# BioNetGen Cpx Pathway model V0.3 (alpha) # # By Paul Turner, University of Leeds 2013 # begin parameters #reaction constants and compartment volumes vol_ECF #volume of extracellualr fluid (i.e. vessel volume) effvol_OM #surface area.thickness of outer membrane vol_PP #volume of periplasm effvol_PM #surface area.thickness of Periplasmic Membrane vol_Cp #volume of cell cytoplasm k_block #rate constant of CpxP inhibition/binding to CpxA k_mf_unbind #unbinding rate for CpxP in prescence of misfolded sub-units k_mf_bind #binding rate for CpxP to misfolded sub-unit k_degbind #binding rate of degP to CpxP/misfold complex k_degrade #degradation rate for misfold complex k_autophos #autophophorylation rate of CpxA k_CpxP_CP_PM #transfer rate of CpxP across CP to PM k_CpxP_PM_CP #transfer rate of CpxP across PM to CP k_CpxP_PM_PP #transfer rate of CpxP across PM to PP k_CpxP_PP_PM #transfer rate of CpxP across PP to PM k_degP_CP_PM #transfer rate of degP across CP to PM k_degP_PM_CP #transfer rate of degP across PM to CP k_degP_PM_PP #transfer rate of degP across PM to PP k_degP_PP_PM #transfer rate of degP across PP to PM k_PhosPro #Phosphate production rate in CP k_Phos_CP_PM #transfer rate of Phosphate across CP to PM k_Phos_PM_CP #transfer rate of Phosphate across PM to CP k_Phos_PM_PP #transfer rate of Phosphate across PM to PP k_Phos_PP_PM #transfer rate of Phosphate across PP to PM k_AR_bind #binding rate of CpxA and CpxR k_AR_dephos #Dephosphorylation rate of CpxR k_AR_phos #Phosphorylation rate of CpxR k_transcription #binding rate to transcription factors k_DenatPro #Denaturant production rate from transcription k_GFPPro #GFP production rate from transcription k_CpxPPro #CpxP production rate from transcription k_degPPro #degP production rate from transcription k_lambdaGFP #Half life rate constant for GFP k_lambdaDenat #Half life rate constant for denaturants end parameters begin molecule types #all molecules involved in pathway CpxP(b) CpxA(Phos~U~P,R) CpxR(Phos~U~P,T) PapE(b,dP) degP(b) Phosphate() Denat() GFP() pdegP(pR) pGFP(pR) pCpxP(pR) pDenat(pR) end molecule types #start of compartmentalization for mimicry of membranes and plasmas begin compartments ECF 3 vol_ECF #Extra-cellular Fluid OM 2 effvol_OM ECF #Outer Membrane (Surface) with effvol = surface area.thickness PP 3 vol_PP OM #Periplasm PM 2 effvol_PM PP #Periplasmic Membrane (surface) with effvol = surface area.thickness CP 3 vol_CP PM #Cytoplasm end compartments #Specify starting concentrations and comparments occupied begin seed species CpxP(b)@PP CpxA(Phos~U,R)@PM CpxR(Phos~U,T)@CP pdegP(pR)@CP pDenat(pR)@CP pGFP(pR)@CP Phosphate()@PP end seed species #Specify which species one wants to observe, eg. GFP production etc begin observables Molecules GFP GFP() #Observable that we actually wish to measure Molecules Misfolds PapE(b,dP) #Model check to ensure that misfolded units are being degraded Molecules CpxA CpxA() #Check to ensure that CpxA concentration remains constant. Molecules Denaturants Denat() #Measure for relative proportions of GFP to Denaturants. end observables #The important bit - need to be careful with how things are specified. begin reaction rules CpxP(b)@PP+CpxA(Phos~U,R)@PM -> CpxP(b!0)@PP.CpxA(Phos~U!0,R)@PM k_block CpxP(b)@PP+CpxA(Phos~P,R)@PM -> CpxP(b!0)@PP.CpxA(Phos~U!0,R)@PM k_block #CpxP/A binding rules, P binds to A, no unbinding allowed until later CpxP(b!0)@PP.CpxA(Phos~U!0,R)@PM+PapE(b,dP)@PP -> CpxP(b)@PP+CpxA(Phos~U,R)@PM+PapE(b,dP)@PP k_mf_unbind CpxP(b)@PP+PapE(b,dP)@PP -> CpxP(b!0)@PP.PapE(b!0,dP)@PP k_mf_bind #Misfolded Unit protocol, causing CpxP to unbind from A and to bind to the misfold CpxP(b!0)@PP.PapE(b!0,dP)@PP+degP(b)@PP -> CpxP(b!0)@PP.PapE(b!0,dP!1)@PP.degP(b!1)@PP k_degbind CpxP(b!0)@PP.PapE(b!0,dP!1)@PP.degP(b!1)@PP -> 0 k_degrade #Degradation rate CpxA(Phos~U,R)@PM+Phosphate()@PP -> CpxA(Phos~P,)@PM k_autophos #Autophosphorylation of CpxA CpxP(b)@CP <-> CpxP(b)@PM k_CpxP_CP_PM,k_CpxP_PM_CP #CpxP transfer across CP-PM interface CpxP(b)@PM <-> CpxP(b)@PP k_CpxP_PM_PP,k_CpxP_PP_PM #CpxP transfer across PM-PP interface degP(b)@CP <-> degP(b)@PM k_degP_CP_PM,k_degP_PM_CP #degP transfer across CP-PM interface degP(b)@PM <-> degP(b)@PP k_degP_PM_PP,k_degP_PP_PM #degP transfer across PM-PP interface 0 -> Phosphat()@CP k_PhosPro #Phosphate production Phosphate()@CP <-> Phosphate()@PM k_Phos_CP_PM,k_Phos_PM_CP #Phosphate transfer across CP-PM interface Phosphate()@PM <-> Phosphate()@PP l_Phos_PM_PP,k_Phos_PP_PM #Phosphate transfer across PM-PP interface 0 -> PapE(b,dP)@PP k_misfoldrate #misfolding rate CpxA(Phos~U,R)@PM+CpxR(Phos~P,T)@CP -> CPxA(Phos~U,R!0)@PM.CpxR(Phos~P!0,T)@CP k_AR_Bind #Dephos of CpxR CpxA(Phos~U,R!0)@PM.CpxR(Phos~P!0,T)@CP -> CpxA(Phos~P,R)@PM+CpxR(Phos~U,T)@CP k_AR_dephos #Dephos of CpxR CpxA(Phos~P,R)@PM+CpxR(Phos~U,T)@CP -> CpxA(Phos~P,R!0)@PM.CpxR(Phos~U!0,T)@CP k_AR_Bind #Phos of CpxR CpxA(Phos~P,R!0)@PM.CpxR(Phos~U!0,T)@CP -> CpxA(Phos~U,R)@PM+CpxR(Phos~P,T)@CP k_AR_phos #Phos of CpxR CpxR(Phos~P,T)@CP+pDenat(pR)@CP -> CpxR(Phos~P,T!0)@CP.pDenat(pR!0)@CP k_transcription #transcription of Denaturants CpxR(Phos~P,T)@CP+pGFP(pR)@CP -> CpxR(Phos~P,T!0)@CP.pGFP(pR!0)@CP k_transcription #transcription of GFP CpxR(Phos~P,T)@CP+pCpxP(pR)@CP -> CpxR(Phos~P,T!0)@CP.pCpxP(pR!0)@CP k_transcription #transcription of CpxP CpxR(Phos~P,T)@CP+pdegP(pR)@CP -> CpxR(Phos~P,T!0)@CP.pdegP(pR!0)@CP k_transcription #transcription of degP CpxR(Phos~P,T!0)@CP.pDenat(pR!0)@CP -> CpxR(Phos~P,T)@CP+pDenat(pR)@CP+Denat()@CP k_DenatPro #Denaturant production CpxR(Phos~P,T!0)@CP.pGFP(pR!0)@CP -> CpxR(Phos~P,T)@CP+pGFP(pR)@CP+GFP()@CP k_GFPPro #GFP production CpxR(Phos~P,T!0)@CP.pCpxP(pR!0)@CP -> CpxR(Phos~P,T)@CP+pCpxP(pR)@CP+CpxP()@CP k_CpxPPro #CpxP Production CpxR(Phos~P,T!0)@CP.pdegP(pR!0)@CP -> CpxR(Phos~P,T)@CP+pdegP(pR)@CP+degP()@CP k_degPPro #degP Production GFP()@CP -> 0 k_lambdaGFP #GFP halflife Denat()@CP -> 0 k_lambdaDenat #Denaturant halflives end reaction rules ##actions, inc. writing of SBML file for VCell integration## generate_network({overwrite=>1}) writeSBML(prefix=CpxPathway_v0.3) %VC% mergereversibleReactions %VC% speciesRenamePattern("\.","_") %VC% speciesRenamePattern("[\(,][a-ZA-Z]\w*","") %VC% speciesRenamePattern("~|!\d*","") %VC% speciesRenamePattern("\(","") %VC% speciesRenamePattern("\)","") %VC% speciesRenamePattern("SH2","s") %VC% compartmentalizeSpecies("@CP","3","Cytoplasm","Periplasmic Membrane") %VC% compartmentalizeSpecies("@PM","2","Periplasmic Membrane","Periplasm") %VC% compartmentalizeSpecies("@PP","3","Periplasm","Outer Membrane") %VC% compartmentalizeSpecies("@OM","2","Outer Membrane","Extracellular Fluid") %VC% compartmentalizeSpecies("@ECF","3","Extracellular Fluid","") #Equilibration simulate_ode({t_end->10000,n_steps->10000})