EGFR (minimal)

This passage was processed and assembled automatically by INDRA:

The receptor tyrosine kinase EGFR binds the growth factor ligand EGF. The EGFR-EGF complex binds another EGFR-EGF complex. EGFR, bound to EGFR, transphosphorylates itself on a tyrosine residue. The adaptor protein GRB2 can bind EGFR that is phosphorylated on tyrosine. EGFR-bound GRB2 binds SOS1.

INDRA-assembled model components

from pysb import Monomer, Parameter, Rule, Annotation, ANY
from pysb.util import alias_model_components

def egfr_minimal():
    Monomer(u'GRB2', [u'egfr', u'sos1'])
    Monomer(u'EGFR', [u'egf', u'egfr', 'Y', u'grb2'], {'Y': ['u', 'p']})
    Monomer(u'EGF', [u'egfr'])
    Monomer(u'SOS1', [u'grb2', 'ras'])

    Parameter(u'kf_ee_bind_1', 1e-06)
    Parameter(u'kr_ee_bind_1', 1e-06)
    Parameter(u'kf_ee_bind_2', 1e-06)
    Parameter(u'kr_ee_bind_2', 1e-06)
    Parameter(u'kf_ge_bind_1', 1e-06)
    Parameter(u'kr_ge_bind_1', 1e-06)
    Parameter(u'kf_gs_bind_1', 1e-06)
    Parameter(u'kr_gs_bind_1', 1e-06)
    Parameter(u'kf_ee_transphos_1', 0.001)


    Rule(u'EGFR_EGF_bind', EGFR(egf=None) + EGF(egfr=None) >>
        EGFR(egf=1) % EGF(egfr=1), kf_ee_bind_1)

    Rule(u'EGFR_EGF_dissociate', EGFR(egf=1) % EGF(egfr=1) >>
        EGFR(egf=None) + EGF(egfr=None), kr_ee_bind_1)

    Rule(u'EGFR_EGF_EGFR_EGF_bind', EGFR(egf=ANY, egfr=None) +
        EGFR(egf=ANY, egfr=None) >> EGFR(egf=ANY, egfr=1) %\
        EGFR(egf=ANY, egfr=1), kf_ee_bind_2)

    Rule(u'EGFR_EGF_EGFR_EGF_dissociate', EGFR(egfr=1) % EGFR(egfr=1) >>
        EGFR(egfr=None) + EGFR(egfr=None), kr_ee_bind_2)

    Rule(u'GRB2_EGFR_bind', GRB2(egfr=None) + EGFR(grb2=None) >>
        GRB2(egfr=1) % EGFR(grb2=1), kf_ge_bind_1)

    Rule(u'GRB2_EGFR_dissociate', GRB2(egfr=1) % EGFR(grb2=1) >>
        GRB2(egfr=None) + EGFR(grb2=None), kr_ge_bind_1)

    Rule(u'GRB2_EGFR_SOS1_bind', GRB2(egfr=ANY, sos1=None) +\
        SOS1(grb2=None) >> GRB2(egfr=ANY, sos1=1) % SOS1(grb2=1),

    Rule(u'GRB2_EGFR_SOS1_dissociate', GRB2(sos1=1) % SOS1(grb2=1) >>
        GRB2(sos1=None) + SOS1(grb2=None), kr_gs_bind_1)

        EGFR(egfr=ANY) % EGFR(Y='u') >> EGFR(egfr=ANY) % EGFR(Y='p'),

    Annotation(GRB2, '', 'is')
    Annotation(GRB2, '', 'is')
    Annotation(EGFR, '', 'is')
    Annotation(EGFR, '', 'is')
    Annotation(EGF, '', 'is')
    Annotation(EGF, '', 'is')
    Annotation(SOS1, '', 'is')
    Annotation(SOS1, '', 'is')
    Annotation(SOS1, '', 'is')