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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A dynamic network model of mTOR signaling reveals TSC-independent mTORC2 regulation.

  • Piero Dalle Pezze
  • Annika G Sonntag
  • Antje Thien
  • Mirja T Prentzell
  • Markus Gödel
  • Sven Fischer
  • Elke Neumann-Haefelin
  • Tobias B Huber
  • Ralf Baumeister
  • Daryl P Shanley
  • Kathrin Thedieck
Sci Signal 2012; 5 (217):
Abstract
The kinase mammalian target of rapamycin (mTOR) exists in two multiprotein complexes (mTORC1 and mTORC2) and is a central regulator of growth and metabolism. Insulin activation of mTORC1, mediated by phosphoinositide 3-kinase (PI3K), Akt, and the inhibitory tuberous sclerosis complex 1/2 (TSC1-TSC2), initiates a negative feedback loop that ultimately inhibits PI3K. We present a data-driven dynamic insulin-mTOR network model that integrates the entire core network and used this model to investigate the less well understood mechanisms by which insulin regulates mTORC2. By analyzing the effects of perturbations targeting several levels within the network in silico and experimentally, we found that, in contrast to current hypotheses, the TSC1-TSC2 complex was not a direct or indirect (acting through the negative feedback loop) regulator of mTORC2. Although mTORC2 activation required active PI3K, this was not affected by the negative feedback loop. Therefore, we propose an mTORC2 activation pathway through a PI3K variant that is insensitive to the negative feedback loop that regulates mTORC1. This putative pathway predicts that mTORC2 would be refractory to Akt, which inhibits TSC1-TSC2, and, indeed, we found that mTORC2 was insensitive to constitutive Akt activation in several cell types. Our results suggest that a previously unknown network structure connects mTORC2 to its upstream cues and clarifies which molecular connectors contribute to mTORC2 activation.

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

Global parameters

Id Value

Local parameters

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)

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments