Name: “Podocyte Nested FFM model”
Saved: Tue, 14 May 2013  10:18:47 GMT
vcell identifier: biomodel-81992349
Owned by: “sihar”

download model (.vcml)

Compartments, Species, Reactions
  • Compartment "cell".   (type: Volume)
    • Species "R2C2_cell"
    • Species "ATP_cell"
    • Species "MKP1_cell"
    • Species "AMP_cell"
    • Species "BRaf_cell"
    • Species "MAPK_act_cell"
    • Species "cAMP4_R2C2_cell"
    • Species "cAMP4_R2C_cell"
    • Species "cAMP4_R2_cell"
    • Species "MKP1p_cell"
    • Species "MKP2_cell"
    • Species "PDE_star_cell"
    • Species "PP2A_cell"
    • Species "cAMP_R2C2_cell"
    • Species "Epac_cAMP_cell"
    • Species "cAMP2_R2C2_cell"
    • Species "PKA_cell"
    • Species "MAPKK_Ser_cell"
    • Species "PKI_cell"
    • Species "inhibitedPKA_cell"
    • Species "MAPK_active_cell"
    • Species "Rap1GAP_cell"
    • Species "MAPKK_cell"
    • Species "cAMP3_R2C2_cell"
    • Species "cAMP_cell"
    • Species "PP1_cell"
    • Species "PTPSL_star_cell"
    • Species "Epac_cell"
    • Species "MKP1_RNA_cell"
    • Species "MAPKK_active_cell"
    • Species "GRK_cell"
    • Species "PDE_cell"
    • Species "PTPSL_cell"
    • Species "MAPK_Thr_cell"
    • Species "PDE_PP_cell"
    • Species "PDE_highKm_cell"
    • Species "BRaf_star_cell"
    • Species "MAPK_cell"
    • Reaction "PP_deact_BRaf"   (BRaf_star_cell → BRaf_cell)
    • Reaction "PKA_act_BRaf"   (BRaf_cell → BRaf_star_cell)
    • Reaction "Release of C1"   (cAMP4_R2C2_cell → cAMP4_R2C_cell + PKA_cell)
    • Reaction "MKP1 phospho by MAPKactive"   (MKP1_cell → MKP1p_cell)
    • Reaction "07: PDE"   (cAMP_cell → AMP_cell)
    • Reaction "PTPSL_dephos"   (PTPSL_star_cell → PTPSL_cell)
    • Reaction "MAPKK_act_MAPK_thr"   (MAPK_Thr_cell → MAPK_active_cell)
    • Reaction "PKA_act_PDE"   (PDE_cell → PDE_star_cell)
    • Reaction "PP2A_inact_MAPKK_active"   (MAPKK_active_cell → MAPKK_Ser_cell)
    • Reaction "PKA release by PKI"   (inhibitedPKA_cell → PKI_cell + PKA_cell)
    • Reaction "cAMP_binds_A2"   (cAMP3_R2C2_cell + cAMP_cell → cAMP4_R2C2_cell)
    • Reaction "BRaf_act_MAPKK"   (MAPKK_cell → MAPKK_Ser_cell)
    • Reaction "Epac-cAMP binding"   (cAMP_cell + Epac_cell → Epac_cAMP_cell)
    • Reaction "MKPp_decat_MAPKtyr"   (MAPK_Thr_cell → MAPK_cell)
    • Reaction "PKA_deact_PTPSL"   (PTPSL_cell → PTPSL_star_cell)
    • Reaction "PDE_highKm deact cAMP"   (cAMP_cell → AMP_cell)
    • Reaction "MAPK dephosph by PTP"   (MAPK_active_cell → MAPK_Thr_cell)
    • Reaction "cAMP_bind_cAMP2R2C2"   (cAMP_cell + cAMP2_R2C2_cell → cAMP3_R2C2_cell)
    • Reaction "MKP1_deact_MAPKactive"   (MAPK_active_cell → MAPK_Thr_cell)
    • Reaction "cAMP bind R2C2"   (R2C2_cell + cAMP_cell → cAMP_R2C2_cell)
    • Reaction "PDEstar_deact_cAMP"   (cAMP_cell → AMP_cell)
    • Reaction "Release of C2"   (cAMP4_R2C_cell → cAMP4_R2_cell + PKA_cell)
    • Reaction "MKP1 turnover"   (MKP1_cell → ∅)
    • Reaction "cAMP_binds_cAMPR2C2"   (cAMP_R2C2_cell + cAMP_cell → cAMP2_R2C2_cell)
    • Reaction "PP2A_inact_MAPKKSer"   (MAPKK_Ser_cell → MAPKK_cell)
    • Reaction "MAPKK_act_MAPK"   (MAPK_cell → MAPK_Thr_cell)
    • Reaction "MKP_translation"   (MKP1_RNA_cell → MKP1_cell)
    • Reaction "reaction1"   (MAPKK_Ser_cell → MAPKK_active_cell)
    • Reaction "PP2A_dephos_PDEstar"   (PDE_star_cell → PDE_cell)
    • Reaction "reaction0"   (MAPK_Thr_cell → MAPK_cell)
    • Reaction "reaction3"   (MAPK_active_cell → MAPK_Thr_cell)
    • Reaction "MKP_decat_MAPKtyr"   (MAPK_Thr_cell → MAPK_cell)
    • Reaction "MKP1p turnover"   (MKP1p_cell → ∅)
    • Reaction "MKP1 dephosph"   (MKP1p_cell → MKP1_cell)
    • Reaction "MKP1p_deact_MAPKactive"   (MAPK_active_cell → MAPK_Thr_cell)
  • Compartment "ec".   (type: Volume)
    • Species "isoprenaline_ec"
  • Compartment "golgi".   (type: Volume)
  • Compartment "nucleus".   (type: Volume)
    • Species "MSK_nucleus"
    • Species "MSK_active_nucleus"
    • Species "MAPK_nucleus"
    • Species "MKP1_nucleus"
    • Species "MKP2_nucleus"
    • Species "MAPK_thr_nucleus"
    • Species "MKP1p_nucleus"
    • Species "MKP1gene_nucleus"
    • Species "MAPK_active_nucleus"
    • Species "MKP1_RNA_nucleus"
    • Species "inhibitedPKA_nucleus"
    • Species "PP1A_nucleus"
    • Species "CREB_Ser_nucleus"
    • Species "PKI_nucleus"
    • Species "pp2a_nucleus"
    • Species "CREB_nucleus"
    • Species "PKA_nucleus"
    • Reaction "MKP1p turnover nucleus"   (MKP1p_nucleus → ∅)
    • Reaction "MKP1p deact MAPKact"   (MAPK_active_nucleus → MAPK_thr_nucleus)
    • Reaction "MKP1 turnover in nucleus"   (MKP1_nucleus → ∅)
    • Reaction "MKP1p deact MAPKtyr"   (MAPK_thr_nucleus → MAPK_nucleus)
    • Reaction "MSK_act_CREB"   (CREB_nucleus → CREB_Ser_nucleus)
    • Reaction "MSK_dephos"   (MSK_active_nucleus → MSK_nucleus)
    • Reaction "PKA_act_CREB"   (CREB_nucleus → CREB_Ser_nucleus)
    • Reaction "PP1A_dephos_CREB"   (CREB_Ser_nucleus → CREB_nucleus)
    • Reaction "MKP1 deact MAPKact"   (MAPK_active_nucleus → MAPK_thr_nucleus)
    • Reaction "MKP1 deact MAPKtyr "   (MAPK_thr_nucleus → MAPK_nucleus)
    • Reaction "reaction2"   (MSK_nucleus → MSK_active_nucleus)
    • Reaction "MKP2 deact MAPKact"   (MAPK_active_nucleus → MAPK_thr_nucleus)
    • Reaction "MKP2 deact MAPK tyr"   (MAPK_thr_nucleus → MAPK_nucleus)
    • Reaction "MKP1 phosph by MAPKactive_nucleus"   (MKP1_nucleus → MKP1p_nucleus)
    • Reaction "MKP1 dephosph in nucleus"   (MKP1p_nucleus → MKP1_nucleus)
    • Reaction "PKA inhibition by PKI"   (PKI_nucleus + PKA_nucleus → inhibitedPKA_nucleus)
    • Reaction "Pp2A_deact_CREB"   (CREB_Ser_nucleus → CREB_nucleus)
    • Reaction "MAPK_act_MKPtranscription"   (MKP1gene_nucleus → MKP1_RNA_nucleus)
    • Reaction "MKP1 basal transcription"   (MKP1gene_nucleus → MKP1_RNA_nucleus)
  • Compartment "GM".   (type: Membrane)
    • Species "Rap1_RGII_GM"
    • Species "Rap1_GDP_GM"
    • Species "Rap1_Epac_GM"
    • Species "Rap1_BRaf_GM"
    • Species "Rap1_GTP_GM"
    • Reaction "08: Epac exchange"   (Rap1_Epac_GM → Epac_cAMP_cell + Rap1_GTP_GM)
    • Reaction "Rap1raf_act_MAPKK"   (MAPKK_cell → MAPKK_Ser_cell)
    • Reaction "8a: Rap1-Epac binding"   (Rap1_GDP_GM + Epac_cAMP_cell → Rap1_Epac_GM)
    • Reaction "constit exch+hydrolysis"   (Rap1_GDP_GM → Rap1_GTP_GM)
    • Reaction "10a: Rap1-RGII binding"   (Rap1GAP_cell + Rap1_GTP_GM → Rap1_RGII_GM)
    • Reaction "10: Rap1 GTPase"   (Rap1_RGII_GM → Rap1_GDP_GM + Rap1GAP_cell)
    • Reaction "RapRaf_act_MAPKKSer"   (MAPKK_Ser_cell → MAPKK_active_cell)
    • Reaction "Rap1_binds_BRaf"   (BRaf_cell + Rap1_GTP_GM → Rap1_BRaf_GM)
  • Compartment "PM".   (type: Membrane)
    • Species "G_bg_PM"
    • Species "Gsa_GDP_PM"
    • Species "beta_isop_PM"
    • Species "beta_PM"
    • Species "beta_P_PM"
    • Species "Gs_trimer_PM"
    • Species "GRK_Gbg_PM"
    • Species "Gs_a_PM"
    • Species "AC_PM"
    • Species "AC_Gsa_PM"
    • Species "GRK_PM"
    • Species "betaAR_Gs_PM"
    • Reaction "GRK to cytosol"   (GRK_PM → GRK_cell)
    • Reaction "01b: isoprenaline binding"   (isoprenaline_ec + beta_PM → beta_isop_PM)
    • Reaction "Receptor recycling"   (beta_P_PM → beta_PM)
    • Reaction "GRK-Gbg binding"   (G_bg_PM + GRK_cell → GRK_Gbg_PM)
    • Reaction "14b: Gs trimerization"   (Gsa_GDP_PM + G_bg_PM → Gs_trimer_PM)
    • Reaction "04: Gs-AC binding"   (Gs_a_PM + AC_PM → AC_Gsa_PM)
    • Reaction "05b: cAMP production"   (ATP_cell → cAMP_cell)
    • Reaction "2: ARbeta-Gs binding"   (beta_isop_PM + Gs_trimer_PM → betaAR_Gs_PM)
    • Reaction "03: GRK activity"   (beta_isop_PM → beta_P_PM)
    • Reaction "Gs GTPase"   (Gs_a_PM → Gsa_GDP_PM)
    • Reaction "GRK PM recruitment"   (GRK_Gbg_PM → GRK_PM + G_bg_PM)
    • Reaction "02b: Gs activation"   (betaAR_Gs_PM → beta_isop_PM + Gs_a_PM + G_bg_PM)
  • Compartment "nuclear membrane".   (type: Membrane)
    • Reaction "PKI translocation"   (PKI_cell → PKI_nucleus)
    • Reaction "MKP1p translocation"   (MKP1p_cell → MKP1p_nucleus)
    • Reaction "MAPK translocation"   (MAPK_cell → MAPK_nucleus)
    • Reaction "MKP1 translocation"   (MKP1_cell → MKP1_nucleus)
    • Reaction "MAPKactive_translocation"   (MAPK_active_cell → MAPK_active_nucleus)
    • Reaction "PKA_translocation"   (PKA_cell → PKA_nucleus)
    • Reaction "inhibited PKA export"   (inhibitedPKA_cell → inhibitedPKA_nucleus)
    • Reaction "MKPRNA_export"   (MKP1_RNA_cell → MKP1_RNA_nucleus)
2018-07-12T19:23:22+00:00 February 16th, 2018|biomodel|