simulation.hsim

title="FNR regulator simulation"; geometry = 200:50; // size of E.coli in unit of 10nm 200 : 50=2:0.5 µm //molecules list molecule Pfnr;//fnr promotor molecule Ise,ClpXP;//Ise: iron-sulfur cluster assembly proteins : enzyme of dimerisation ; ClpXP: ATP dependent protease that induces degradation for all protein molecule QFeFNRa,apoFNR,DFeFNRi;//3 states of FNR: activated, without Fe (inactivated), and inactivated molecule GPV,PV;//GPV green protein gene, PV green protein molecule GPR,PR;//GPR red protein gene, PR red protein molecule QFeFNRa_GPR_binded,QFeFNRa_GPV_binded;//molecule FNR binds on mRNA from GPR and GPV molecule rep;//complexe of 4 FNRs, prevent production of red protein metabolite o2;//declare the o2 as a cytosolic molecule leads to be treated as an homogeneous population //size in 10nm unit size(Pfnr)=0.01; size(Ise)=0.5; size(ClpXP)=0.5; size(QFeFNRa)=2; size(apoFNR)=1; size(DFeFNRi)=2; size(GPV)=0.01; size(PV)=1; size(GPR)=0.01; size(PR)=1; size(QFeFNRa_GPR_binded)=2.01; size(QFeFNRa_GPV_binded)=2.01; size(rep)=4.02; //speed speed(Pfnr)=0; speed(Ise)=0.5; speed(ClpXP)=0.5; speed(QFeFNRa)=0.3; speed(DFeFNRi)=0.3; speed(apoFNR)=0.3; speed(GPV)=0; speed(PV)=0.3; speed(GPR)=0; speed(PR)=0.3; speed(QFeFNRa_GPR_binded)=0; speed(QFeFNRa_GPV_binded)=0; speed(rep)=0; //reactions //translating Pfnr to FNR Pfnr -> Pfnr + apoFNR [0.1];//fnr mRNA generates steagyly apoFNR(inactived) //dimerisation apoFNR + Ise -> QFeFNRa + Ise[0.8];//production of 4Fe-FNR by Ise is steady //oxydation QFeFNRa + o2 -> DFeFNRi +o2 [0.8];//aerobically, oxygen inactivates FNR DFeFNRi + Ise -> QFeFNRa + Ise [0.5];//but cell continues to reactivate it steadly DFeFNRi + o2 -> apoFNR +o2 [0.6];//return to apoFNR //degradation FNR apoFNR + ClpXP -> ClpXP [0.05]; DFeFNRi + ClpXP -> ClpXP [0.05]; QFeFNRa + ClpXP -> ClpXP [0.05]; //activation/inactivation of green gene QFeFNRa + GPV -> QFeFNRa_GPV_binded [0.8];//association QFeFNRa_GPV_binded -> QFeFNRa + GPV [0.4];//dissociation QFeFNRa_GPV_binded -> PV + QFeFNRa_GPV_binded [0.3];//production of green protein //green protein degradation PV + ClpXP -> ClpXP [0.05]; //repression of red gene QFeFNRa + GPR -> QFeFNRa_GPR_binded [0.8]; QFeFNRa_GPR_binded -> QFeFNRa + GPR [0.1]; QFeFNRa_GPR_binded + QFeFNRa_GPR_binded -> rep [0.5]; rep -> QFeFNRa_GPR_binded + QFeFNRa_GPR_binded [0.05]; //expression the red gene in aerobic condition GPR -> GPR + PR [0.3];//production of red protein QFeFNRa_GPR_binded -> QFeFNRa_GPR_binded + PR [0.1]; //degradation of red protein PR + ClpXP -> ClpXP [0.05]; //initialtion init(100,Pfnr); init(100,Ise); init(100,ClpXP); init(100,QFeFNRa); init(100,DFeFNRi); init(100,apoFNR); init(100,GPV); init(10,PV); init(100,GPR); init(10,PR); init(10,o2); init(10,QFeFNRa_GPR_binded); init(10,QFeFNRa_GPV_binded); init(10,rep);