def _reactions_to_remove(self):
# aApaf + pC9 <--> Apop
yield ReversibleSynthesis(self.Apaf.A, self.C9, self.Apop, self.k_Apop, self.KR)
# Apop + XIAP <--> Apop:XIAP
yield ReversibleSynthesis(
self.Apop, self.XIAP, self.Apop & self.XIAP, self.k_Apop_XIAP, self.KR
)
def add_reactions(self):
yield ReversibleSynthesis(
self.Bax.M4,
self.Mito.I,
self.Bax.M4 & self.Mito.I,
self.Bax.KF,
self.KR,
)
yield Conversion(self.Bax.M4 & self.Mito.I, self.Mito.A, self.KC)
def add_reactions(self):
yield MichaelisMenten(
self.Bid.T,
self.Bax.C,
self.Bid.T & self.Bax.C,
self.Bax.A,
self.k_Bax_C_Bid_T,
self.KR,
self.KC,
)
yield ReversibleSynthesis(
self.Bax.A,
self.Bcl2,
self.Bax.A & self.Bcl2,
self.KF,
self.KR,
)
def add_reactions(self):
yield MichaelisMenten(
self.Bid.T,
self.Bax.C,
self.Bid.T & self.Bax.C,
self.Bax.A,
self.k_Bax_C_Bid_T,
self.KR,
self.KC,
)
# Bcl2 inhibits Bax, Bax2, and Bax4
for x in (self.Bax.M, self.Bax.M2, self.Bax.M4):
yield ReversibleSynthesis(
x,
self.Bcl2,
x & self.Bcl2,
self.Bax.KF,
self.KR,
)
def add_reactions(self):
yield CatalyzeConvert(
self.L,
self.R,
self.L & self.R,
self.DISC,
self.k_L_R,
self.KR,
self.k_DISC,
)
yield MichaelisMenten(
self.DISC,
self.C8.pro,
self.DISC & self.C8.pro,
self.C8.A,
self.KF,
self.KR,
self.KC,
)
yield MichaelisMenten(
self.C8.A,
self.Bid.U,
self.C8.A & self.Bid.U,
self.Bid.T,
self.KF,
self.KR,
self.KC,
)
# ---------------------
# Inhibition Rules
# ---------------------
# flip + DISC <--> flip:DISC
# C8 + BAR <--> BAR:C8
# ---------------------
yield ReversibleSynthesis(self.DISC, self.flip, self.DISC & self.flip,
self.KF, self.KR)
yield ReversibleSynthesis(self.BAR, self.C8.A, self.BAR & self.C8.A,
self.KF, self.KR)
# Apoptosome formation
# --------------------
# Apaf + cCytoC <--> Apaf:cCytoC --> aApaf + cCytoC
# aApaf + pC9 <--> Apop
# Apop + pC3 <--> Apop:pC3 --> Apop + C3
yield MichaelisMenten(
self.CytoC.A,
self.Apaf.I,
self.CytoC.A & self.Apaf.I,
self.Apaf.A,
self.k_Apaf_I_Cyto_C,
self.KR,
self.KC,
)
yield ReversibleSynthesis(self.Apaf.A, self.C9, self.Apop, self.k_Apop,
self.KR)
yield MichaelisMenten(
self.Apop,
self.C3.pro,
self.Apop & self.C3.pro,
self.C3.A,
self.k_Apop_C3_pro,
self.KR,
self.KC,
)
# Apoptosome-related inhibitors
# -----------------------------
# Apop + XIAP <--> Apop:XIAP
# cSmac + XIAP <--> cSmac:XIAP
yield ReversibleSynthesis(self.Apop, self.XIAP, self.Apop & self.XIAP,
self.k_Apop_XIAP, self.KR)
yield ReversibleSynthesis(self.Smac.A, self.XIAP,
self.Smac.A & self.XIAP, self.k_Smac_A_XIAP,
self.KR)
# Caspase reactions
# -----------------
# Includes effectors, inhibitors, and feedback initiators:
#
# pC3 + C8 <--> pC3:C8 --> C3 + C8 CSPS
# pC6 + C3 <--> pC6:C3 --> C6 + C3 CSPS
# XIAP + C3 <--> XIAP:C3 --> XIAP + C3_U CSPS
# PARP + C3 <--> PARP:C3 --> CPARP + C3 CSPS
# pC8 + C6 <--> pC8:C6 --> C8 + C6 CSPS
yield MichaelisMenten(
self.C8.A,
self.C3.pro,
self.C8.A & self.C3.pro,
self.C3.A,
self.k_C3_pro_C8_A,
self.KR,
self.KC,
)
yield MichaelisMenten(
self.XIAP,
self.C3.A,
self.XIAP & self.C3.A,
self.C3.ub,
self.k_C3_A_XIAP,
self.KR,
self.k_C3_ub,
)
yield MichaelisMenten(
self.C3.A,
self.PARP.U,
self.C3.A & self.PARP.U,
self.PARP.C,
self.KF,
self.k_PARP_C,
self.KC,
)
yield MichaelisMenten(
self.C3.A,
self.C6.pro,
self.C3.A & self.C6.pro,
self.C6.A,
self.KF,
self.KR,
self.KC,
)
yield MichaelisMenten(
self.C6.A,
self.C8.pro,
self.C6.A & self.C8.pro,
self.C8.A,
self.k_C6_A_C8_pro,
self.KR,
self.KC,
)
def add_reactions(self):
# Apoptosome formation
# aApaf + pC3 <--> aApaf:pC3 --> aApaf + C3
# C3 + aApaf <--> C3:aApaf --> C3 + Apop
yield MichaelisMenten(
self.Apaf.A,
self.C3.pro,
self.Apaf.A & self.C3.pro,
self.C3.A,
self.k_Apaf_A_C3_pro,
self.KR,
self.KC,
)
yield MichaelisMenten(
self.C3.A,
self.Apaf.A,
self.Apaf.A & self.C3.A,
self.Apop,
self.k_Apaf_A_C3_A,
self.KR,
self.KC,
)
# Apoptosome-related inhibitors
# Apaf + XIAP <--> Apaf:XIAP
yield ReversibleSynthesis(
self.Apaf.A, self.XIAP, self.Apaf.A & self.XIAP, self.k_Apaf_A_XIAP, self.KR
)
# Sensors
yield MichaelisMenten(
self.C3.A,
self.Sensor.sCas3_dimer,
self.C3.A & self.Sensor.sCas3_dimer,
2 * self.Sensor.sCas3,
self.Sensor.kf_sCas3,
self.Sensor.kr_sCas3,
self.Sensor.kc_sCas3,
)
yield MichaelisMenten(
self.Apop,
self.Sensor.sCas9_dimer,
self.Apop & self.Sensor.sCas9_dimer,
2 * self.Sensor.sCas9,
self.Sensor.kf_sCas9,
self.Sensor.kr_sCas9,
self.Sensor.kc_sCas9,
)
yield MichaelisMenten(
self.C8.A,
self.Sensor.sCas8_dimer,
self.C8.A & self.Sensor.sCas8_dimer,
2 * self.Sensor.sCas8,
self.Sensor.kf_sCas8,
self.Sensor.kr_sCas8,
self.Sensor.kc_sCas8,
)
# Add interaction between single activation
yield MichaelisMenten(
self.Apaf.A,
self.Sensor.sCas9_dimer,
self.Apaf.A & self.Sensor.sCas9_dimer,
2 * self.Sensor.sCas9,
self.Sensor.kf_sCas92,
self.Sensor.kr_sCas9,
self.Sensor.kc_sCas9,
)
yield MichaelisMenten(
self.IntrinsicStimuli,
self.Bid.U,
self.IntrinsicStimuli & self.Bid.U,
self.Bid.T,
self.KF,
self.KR,
self.KC,
)
def add_reactions(self):
yield ReversibleSynthesis(
self.Bid.T, self.Bcl2c, self.Bid.T & self.Bcl2c, self.KF, self.KR
)