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A Systems Biology Approach to Cancer Therapy and Early Detection A Systems Biology Approach to Cancer Therapy and Early

A Systems Biology Approach to Cancer Therapy and Early Detection A Systems Biology Approach to Cancer Therapy and Early Detection. Avijit Ghosh Dhruv Pant , Rui Zou, Dave Miller Yihua Wang, Hanbing Lin Travis Hoppe, Aparna Kumar. Department of Physics Drexel University. Outline.

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A Systems Biology Approach to Cancer Therapy and Early Detection A Systems Biology Approach to Cancer Therapy and Early

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  1. A Systems Biology Approach to Cancer Therapy and Early DetectionA Systems Biology Approach to Cancer Therapy and Early Detection Avijit Ghosh Dhruv Pant, Rui Zou, Dave Miller Yihua Wang, Hanbing Lin Travis Hoppe, Aparna Kumar Department of Physics Drexel University

  2. Outline • Signal Transduction • Overview • Mutations, Oncogenes, Proto-Oncogenes • Mathematical Models • Enzymes • Mutations • Predicting Putative Oncogenes using Systems Biology • D. Pant A. Ghosh (2005) Biophys. Chem 113(3) 275-288 • The Results • Experimentally Validated Results • New Predictions • Drugs! • Spatio-Temporal Modeling • CellSim • Overview Special topics on Electrical and Systems Engineering 2007 Systems Biology

  3. Signal Transduction • Controls behavior of cells • Ion Channels • Metabolic Pathways • Cytoskeletal Proteins • Gene Regulatory Proteins • Cell cycle • Cytoskeletal rearrangement D. Slish Mechanism of Tyrosine Kinase Receptors U.Platt. Special topics on Electrical and Systems Engineering 2007 Systems Biology

  4. The Normal Functioning MAPK Signal Cascade Special topics on Electrical and Systems Engineering 2007 Systems Biology

  5. Signaling and Cell Growth • Input : • EGF – Epidermal Growth Factor • Output: • Signal for gene transcription :: ERK • Activation: • Phosphorylation • GTP/GDP binding Special topics on Electrical and Systems Engineering 2007 Systems Biology

  6. EGF stimulation and ERK response Special topics on Electrical and Systems Engineering 2007 Systems Biology

  7. Oncogenes and Tumor Suppressor Genes • Oncogene - A gene (protein) that when mutated or inappropriately expressed contributes to cancer formation • Mutations in signal transduction genes • Mutations in Tumor Suppressor genes • INHERITED • Activation • Point Mutation • Chromosomal rearrangement • Gene amplification • Viral Insertion Special topics on Electrical and Systems Engineering 2007 Systems Biology

  8. The Ras Protein • Ras Protein • Active – GTP Bound • Inactive – GDP Bound • GAP (GTPase Activating Protein) • Hydrolyzes GTP in Ras • Gly12 – Stops Ras Gap Interactions • Gln61 – Stops hydrolysis Scheffzick et.al. (1997) Science 277 pp 333-338 Special topics on Electrical and Systems Engineering 2007 Systems Biology

  9. Interactions Special topics on Electrical and Systems Engineering 2007 Systems Biology

  10. EGF / MAPK / PLC / PLC-γ/ PKC / Calcium / PLA2 Pathways Ca +CaTransp +Ca <> CaTransp-2Ca :: 1e-08 144 IP3R +IP3 +IP3 +IP3 <> IP3R* :: 1e-20 1 Ca-sequester +Ca-sequester +capacitive_Ca_entry* <> inact_cap_entry :: 1.2e-11 1 EGFR +EGF <> L.EGFR :: 7e-06 0.25 SHC* -> SHC :: 0.0016667 L.EGFR <> Internal_L.EGFR :: 0.002 0.00033 mGluR +Glu <> Rec-Glu :: 2.8e-05 10 G-GDP -> G*GTP + BetaGamma :: 0.0001 G*GDP +BetaGamma -> G-GDP :: 1e-05 G*GTP -> G*GDP :: 0.0133 G-GDP +Rec-Glu <> Rec-Glu-Gq :: 1e-08 0.0001 Glu +Rec-Gq <> Rec-Glu-Gq :: 2.8e-05 0.1 Rec-Glu-Gq -> G*GTP + BetaGamma + Rec-Glu :: 0.01 G-GDP +mGluR <> Rec-Gq :: 1e-06 1 Rec-Gq +mGluRAntag <> Blocked-rec-Gq :: 0.0001 0.01 craf-1* +GTP-Ras <> Raf-GTP-Ras* :: 4e-05 0.5 PKC-cytosolic +Ca <> PKC-Ca :: 1e-06 0.5 DAG +PKC-Ca <> PKC-Ca-DAG :: 1.3333e-08 8.6348 PKC-Ca <> PKC-Ca-memb* :: 1.2705 3.5026 PKC-Ca-DAG <> PKC-DAG-memb* :: 1 0.1 PKC-Ca +AA <> PKC-Ca-AA* :: 2e-09 0.1 PKC-DAG-AA <> PKC-DAG-AA* :: 2 0.2 PKC-cytosolic <> PKC-basal* :: 1 50 AA +PKC-cytosolic <> PKC-AA* :: 2e-10 0.1 PKC-cytosolic +DAG <> PKC-DAG :: 1e-09 0.1 PKC-DAG +AA <> PKC-DAG-AA :: 3e-08 2 PLA2-cytosolic +Ca <> PLA2-Ca* :: 1.6667e-06 0.1 temp-PIP2 +PLA2-cytosolic <> PIP2-PLA2* :: 2e-09 0.5 temp-PIP2 +PLA2-Ca* <> PIP2-Ca-PLA2* :: 2e-08 0.1 DAG +PLA2-Ca* <> DAG-Ca-PLA2* :: 5e-09 4 AA -> APC :: 0.4 PLA2* +Ca <> PLA2*-Ca :: 1e-05 0.1 PLA2* -> PLA2-cytosolic :: 0.17 Ca +PLC <> PLC-Ca :: 5e-06 1 IP3 -> Inositol :: 2.5 DAG -> PC :: 0.15 G*GTP +PLC-Ca <> PLC-Ca-Gq :: 4.2e-05 1 PLC-Ca-Gq -> G*GDP + PLC-Ca :: 0.0133 PLC +G*GTP <> PLC-Gq :: 4.2e-06 1 Ca +PLC-Gq <> PLC-Ca-Gq :: 5e-05 1 PLC_g +Ca <> Ca.PLC_g :: 0.0003 10 Ca +PLC_G* <> Ca.PLC_g* :: 2e-05 10 Ca.PLC_g* -> Ca.PLC_g :: 0.05 BetaGamma +inact-GEF <> GEF-Gprot-bg :: 1e-05 1 GEF* -> inact-GEF :: 1 GTP-Ras -> GDP-Ras :: 0.0001 GAP* -> GAP :: 0.1 inact-GEF +CaM-Ca4 <> CaM-GEF :: 0.0001 1 inact-GEF* -> inact-GEF :: 1 Sos.Grb2 +SHC* <> Shc*.Sos.Grb2 :: 8.333e-07 0.1 Sos* +Grb2 <> Sos*.Grb2 :: 4.1667e-08 0.0168 Sos* -> Sos :: 0.001 Grb2 +Sos <> Sos.Grb2 :: 4.1667e-08 0.0168 ## locations# the volume is a optional parameter# our volume units are Llocation extracellular 1E-10 Ca-extlocation cytosol 1E-12location endosome 1.6E-13 Ca-sequester# Channelschannel capacitive_Ca_entry* Ca-ext -> Ca :: 0.005channel Ca-leak-from-extracell Ca-ext -> Ca :: 0.004channel Ca-leak-to-cytoplasm Ca-sequester->Ca :: 8channel IP3R* Ca-sequester -> Ca :: 19.2# conservationReactions#conserve CaEPump :: Ca_CaEPump#conserve CaTransp-2Ca :: CaTransp#conserve mGluR :: Rec-Glu Rec-Glu-Gq Rec-Gq Blocked-rec-Gq#conserve PLC :: match /PLC-/#conserve PLA2-cytosolic :: match /PLA2/# sum up#sum PKC-active :: PKC-DAG-AA* PKC-Ca-memb* PKC-Ca-AA* PKC-DAG-memb*# sumReactions# (native units are #/compartment)Ca + CaEPump <> Ca_CaEPump :: 0.003 288Ca_CaEPump -> CaEPump +Ca-ext :: 72 Ca.PLC_g + L.EGFR <> Ca.PLC_g_L.EGFR :: 5e-06 0.8Ca.PLC_g_L.EGFR -> L.EGFR +Ca.PLC_g* :: 0.2 SHC + L.EGFR <> SHC_L.EGFR :: 2e-06 0.8SHC_L.EGFR -> L.EGFR +SHC* :: 0.2 MAPK + MAPKK* <> MAPK_MAPKK* :: 2.7e-05 0.6MAPK_MAPKK* -> MAPKK* +MAPK-tyr :: 0.15 MAPK-tyr + MAPKK* <> MAPK-tyr_MAPKK* :: 2.7e-05 0.6MAPK-tyr_MAPKK* -> MAPKK* +MAPK* :: 0.15 MAPKK + Raf-GTP-Ras* <> MAPKK_Raf-GTP-Ras* :: 5.5e-06 0.42MAPKK_Raf-GTP-Ras* -> Raf-GTP-Ras* +MAPKK-ser :: 0.105 MAPKK-ser + Raf-GTP-Ras* <> MAPKK-ser_Raf-GTP-Ras* :: 5.5e-06 0.42MAPKK-ser_Raf-GTP-Ras* -> Raf-GTP-Ras* +MAPKK* :: 0.105 #craf-1 + PKC-active <> craf-1_PKC-active :: 5e-07 16#craf-1_PKC-active -> PKC-active +craf-1* :: 4 #GAP + PKC-active <> GAP_PKC-active :: 1e-05 16#GAP_PKC-active -> PKC-active +GAP* :: 4 #inact-GEF + PKC-active <> inact-GEF_PKC-active :: 1e-05 16#inact-GEF_PKC-active -> PKC-active +GEF* :: 4 craf-1 + PKC-DAG-AA* <> craf-1_PKC-DAG-AA* :: 5e-07 16craf-1_PKC-DAG-AA* -> PKC-DAG-AA* +craf-1* :: 4 GAP + PKC-DAG-AA* <> GAP_PKC-DAG-AA* :: 1e-05 16GAP_PKC-DAG-AA* -> PKC-DAG-AA* +GAP* :: 4 inact-GEF + PKC-DAG-AA* <> inact-GEF_PKC-DAG-AA* :: 1e-05 16inact-GEF_PKC-DAG-AA* -> PKC-DAG-AA* +GEF* :: 4 craf-1 + PKC-Ca-memb* <> craf-1_PKC-Ca-memb* :: 5e-07 16craf-1_PKC-Ca-memb* -> PKC-Ca-memb* +craf-1* :: 4 GAP + PKC-Ca-memb* <> GAP_PKC-Ca-memb* :: 1e-05 16GAP_PKC-Ca-memb* -> PKC-Ca-memb* +GAP* :: 4 inact-GEF + PKC-Ca-memb* <> inact-GEF_PKC-Ca-memb* :: 1e-05 16inact-GEF_PKC-Ca-memb* -> PKC-Ca-memb* +GEF* :: 4 craf-1 + PKC-Ca-AA* <> craf-1_PKC-Ca-AA* :: 5e-07 16craf-1_PKC-Ca-AA* -> PKC-Ca-AA* +craf-1* :: 4 GAP + PKC-Ca-AA* <> GAP_PKC-Ca-AA* :: 1e-05 16GAP_PKC-Ca-AA* -> PKC-Ca-AA* +GAP* :: 4 inact-GEF + PKC-Ca-AA* <> inact-GEF_PKC-Ca-AA* :: 1e-05 16inact-GEF_PKC-Ca-AA* -> PKC-Ca-AA* +GEF* :: 4 craf-1 + PKC-DAG-memb* <> craf-1_PKC-DAG-memb* :: 5e-07 16 craf-1_PKC-DAG-memb* -> PKC-DAG-memb* +craf-1* :: 4 GAP + PKC-DAG-memb* <> GAP_PKC-DAG-memb* :: 1e-05 16GAP_PKC-DAG-memb* -> PKC-DAG-memb* +GAP* :: 4 inact-GEF + PKC-DAG-memb* <> inact-GEF_PKC-DAG-memb* :: 1e-05 16inact-GEF_PKC-DAG-memb* -> PKC-DAG-memb* +GEF* :: 4 craf-1 + PKC-basal* <> craf-1_PKC-basal* :: 5e-07 16craf-1_PKC-basal* -> PKC-basal* +craf-1* :: 4 GAP + PKC-basal* <> GAP_PKC-basal* :: 1e-05 16GAP_PKC-basal* -> PKC-basal* +GAP* :: 4 inact-GEF + PKC-basal* <> inact-GEF_PKC-basal* :: 1e-05 16inact-GEF_PKC-basal* -> PKC-basal* +GEF* :: 4 craf-1 + PKC-AA* <> craf-1_PKC-AA* :: 5e-07 16craf-1_PKC-AA* -> PKC-AA* +craf-1* :: 4 GAP + PKC-AA* <> GAP_PKC-AA* :: 1e-05 16GAP_PKC-AA* -> PKC-AA* +GAP* :: 4 inact-GEF + PKC-AA* <> inact-GEF_PKC-AA* :: 1e-05 16inact-GEF_PKC-AA* -> PKC-AA* +GEF* :: 4 # end expandAPC + PLA2-Ca* <> APC_PLA2-Ca* :: 2.25e-06 21.6APC_PLA2-Ca* -> PLA2-Ca* +AA :: 5.4 APC + PIP2-PLA2* <> APC_PIP2-PLA2* :: 4.6e-06 44.16APC_PIP2-PLA2* -> PIP2-PLA2* +AA :: 11.04 APC + PIP2-Ca-PLA2* <> APC_PIP2-Ca-PLA2* :: 1.5e-05 144APC_PIP2-Ca-PLA2* -> PIP2-Ca-PLA2* +AA :: 36 APC + DAG-Ca-PLA2* <> APC_DAG-Ca-PLA2* :: 2.5e-05 240APC_DAG-Ca-PLA2* -> DAG-Ca-PLA2* +AA :: 60 APC + PLA2*-Ca <> APC_PLA2*-Ca :: 5e-05 480APC_PLA2*-Ca -> PLA2*-Ca +AA :: 120 PLA2-cytosolic + MAPK* <> PLA2-cytosolic_MAPK* :: 6.5e-06 80PLA2-cytosolic_MAPK* -> MAPK* +PLA2* :: 20 craf-1* + MAPK* <> craf-1*_MAPK* :: 3.25e-06 40craf-1*_MAPK* -> MAPK* +craf-1** :: 10 Sos + MAPK* <> Sos_MAPK* :: 3.25e-05 40Sos_MAPK* -> MAPK* +Sos* :: 10 MAPK-tyr + MKP-1 <> MAPK-tyr_MKP-1 :: 0.000125 4MAPK-tyr_MKP-1 -> MKP-1 +MAPK :: 1 MAPK* + MKP-1 <> MAPK*_MKP-1 :: 0.000125 4MAPK*_MKP-1 -> MKP-1 +MAPK-tyr :: 1 craf-1* + PPhosphatase2A <> craf-1*_PPhosphatase2A :: 3.3e-06 25craf-1*_PPhosphatase2A -> PPhosphatase2A +craf-1 :: 6 MAPKK* + PPhosphatase2A <> MAPKK*_PPhosphatase2A :: 3.3e-06 25MAPKK*_PPhosphatase2A -> PPhosphatase2A +MAPKK-ser :: 6 MAPKK-ser + PPhosphatase2A <> MAPKK-ser_PPhosphatase2A :: 3.3e-06 25MAPKK-ser_PPhosphatase2A -> PPhosphatase2A +MAPKK :: 6 craf-1** + PPhosphatase2A <> craf-1**_PPhosphatase2A :: 3.3e-06 25craf-1**_PPhosphatase2A -> PPhosphatase2A +craf-1* :: 6 inact-GEF + PKA-active <> inact-GEF_PKA-active :: 1e-05 36inact-GEF_PKA-active -> PKA-active +inact-GEF* :: 9 GDP-Ras + Shc*.Sos.Grb2 <> GDP-Ras_Shc*.Sos.Grb2 :: 3.3e-07 0.08GDP-Ras_Shc*.Sos.Grb2 -> Shc*.Sos.Grb2 +GTP-Ras :: 0.02 PIP2 + PLC-Ca <> PIP2_PLC-Ca :: 4.2e-06 40 PIP2_PLC-Ca -> PLC-Ca +DAG + IP3 :: 10 PIP2 + PLC-Ca-Gq <> PIP2_PLC-Ca-Gq :: 8e-05 192PIP2_PLC-Ca-Gq -> PLC-Ca-Gq +DAG + IP3 :: 48 PIP2 + Ca.PLC_g <> PIP2_Ca.PLC_g :: 1.2e-06 56PIP2_Ca.PLC_g -> Ca.PLC_g +DAG + IP3 :: 14 PIP2 + Ca.PLC_g* <> PIP2_Ca.PLC_g* :: 2.4e-05 228PIP2_Ca.PLC_g* -> Ca.PLC_g* +DAG + IP3 :: 57 GDP-Ras + GEF-Gprot-bg <> GDP-Ras_GEF-Gprot-bg :: 3.3e-07 0.08GDP-Ras_GEF-Gprot-bg -> GEF-Gprot-bg +GTP-Ras :: 0.02 GDP-Ras + GEF* <> GDP-Ras_GEF* :: 3.3e-07 0.08GDP-Ras_GEF* -> GEF* +GTP-Ras :: 0.02 GTP-Ras + GAP <> GTP-Ras_GAP :: 0.001666 1000GTP-Ras_GAP -> GAP +GDP-Ras :: 10 GDP-Ras + CaM-GEF <> GDP-Ras_CaM-GEF :: 3.3e-07 0.08GDP-Ras_CaM-GEF -> CaM-GEF +GTP-Ras :: 0.02 CaTransp-2Ca -> CaTransp + Ca-sequester + Ca-sequester :: 25 Special topics on Electrical and Systems Engineering 2007 Systems Biology

  11. Leads to.. d[capacitive_ca_entry*]/dt = 1[inact_cap_entry] - 1.2e-11[ca-sequester][ca-sequester][capacitive_ca_entry*]d[ca]/dt = 288[ca_caepump] + 144[catransp-2ca] + 144[catransp-2ca] + 0.5[pkc-ca] + 0.1[pla2-ca*] + 0.1[pla2*-ca] + 1[plc-ca] + 1[plc-ca-gq] + 10[ca.plc_g] + 10[ca.plc_g*] - 0.003[ca][caepump] - 1e-08[ca][catransp][ca] - 1e-08[ca][catransp][ca] - 1e-06[pkc-cytosolic][ca] - 1.6667e-06[pla2-cytosolic][ca] - 1e-05[pla2*][ca] - 5e-06[ca][plc] - 5e-05[ca][plc-gq] - 0.0003[plc_g][ca] - 2e-05[ca][plc_g*] + 0.005 * [capacitive_ca_entry*] * ( [ca-ext] - [ca] ) + 0.004 * [ca-leak-from-extracell] * ( [ca-ext] - [ca] ) + 8 * [ca-leak-to-cytoplasm] * ( [ca-sequester] - [ca] ) + 19.2 * [ip3r*] * ( [ca-sequester] - [ca] ) d[ca-leak-from-extracell]/dt = d[ca-leak-to-cytoplasm]/dt = d[ip3r*]/dt = 1e-20[ip3r][ip3][ip3][ip3] - 1[ip3r*]d[caepump]/dt = 288[ca_caepump] + 72[ca_caepump] - 0.003[ca][caepump]d[ca_caepump]/dt = 0.003[ca][caepump] - 288[ca_caepump] - 72[ca_caepump]d[ca.plc_g]/dt = 0.8[ca.plc_g_l.egfr] + 56[pip2_ca.plc_g] + 14[pip2_ca.plc_g] + 0.0003[plc_g][ca] + 0.05[ca.plc_g*] - 5e-06[ca.plc_g][l.egfr] - 1.2e-06[pip2][ca.plc_g] - 10[ca.plc_g]d[l.egfr]/dt = 0.8[ca.plc_g_l.egfr] + 0.2[ca.plc_g_l.egfr] + 0.8[shc_l.egfr] + 0.2[shc_l.egfr] + 7e-06[egfr][egf] + 0.00033[internal_l.egfr] - 5e-06[ca.plc_g][l.egfr] - 2e-06[shc][l.egfr] - 0.25[l.egfr] - 0.002[l.egfr]d[ca.plc_g_l.egfr]/dt = 5e-06[ca.plc_g][l.egfr] - 0.8[ca.plc_g_l.egfr] - 0.2[ca.plc_g_l.egfr]d[ca.plc_g*]/dt = 0.2[ca.plc_g_l.egfr] + 228[pip2_ca.plc_g*] + 57[pip2_ca.plc_g*] + 2e-05[ca][plc_g*] - 2.4e-05[pip2][ca.plc_g*] - 10[ca.plc_g*] - 0.05[ca.plc_g*]d[shc]/dt = 0.8[shc_l.egfr] + 0.0016667[shc*] - 2e-06[shc][l.egfr]d[shc_l.egfr]/dt = 2e-06[shc][l.egfr] - 0.8[shc_l.egfr] - 0.2[shc_l.egfr]d[shc*]/dt = 0.2[shc_l.egfr] + 0.1[shc*.sos.grb2] - 0.0016667[shc*] - 8.333e-07[sos.grb2][shc*]d[mapk]/dt = 0.6[mapk_mapkk*] + 1[mapk-tyr_mkp-1] - 2.7e-05[mapk][mapkk*]d[mapkk*]/dt = 0.6[mapk_mapkk*] + 0.15[mapk_mapkk*] + 0.6[mapk-tyr_mapkk*] + 0.15[mapk-tyr_mapkk*] + 0.105[mapkk-ser_raf-gtp-ras*] + 25[mapkk*_pphosphatase2a] - 2.7e-05[mapk][mapkk*] - 2.7e-05[mapk-tyr][mapkk*] - 3.3e-06[mapkk*][pphosphatase2a]d[mapk_mapkk*]/dt = 2.7e-05[mapk][mapkk*] - 0.6[mapk_mapkk*] - 0.15[mapk_mapkk*]d[mapk-tyr]/dt = 0.15[mapk_mapkk*] + 0.6[mapk-tyr_mapkk*] + 4[mapk-tyr_mkp-1] + 1[mapk*_mkp-1] - 2.7e-05[mapk-tyr][mapkk*] - 0.000125[mapk-tyr][mkp-1]d[mapk-tyr_mapkk*]/dt = 2.7e-05[mapk-tyr][mapkk*] - 0.6[mapk-tyr_mapkk*] - 0.15[mapk-tyr_mapkk*]d[mapk*]/dt = 0.15[mapk-tyr_mapkk*] + 80[pla2-cytosolic_mapk*] + 20[pla2-cytosolic_mapk*] + 40[craf-1*_mapk*] + 10[craf-1*_mapk*] + 40[sos_mapk*] + 10[sos_mapk*] + 4[mapk*_mkp-1] - 6.5e-06[pla2-cytosolic][mapk*] - 3.25e-06[craf-1*][mapk*] - 3.25e-05[sos][mapk*] - 0.000125[mapk*][mkp-1]d[mapkk]/dt = 0.42[mapkk_raf-gtp-ras*] + 6[mapkk-ser_pphosphatase2a] - 5.5e-06[mapkk][raf-gtp-ras*]d[raf-gtp-ras*]/dt = 0.42[mapkk_raf-gtp-ras*] + 0.105[mapkk_raf-gtp-ras*] + 0.42[mapkk-ser_raf-gtp-ras*] + 0.105[mapkk-ser_raf-gtp-ras*] + 4e-05[craf-1*][gtp-ras] - 5.5e-06[mapkk][raf-gtp-ras*] - 5.5e-06[mapkk-ser][raf-gtp-ras*] - 0.5[raf-gtp-ras*]d[mapkk_raf-gtp-ras*]/dt = 5.5e-06[mapkk][raf-gtp-ras*] - 0.42[mapkk_raf-gtp-ras*] - 0.105[mapkk_raf-gtp-ras*]d[mapkk-ser]/dt = 0.105[mapkk_raf-gtp-ras*] + 0.42[mapkk-ser_raf-gtp-ras*] + 6[mapkk*_pphosphatase2a] + 25[mapkk-ser_pphosphatase2a] - 5.5e-06[mapkk-ser][raf-gtp-ras*] - 3.3e-06[mapkk-ser][pphosphatase2a]d[mapkk-ser_raf-gtp-ras*]/dt = 5.5e-06[mapkk-ser][raf-gtp-ras*] - 0.42[mapkk-ser_raf-gtp-ras*] - 0.105[mapkk-ser_raf-gtp-ras*]d[craf-1]/dt = 16[craf-1_pkc-dag-aa*] + 16[craf-1_pkc-ca-memb*] + 16[craf-1_pkc-ca-aa*] + 16[craf-1_pkc-dag-memb*] + 16[craf-1_pkc-basal*] + 16[craf-1_pkc-aa*] + 6[craf-1*_pphosphatase2a] - 5e-07[craf-1][pkc-dag-aa*] - 5e-07[craf-1][pkc-ca-memb*] - 5e-07[craf-1][pkc-ca-aa*] - 5e-07[craf-1][pkc-dag-memb*] - 5e-07[craf-1][pkc-basal*] - 5e-07[craf-1][pkc-aa*]d[pkc-dag-aa*]/dt = 16[craf-1_pkc-dag-aa*] + 4[craf-1_pkc-dag-aa*] + 16[gap_pkc-dag-aa*] + 4[gap_pkc-dag-aa*] + 16[inact-gef_pkc-dag-aa*] + 4[inact-gef_pkc-dag-aa*] + 2[pkc-dag-aa] - 5e-07[craf-1][pkc-dag-aa*] - 1e-05[gap][pkc-dag-aa*] - 1e-05[inact-gef][pkc-dag-aa*] - 0.2[pkc-dag-aa*]d[craf-1_pkc-dag-aa*]/dt = 5e-07[craf-1][pkc-dag-aa*] - 16[craf-1_pkc-dag-aa*] - 4[craf-1_pkc-dag-aa*]d[craf-1*]/dt = 4[craf-1_pkc-dag-aa*] + 4[craf-1_pkc-ca-memb*] + 4[craf-1_pkc-ca-aa*] + 4[craf-1_pkc-dag-memb*] + 4[craf-1_pkc-basal*] + 4[craf-1_pkc-aa*] + 40[craf-1*_mapk*] + 25[craf-1*_pphosphatase2a] + 6[craf-1**_pphosphatase2a] + 0.5[raf-gtp-ras*] - 3.25e-06[craf-1*][mapk*] - 3.3e-06[craf-1*][pphosphatase2a] - 4e-05[craf-1*][gtp-ras]d[gap]/dt = 16[gap_pkc-dag-aa*] + 16[gap_pkc-ca-memb*] + 16[gap_pkc-ca-aa*] + 16[gap_pkc-dag-memb*] + 16[gap_pkc-basal*] + 16[gap_pkc-aa*] + 1000[gtp-ras_gap] + 10[gtp-ras_gap] + 0.1[gap*] - 1e-05[gap][pkc-dag-aa*] - 1e-05[gap][pkc-ca-memb*] - 1e-05[gap][pkc-ca-aa*] - 1e-05[gap][pkc-dag-memb*] - 1e-05[gap][pkc-basal*] - 1e-05[gap][pkc-aa*] - 0.001666[gtp-ras][gap]d[gap_pkc-dag-aa*]/dt = 1e-05[gap][pkc-dag-aa*] - 16[gap_pkc-dag-aa*] - 4[gap_pkc-dag-aa*]d[gap*]/dt = 4[gap_pkc-dag-aa*] + 4[gap_pkc-ca-memb*] + 4[gap_pkc-ca-aa*] + 4[gap_pkc-dag-memb*] + 4[gap_pkc-basal*] + 4[gap_pkc-aa*] - 0.1[gap*]d[inact-gef]/dt = 16[inact-gef_pkc-dag-aa*] + 16[inact-gef_pkc-ca-memb*] + 16[inact-gef_pkc-ca-aa*] + 16[inact-gef_pkc-dag-memb*] + 16[inact-gef_pkc-basal*] + 16[inact-gef_pkc-aa*] + 36[inact-gef_pka-active] + 1[gef-gprot-bg] + 1[gef*] + 1[cam-gef] + 1[inact-gef*] - 1e-05[inact-gef][pkc-dag-aa*] - 1e-05[inact-gef][pkc-ca-memb*] - 1e-05[inact-gef][pkc-ca-aa*] - 1e-05[inact-gef][pkc-dag-memb*] - 1e-05[inact-gef][pkc-basal*] - 1e-05[inact-gef][pkc-aa*] - 1e-05[inact-gef][pka-active] - 1e-05[betagamma][inact-gef] - 0.0001[inact-gef][cam-ca4]d[inact-gef_pkc-dag-aa*]/dt = 1e-05[inact-gef][pkc-dag-aa*] - 16[inact-gef_pkc-dag-aa*] - 4[inact-gef_pkc-dag-aa*]d[gef*]/dt = 4[inact-gef_pkc-dag-aa*] + 4[inact-gef_pkc-ca-memb*] + 4[inact-gef_pkc-ca-aa*] + 4[inact-gef_pkc-dag-memb*] + 4[inact-gef_pkc-basal*] + 4[inact-gef_pkc-aa*] + 0.08[gdp-ras_gef*] + 0.02[gdp-ras_gef*] - 3.3e-07[gdp-ras][gef*] - 1[gef*]d[pkc-ca-memb*]/dt = 16[craf-1_pkc-ca-memb*] + 4[craf-1_pkc-ca-memb*] + 16[gap_pkc-ca-memb*] + 4[gap_pkc-ca-memb*] + 16[inact-gef_pkc-ca-memb*] + 4[inact-gef_pkc-ca-memb*] + 1.2705[pkc-ca] - 5e-07[craf-1][pkc-ca-memb*] - 1e-05[gap][pkc-ca-memb*] - 1e-05[inact-gef][pkc-ca-memb*] - 3.5026[pkc-ca-memb*]d[craf-1_pkc-ca-memb*]/dt = 5e-07[craf-1][pkc-ca-memb*] - 16[craf-1_pkc-ca-memb*] - 4[craf-1_pkc-ca-memb*]d[gap_pkc-ca-memb*]/dt = 1e-05[gap][pkc-ca-memb*] - 16[gap_pkc-ca-memb*] - 4[gap_pkc-ca-memb*]d[inact-gef_pkc-ca-memb*]/dt = 1e-05[inact-gef][pkc-ca-memb*] - 16[inact-gef_pkc-ca-memb*] - 4[inact-gef_pkc-ca-memb*]d[pkc-ca-aa*]/dt = 16[craf-1_pkc-ca-aa*] + 4[craf-1_pkc-ca-aa*] + 16[gap_pkc-ca-aa*] + 4[gap_pkc-ca-aa*] + 16[inact-gef_pkc-ca-aa*] + 4[inact-gef_pkc-ca-aa*] + 2e-09[pkc-ca][aa] - 5e-07[craf-1][pkc-ca-aa*] - 1e-05[gap][pkc-ca-aa*] - 1e-05[inact-gef][pkc-ca-aa*] - 0.1[pkc-ca-aa*]d[craf-1_pkc-ca-aa*]/dt = 5e-07[craf-1][pkc-ca-aa*] - 16[craf-1_pkc-ca-aa*] - 4[craf-1_pkc-ca-aa*]d[gap_pkc-ca-aa*]/dt = 1e-05[gap][pkc-ca-aa*] - 16[gap_pkc-ca-aa*] - 4[gap_pkc-ca-aa*] d[glu]/dt = 10[rec-glu] + 0.1[rec-glu-gq] - 2.8e-05[mglur][glu] - 2.8e-05[glu][rec-gq]d[rec-glu]/dt = 2.8e-05[mglur][glu] + 0.0001[rec-glu-gq] + 0.01[rec-glu-gq] - 10[rec-glu] - 1e-08[g-gdp][rec-glu]d[g-gdp]/dt = 1e-05[g*gdp][betagamma] + 0.0001[rec-glu-gq] + 1[rec-gq] - 0.0001[g-gdp] - 1e-08[g-gdp][rec-glu] - 1e-06[g-gdp][mglur]d[g*gtp]/dt = 0.0001[g-gdp] + 0.01[rec-glu-gq] + 1[plc-ca-gq] + 1[plc-gq] - 0.0133[g*gtp] - 4.2e-05[g*gtp][plc-ca] - 4.2e-06[plc][g*gtp]d[betagamma]/dt = 0.0001[g-gdp] + 0.01[rec-glu-gq] + 1[gef-gprot-bg] - 1e-05[g*gdp][betagamma] - 1e-05[betagamma][inact-gef]d[g*gdp]/dt = 0.0133[g*gtp] + 0.0133[plc-ca-gq] - 1e-05[g*gdp][betagamma]d[rec-glu-gq]/dt = 1e-08[g-gdp][rec-glu] + 2.8e-05[glu][rec-gq] - 0.0001[rec-glu-gq] - 0.1[rec-glu-gq] - 0.01[rec-glu-gq]d[rec-gq]/dt = 0.1[rec-glu-gq] + 1e-06[g-gdp][mglur] + 0.01[blocked-rec-gq] - 2.8e-05[glu][rec-gq] - 1[rec-gq] - 0.0001[rec-gq][mglurantag]d[mglurantag]/dt = 0.01[blocked-rec-gq] - 0.0001[rec-gq][mglurantag]d[blocked-rec-gq]/dt = 0.0001[rec-gq][mglurantag] - 0.01[blocked-rec-gq]d[pkc-cytosolic]/dt = 0.5[pkc-ca] + 50[pkc-basal*] + 0.1[pkc-aa*] + 0.1[pkc-dag] - 1e-06[pkc-cytosolic][ca] - 1[pkc-cytosolic] - 2e-10[aa][pkc-cytosolic] - 1e-09[pkc-cytosolic][dag]d[pkc-ca]/dt = 1e-06[pkc-cytosolic][ca] + 8.6348[pkc-ca-dag] + 3.5026[pkc-ca-memb*] + 0.1[pkc-ca-aa*] - 0.5[pkc-ca] - 1.3333e-08[dag][pkc-ca] - 1.2705[pkc-ca] - 2e-09[pkc-ca][aa]d[pkc-ca-dag]/dt = 1.3333e-08[dag][pkc-ca] + 0.1[pkc-dag-memb*] - 8.6348[pkc-ca-dag] - 1[pkc-ca-dag]d[pkc-dag-aa]/dt = 0.2[pkc-dag-aa*] + 3e-08[pkc-dag][aa] - 2[pkc-dag-aa] - 2[pkc-dag-aa]d[pkc-dag]/dt = 1e-09[pkc-cytosolic][dag] + 2[pkc-dag-aa] - 0.1[pkc-dag] - 3e-08[pkc-dag][aa]d[temp-pip2]/dt = 0.5[pip2-pla2*] + 0.1[pip2-ca-pla2*] - 2e-09[temp-pip2][pla2-cytosolic] - 2e-08[temp-pip2][pla2-ca*]d[plc]/dt = 1[plc-ca] + 1[plc-gq] - 5e-06[ca][plc] - 4.2e-06[plc][g*gtp]d[inositol]/dt = 2.5[ip3]d[pc]/dt = 0.15[dag]d[plc-gq]/dt = 4.2e-06[plc][g*gtp] + 1[plc-ca-gq] - 1[plc-gq] - 5e-05[ca][plc-gq]d[plc_g]/dt = 10[ca.plc_g] - 0.0003[plc_g][ca]d[plc_g*]/dt = 10[ca.plc_g*] - 2e-05[ca][plc_g*]d[cam-ca4]/dt = 1[cam-gef] - 0.0001[inact-gef][cam-ca4]d[sos.grb2]/dt = 0.1[shc*.sos.grb2] + 4.1667e-08[grb2][sos] - 8.333e-07[sos.grb2][shc*] - 0.0168[sos.grb2]d[grb2]/dt = 0.0168[sos*.grb2] + 0.0168[sos.grb2] - 4.1667e-08[sos*][grb2] - 4.1667e-08[grb2][sos]d[sos*.grb2]/dt = 4.1667e-08[sos*][grb2] - 0.0168[sos*.grb2]d[ca-ext]/dt = 72[ca_caepump] - 0.005 * [capacitive_ca_entry*] * ( [ca-ext] - [ca] ) - 0.004 * [ca-leak-from-extracell] * ( [ca-ext] - [ca] ) d[ca-sequester]/dt = 25[catransp-2ca] + 25[catransp-2ca] + 1[inact_cap_entry] + 1[inact_cap_entry] - 1.2e-11[ca-sequester][ca-sequester][capacitive_ca_entry*] - 1.2e-11[ca-sequester][ca-sequester][capacitive_ca_entry*] - 8 * [ca-leak-to-cytoplasm] * ( [ca-sequester] - [ca] ) - 19.2 * [ip3r*] * ( [ca-sequester] - [ca] ) d[inact-gef_pkc-ca-aa*]/dt = 1e-05[inact-gef][pkc-ca-aa*] - 16[inact-gef_pkc-ca-aa*] - 4[inact-gef_pkc-ca-aa*]d[pkc-dag-memb*]/dt = 16[craf-1_pkc-dag-memb*] + 4[craf-1_pkc-dag-memb*] + 16[gap_pkc-dag-memb*] + 4[gap_pkc-dag-memb*] + 16[inact-gef_pkc-dag-memb*] + 4[inact-gef_pkc-dag-memb*] + 1[pkc-ca-dag] - 5e-07[craf-1][pkc-dag-memb*] - 1e-05[gap][pkc-dag-memb*] - 1e-05[inact-gef][pkc-dag-memb*] - 0.1[pkc-dag-memb*]d[craf-1_pkc-dag-memb*]/dt = 5e-07[craf-1][pkc-dag-memb*] - 16[craf-1_pkc-dag-memb*] - 4[craf-1_pkc-dag-memb*]d[gap_pkc-dag-memb*]/dt = 1e-05[gap][pkc-dag-memb*] - 16[gap_pkc-dag-memb*] - 4[gap_pkc-dag-memb*]d[inact-gef_pkc-dag-memb*]/dt = 1e-05[inact-gef][pkc-dag-memb*] - 16[inact-gef_pkc-dag-memb*] - 4[inact-gef_pkc-dag-memb*]d[pkc-basal*]/dt = 16[craf-1_pkc-basal*] + 4[craf-1_pkc-basal*] + 16[gap_pkc-basal*] + 4[gap_pkc-basal*] + 16[inact-gef_pkc-basal*] + 4[inact-gef_pkc-basal*] + 1[pkc-cytosolic] - 5e-07[craf-1][pkc-basal*] - 1e-05[gap][pkc-basal*] - 1e-05[inact-gef][pkc-basal*] - 50[pkc-basal*]d[craf-1_pkc-basal*]/dt = 5e-07[craf-1][pkc-basal*] - 16[craf-1_pkc-basal*] - 4[craf-1_pkc-basal*]d[gap_pkc-basal*]/dt = 1e-05[gap][pkc-basal*] - 16[gap_pkc-basal*] - 4[gap_pkc-basal*]d[inact-gef_pkc-basal*]/dt = 1e-05[inact-gef][pkc-basal*] - 16[inact-gef_pkc-basal*] - 4[inact-gef_pkc-basal*]d[pkc-aa*]/dt = 16[craf-1_pkc-aa*] + 4[craf-1_pkc-aa*] + 16[gap_pkc-aa*] + 4[gap_pkc-aa*] + 16[inact-gef_pkc-aa*] + 4[inact-gef_pkc-aa*] + 2e-10[aa][pkc-cytosolic] - 5e-07[craf-1][pkc-aa*] - 1e-05[gap][pkc-aa*] - 1e-05[inact-gef][pkc-aa*] - 0.1[pkc-aa*]d[craf-1_pkc-aa*]/dt = 5e-07[craf-1][pkc-aa*] - 16[craf-1_pkc-aa*] - 4[craf-1_pkc-aa*]d[gap_pkc-aa*]/dt = 1e-05[gap][pkc-aa*] - 16[gap_pkc-aa*] - 4[gap_pkc-aa*]d[inact-gef_pkc-aa*]/dt = 1e-05[inact-gef][pkc-aa*] - 16[inact-gef_pkc-aa*] - 4[inact-gef_pkc-aa*]d[apc]/dt = 21.6[apc_pla2-ca*] + 44.16[apc_pip2-pla2*] + 144[apc_pip2-ca-pla2*] + 240[apc_dag-ca-pla2*] + 480[apc_pla2*-ca] + 0.4[aa] - 2.25e-06[apc][pla2-ca*] - 4.6e-06[apc][pip2-pla2*] - 1.5e-05[apc][pip2-ca-pla2*] - 2.5e-05[apc][dag-ca-pla2*] - 5e-05[apc][pla2*-ca]d[pla2-ca*]/dt = 21.6[apc_pla2-ca*] + 5.4[apc_pla2-ca*] + 1.6667e-06[pla2-cytosolic][ca] + 0.1[pip2-ca-pla2*] + 4[dag-ca-pla2*] - 2.25e-06[apc][pla2-ca*] - 0.1[pla2-ca*] - 2e-08[temp-pip2][pla2-ca*] - 5e-09[dag][pla2-ca*]d[apc_pla2-ca*]/dt = 2.25e-06[apc][pla2-ca*] - 21.6[apc_pla2-ca*] - 5.4[apc_pla2-ca*]d[aa]/dt = 5.4[apc_pla2-ca*] + 11.04[apc_pip2-pla2*] + 36[apc_pip2-ca-pla2*] + 60[apc_dag-ca-pla2*] + 120[apc_pla2*-ca] + 0.1[pkc-ca-aa*] + 0.1[pkc-aa*] + 2[pkc-dag-aa] - 2e-09[pkc-ca][aa] - 2e-10[aa][pkc-cytosolic] - 3e-08[pkc-dag][aa] - 0.4[aa]d[pip2-pla2*]/dt = 44.16[apc_pip2-pla2*] + 11.04[apc_pip2-pla2*] + 2e-09[temp-pip2][pla2-cytosolic] - 4.6e-06[apc][pip2-pla2*] - 0.5[pip2-pla2*]d[apc_pip2-pla2*]/dt = 4.6e-06[apc][pip2-pla2*] - 44.16[apc_pip2-pla2*] - 11.04[apc_pip2-pla2*]d[pip2-ca-pla2*]/dt = 144[apc_pip2-ca-pla2*] + 36[apc_pip2-ca-pla2*] + 2e-08[temp-pip2][pla2-ca*] - 1.5e-05[apc][pip2-ca-pla2*] - 0.1[pip2-ca-pla2*]d[apc_pip2-ca-pla2*]/dt = 1.5e-05[apc][pip2-ca-pla2*] - 144[apc_pip2-ca-pla2*] - 36[apc_pip2-ca-pla2*]d[dag-ca-pla2*]/dt = 240[apc_dag-ca-pla2*] + 60[apc_dag-ca-pla2*] + 5e-09[dag][pla2-ca*] - 2.5e-05[apc][dag-ca-pla2*] - 4[dag-ca-pla2*]d[apc_dag-ca-pla2*]/dt = 2.5e-05[apc][dag-ca-pla2*] - 240[apc_dag-ca-pla2*] - 60[apc_dag-ca-pla2*]d[pla2*-ca]/dt = 480[apc_pla2*-ca] + 120[apc_pla2*-ca] + 1e-05[pla2*][ca] - 5e-05[apc][pla2*-ca] - 0.1[pla2*-ca]d[apc_pla2*-ca]/dt = 5e-05[apc][pla2*-ca] - 480[apc_pla2*-ca] - 120[apc_pla2*-ca]d[pla2-cytosolic]/dt = 80[pla2-cytosolic_mapk*] + 0.1[pla2-ca*] + 0.5[pip2-pla2*] + 0.17[pla2*] - 6.5e-06[pla2-cytosolic][mapk*] - 1.6667e-06[pla2-cytosolic][ca] - 2e-09[temp-pip2][pla2-cytosolic]d[pla2-cytosolic_mapk*]/dt = 6.5e-06[pla2-cytosolic][mapk*] - 80[pla2-cytosolic_mapk*] - 20[pla2-cytosolic_mapk*]d[pla2*]/dt = 20[pla2-cytosolic_mapk*] + 0.1[pla2*-ca] - 1e-05[pla2*][ca] - 0.17[pla2*]d[craf-1*_mapk*]/dt = 3.25e-06[craf-1*][mapk*] - 40[craf-1*_mapk*] - 10[craf-1*_mapk*]d[craf-1**]/dt = 10[craf-1*_mapk*] + 25[craf-1**_pphosphatase2a] - 3.3e-06[craf-1**][pphosphatase2a]d[sos]/dt = 40[sos_mapk*] + 0.001[sos*] + 0.0168[sos.grb2] - 3.25e-05[sos][mapk*] - 4.1667e-08[grb2][sos]d[sos_mapk*]/dt = 3.25e-05[sos][mapk*] - 40[sos_mapk*] - 10[sos_mapk*]d[sos*]/dt = 10[sos_mapk*] + 0.0168[sos*.grb2] - 4.1667e-08[sos*][grb2] - 0.001[sos*]d[mkp-1]/dt = 4[mapk-tyr_mkp-1] + 1[mapk-tyr_mkp-1] + 4[mapk*_mkp-1] + 1[mapk*_mkp-1] - 0.000125[mapk-tyr][mkp-1] - 0.000125[mapk*][mkp-1]d[mapk-tyr_mkp-1]/dt = 0.000125[mapk-tyr][mkp-1] - 4[mapk-tyr_mkp-1] - 1[mapk-tyr_mkp-1]d[mapk*_mkp-1]/dt = 0.000125[mapk*][mkp-1] - 4[mapk*_mkp-1] - 1[mapk*_mkp-1]d[pphosphatase2a]/dt = 25[craf-1*_pphosphatase2a] + 6[craf-1*_pphosphatase2a] + 25[mapkk*_pphosphatase2a] + 6[mapkk*_pphosphatase2a] + 25[mapkk-ser_pphosphatase2a] + 6[mapkk-ser_pphosphatase2a] + 25[craf-1**_pphosphatase2a] + 6[craf-1**_pphosphatase2a] - 3.3e-06[craf-1*][pphosphatase2a] - 3.3e-06[mapkk*][pphosphatase2a] - 3.3e-06[mapkk-ser][pphosphatase2a] - 3.3e-06[craf-1**][pphosphatase2a]d[craf-1*_pphosphatase2a]/dt = 3.3e-06[craf-1*][pphosphatase2a] - 25[craf-1*_pphosphatase2a] - 6[craf-1*_pphosphatase2a]d[mapkk*_pphosphatase2a]/dt = 3.3e-06[mapkk*][pphosphatase2a] - 25[mapkk*_pphosphatase2a] - 6[mapkk*_pphosphatase2a]d[mapkk-ser_pphosphatase2a]/dt = 3.3e-06[mapkk-ser][pphosphatase2a] - 25[mapkk-ser_pphosphatase2a] - 6[mapkk-ser_pphosphatase2a]d[craf-1**_pphosphatase2a]/dt = 3.3e-06[craf-1**][pphosphatase2a] - 25[craf-1**_pphosphatase2a] - 6[craf-1**_pphosphatase2a]d[pka-active]/dt = 36[inact-gef_pka-active] + 9[inact-gef_pka-active] - 1e-05[inact-gef][pka-active]d[inact-gef_pka-active]/dt = 1e-05[inact-gef][pka-active] - 36[inact-gef_pka-active] - 9[inact-gef_pka-active]d[inact-gef*]/dt = 9[inact-gef_pka-active] - 1[inact-gef*]d[gdp-ras]/dt = 0.08[gdp-ras_shc*.sos.grb2] + 0.08[gdp-ras_gef-gprot-bg] + 0.08[gdp-ras_gef*] + 10[gtp-ras_gap] + 0.08[gdp-ras_cam-gef] + 0.0001[gtp-ras] - 3.3e-07[gdp-ras][shc*.sos.grb2] - 3.3e-07[gdp-ras][gef-gprot-bg] - 3.3e-07[gdp-ras][gef*] - 3.3e-07[gdp-ras][cam-gef]d[shc*.sos.grb2]/dt = 0.08[gdp-ras_shc*.sos.grb2] + 0.02[gdp-ras_shc*.sos.grb2] + 8.333e-07[sos.grb2][shc*] - 3.3e-07[gdp-ras][shc*.sos.grb2] - 0.1[shc*.sos.grb2]d[gdp-ras_shc*.sos.grb2]/dt = 3.3e-07[gdp-ras][shc*.sos.grb2] - 0.08[gdp-ras_shc*.sos.grb2] - 0.02[gdp-ras_shc*.sos.grb2]d[gtp-ras]/dt = 0.02[gdp-ras_shc*.sos.grb2] + 0.02[gdp-ras_gef-gprot-bg] + 0.02[gdp-ras_gef*] + 1000[gtp-ras_gap] + 0.02[gdp-ras_cam-gef] + 0.5[raf-gtp-ras*] - 0.001666[gtp-ras][gap] - 4e-05[craf-1*][gtp-ras] - 0.0001[gtp-ras]d[pip2]/dt = 40[pip2_plc-ca] + 192[pip2_plc-ca-gq] + 56[pip2_ca.plc_g] + 228[pip2_ca.plc_g*] - 4.2e-06[pip2][plc-ca] - 8e-05[pip2][plc-ca-gq] - 1.2e-06[pip2][ca.plc_g] - 2.4e-05[pip2][ca.plc_g*]d[plc-ca]/dt = 40[pip2_plc-ca] + 10[pip2_plc-ca] + 5e-06[ca][plc] + 1[plc-ca-gq] + 0.0133[plc-ca-gq] - 4.2e-06[pip2][plc-ca] - 1[plc-ca] - 4.2e-05[g*gtp][plc-ca]d[pip2_plc-ca]/dt = 4.2e-06[pip2][plc-ca] - 40[pip2_plc-ca] - 10[pip2_plc-ca]d[dag]/dt = 10[pip2_plc-ca] + 48[pip2_plc-ca-gq] + 14[pip2_ca.plc_g] + 57[pip2_ca.plc_g*] + 8.6348[pkc-ca-dag] + 0.1[pkc-dag] + 4[dag-ca-pla2*] - 1.3333e-08[dag][pkc-ca] - 1e-09[pkc-cytosolic][dag] - 5e-09[dag][pla2-ca*] - 0.15[dag]d[ip3]/dt = 10[pip2_plc-ca] + 48[pip2_plc-ca-gq] + 14[pip2_ca.plc_g] + 57[pip2_ca.plc_g*] + 1[ip3r*] + 1[ip3r*] + 1[ip3r*] - 1e-20[ip3r][ip3][ip3][ip3] - 1e-20[ip3r][ip3][ip3][ip3] - 1e-20[ip3r][ip3][ip3][ip3] - 2.5[ip3]d[plc-ca-gq]/dt = 192[pip2_plc-ca-gq] + 48[pip2_plc-ca-gq] + 4.2e-05[g*gtp][plc-ca] + 5e-05[ca][plc-gq] - 8e-05[pip2][plc-ca-gq] - 1[plc-ca-gq] - 0.0133[plc-ca-gq] - 1[plc-ca-gq]d[pip2_plc-ca-gq]/dt = 8e-05[pip2][plc-ca-gq] - 192[pip2_plc-ca-gq] - 48[pip2_plc-ca-gq]d[pip2_ca.plc_g]/dt = 1.2e-06[pip2][ca.plc_g] - 56[pip2_ca.plc_g] - 14[pip2_ca.plc_g]d[pip2_ca.plc_g*]/dt = 2.4e-05[pip2][ca.plc_g*] - 228[pip2_ca.plc_g*] - 57[pip2_ca.plc_g*]d[gef-gprot-bg]/dt = 0.08[gdp-ras_gef-gprot-bg] + 0.02[gdp-ras_gef-gprot-bg] + 1e-05[betagamma][inact-gef] - 3.3e-07[gdp-ras][gef-gprot-bg] - 1[gef-gprot-bg]d[gdp-ras_gef-gprot-bg]/dt = 3.3e-07[gdp-ras][gef-gprot-bg] - 0.08[gdp-ras_gef-gprot-bg] - 0.02[gdp-ras_gef-gprot-bg]d[gdp-ras_gef*]/dt = 3.3e-07[gdp-ras][gef*] - 0.08[gdp-ras_gef*] - 0.02[gdp-ras_gef*]d[gtp-ras_gap]/dt = 0.001666[gtp-ras][gap] - 1000[gtp-ras_gap] - 10[gtp-ras_gap]d[cam-gef]/dt = 0.08[gdp-ras_cam-gef] + 0.02[gdp-ras_cam-gef] + 0.0001[inact-gef][cam-ca4] - 3.3e-07[gdp-ras][cam-gef] - 1[cam-gef]d[gdp-ras_cam-gef]/dt = 3.3e-07[gdp-ras][cam-gef] - 0.08[gdp-ras_cam-gef] - 0.02[gdp-ras_cam-gef]d[catransp-2ca]/dt = 1e-08[ca][catransp][ca] - 25[catransp-2ca] - 144[catransp-2ca]d[catransp]/dt = 25[catransp-2ca] + 144[catransp-2ca] - 1e-08[ca][catransp][ca]d[ip3r]/dt = 1[ip3r*] - 1e-20[ip3r][ip3][ip3][ip3]d[inact_cap_entry]/dt = 1.2e-11[ca-sequester][ca-sequester][capacitive_ca_entry*] - 1[inact_cap_entry]d[egfr]/dt = 0.25[l.egfr] - 7e-06[egfr][egf]d[egf]/dt = 0.25[l.egfr] - 7e-06[egfr][egf]d[internal_l.egfr]/dt = 0.002[l.egfr] - 0.00033[internal_l.egfr]d[mglur]/dt = 10[rec-glu] + 1[rec-gq] - 2.8e-05[mglur][glu] - 1e-06[g-gdp][mglur] Special topics on Electrical and Systems Engineering 2007 Systems Biology

  12. Parameters • 1: Science. 1999 Jan 15;283(5400):381-7. Emergent properties of networks of biological signaling pathways.Bhalla US, Iyengar R. Special topics on Electrical and Systems Engineering 2007 Systems Biology

  13. How may a mutation affect kinetics? δ Special topics on Electrical and Systems Engineering 2007 Systems Biology

  14. Effects on signaling • A mutation between two unique species • Affects Reactant State • Affects Product State • Affects Transition State Special topics on Electrical and Systems Engineering 2007 Systems Biology

  15. Cancer as a cumulative process • Multiple Mutations at different sites contribute to tumor transformation • Tumor may exist as “families” of differentially mutated cells • Overrides resistance of tumor to treatment Special topics on Electrical and Systems Engineering 2007 Systems Biology

  16. “In Silico” Interaction Knockout experiments Special topics on Electrical and Systems Engineering 2007 Systems Biology

  17. Single Site Transformations(kf’/kf) Special topics on Electrical and Systems Engineering 2007 Systems Biology

  18. Top Ranked Mutations Special topics on Electrical and Systems Engineering 2007 Systems Biology

  19. Top Ranked expression level mutations Species Species Special topics on Electrical and Systems Engineering 2007 Systems Biology

  20. Advantages of In Silico Pathway Analysis • Using experimentally validated models of a working signal pathway and a simple kinetic view of mutations • One can: • Quantify (and rank) • Single Interaction Mutations • Multiple Interaction Mutations • Initial State Mutations • Many results are validated in the literature • Several new and non-obvious predictions Special topics on Electrical and Systems Engineering 2007 Systems Biology

  21. In Silico Cancer Cells • We have developed a family of “in silico” cancer cells as models of pathways What is this good for? Special topics on Electrical and Systems Engineering 2007 Systems Biology

  22. The effect of Drugs on Signaling in mutated cells Competitive Binding Noncompetitive binding Special topics on Electrical and Systems Engineering 2007 Systems Biology

  23. ERK Target Special topics on Electrical and Systems Engineering 2007 Systems Biology

  24. MEK Target Special topics on Electrical and Systems Engineering 2007 Systems Biology

  25. Calciumblockers Special topics on Electrical and Systems Engineering 2007 Systems Biology

  26. Threshold “Ranking” Special topics on Electrical and Systems Engineering 2007 Systems Biology

  27. Experimental Assays • PLC- - peptide based inhibitors • PLC - U73122 • PKC - Tamoxifen , Go6976, SPC-100221 • PLA-2 - Quinacrine (anti-inflammatory) • ERK - • MEK - AZD6244/ARRY-142886, CI-1040 , PD98059 • Ras - R115577, BMS-214462 SCH-66336 • Raf - Bay43-9006 ISIS-5132 • GEF - • Calcium Blockers Verapamil , Nicardipine Special topics on Electrical and Systems Engineering 2007 Systems Biology

  28. Overview • Ras/Gap mutations predicted • PP2A mutations predicted • Ras/Raf interaction “importance” predicted • Much of the overexpression/underexpression mutations predicted • Drug targets are for the most part have experimental counter parts. Special topics on Electrical and Systems Engineering 2007 Systems Biology

  29. Transport? Special topics on Electrical and Systems Engineering 2007 Systems Biology

  30. How to treat real cells? Special topics on Electrical and Systems Engineering 2007 Systems Biology

  31. Confocal Imaging and Quantum Dots (Andres Kriete) QDots Tunable Photostable Narrow Emission Spectra Broad Absorption Spectrum Confocal Imaging Live Cells and fixed cells sub micron imaging Special topics on Electrical and Systems Engineering 2007 Systems Biology

  32. Quantitative Signaling Analysis Data from Confocal Imaging - derivation of “in vivo” rate constants through global analysis Given time sliced images and model Derived rate constants will “fit” experimental images best (global optimization problem) with confidence intervals - wealth of data helps prevent over fitting C(x,y,z,t) - “Automated” Sensitivity Analysis will be used for fitting Special topics on Electrical and Systems Engineering 2007 Systems Biology

  33. Cell(ular)Sim(ulator) • Cross Platform (Linux, Windows, MacOS X, Solaris) • Multiprocessor (MPI) (linear scaling) • Freely Available (GPL) • Pseudo-C Scripting Language • Adaptive Integrators (Reaction Diffusion) with Sensitivity Analysis • - (Adaptive 2nd and 4th order Rosenbrock, Euler RK2,RK4,ARK4) • - Strang Split RDR Coupled Diffusion Special topics on Electrical and Systems Engineering 2007 Systems Biology

  34. Analysis Optimization Tools • Sensitivity Analysis Module (Automatic generation of Jacobian, Hessian) • MCA Module (Conservation Relationships) • Global Optimization Tools • - Use tools derived by the Protein Folding Community (and elsewhere) • - Simulated Annealing • - Monte Carlo + Minimization • - GA / Evolutionary Programming Special topics on Electrical and Systems Engineering 2007 Systems Biology

  35. Numerical Methods Equations are stiff, Jacobian is Sparse Reaction - Diffusion Reaction - Advection RADAR Must ||’ize well and must be accurate Special topics on Electrical and Systems Engineering 2007 Systems Biology

  36. Reaction Operator :: Rosenbrock We have this for solving Inherently || for our distribution scheme Special topics on Electrical and Systems Engineering 2007 Systems Biology

  37. Diffusion Operator Simple || algorithm based on explicit (FTCS) method Simple single processor method based on Crank-Nicolson || Crank-Nicolson method based on the fact that you are solving a slew of independent 1D tri-diagonal solves Special topics on Electrical and Systems Engineering 2007 Systems Biology

  38. Advection Operator Based on Lax (explicit, inherently || ) Nonlinear part of advection operator moved to reaction Operator Special topics on Electrical and Systems Engineering 2007 Systems Biology

  39. Time Step Adaptability Calculate the splitting error (and local errors) : use total error for estimating time step Currently we have this for Reaction-Diffusion Special topics on Electrical and Systems Engineering 2007 Systems Biology

  40. Visualization Cross Platform QT/OpenGL Code Base Client / Server (Socket Based) GUI “Live” Interaction with Numerical Code 1D/2D/3D time lapse contour plots Mouse-based interactive manipulation Flexible Modular Design To Be Implemented Point and Click graphical Entry of Biological Pathways, Grid Geometry, Initial Parameters and Control Special topics on Electrical and Systems Engineering 2007 Systems Biology

  41. Who did the real work? • Dhruv Pant Ph.D. • Dave Miller • Ray Zou • Yihua Wang • Hanbing Lin • Tom Shortell • Travis Hoppe • Aparna Kumar http://bio.physics.drexel.edu http://bio.physics.drexel.edu/systemsBiology Email : avijit@physics.drexel.edu Special topics on Electrical and Systems Engineering 2007 Systems Biology

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