# A model for WT Ras signaling in vitro # A single well-mixed reaction compartment is assumed. # # Author information: # William S. Hlavacek # Theoretical Division # Los Alamos National Laboratory # # Date: # 16-December-2013 # # Platform information: # Mac OS X, version 10.5.8 # # Software information: # BioNetGen, version 2.1.7 (http://bionetgen.org) # RuleBender, version 1.1.415 (http://rulebender.cs.pitt.edu) begin model begin parameters # simulation 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 # molecular parameters (e.g., copy numbers) # NB: concentrations are each given in M # and then converted to molecules per volume of reaction compartment GTP_conc 1.8e-4*NA*V # [=] M GDP_conc 1.8e-5*NA*V # [=] M KRAS_conc 4.0e-7*NA*V # [=] M CRAF_conc 4.0e-7*NA*V # [=] M SOS1_conc 2.0e-11*NA*V # [=] M RASA1_conc 6.0e-11*NA*V # [=] M # interaction parameters (e.g., rate constants) # NB: biomolecular assocication rate constants are each given in /M/s # and then converted to /(molecules per volume of reaction compartment)/s # binding # GDP binding to apo Ras # KD1 = 9.0e-12 M km1 2.0e-5 # [=] /s kp1 2.2e6/(NA*V) # [=] /M/s # GEF binding to apo Ras # KD2 = 3.3e-9 M km2 1.0e-3 # [=] /s kp2 3.3e5/(NA*V) # [=] /M/s # GEF binding to RasGDP # KD3 = 2.2e-4 M km3 5.0 # [=] /s kp3 2.3e4/(NA*V) # [=] /M/s # GDP binding to apo Ras-GEF complex # KD4 = 6.0e-7 M km4 3.9 # [=] /s kp4 6.5e6/(NA*V) # [=] /M/s # GTP binding to apo Ras # KD5 = 5.0e-12 M km5 1.0e-5 # [=] /s kp5 2.0e6/(NA*V) # [=] /M/s # GTP binding to apo Ras-GEF complex # KD6 = 3.0e-7 M km6 1.1 # [=] /s kp6 3.7e6/(NA*V) # [=] /M/s # GEF binding to RasGTP # KD7 = 2.0e-4 M km7 5.0 # [=] /s kp7 2.5e4/(NA*V) # [=] /M/s # Effector binding # KD = 8.0e-8 M kaEff 4.5e7/(NA*V) # [=] /M/s kdEff 3.6 # [=] /s # catalysis # GTP hyrdolysis via the intrinsic GTPase activity of Ras khyd 3.5e-4 # [=] /s # GAP activity via a Michaelis-Menten mechanism # KM = 2.3e-7 M kf 4.0e7/(NA*V) # [=] /M/s kr 3.8 # [=] /s kcat 5.4 # [=] /s end parameters begin molecule types # Except as noted, proteins are named in accordance with the recommendations of # the HUGO Gene Nomenclature Committee (HGNC). # http://www.genenames.org # Organism information: # Homo sapiens (human) # small molecules ## GDP ## ################################################################################ # guanosine diphosphate ################################################################################ GDP ## GTP ## ################################################################################ # guanosine-5'-triphosphate ################################################################################ GTP # proteins ## KRAS ## ################################################################################ # KRAS consists of a G domain # The G domain can be free (the apo form of Ras), bound to GDP, or bound to GTP. ################################################################################ KRAS(G~apo~GDP~GTP) ## RASA1 ## ################################################################################ # RASA1 contains a GAP domain ################################################################################ RASA1(GAP) ## SOS1 ## ################################################################################ # SOS1 contains a GEF domain ################################################################################ SOS1(GEF) ## CRAF ## ################################################################################ # CRAF contains an RDB (Ras binding domain) ################################################################################ CRAF(RBD) end molecule types begin seed species # small molecules GDP GDP_conc GTP GTP_conc # proteins # Set apo Ras, RasGDP and RasGTP concentrations to their near equilibrium values KRAS(G~apo) KRAS_conc/(1.+(kp1/km1)*GDP_conc+(kp5/km5)*GTP_conc) KRAS(G~GDP) \ (kp1/km1)*GDP_conc*KRAS_conc/(1.+(kp1/km1)*GDP_conc+(kp5/km5)*GTP_conc) KRAS(G~GTP) \ (kp5/km5)*GTP_conc*KRAS_conc/(1.+(kp1/km1)*GDP_conc+(kp5/km5)*GTP_conc) # The settings below simulate addition of SOS1, RASA1 and CRAF at time t=0 SOS1(GEF) SOS1_conc RASA1(GAP) RASA1_conc CRAF(RBD) CRAF_conc end seed species begin observables Molecules RasGTP KRAS(G~GTP!?) Molecules RasGDP KRAS(G~GDP!?) Molecules ActiveEff CRAF(RBD!+) # conservation laws Molecules KRAStot KRAS() Molecules Gtot GDP GTP KRAS(G~GDP!?) KRAS(G~GTP!?) Molecules SOS1tot SOS1() Molecules RASA1tot RASA1() Molecules CRAFtot CRAF() end observables begin reaction rules # GDP binds the apo form of Ras KRAS(G~apo)+GDP->KRAS(G~GDP) kp1 # GDP spontaneously dissociates from Ras KRAS(G~GDP)->KRAS(G~apo)+GDP km1 # GEF reversibly binds apo Ras KRAS(G~apo)+SOS1(GEF)<->KRAS(G~apo!1).SOS1(GEF!1) kp2,km2 # GEF reversibly binds RasGDP KRAS(G~GDP)+SOS1(GEF)<->KRAS(G~GDP!1).SOS1(GEF!1) kp3,km3 # GDP binds apo Ras-GEF complex KRAS(G~apo!1).SOS1(GEF!1)+GDP->KRAS(G~GDP!1).SOS1(GEF!1) kp4 # GDP dissociates from RasGDP-GEF complex KRAS(G~GDP!1).SOS1(GEF!1)->KRAS(G~apo!1).SOS1(GEF!1)+GDP km4 # GTP binds the apo form of Ras KRAS(G~apo)+GTP->KRAS(G~GTP) kp5 # GTP spontaneoulsy dissociates from Ras KRAS(G~GTP)->KRAS(G~apo)+GTP km5 # GTP binds apo Ras-GEF complex KRAS(G~apo!1).SOS1(GEF!1)+GTP->KRAS(G~GTP!1).SOS1(GEF!1) kp6 # GTP dissociates from RasGTP-GEF complex KRAS(G~GTP!1).SOS1(GEF!1)->KRAS(G~apo!1).SOS1(GEF!1)+GTP km6 # GEF reversibly binds RasGTP KRAS(G~GTP)+SOS1(GEF)<->KRAS(G~GTP!1).SOS1(GEF!1) kp7,km7 # Effector reversibly binds RasGTP KRAS(G~GTP)+CRAF(RBD)<->KRAS(G~GTP!1).CRAF(RBD!1) kaEff,kdEff # GTP hydrolysis via the intrinsic GTPase activity of Ras # RasGTP is free KRAS(G~GTP)->KRAS(G~GDP) khyd # RasGTP is bound to effector, fast release of effector after hydrolysis KRAS(G~GTP!1).CRAF(RBD!1)->KRAS(G~GDP)+CRAF(RBD) khyd # GAP-assisted hydrolysis of GTP via a Michaelis-Menten mechanism # Enzyme-substrate association KRAS(G~GTP)+RASA1(GAP)->KRAS(G~GTP!1).RASA1(GAP!1) kf # Enzyyme-substrate dissociation (no reaction) KRAS(G~GTP!1).RASA1(GAP!1)->KRAS(G~GTP)+RASA1(GAP) kr # Hydrolysis (reaction), fast dissoc of enzyme and product after hydrolysis KRAS(G~GTP!1).RASA1(GAP!1)->KRAS(G~GDP)+RASA1(GAP) kcat end reaction rules end model # actions generate_network({overwrite=>1}); simulate_ode({t_end=>10,n_steps=>100});