PC12RapMinusNetwork.cpp Source File

00001 #include "PC12RapMinusNetwork.h"
00002 
00003 CPC12RapMinusNetwork::CPC12RapMinusNetwork(void)
00004 {
00005         // CFactor = #molecules/1uM
00006         double CFactor = 600000.0, SecToMin = 60.0;
00007 
00008         // 1
00009         Chemical *EGF = new Chemical(chemicals.size(), 0.0, "EGF");
00010         chemicals.push_back(EGF);
00011 
00012         // 2
00013         Chemical *NGF = new Chemical(chemicals.size(), 0.0, "NGF");
00014         chemicals.push_back(NGF);
00015 
00016         // 3 (ref - constraint on [EGFR]_T)
00017         Chemical *freeEGFReceptor = new Chemical(chemicals.size(), 80000, "freeEGFReceptor");
00018         chemicals.push_back(freeEGFReceptor);
00019 
00020         // 4 (ref)
00021         Chemical *boundEGFReceptor = new Chemical(chemicals.size(), 0.0, "boundEGFReceptor");
00022         chemicals.push_back(boundEGFReceptor);
00023 
00024         // 5 (ref)
00025         Chemical *freeNGFReceptor = new Chemical(chemicals.size(), 10000, "freeNGFReceptor");
00026         chemicals.push_back(freeNGFReceptor);
00027 
00028         // 6
00029         Chemical *boundNGFReceptor = new Chemical(chemicals.size(), 0.0, "boundNGFReceptor");
00030         chemicals.push_back(boundNGFReceptor);
00031 
00032         // 7
00033         Chemical *SosInactive = new Chemical(chemicals.size(), 0.2*CFactor, "SosInactive");
00034         chemicals.push_back(SosInactive);
00035                 
00036         // 8
00037         Chemical *SosActive = new Chemical(chemicals.size(), 0.0, "SosActive");
00038         chemicals.push_back(SosActive);
00039 
00040         // 9
00041         Chemical *P90RskInactive = new Chemical(chemicals.size(), 0.2*CFactor, "P90RskInactive");
00042         chemicals.push_back(P90RskInactive);
00043 
00044         // 10
00045         Chemical *P90RskActive = new Chemical(chemicals.size(), 0.0, "P90RskActive");
00046         chemicals.push_back(P90RskActive);
00047 
00048         // 11
00049         Chemical *RasInactive = new Chemical(chemicals.size(), 0.2*CFactor,"RasInactive");
00050         chemicals.push_back(RasInactive);
00051 
00052         // 12
00053         Chemical *RasActive = new Chemical(chemicals.size(), 0.0, "RasActive");
00054         chemicals.push_back(RasActive);
00055 
00056         // 13
00057         Chemical *RasGapActive = new Chemical(chemicals.size(), CFactor*0.2, "RasGapActive");
00058         chemicals.push_back(RasGapActive);
00059 
00060         
00061         // 14 (ref - constraint on [Raf1]_T = CFactor*0.003)
00062         Chemical *Raf1Inactive = new Chemical(chemicals.size(), CFactor*0.2, "Raf1Inactive");
00063         chemicals.push_back(Raf1Inactive);
00064                 
00065         // 15 (ref)
00066         Chemical *Raf1Active = new Chemical(chemicals.size(), 0.0, "Raf1Active");
00067         chemicals.push_back(Raf1Active);
00068 
00069         // 16 (ref - constraint on [Mek]_T)
00070         Chemical *MekInactive = new Chemical(chemicals.size(), CFactor, "MekInactive");
00071         chemicals.push_back(MekInactive);
00072 
00073         // 17 (ref)
00074         Chemical *MekActive = new Chemical(chemicals.size(), 0.0, "MekActive");
00075         chemicals.push_back(MekActive);
00076 
00077         // 18 (ref - constraint on [Erk]_T)
00078         Chemical *ErkInactive = new Chemical(chemicals.size(), CFactor,"ErkInactive");
00079         chemicals.push_back(ErkInactive);
00080 
00081         // 19 (ref)
00082         Chemical *ErkActive = new Chemical(chemicals.size(), 0.0, "ErkActive");
00083         chemicals.push_back(ErkActive);
00084 
00085         // 20
00086         Chemical *PI3KInactive = new Chemical(chemicals.size(), 0.2*CFactor, "PI3KInactive");
00087         chemicals.push_back(PI3KInactive);
00088 
00089         // 21
00090         Chemical *PI3KActive = new Chemical(chemicals.size(), 0.0, "PI3KActive");
00091         chemicals.push_back(PI3KActive);
00092 
00093         // 22
00094         Chemical *AktInactive = new Chemical(chemicals.size(), 0.2*CFactor, "AktInactive");
00095         chemicals.push_back(AktInactive);
00096 
00097         // 23
00098         Chemical *AktActive = new Chemical(chemicals.size(), 0.0, "AktActive");
00099         chemicals.push_back(AktActive);
00100         
00101         // 24
00102         Chemical *PP2AActive = new Chemical(chemicals.size(), 0.2*CFactor, "PP2AActive");
00103         chemicals.push_back(PP2AActive);
00104 
00105         // 25 
00106         Chemical *Raf1PPtase = new Chemical(chemicals.size(), 0.2*CFactor, "Raf1PPtase");
00107         chemicals.push_back(Raf1PPtase);
00108 
00109 
00110         RateConstant *k_rb_EGF = new RateConstant(SecToMin*0.00001, "krbEGF");
00111         rateConstants.push_back(k_rb_EGF);
00112         RateConstant *k_ru_EGF = new RateConstant(SecToMin*0.01, "kruEGF");
00113         rateConstants.push_back(k_ru_EGF);
00114         RateConstant *k_rb_NGF = new RateConstant(SecToMin*0.00005, "krbNGF");
00115         rateConstants.push_back(k_rb_NGF);
00116         RateConstant *k_ru_NGF = new RateConstant(SecToMin*0.02, "kruNGF");
00117         rateConstants.push_back(k_ru_NGF);
00118 
00119         RateConstant *k_EGF = new RateConstant(SecToMin*0.2, "kEGF");
00120         rateConstants.push_back(k_EGF);
00121         RateConstant *Km_EGF = new RateConstant(CFactor*0.8333, "KmEGF");
00122         rateConstants.push_back(Km_EGF);
00123         RateConstant *k_NGF = new RateConstant(SecToMin*0.4, "kNGF");
00124         rateConstants.push_back(k_NGF);
00125         RateConstant *Km_NGF = new RateConstant(CFactor*0.8333, "KmNGF");
00126         rateConstants.push_back(Km_NGF);
00127 
00128         RateConstant *k_dSos = new RateConstant(0.01*SecToMin, "kdSos");
00129         rateConstants.push_back(k_dSos);
00130         RateConstant *Km_dSos = new RateConstant(100000.0, "KmdSos");
00131         rateConstants.push_back(Km_dSos);       
00132         RateConstant *k_Sos = new RateConstant(0.075*SecToMin, "kSos");
00133         rateConstants.push_back(k_Sos);
00134         RateConstant *Km_Sos = new RateConstant(0.25*CFactor, "KmSos");
00135         rateConstants.push_back(Km_Sos);
00136 
00137         RateConstant *k_RasGap = new RateConstant(0.2*SecToMin, "kRasGap");
00138         rateConstants.push_back(k_RasGap);
00139         RateConstant *Km_RasGap = new RateConstant(CFactor*1.0104, "KmRasGap");
00140         rateConstants.push_back(Km_RasGap);
00141         RateConstant *k_RasToRaf1 = new RateConstant(0.08*SecToMin, "kRasToRaf1");
00142         rateConstants.push_back(k_RasToRaf1);
00143         RateConstant *Km_RasToRaf1 = new RateConstant(150000.0, "KmRasToRaf1");
00144         rateConstants.push_back(Km_RasToRaf1);
00145         
00146         RateConstant *k_pRaf1 = new RateConstant(0.05*SecToMin, "kpRaf1");
00147         rateConstants.push_back(k_pRaf1);
00148         // (ref)
00149         RateConstant *Km_pRaf1 = new RateConstant(0.6*CFactor, "KmpRaf1");
00150         rateConstants.push_back(Km_pRaf1);
00151 
00152         RateConstant *k_dMek = new RateConstant(0.03*SecToMin, "kdMek");
00153         rateConstants.push_back(k_dMek);
00154         RateConstant *Km_dMek = new RateConstant(125000.0, "KmdMek");
00155         rateConstants.push_back(Km_dMek);
00156         
00157         RateConstant *k_pMek_Cytoplasmic = new RateConstant(0.01*SecToMin, "kpMekCytoplasmic");
00158         rateConstants.push_back(k_pMek_Cytoplasmic);
00159         // (ref)
00160         RateConstant *Km_pMek_Cytoplasmic = new RateConstant(125000.0, "KmpMekCytoplasmic");
00161         rateConstants.push_back(Km_pMek_Cytoplasmic);
00162         RateConstant *k_dErk = new RateConstant(0.01*SecToMin, "kdErk");
00163         rateConstants.push_back(k_dErk);
00164         RateConstant *Km_dErk = new RateConstant(300000.0, "KmdErk");
00165         rateConstants.push_back(Km_dErk);
00166         RateConstant *k_pP90Rsk = new RateConstant(0.01*SecToMin, "kpP90Rsk");
00167         rateConstants.push_back(k_pP90Rsk);
00168         RateConstant *Km_pP90Rsk = new RateConstant(300000.0, "KmpP90Rsk");
00169         rateConstants.push_back(Km_pP90Rsk);
00170                 
00171         
00172         RateConstant *k_PI3K = new RateConstant(0.05*SecToMin, "kPI3K");
00173         rateConstants.push_back(k_PI3K);
00174         RateConstant *Km_PI3K = new RateConstant(100000.0, "KmPI3K");
00175         rateConstants.push_back(Km_PI3K);
00176         RateConstant *k_PI3K_Ras = new RateConstant(0.025*SecToMin, "kPI3KRas");
00177         rateConstants.push_back(k_PI3K_Ras);
00178         RateConstant *Km_PI3K_Ras = new RateConstant(300000.0, "KmPI3KRas");
00179         rateConstants.push_back(Km_PI3K_Ras);
00180         RateConstant *k_Akt = new RateConstant(0.01*SecToMin, "kAkt");
00181         rateConstants.push_back(k_Akt);
00182         RateConstant *Km_Akt = new RateConstant(300000.0, "KmAkt");
00183         rateConstants.push_back(Km_Akt);
00184         RateConstant *k_dRaf1ByAkt = new RateConstant(0.1*SecToMin, "kdRaf1ByAkt");
00185         rateConstants.push_back(k_dRaf1ByAkt);
00186         RateConstant *Km_Raf1ByAkt = new RateConstant(300000.0, "KmRaf1ByAkt"); 
00187         rateConstants.push_back(Km_Raf1ByAkt);
00188         
00189 
00190         RateConstant *k_dRaf1 = new RateConstant(0.1*SecToMin, "kdRaf1");
00191         rateConstants.push_back(k_dRaf1);
00192         RateConstant *Km_dRaf1 = new RateConstant(300000.0, "KmdRaf1");
00193         rateConstants.push_back(Km_dRaf1);
00194 
00195 
00196         ReceptorBindingReaction *EGFBindingReaction = new ReceptorBindingReaction(EGF, freeEGFReceptor, boundEGFReceptor, k_rb_EGF, "EGFBindingReaction");
00197         reactions.push_back(EGFBindingReaction);
00198         ReceptorUnbindingReaction *EGFUnbindingReaction = new ReceptorUnbindingReaction(boundEGFReceptor, freeEGFReceptor, EGF, k_ru_EGF, "EGFUnbindingReaction");
00199         reactions.push_back(EGFUnbindingReaction);
00200         ReceptorBindingReaction *NGFBindingReaction = new ReceptorBindingReaction(NGF, freeNGFReceptor, boundNGFReceptor, k_rb_NGF, "NGFBindingReaction");
00201         reactions.push_back(NGFBindingReaction);
00202         ReceptorUnbindingReaction *NGFUnbindingReaction = new ReceptorUnbindingReaction(boundNGFReceptor, freeNGFReceptor, NGF, k_ru_NGF, "NGFUnbindingReaction");
00203         reactions.push_back(NGFUnbindingReaction);
00204 
00205         MichaelisMentenPhosphorylationReaction *SosActivationByEGFReaction = new MichaelisMentenPhosphorylationReaction(boundEGFReceptor, SosInactive, SosActive, k_EGF, Km_EGF, "SosActivationbyEGFReaction");
00206         reactions.push_back(SosActivationByEGFReaction);
00207         MichaelisMentenPhosphorylationReaction *SosActivationByNGFReaction = new MichaelisMentenPhosphorylationReaction(boundNGFReceptor, SosInactive, SosActive, k_NGF, Km_NGF, "SosActivationbyNGFReaction");
00208         reactions.push_back(SosActivationByNGFReaction);
00209         MichaelisMentenDephosphorylationReaction *SosDeactivationReaction = new MichaelisMentenDephosphorylationReaction(P90RskActive, SosActive, SosInactive, k_dSos, Km_dSos, "SosDeactivationReaction");
00210         reactions.push_back(SosDeactivationReaction);
00211         MichaelisMentenGProteinActivationReaction *RasActivationReaction = new MichaelisMentenGProteinActivationReaction(SosActive, RasInactive, RasActive, k_Sos, Km_Sos, "RasActivationReaction");
00212         reactions.push_back(RasActivationReaction);
00213         
00214         MichaelisMentenGProteinDeactivationReaction *RasDeactivationReaction = new MichaelisMentenGProteinDeactivationReaction(RasGapActive, RasActive, RasInactive, k_RasGap, Km_RasGap, "RasDeactivationReaction");
00215         reactions.push_back(RasDeactivationReaction);
00216         MichaelisMentenProteinProteinActivationReaction *Raf1ByRasActivationReaction = new MichaelisMentenProteinProteinActivationReaction(RasActive, Raf1Inactive, Raf1Active, k_RasToRaf1, Km_RasToRaf1, "Raf1ByRasActivationReaction");
00217         reactions.push_back(Raf1ByRasActivationReaction);
00218 
00219         MichaelisMentenPhosphorylationReaction *MekbyRaf1ActivationReaction = new MichaelisMentenPhosphorylationReaction(Raf1Active, MekInactive, MekActive, k_pRaf1, Km_pRaf1, "MekbyRaf1ActivationReaction");
00220         reactions.push_back(MekbyRaf1ActivationReaction);
00221         MichaelisMentenPhosphorylationReaction *ErkActivationReaction = new MichaelisMentenPhosphorylationReaction(MekActive, ErkInactive, ErkActive, k_pMek_Cytoplasmic, Km_pMek_Cytoplasmic, "ErkActivationReaction");
00222         reactions.push_back(ErkActivationReaction);
00223 
00224         
00225         MichaelisMentenDephosphorylationReaction *MekDeactivationReaction = new MichaelisMentenDephosphorylationReaction(PP2AActive, MekActive, MekInactive, k_dMek, Km_dMek, "MekDeactivationReaction");
00226         reactions.push_back(MekDeactivationReaction);
00227         MichaelisMentenDephosphorylationReaction *ErkDeactivationReaction = new MichaelisMentenDephosphorylationReaction(PP2AActive, ErkActive, ErkInactive, k_dErk, Km_dErk, "ErkDeactivationReaction");
00228         reactions.push_back(ErkDeactivationReaction);
00229 
00230         MichaelisMentenDephosphorylationReaction *Raf1byPPtaseDeactivationReaction = new MichaelisMentenDephosphorylationReaction(Raf1PPtase, Raf1Active, Raf1Inactive, k_dRaf1, Km_dRaf1, "Raf1byPPtaseDeactivationReaction");
00231         reactions.push_back(Raf1byPPtaseDeactivationReaction);
00232 
00233         MichaelisMentenPhosphorylationReaction *P90RskActivationReaction = new MichaelisMentenPhosphorylationReaction(ErkActive, P90RskInactive, P90RskActive, k_pP90Rsk, Km_pP90Rsk, "P90RskActivationReaction");
00234         reactions.push_back(P90RskActivationReaction);
00235         
00236         
00237         MichaelisMentenPhosphorylationReaction *PI3KbyEGFRActivationReaction = new MichaelisMentenPhosphorylationReaction(boundEGFReceptor, PI3KInactive, PI3KActive, k_PI3K, Km_PI3K, "PI3KbyEGFRActivationReaction");
00238         reactions.push_back(PI3KbyEGFRActivationReaction);
00239         MichaelisMentenProteinProteinActivationReaction *PI3KbyRasActivationReaction = new MichaelisMentenProteinProteinActivationReaction(RasActive, PI3KInactive, PI3KActive, k_PI3K_Ras, Km_PI3K_Ras, "PI3KbyRasActivationReaction");
00240         reactions.push_back(PI3KbyRasActivationReaction);
00241 
00242         
00243         MichaelisMentenPhosphorylationReaction *AktActivationReaction = new MichaelisMentenPhosphorylationReaction(PI3KActive, AktInactive, AktActive, k_Akt, Km_Akt, "AktActivationReaction");
00244         reactions.push_back(AktActivationReaction);
00245         MichaelisMentenProteinProteinDeactivationReaction *Raf1ByAktDeactivationReaction = new MichaelisMentenProteinProteinDeactivationReaction(AktActive, Raf1Active, Raf1Inactive, k_dRaf1ByAkt, Km_Raf1ByAkt, "RafByAktDeactivationReaction");
00246         reactions.push_back(Raf1ByAktDeactivationReaction);     
00247         
00248 }
00249 
00250 CPC12RapMinusNetwork::~CPC12RapMinusNetwork(void)
00251 {
00252 }