begin parameters # Agrees with Table 1 of Lipniacki, et al. TCR model N1 30 N2 0 TCR 30000 LCK 100000 ZAP 100000 MEK 100000 ERK 300000 SHP 300000 b1 0.3/TCR b2 0.3/TCR d1 0.05 d2 1 lb 0.3/LCK ly1 5/SHP ly2 0.3 ls1 0.1 ls2 0.5/ERK tp 0.05 s0 1e-5 s1 30/SHP s2 0.0006 s3 0.05 z0 2e-6 z1 5/ZAP z2 0.02 m1 5/MEK m2 0.02 e1 5/ERK e2 0.02 end parameters begin molecule types pMHC(p~ag~en) TCR(ab,ITAM~U~P~PP,lck,shp) Lck(tcr,Y~U~P,S~U~P) SHP(tcr,Y~U~P) ZAP(Y~U~P) MEK(S~U~P~PP) ERK(S~U~P~PP) end molecule types begin species pMHC(p~ag) 0 pMHC(p~en) 0 TCR(ab,ITAM~U,lck,shp) TCR Lck(tcr,Y~U,S~U) LCK SHP(tcr,Y~U) SHP ZAP(Y~U) ZAP MEK(S~U) MEK ERK(S~U) ERK end species begin reaction rules # pMHC binding to TCR: TCR(ab,shp)+pMHC(p~ag) -> TCR(ab!1,shp).pMHC(p~ag!1) b1 TCR(ab,shp)+pMHC(p~en) -> TCR(ab!1,shp).pMHC(p~en!1) b2 #recruitment of Lck to TCR bound to pMHC: #All unbound Lck is unphosphorylated TCR(ab!+,lck,shp) + Lck(tcr) -> TCR(ab!+,lck!1,shp).Lck(tcr!1) lb #Lck phosphorylation on Y: # What is phosphorylating Lck? TCR(lck!1,shp).Lck(tcr!1,Y~U) -> TCR(lck!1,shp).Lck(tcr!1,Y~P) ly2 #Lck phosphorylation on S: ERK(S~PP) + TCR(lck!1,shp).Lck(tcr!1,S~U) -> ERK(S~PP) + TCR(lck!1,shp).Lck(tcr!1,S~P) ls2 #Lck dephosphorylation on S: Lck(tcr!+,S~P) -> Lck(tcr!+,S~U) ls1 #TCR phosphorylation by Lck: TCR(ITAM~U,lck!1,shp).Lck(tcr!1,Y~P) -> TCR(ITAM~P,lck!1,shp).Lck(tcr!1,Y~P) tp TCR(ITAM~P,lck!1,shp).Lck(tcr!1,Y~P) -> TCR(ITAM~PP,lck!1,shp).Lck(tcr!1,Y~P) tp #Spontaneous ZAP phosphorylation: ZAP(Y~U) -> ZAP(Y~P) z0 #ZAP phosphorylation: TCR(ITAM~PP) + ZAP(Y~U) -> TCR(ITAM~PP) + ZAP(Y~P) z1 #ZAP dephosphorylation: ZAP(Y~P) -> ZAP(Y~U) z2 #MEK phosphorylation by ZAP ZAP(Y~P) + MEK(S~U) -> ZAP(Y~P) + MEK(S~P) m1 ZAP(Y~P) + MEK(S~P) -> ZAP(Y~P) + MEK(S~PP) m1 #MEK dephosphorylation: MEK(S~P) -> MEK(S~U) m2 MEK(S~PP) -> MEK(S~U) m2 #ERK phosphorylation by MEK: MEK(S~PP) + ERK(S~U) -> MEK(S~PP) + ERK(S~P) e1 MEK(S~PP) + ERK(S~P) -> MEK(S~PP) + ERK(S~PP) e1 #ERK dephosphorylation: ERK(S~P) -> ERK(S~U) e2 ERK(S~PP) -> ERK(S~U) e2 #Spontaneous phosphorylation of SHP SHP(Y~U) -> SHP(Y~P) s0 #SHP phosphorylation by Lck: # All SHP(Y~U) is unbound, all LckYP is bound to TCR Lck(Y~P,S~U) + SHP(Y~U) -> Lck(Y~P,S~U) + SHP(Y~P) s1 #pMH dissociation from TCR not associated with Lck and simultaneous dephosphorylation pMHC(p~ag!1).TCR(ab!1,ITAM~*,lck)-> pMHC(p~ag) + TCR(ab,ITAM~U,lck) d1 pMHC(p~en!1).TCR(ab!1,ITAM~*,lck)-> pMHC(p~en) + TCR(ab,ITAM~U,lck) d2 #pMHC dissociation causes Lck dissociation and simultaneous dephosphorylation: pMHC(p~ag!1).TCR(ab!1,ITAM~*,lck!2).Lck(tcr!2,Y~*,S~*) -> pMHC(p~ag) + TCR(ab,ITAM~U,lck) + Lck(tcr,Y~U,S~U) d1 pMHC(p~en!1).TCR(ab!1,ITAM~*,lck!2).Lck(tcr!2,Y~*,S~*) -> pMHC(p~en) + TCR(ab,ITAM~U,lck) + Lck(tcr,Y~U,S~U) d2 #Recruitment of phosphorylated SHP to receptor complex without Lck: TCR(ITAM~*,lck,shp) + SHP(tcr,Y~P) -> TCR(ITAM~U,lck,shp!1).SHP(tcr!1,Y~P) ly1 #Recruitment of phosphorylated SHP to receptor complex with Lck: #Phosphorylation of Lck on S inhibits this reaction TCR(ITAM~*,lck!1,shp).Lck(tcr!1,Y~*,S~U) + SHP(tcr,Y~P) -> TCR(ITAM~U,lck!1,shp!2).Lck(tcr!1,Y~U,S~U).SHP(tcr!2,Y~P) ly1 #SHP dissociation from TCR with dephosphorylation: TCR(shp!1).SHP(tcr!1,Y~P) -> TCR(shp) + SHP(tcr,Y~U) s2 #SHP dissociation from TCR without dephosphorylation: TCR(shp!1).SHP(tcr!1,Y~P) -> TCR(shp) + SHP(tcr,Y~P) s3 #free SHP dephosphorylation: SHP(tcr,Y~P) -> SHP(tcr,Y~U) s2 end reaction rules begin observables Molecules ppERK ERK(S~PP) Molecules ppTCR TCR(ITAM~PP) Molecules pTCR TCR(ITAM~P) Molecules pSHP SHP(Y~P) Molecules pZAP ZAP(Y~P) Molecules pMEK MEK(S~P) Molecules ppMEK MEK(S~PP) end observables generate_network({overwrite=>1}); writeMfile({}); simulate_ode({suffix=>equil_ode,t_end=>10000,n_steps=>200}); saveConcentrations(); setConcentration("pMHC(p~ag)",N1); simulate_ode({suffix=>ode,t_end=>4000,n_steps=>200}); resetConcentrations(); simulate_ssa({suffix=>ssa,t_end=>20000,n_steps=>1000});