Team:Johns Hopkins/Modeling/VitAPathLBS

The Beta-Carotene Pathway Model in LBS

directive sample 900.0 5000
 
// Compartments
comp cytosol = new comp;
 
//Enzymes
spec GGPP_synth_exo = new{};
spec GGPP_synth_endo = new{};
spec carotene_desat = new{};
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;
 
module mmRXN(spec sub, enz, prod; rate km, kcat) {
	rate rxn_rate = kcat*enz/(sub+km);
	sub + enz ->[rxn_rate] enz + prod
};
 
cytosol[ 
	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) |
	->{100} farnesyl_PP |
		init GGPP_synth_exo 1 |
		init GGP_synth_endo 0 |
		init carotene_desat 1 |
		init phytoene_synth_lycopene_cyc 1
]