biocrnpyler.mechanisms.signaling

Classes

Membrane_Signaling_Pathway_MM([name, ...])

A mechanism to model a two-component system (TCS) membrane sensor.

class biocrnpyler.mechanisms.signaling.Membrane_Signaling_Pathway_MM(name='two_component_membrane_signaling', mechanism_type='membrane_sensor', **keywords)[source]

A mechanism to model a two-component system (TCS) membrane sensor. Includes the sensing of signal substrate (SigSub) and the phosphorylation of the response protein (RP) but not include the reporter circuit. Mechanism follows Michaelis-Menten Type Reactions. Mechanism for the activation of the membrane sensor protein (MSP): SP + SigSub <–> SP:SigSub –> SP* Mechanism for the auto-phosphorylation: SP* + nATP <–> SP*:nATP –> SP**:nADP –> SP** + nADP Mechanism for the phosphorylation of response protein: SP** + RP <–> SP**:RP –> SP*:RP* –> SP*+RP* Mechanism for the dephosphorylation of phosphoryled response protein: RP* –> RP + Pi

Initializes a Mechanism instance.

Parameters:

name – name of the Mechanism
mechanism_type – mechanism_type in string

update_reactions(membrane_sensor_protein, response_protein, assigned_substrate, signal_substrate, product, energy, waste, complex_dict=None, component=None, part_id=None, **keywords)[source]: This always requires the inputs component and part_id to find the relevant parameters

update_species(membrane_sensor_protein, response_protein, assigned_substrate, signal_substrate, product, energy, waste, complex_dict=None, **keywords)[source]

the child class should implement this method.

Returns:: empty list