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The Full Pathway+Expression Beta-Carotene Model in LBS
directive sample 90000.0 5000
// Compartments comp cytosol = new comp; comp nucleus = new comp inside cytosol;
// Transcriptional machinery spec Ribo = new{mrna:binding}; spec RNAP = new{dna:binding,mrna:binding};
//Gene-Ezyme Pairs spec crtE = new{bind:binding}; spec GGPP_synth_exo = new{}; spec BTS1 = new{bind:binding}; spec GGPP_synth_endo = new{}; spec crtYB = new{bind:binding}; spec carotene_desat = new{}; spec crtI = new{bind:binding}; spec phytoene_synth_lycopene_cyc = new{};
// Metabolites spec farnesyl_PP = new{}; spec GGPP = new{}; spec phytoene = new{}; spec neurosporene = new{}; spec lycopene = new{}; spec beta_carotene = new{}; spec hh_beta_carotene = new{};
// Rate constants rate GGPP_synth_endo_Km = 0.0032; rate GGPP_synth_endo_Kcat = 0.025; rate GGPP_synth_exo_Km = 0.0032; rate GGPP_synth_exo_Kcat = 0.025; rate phytoene_synth_Km = 0.0030; rate phytoene_synth_Kcat = 0.0526; rate carotene_desat_neurosporene_Km = 0.0084; rate carotene_desat_neurosporene_Kcat = 11.9665; rate carotene_desat_lycopene_Km = 0.0090; rate carotene_desat_lycopene_Kcat = 0.9703; rate phytoene_synth_hh_beta_carotene_Km = 0.0090; rate phytoene_synth_hh_beta_carotene_Kcat = 0.3881; rate phytoene_synth_beta_carotene_Km = 0.0018; rate phytoene_synth_beta_carotene_Kcat = 0.00038623;
//Transcription Kinetics rate rna_deg = 0.0058; rate rna_falloff = 0.01; rate rnap_bind = 0.5; rate transcription = 10; rate termination = 10; rate ribo_bind = 0.1; rate ribo_unbind = 0.01; rate translation = 10; rate export = 0.01; rate prot_deg = 0.01;
module transcribe(spec DNA:{bind}, mRNA:{down}) { RNAP{dna} + DNA{bind} ->{rnap_bind} RNAP{dna!1}-DNA{bind!1} | RNAP{dna!1}-DNA{bind!1} ->{transcription} mRNA{down!2}-RNAP{dna!1,mrna!2}-DNA{bind!1} | mRNA{down!2}-RNAP{dna!1,mrna!2}-DNA{bind!1} ->{termination} mRNA{down} + RNAP{dna,mrna} + DNA{bind} };
module translate(spec mRNA:{up}, Prot) { Ribo{mrna} + mRNA{up} <->{ribo_bind}{ribo_unbind} Ribo{mrna!1}-mRNA{up!1} | Ribo{mrna!1}-mRNA{up!1} ->{translation} Ribo{mrna} + mRNA{up} + Prot };
module express(comp nuc; spec DNA:{bind}, Prot) { spec mRNA = new{up:binding,down:binding}; nuc[ transcribe(DNA:{bind}, mRNA:{down}) | mRNA ->{rna_deg} ] | nuc[ mRNA ] ->{export} mRNA | translate(mRNA:{up}, Prot) | mRNA -> {rna_deg} };
module mmRXN(spec sub, enz, prod; rate km, kcat) { rate rxn_rate = kcat*enz/(sub+km); sub + enz ->[rxn_rate] enz + prod };
cytosol[ express(nucleus, crtE:{bind}, GGPP_synth_exo) | express(nucleus, BTS1:{bind}, GGPP_synth_endo) | express(nucleus, crtYB:{bind}, phytoene_synth_lycopene_cyc) | express(nucleus, crtI:{bind}, carotene_desat) | mmRXN(farnesyl_PP, GGPP_synth_endo, GGPP, GGPP_synth_endo_Km, GGPP_synth_endo_Kcat) | mmRXN(farnesyl_PP, GGPP_synth_exo, GGPP, GGPP_synth_exo_Km, GGPP_synth_exo_Kcat) | mmRXN(GGPP, phytoene_synth_lycopene_cyc, phytoene, phytoene_synth_Km, phytoene_synth_Kcat) | mmRXN(phytoene, carotene_desat, neurosporene, carotene_desat_neurosporene_Km, carotene_desat_neurosporene_Kcat) | mmRXN(neurosporene, carotene_desat, lycopene, carotene_desat_lycopene_Km, carotene_desat_lycopene_Kcat) | mmRXN(neurosporene, carotene_desat, hh_beta_carotene, phytoene_synth_hh_beta_carotene_Km, phytoene_synth_hh_beta_carotene_Kcat) | mmRXN(lycopene, phytoene_synth_lycopene_cyc, beta_carotene, phytoene_synth_beta_carotene_Km, phytoene_synth_beta_carotene_Kcat) | GGPP_synth_exo ->{prot_deg} | GGPP_synth_endo ->{prot_deg} | carotene_desat ->{prot_deg} | phytoene_synth_lycopene_cyc ->{prot_deg} | ->{100} farnesyl_PP | init Ribo 10 | nucleus[ init crtE 5 | init crtYB 5 | init crtI 5 | init RNAP 1 ] ]
