#rehm1



#reactions
Apo_formation:
 {1.0}PC9 + {1.0}APAF1 = {1.0}C9
  cell * apo_lim * log(2) / th_Apop
CytC_release:
 {1.0}CytC_mit = {1.0}CytC_cell
  cell * CytC_mit * log(2) / th_CytC
SMAC_release:
 {1.0}SMAC_mito = {1.0}SMAC
  cell * SMAC_mito * log(2) / th_SMAC
reaction1:
 $pool = {1.0}PC3
  cell * (k1 - k1r * PC3)
reaction10:
 {1.0}C3 + {1.0}BIR12 = {1.0}BIR12_C3
  cell * (k10 * C3 * BIR12 - k10r * BIR12_C3)
reaction11:
 {1.0}C3 + {1.0}XIAP = {1.0}BIR12 + {1.0}BIR3R + {1.0}C3
  cell * k11 * C3 * XIAP
reaction12:
 {1.0}C3 + {1.0}XIAP_C9 = {1.0}BIR12 + {1.0}BIR3R_C9 + {1.0}C3
  cell * k12 * C3 * XIAP_C9
reaction13:
 {1.0}C3 + {1.0}XIAP_C3 = {1.0}C3 + {1.0}BIR12_C3 + {1.0}BIR3R
  cell * k13 * C3 * XIAP_C3
reaction14:
 {1.0}C3 + {1.0}XIAP_p2frag = {1.0}C3 + {1.0}BIR12 + {1.0}BIR3R_p2frag
  cell * k14 * C3 * XIAP_p2frag
reaction15:
 {1.0}C3 + {1.0}XIAP_p2frag_C3 = {1.0}C3 + {1.0}BIR12_C3 + {1.0}BIR3R_p2frag
  cell * k15 * C3 * XIAP_p2frag_C3
reaction16:
 {1.0}C3 + {1.0}XIAP_C9_C3 = {1.0}C3 + {1.0}BIR12_C3 + {1.0}BIR3R_C9
  cell * k16 * C3 * XIAP_C9_C3
reaction17:
 {1.0}C3 + {1.0}XIAP_2SMAC = {1.0}C3 + {1.0}BIR12_SMAC + {1.0}BIR3R_SMAC
  cell * k17 * C3 * XIAP_2SMAC
reaction18:
 {1.0}C3 + {1.0}XIAP_C9_C3 = {1.0}C3 + {1.0}C9P + {1.0}XIAP_p2frag_C3
  cell * k18 * C3 * XIAP_C9_C3
reaction19:
 {1.0}C3 + {1.0}XIAP_C9 = {1.0}C3 + {1.0}C9P + {1.0}XIAP_p2frag
  cell * k19 * C3 * XIAP_C9
reaction2:
 $pool = {1.0}XIAP
  cell * (k2 - k2r * XIAP)
reaction20:
 {1.0}C3 + {1.0}BIR3R_C9 = {1.0}C3 + {1.0}BIR3R_p2frag + {1.0}C9P
  cell * k20 * C3 * BIR3R_C9
reaction21:
 {1.0}C9 + {1.0}XIAP = {1.0}XIAP_C9
  cell * (k21 * C9 * XIAP - k21r * XIAP_C9)
reaction22:
 {1.0}C9 + {1.0}XIAP_C3 = {1.0}XIAP_C9_C3
  cell * (k22 * C9 * XIAP_C3 - k22r * XIAP_C9_C3)
reaction23:
 {1.0}C9 + {1.0}BIR3R = {1.0}BIR3R_C9
  cell * (k23 * C9 * BIR3R - k23r * BIR3R_C9)
reaction24:
 {1.0}BIR3R_p2frag = {1.0}BIR3R
  cell * k24 * BIR3R_p2frag
reaction25:
 {1.0}XIAP_p2frag = {1.0}XIAP
  cell * k25 * XIAP_p2frag
reaction26:
 {1.0}XIAP + {2.0}SMAC = {1.0}XIAP_2SMAC
  cell * (k26 * XIAP * SMAC * SMAC - k26r * XIAP_2SMAC)
reaction27:
 {1.0}XIAP_C9 + {2.0}SMAC = {1.0}XIAP_2SMAC + {1.0}C9
  cell * (k27 * XIAP_C9 * SMAC * SMAC - k27r * XIAP_2SMAC * C9)
reaction28:
 {1.0}XIAP_C3 + {2.0}SMAC = {1.0}XIAP_2SMAC + {1.0}C3
  cell * (k28 * XIAP_C3 * SMAC * SMAC - k28r * XIAP_2SMAC * C3)
reaction29:
 {1.0}XIAP_C9_C3 + {2.0}SMAC = {1.0}XIAP_2SMAC + {1.0}C3 + {1.0}C9
  cell * (k29 * XIAP_C9_C3 * SMAC * SMAC - k29r * XIAP_2SMAC * C3 * C9)
reaction3:
 {1.0}C9 + {1.0}PC3 = {1.0}C3 + {1.0}C9
  cell * k3 * C9 * PC3
reaction30:
 {1.0}BIR12 + {1.0}SMAC = {1.0}BIR12_SMAC
  cell * (k30 * BIR12 * SMAC - k30r * BIR12_SMAC)
reaction31:
 {1.0}BIR3R + {1.0}SMAC = {1.0}BIR3R_SMAC
  cell * (k31 * BIR3R * SMAC - k31r * BIR3R_SMAC)
reaction32:
 {1.0}BIR12_C3 + {1.0}SMAC = {1.0}BIR12_SMAC + {1.0}C3
  cell * (k32 * BIR12_C3 * SMAC - k32r * BIR12_SMAC * C3)
reaction33:
 {1.0}BIR3R_C9 + {1.0}SMAC = {1.0}BIR3R_SMAC + {1.0}C9
  cell * (k33 * BIR3R_C9 * SMAC - k33r * BIR3R_SMAC * C9)
reaction34:
 {1.0}XIAP_p2frag + {2.0}SMAC = {1.0}XIAP_p2frag_2SMAC
  cell * (k34 * XIAP_p2frag * SMAC * SMAC - k34r * XIAP_p2frag_2SMAC)
reaction35:
 {1.0}C9P = $pool
  cell * k35 * C9P
reaction36:
 {1.0}C9 = $pool
  cell * k36 * C9
reaction37:
 {1.0}C3 = $pool
  cell * k37 * C3
reaction38:
 {1.0}XIAP_C3 = $pool
  cell * k38 * XIAP_C3
reaction39:
 {1.0}XIAP_C9_C3 = $pool
  cell * k39 * XIAP_C9_C3
reaction4:
 {1.0}C9 + {1.0}C3 = {1.0}C9P + {1.0}C3
  cell * k4 * C9 * C3
reaction40:
 {1.0}XIAP_C9 = $pool
  cell * k40 * XIAP_C9
reaction41:
 {1.0}XIAP_p2frag = $pool
  cell * k41 * XIAP_p2frag
reaction42:
 {1.0}XIAP_p2frag_C3 = $pool
  cell * k42 * XIAP_p2frag_C3
reaction43:
 {1.0}XIAP_p2frag_2SMAC = $pool
  cell * k43 * XIAP_p2frag_2SMAC
reaction44:
 {1.0}XIAP_2SMAC = $pool
  cell * k44 * XIAP_2SMAC
reaction45:
 {1.0}BIR12 = $pool
  cell * k45 * BIR12
reaction46:
 {1.0}BIR3R = $pool
  cell * k46 * BIR3R
reaction47:
 {1.0}BIR12_SMAC = $pool
  cell * k47 * BIR12_SMAC
reaction48:
 {1.0}BIR3R_SMAC = $pool
  cell * k48 * BIR3R_SMAC
reaction49:
 {1.0}BIR12_C3 = $pool
  cell * k49 * BIR12_C3
reaction5:
 {1.0}C9P + {1.0}PC3 = {1.0}C9P + {1.0}C3
  cell * k5 * C9P * PC3
reaction50:
 {1.0}BIR3R_C9 = $pool
  cell * k50 * BIR3R_C9
reaction51:
 {1.0}BIR3R_p2frag = $pool
  cell * k51 * BIR3R_p2frag
reaction52:
 {1.0}SMAC = $pool
  cell * k52 * SMAC
reaction53:
 {1.0}C3 + {1.0}Substrate = {1.0}C3 + {1.0}ClvgPrds
  cell * k53 * C3 * Substrate
reaction6:
 {1.0}PC3 + {1.0}C3 = {2.0}C3
  cell * k6 * PC3 * C3
reaction7:
 {1.0}C3 + {1.0}XIAP = {1.0}XIAP_C3
  cell * (k7 * C3 * XIAP - k7r * XIAP_C3)
reaction8:
 {1.0}C3 + {1.0}XIAP_C9 = {1.0}XIAP_C9_C3
  cell * (k8 * C3 * XIAP_C9 - k8r * XIAP_C9_C3)
reaction9:
 {1.0}C3 + {1.0}XIAP_p2frag = {1.0}XIAP_p2frag_C3
  cell * (k9 * C3 * XIAP_p2frag - k9r * XIAP_p2frag_C3)


#parameters
APAF1_tot = APAF1
C3_tot = PC3
C9_tot = PC9
CytC_tot = CytC\[LetterSpace]mit
SMAC_tot = SMAC\[LetterSpace]mito
S_breakdown = 0.01
XIAP_ini = XIAP
k1 = 0.000468
k10 = 156.0
k10r = 0.144
k11 = 12.0
k12 = 12.0
k13 = 12.0
k14 = 12.0
k15 = 12.0
k16 = 12.0
k17 = 12.0
k18 = 12.0
k19 = 12.0
k1r = 0.0039
k2 = 0.0007308
k20 = 12.0
k21 = 156.0
k21r = 0.144
k22 = 156.0
k22r = 0.144
k23 = 156.0
k23r = 0.144
k24 = 0.0
k25 = 0.0
k26 = 420.0
k26r = 0.133
k27 = 420.0
k27r = 156.0
k28 = 420.0
k28r = 156.0
k29 = 420.0
k29r = 156.0
k2r = 0.0116
k3 = 6.0
k30 = 4.45
k30r = 31.9
k31 = 0.33
k31r = 14.2
k32 = 4.45
k32r = 156.0
k33 = 0.33
k33r = 156.0
k34 = 420.0
k34r = 156.0
k35 = 0.0058
k36 = 0.0058
k37 = 0.0058
k38 = 0.0347
k39 = 0.0347
k4 = 12.0
k40 = 0.0347
k41 = 0.0058
k42 = 0.0347
k43 = 0.0347
k44 = 0.0347
k45 = 0.0058
k46 = 0.0347
k47 = 0.0058
k48 = 0.0347
k49 = 0.0058
k5 = 48.0
k50 = 0.0058
k51 = 0.0347
k52 = 0.0058
k53 = 12.0
k6 = 2.4
k7 = 156.0
k7r = 0.144
k8 = 156.0
k8r = 0.144
k9 = 156.0
k9r = 0.144
th_Apop = 2.3
th_CytC = 1.5
th_SMAC = 7.0
cell = 1.0
mito = 1.0


#initial values
APAF1 = 3.372
BIR12 = 0.0
BIR12_C3 = 0.0
BIR12_SMAC = 0.0
BIR3R = 0.0
BIR3R_C9 = 0.0
BIR3R_SMAC = 0.0
BIR3R_p2frag = 0.0
C3 = 0.0
C9 = 0.0
C9P = 0.0
ClvgPrds = 0.0
CytC_cell = 0.0
CytC_mit = 10.0
PC3 = 0.12
PC9 = 0.03
SMAC = 0.0
SMAC_mito = 0.126
Substrate = 1.0
XIAP = 0.063
XIAP_2SMAC = 0.0
XIAP_C3 = 0.0
XIAP_C9 = 0.0
XIAP_C9_C3 = 0.0
XIAP_p2frag = 0.0
XIAP_p2frag_2SMAC = 0.0
XIAP_p2frag_C3 = 0.0


#assignment rules
!F BIR3R_p2frag_norm = BIR3R_p2frag / XIAP_ini
!F BIR3R_C9_norm = BIR3R_C9 / XIAP_ini
!F BIR12_C3_norm = BIR12_C3 / XIAP_ini
!F BIR3R_norm = BIR3R / XIAP_ini
!F BIR12_norm = BIR12 / XIAP_ini
!F XIAP_p2frag_norm = (XIAP_p2frag + XIAP_p2frag_C3) / XIAP_ini
!F XIAP_C9_norm = (XIAP_C9 + XIAP_C9_C3) / XIAP_ini
!F XIAP_C3_norm = (XIAP_C3 + XIAP_C9_C3) / XIAP_ini
!F XIAP_norm = XIAP / XIAP_ini
!F Apoform = 1.0 - PC9 / C9_tot
!F SMAC_rel = 1.0 - SMAC_mito / SMAC_tot
!F PC3norm = PC3 / C3_tot
!F C3norm = C3 / C3_tot
!F C9Pnorm = C9P / C9_tot
!F C9norm = C9 / C9_tot
!F XIAP_2SMAC_norm = XIAP_2SMAC / XIAP_ini
!F SMAC_norm = SMAC / XIAP_ini
!F apo_lim = piecewise(PC9, lt(PC9, APAF1), APAF1)