RBM_Intro_BioNetGen/mapk3.bngl at main · jrfaeder/RBM_Intro_BioNetGen · GitHub

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begin model

begin parameters
  k1 1e-5
  k2 0.1
  kkin 0.1
  kptp 3e-3
end parameters

begin molecule types
  Ras(c)
  Raf(c,S~0~P)
  PP2A(c)
  MKP(c)
  MEK(c,S218~0~P,S222~0~P)
  ERK(c,T185~0~P,Y187~0~P)
end molecule types

begin species
  Ras(c) 6e4
  Raf(c,S~0) 7e4
  PP2A(c)  2e5
  MKP(c) 1.7e4
  MEK(c,S218~0,S222~0) 3e6
  ERK(c,T185~0,Y187~0) 7e5
end species

begin observables
  Molecules RasRaf Ras(c!1).Raf(S!1)
  Molecules pRaf Raf(S~P)
  Molecules ppMEK MEK(S218~P,S222~P)
  Molecules ppERK ERK(T185~P,Y187~P)
end observables

begin reaction rules
  Ras_Raf_bind: \
    Ras(c) + Raf(S~0) <-> Ras(c!1).Raf(S~0!1) k1, k2 # What's the possible problem here?
  Ras_Raf_catalyze: \
    Ras(c!1).Raf(S~0!1) -> Ras(c) + Raf(S~P) kkin
  PP2A_Raf_bind: \
    PP2A(c) + Raf(c,S~P) <-> PP2A(c!1).Raf(c,S~P!1) k1, k2
  PP2A_Raf_catalyze: \
    PP2A(c!1).Raf(c,S~P!1) -> PP2A(c) + Raf(c,S~0) kptp

  # Ordered distributive dual phosphorylation of MEK
  Raf_MEKS218_bind: \
    Raf(c,S~P) + MEK(S218~0,S222~0) <-> Raf(c!1,S~P).MEK(S218~0!1,S222~0) k1, k2
  Raf_MEKS218_catalyze: \
    Raf(c!1,S~P).MEK(S218~0!1) -> Raf(c,S~P) + MEK(S218~P) kkin
  Raf_MEKS222_bind: \
    Raf(c,S~P) + MEK(S218~P,S222~0) <-> Raf(c!1,S~P).MEK(S218~P,S222~0!1) k1, k2
  Raf_MEKS222_catalyze: \
    Raf(c!1,S~P).MEK(S222~0!1) -> Raf(c,S~P) + MEK(S222~P) kkin
  # Ordered dephosphorylation of MEK
  PP2A_MEKS218_bind: \
    PP2A(c) + MEK(c,S218~P,S222~0) <-> PP2A(c!1).MEK(c,S218~P!1,S222~0) k1, k2
  PP2A_MEKS218_catalyze: \
    PP2A(c!1).MEK(c,S218~P!1) -> PP2A(c) + MEK(c,S218~0) kptp
  PP2A_MEKS222_bind: \
    PP2A(c) + MEK(c,S218~P,S222~P) <-> PP2A(c!1).MEK(c,S218~P,S222~P!1) k1, k2
  PP2A_MEKS222_catalyze: \
    PP2A(c!1).MEK(c,S222~P!1) -> PP2A(c) + MEK(c,S222~0) kptp

  # Ordered distributive dual phosphorylation of ERK
  MEK_ERKT185_bind: \
     MEK(c,S218~P,S222~P) + ERK(T185~0,Y187~0) <-> MEK(c!1,S218~P,S222~P).ERK(T185~0!1,Y187~0) k1, k2
  MEK_ERKT185_catalyze: \
    MEK(c!1,S218~P,S222~P).ERK(T185~0!1) -> MEK(c,S218~P,S222~P) + ERK(T185~P) kkin
  MEK_ERKY187_bind: \
     MEK(c,S218~P,S222~P) + ERK(T185~P,Y187~0) <-> MEK(c!1,S218~P,S222~P).ERK(T185~P,Y187~0!1) k1, k2
  MEK_ERKY187_catalyze: \
    MEK(c!1,S218~P,S222~P).ERK(Y187~0!1) -> MEK(c,S218~P,S222~P) + ERK(Y187~P) kkin

  # Ordered dephosphorylation of ERK
  MKP_ERKT185_bind: \
     MKP(c) + ERK(T185~P,Y187~0) <-> MKP(c!1).ERK(T185~P!1,Y187~0) k1, k2
  MKP_ERKT185_catalyze: \
     MKP(c!1).ERK(T185~P!1) -> MKP(c) + ERK(T185~0) kptp
  MKP_ERKY187_bind: \
     MKP(c) + ERK(T185~P,Y187~P) <-> MKP(c!1).ERK(T185~P,Y187~P!1) k1, k2
  MKP_ERKY187_catalyze: \
     MKP(c!1).ERK(Y187~P!1) -> MKP(c) + ERK(Y187~0) kptp

end reaction rules

end model

simulate({method=>"ode",t_end=>5000,n_steps=>200})