def bind(a, b, klist):
"""Alias for pysb.macros.bind with default binding sites."""
return macros.bind(a, 'bf', b, 'bf', klist)
catalyze(COX2(allo=None), 'cat', AG(), 'b', PGG(),
[kf_AG_cat1, kr_AG_cat1, kcat_AG1])
bind_complex(
COX2(allo=1) % AG(b=1), 'cat', AG(), 'b', [kf_AG_cat2, kr_AG_cat2])
bind_complex(
COX2(allo=1) % AA(b=1), 'cat', AG(), 'b', [kf_AG_cat3, kr_AG_cat3])
Rule(
'kcat_AG_3',
COX2(allo=1, cat=2) % AA(b=1) % AG(b=2) >>
COX2(allo=1, cat=None) % AA(b=1) + PGG(), kcat_AG3)
bind(COX2(cat=None), 'allo', AA(), 'b', [kf_AA_allo1, kr_AA_allo1])
Rule(
'bind_COX2AA_AA_allo',
COX2(cat=1, allo=None) % AA(b=1) + AA(b=None)
| COX2(cat=1, allo=2) % AA(b=1) % AA(b=2), kf_AA_allo2, kr_AA_allo2)
Rule(
'bind_COX2AG_AA_allo',
COX2(cat=1, allo=None) % AG(b=1) + AA(b=None)
| COX2(cat=1, allo=2) % AG(b=1) % AA(b=2), kf_AA_allo3, kr_AA_allo3)
bind(COX2(cat=None), 'allo', AG(), 'b', [kf_AG_allo1, kr_AG_allo1])
Rule(
'bind_COX2AA_AG_allo',
def bind(a, b, klist):
"""Alias for pysb.macros.bind with default binding sites."""
return macros.bind(a, 'bf', b, 'bf', klist)
# input the parameter values
#?? Are we going to use the same units?
Parameter('kf', 1.0e-07)
Parameter('kr', 1.0e-03)
Parameter('kc', 1.0)
# now input the rules
#COULD WE SIMPLIFY THE RULES BY ADDING IN A BIND TABLE?
Rule('cplx_bind',
Ca(b=1) % Cdk2(b=1, bp=None) + P27(b=None) <>
Ca(b=1) % Cdk2(b=1, bp=2) % P27(b=2),
KF, KR)
bind(Ca(b=1) % Cdk2(b=1), 'bp' P27(), 'b', [KF, KR])
A. Rule('Ca_Cdk2_bind', Ca(b=None) + Cdk2(b=None) <> Ca(b=1) % Cdk2(b=1), *[kcom3, kdecom3]) *** HOW DO WE DEFINE A STATE FOR THE COMPLEX- ACTIVE AND INACTIVE? OR DO WE MAKE ANOTHER RULE WHERE THE COMPEXT IS ACTIVATED?
B. Rule('Cb_Cdk1_bind', Cb(b=None) + Cdk1(b=None) <> Cb(b=1) % Cdk1(b=1), *[kcom4, kdecom4])
C. Rule('Cd_Cdk4_6_bind', Cd(b=None) + Cdk4_6(b=None) <> Cd(b=1) % Cdk4_6(b=1), *[kcom1, kdecom1])
D. Rule('Ce_Cdk2bind', Ce(b=None) + Cdk2(b=None) <> Ce(b=1) % Cdk2(b=1), *[kcom2, kdecom2])
E. Rule('Ca_Cdk2_p27_bind', Ca(b=1) % Cdk2(b=1) + p27(b=None, S='u') <> Cd(b=2) % Cdk2(b=2) % p27(b=2, S='u'), *[kc5, kc6])
Rule('Cd_Cdk4_6_P27_bind', Cd(b=1) % Cdk4_6(b=1) + p27(b=None, S='u') <> Cd(b=2) % Cdk4_6(b=2) % p27(b=2, S='u'), *[kc1, kc2])
Rule('Ce_Cdk2_P27_bind', Ce(b=1) % Cdk2(b=1) + p27(b=None, S='u') <> Ce(b=2) % Cdk2(b=2) % p27(b=2, S='u'), *[kc3, kc4]
# 1. ptc is actively translated but hh is not.
# 2. PTC but not HH currently present and neither is currently transcribed
# SMO is activated whenever
# 3. hh is currently translated
# 4. PTC and HH are both present but neither is translated
# 5. PTC is both absent and untranslated
# Given this and our interpretation for PH above we conclude that SMO is inactivated
# in the presence of free PTC. As above this will only be apparent when considering
# targets for SMO. For now we need only consider all the binding states. Of course,
# we also don't need to account for the translation of ptc and hh again. Thus we have
bind(SMO_1, "PTC", PTC_1, "SMO", [SMO_PTC_kf, SMO_PTC_kr])
bind(SMO_2, "PTC", PTC_2, "SMO", [SMO_PTC_kf, SMO_PTC_kr])
bind(SMO_3, "PTC", PTC_3, "SMO", [SMO_PTC_kf, SMO_PTC_kr])
bind(SMO_4, "PTC", PTC_4, "SMO", [SMO_PTC_kf, SMO_PTC_kr])
bind(SMO_1, "PH", PH_1, "SMO", [SMO_PH_kf, SMO_PH_kr])
bind(SMO_2, "PH", PH_2, "SMO", [SMO_PH_kf, SMO_PH_kr])
bind(SMO_3, "PH", PH_3, "SMO", [SMO_PH_kf, SMO_PH_kr])
bind(SMO_4, "PH", PH_4, "SMO", [SMO_PH_kf, SMO_PH_kr])
# In order to be consistent with the Boolean model I have renamed the bound entity PTC % HH as PH throughout.
Rule(
"bound_dimerization_SMO_1_PTC_1_HH_4",
SMO_1(PTC=1) % PTC_1(SMO=1, HH=None) + HH_4(PTC=None) <> SMO_1(PTC=1) % PH_1(SMO=1),
SMO_PTC_HH_kf,
Rule('kcat_AA_3',
COX2(allo=1, cat=2) % AA(b=1) % AA(b=2) >> COX2(allo=1, cat=None) % AA(b=1) + PG(),
kcat_AA3)
catalyze(COX2(allo=None), 'cat', AG(), 'b', PGG(), [kf_AG_cat1, kr_AG_cat1, kcat_AG1])
bind_complex(COX2(allo=1) % AG(b=1), 'cat', AG(), 'b', [kf_AG_cat2, kr_AG_cat2])
bind_complex(COX2(allo=1) % AA(b=1), 'cat', AG(), 'b', [kf_AG_cat3, kr_AG_cat3])
Rule('kcat_AG_3',
COX2(allo=1, cat=2) % AA(b=1) % AG(b=2) >> COX2(allo=1, cat=None) % AA(b=1) + PGG(),
kcat_AG3)
bind(COX2(cat=None), 'allo', AA(), 'b', [kf_AA_allo1, kr_AA_allo1])
Rule('bind_COX2AA_AA_allo',
COX2(cat=1, allo=None) % AA(b=1) + AA(b=None) <> COX2(cat=1, allo=2) % AA(b=1) % AA(b=2),
kf_AA_allo2, kr_AA_allo2)
Rule('bind_COX2AG_AA_allo',
COX2(cat=1, allo=None) % AG(b=1) + AA(b=None) <> COX2(cat=1, allo=2) % AG(b=1) % AA(b=2),
kf_AA_allo3, kr_AA_allo3)
bind(COX2(cat=None), 'allo', AG(), 'b', [kf_AG_allo1, kr_AG_allo1])
Rule('bind_COX2AA_AG_allo',
COX2(cat=1, allo=None) % AA(b=1) + AG(b=None) <> COX2(cat=1, allo=2) % AA(b=1) % AG(b=2),
kf_AG_allo2, kr_AG_allo2)
def bind(a, b, klist):
"""Alias for pysb.macros.bind with default binding sites."""
return macros.bind(a, site_name, b, site_name, klist)