begin model begin parameters# fraction of reaction volume to explicitly consider in a stochastic simulation f 1.0 # [=] dimensionless, [0 < f <= 1.0] # physical constants and unit conversion factors # Avogadro constant NA 6.02214e23 # [=] number of molecules per mol # reaction volume V f*1.0e-12 # [=] L # Parameter values from Table S1 in supplementary materials for Stites et. al., # "Network Analysis of Oncogenic Ras Activation in Cancer" GTP_cnpc 1.8e-4*NA*V # Molarity GDP_cnpc 1.8e-5*NA*V # Molarity KRAS_cnpc 4e-7*NA*V # Molarity SOS1_cnpc 2e-10*NA*V # Molarity RASA1_cnpc 6e-11*NA*V # Molarity CRAF_cnpc 2e-7*NA*V # Molarity D 250.0 khyd 3.5e-4 # /sec kdGDP 1.1e-4 # /sec kdGTP 2.5e-4 # /sec kaGDP 2.3e6/(NA*V) # /Mole /sec kaGTP 2.2e6/(NA*V) # /Mole /sec kcatGDP 3.9 # /sec kcatGTP 7.2e-1 # /sec KmGDP 3.86e-4/D*NA*V # M KmGTP 3e-4/D*NA*V # M kcat 5.4 # /sec Km 2.3e-7/D*NA*V # M kaEff 4.5e7/(NA*V) # /Mole /sec kdEff 3.6 # /sec end parameters begin molecule types # Proteins are named in accordance with the recommendatons of the # HUGO Gene Nomenclature Committee (HGNC). # http://www.genenames.org/ GTP GDP # K-Ras is the form of Ras most commonly associated with cancer. # Ras proteins are a family of small GTPases; # they differ mainly at the C-terminal hypervariable region. # The hypervariabl region controls membrane localization; # K-Ras localizes to the plasma membrane. # Ras alone has low GTPase activity. # Ras bound to a GAP protein has high GTPase activity. # ndg: KRAS(?,G~GDP) is RasGDP and KRAS(?,G~GTP) is RasGTP KRAS(GTPase,G~GDP~GTP~O) # The GTPase component is introduced to represent the (overlapping) parts of KRAS # that interact with GEFs, GAPs and effectors. # The G component represents the G motifs (G1-G5); these motifs mediate interaction # with guanine nucleotides (GDP and GTP). # The internal states GDP and GTP are introduced to represent # the GDP- and GTP-loaded forms of KRAS. # The internal state O represents the form of Ras not bound to guanine nucleotide (rare). # Sos1 is a GEF (guanine nucleotide exchange factor). SOS1(REM,RasGEF) # REM is the Ras exchange motif; it preferentially binds GTP-loaded Ras # RasGEF is the CDC25 homology domain; it preferentially binds GDP-loaded Ras # p120 RasGAP (aka RASA1) is a GAP (Ras GTPase activating protein). RASA1(RasGAP) # RasGAP association with Ras is required for full GTPase activity; # the GTPase can be viewed as a heterodimeric enzyme with # Ras contributing one subunit and RasGAP contributing the other subunit. # Raf-1 (aka CRAF) is a Ras effector protein, meaning that is recruited to the plasma # membrane through binding to GTP-loaded Ras. CRAF(RBD) # RBD is the Ras binding domain; it is responsible for interaction with GTP-loaded Ras. end molecule types begin seed species # NB: the settings below are arbitrary - they do not reflect a steady-state condition # Equilibration should be performed to find the steady state of the model. $GTP() GTP_cnpc $GDP() GDP_cnpc KRAS(GTPase,G~GTP) KRAS_cnpc $SOS1(REM,RasGEF) SOS1_cnpc $RASA1(RasGAP) RASA1_cnpc CRAF(RBD) CRAF_cnpc end seed species begin observables Molecules KRAS_total KRAS() Molecules KRAS_GTP_total KRAS(G~GTP) # should match Ras^{WT} column in Table S3 Molecules KRAS_GTP KRAS(GTPase,G~GTP) Molecules KRAS_Eff KRAS(GTPase!1,G~GTP).CRAF(RBD!1) Molecules KRAS_GDP KRAS(GTPase,G~GDP) Molecules KRAS_GDP_total KRAS(G~GDP) # should be close to KRAS_GDP Molecules KRAS_O KRAS(G~O) Molecules KRAS_free KRAS(GTPase) # this definition ignores guanine nucleotide binding Molecules SOS1_total SOS1() Molecules SOS1_free SOS1(REM,RasGEF) Molecules RASA1_total RASA1() Molecules RASA1_free RASA1(RasGAP) Molecules CRAF_total CRAF() Molecules CRAF_free CRAF(RBD) end observables begin reaction rules # Binding and freeing of G(D|T)P to KRAS KRAS(GTPase,G~GTP) <-> KRAS(GTPase,G~O) + GTP kdGTP,kaGTP KRAS(GTPase,G~GDP) <-> KRAS(GTPase,G~O) + GDP kdGDP,kaGDP # GEF-assisted transformation of RasGTP to RasGDP # Treated as a purely catalytic reaction, not an exchange # But perhaps not... see the differential equations in the paper. KRAS(GTPase,G~GTP)+SOS1(REM,RasGEF) -> KRAS(GTPase,G~GDP)+SOS1(REM,RasGEF) (kcatGTP/KmGTP)/(1 + KRAS_GTP/KmGTP + KRAS_GDP/KmGDP) KRAS(GTPase,G~GDP)+SOS1(REM,RasGEF) -> KRAS(GTPase,G~GTP)+SOS1(REM,RasGEF) (kcatGDP/KmGDP)/(1 + KRAS_GDP/KmGDP + KRAS_GTP/KmGTP) # GAP-assisted hydrolysis of GTP->GDP KRAS(GTPase,G~GTP) + RASA1(RasGAP) -> KRAS(GTPase,G~GDP) + RASA1(RasGAP) kcat/(Km + KRAS_GTP) # Unassisted hydrolysis of GTP->GDP KRAS(GTPase,G~GTP) -> KRAS(GTPase,G~GDP) khyd # Binding to effector KRAS(GTPase,G~GTP)+CRAF(RBD) <-> KRAS(GTPase!1,G~GTP).CRAF(RBD!1) kaEff,kdEff KRAS(GTPase!1,G~GTP).CRAF(RBD!1) -> KRAS(GTPase,G~GDP)+CRAF(RBD) khyd end reaction rules end model #ACTIONS generate_network({overwrite=>1}); # Equilibration setConcentration("SOS1(REM,RasGEF)","SOS1_cnpc"); simulate_ode({suffix=>"equil",t_end=>10000000,n_steps=>10000000,atol=>1e-12,rtol=>1e-12,steady_state=>1}); saveConcentrations();