | TSC_clx_phosphorylation_by_Akt_pT308_pS473 | species_6 + species_4 > species_8 + species_4 compartment_2 * k1 * species_6 * species_4 | |||
| reaction_31 | Akt_T308_phosphorylation_by_IRS1_phos_PI3K | species_27 + species_7 > species_3 + species_7 compartment_2 * k1 * species_27 * species_7 | |||
| reaction_32 | Akt_pT308_S473_phosphorylation_by_mTORC2_pS2481 | species_3 + species_22 > species_4 + species_22 compartment_2 * k1 * species_3 * species_22 | |||
| reaction_33 | TSC_clx_phosphorylation_by_Akt_pT308 | species_6 + species_3 > species_8 + species_3 compartment_2 * k1 * species_6 * species_3 | |||
| reaction_4 | IRS1_synthesis | species_1 > species_42 compartment_2 * k1 * species_1 | |||
| reaction_40 | mTORC1_S2448_activation_by_Amino_Acids | species_11 + species_28 > species_2 compartment_2 * k1 * species_11 * species_28 | |||
| reaction_41 | IR_beta_Y1146_phosphorylation | species_20 + species_41 > species_21 compartment_1 * k1 * species_20 * species_41 | |||
| reaction_44 | Akt_pT308_pS473_dephosphorylation | species_4 > species_3 compartment_2 * k1 * species_4 | |||
| reaction_46 | IRS1_p_pi3K_phosphorylation_by_p70S6K_pT389 | species_7 + species_17 > species_19 + species_17 compartment_2 * k1 * species_7 * species_17 | |||
| reaction_5 | IR_beta_ready | species_15 > species_20 compartment_1 * k1 * species_15 | |||
| reaction_53 | IRS1_pS636_degradation | species_19 > species_1 compartment_2 * k1 * species_19 | |||
| reaction_55 | IRS1_p_PI3K_dephosphorylation | species_7 > species_42 compartment_2 * k1 * species_7 | |||
| reaction_6 | PRAS40_T246_phosphorylation_by_Akt_pT308_pS473 | species_9 + species_4 > species_10 + species_4 compartment_2 * k1 * species_9 * species_4 | |||
| reaction_61 | Akt_pT308_dephosphorylation | species_3 > species_27 compartment_2 * k1 * species_3 | |||
| reaction_7 | mTORC1_pS2448_dephosphorylation_by_TSC_clx | species_2 + species_6 > species_11 + species_6 compartment_2 * k1 * species_2 * species_6 | |||
| reaction_8 | PRAS40_T246_phosphorylation_by_Akt_pT308 | species_9 + species_3 > species_10 + species_3 compartment_2 * k1 * species_9 * species_3 | |||
| reaction_9 | TSC_p_clx_dephosphorylation | species_8 > species_6 compartment_2 * k1 * species_8 |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| k1 | 0.00812537 | reaction_9 (TSC_p_clx_dephosphorylation) | |
| k1 | 0.00573896 | reaction_16 (p70S6K_T389_phosphorylation_by_mTORC1_pS2448) | |
| k1 | 0.00528455 | reaction_17 (p70S6K_pT389_dephosphorylation) | |
| k1 | 1.0 | reaction_22 (IRS1_S636_phosphorylation_by_p70S6K_pT389) | |
| k1 | 0.134664 | reaction_23 (IRS1_PI3K_phosphorylation_by_IR_beta_pY1146) | |
| k1 | 0.699505 | reaction_31 (Akt_T308_phosphorylation_by_IRS1_phos_PI3K) | |
| k1 | 4.50769 | reaction_32 (Akt_pT308_S473_phosphorylation_by_mTORC2_pS2481) | |
| k1 | 0.00627315 | reaction_33 (TSC_clx_phosphorylation_by_Akt_pT308) | |
| k1 | 0.0513784 | reaction_40 (mTORC1_S2448_activation_by_Amino_Acids) | |
| k1 | 0.0253763 | reaction_41 (IR_beta_Y1146_phosphorylation) | |
| k1 | 0.0001 | reaction_46 (IRS1_p_pi3K_phosphorylation_by_p70S6K_pT389) | |
| k1 | 0.000100001 | reaction_53 (IRS1_pS636_degradation) | |
| k1 | 0.00328283 | reaction_55 (IRS1_p_PI3K_dephosphorylation) | |
| k1 | 7.52842 | reaction_44 (Akt_pT308_pS473_dephosphorylation) | |
| k1 | 4.0739 | reaction_61 (Akt_pT308_dephosphorylation) | |
| k1 | 0.0255714 | reaction_1 (mTORC2_pS2481_dephosphorylation) | |
| k1 | 0.149328 | reaction_2 (IR_beta_pY1146_dephosphorylation) | |
| k1 | 0.000100039 | reaction_3 (TSC_clx_phosphorylation_by_Akt_pT308_pS473) | |
| k1 | 0.0999968 | reaction_4 (IRS1_synthesis) | |
| k1 | 0.0309731 | reaction_5 (IR_beta_ready) | |
| k1 | 0.000100001 | reaction_6 (PRAS40_T246_phosphorylation_by_Akt_pT308_pS473) | |
| k1 | 0.999989 | reaction_7 (mTORC1_pS2448_dephosphorylation_by_TSC_clx) | |
| k1 | 0.0239178 | reaction_8 (PRAS40_T246_phosphorylation_by_Akt_pT308) | |
| k1 | 0.999991 | reaction_10 (PRAS40_pT246_dephosphorylation) | |
| k1 | 0.403706 | reaction_11 (PRAS40_pS183_dephosphorylation) | |
| k1 | 0.073093 | reaction_12 (PRAS40_S183_phosphorylation_by_mTORC1_pS2448) | |
| k1 | 0.0318902 | reaction_18 (mTORC2_S2481_phosphorylation_by_PI3K_variant_p) | |
| k1 | 5.90372 | reaction_13 (Akt_pT308_S473_phosphorylation_by_PDK2) | |
| k1 | 1.0 | reaction_14 (PDK2_p_dephosphorylation) | |
| k1 | 0.1 | reaction_15 (PDK2_phosphorylation) | |
| k1 | 0.999985 | reaction_19 (PI3K_variant_phosphorylation_by_IR_beta_pY1146) | |
| k1 | 0.000232165 | reaction_20 (PI3K_variant_p_dephosphorylation) |
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| Trigger | Assignments |
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