ecoli.processes.chemotaxis.chemoreceptor_cluster

Chemoreceptor Cluster

This ReceptorCluster Process models the activity of a chemoreceptor cluster composed of Tsr and Tar amino acid chemoreceptors. The model is a Monod-Wyman-Changeux (MWC) model adapted from “Endres, R. G., & Wingreen, N. S. (2006). Precise adaptation in bacterial chemotaxis through assistance neighborhoods”. Each receptor homodimer is modeled as a two-state system (on or off) with energy values based on ligand concentration and methylation levels. This results in four energy levels: 1) on without ligand, on with ligand, off without ligand, off with ligand. Sensory adaptation comes from the methylation of receptors, which alters the free-energy offset and transition rate to favor the on state; attractant ligand binding favors the off state.

class ecoli.processes.chemotaxis.chemoreceptor_cluster.ReceptorCluster(parameters=None)

Bases: Process

Models the activity of a chemoreceptor cluster

Ports:

• internal: Expects a store with ‘chemoreceptor_activity’, ‘CheR’, ‘CheB’, ‘CheB_P’, and ‘n_methyl’.

• external: Expects a store with the ligand.

Parameters:

parameters –

A dictionary of configuration options. The following configuration options may be provided:

• ligand_id (str): The name of the external ligand sensed by the cluster.

• initial_ligand (float): The initial concentration of the ligand. The initial state of the cluster is set to steady state relative to this concetnration.

• n_Tar (int): number of Tar receptors in a cluster

• n_Tsr (int): number of Tsr receptors in a cluster

• K_Tar_off (float): (mM) MeAsp binding by Tar (Endres06)

• K_Tar_on (float): (mM) MeAsp binding by Tar (Endres06)

• K_Tsr_off (float): (mM) MeAsp binding by Tsr (Endres06)

• K_Tsr_on (float): (mM) MeAsp binding by Tsr (Endres06)

• k_meth (float): Catalytic rate of methylation

• k_demeth (float): Catalytic rate of demethylation

• adapt_rate (float): adaptation rate relative to wild-type. cell-to-cell variation cause by variability in CheR and CheB

Note

• dissociation constants (mM)

• K_Tar_on = 12e-3 # Tar to Asp (Emonet05)

• K_Tar_off = 1.7e-3 # Tar to Asp (Emonet05)

• (Endres & Wingreen, 2006) has dissociation constants for serine binding, NiCl2 binding

defaults: Dict[str, Any]

{   'K_Tar_off': 0.02,
    'K_Tar_on': 0.5,
    'K_Tsr_off': 100.0,
    'K_Tsr_on': 10000000.0,
    'adapt_rate': 1.2,
    'initial_internal_state': {   'CheB': 0.00028,
                                  'CheB_P': 0.0,
                                  'CheR': 0.00016,
                                  'chemoreceptor_activity': 0.3333333333333333,
                                  'n_methyl': 2.0},
    'initial_ligand': 5.0,
    'k_demeth': 0.0714,
    'k_meth': 0.0625,
    'ligand_id': 'MeAsp',
    'n_Tar': 6,
    'n_Tsr': 12}

name = 'chemoreceptor_cluster'

next_update(timestep, states)

calculate update to chemoreceptor_activity and n_methyl from ligand concentration, CheR, and CheB

ports_schema()

initialize internal and external ports

ecoli.processes.chemotaxis.chemoreceptor_cluster.get_brownian_ligand_timeline(environment_port=('external',), ligand_id='MeAsp', initial_conc=0.01, total_time=10, timestep=1, base=1.0003, speed=14)

ecoli.processes.chemotaxis.chemoreceptor_cluster.get_exponential_random_timeline(config)

get timeline with random walk in exponential space

ecoli.processes.chemotaxis.chemoreceptor_cluster.get_pulse_timeline(ligand='MeAsp')

get a timeline with pulses applied to the external ligand

ecoli.processes.chemotaxis.chemoreceptor_cluster.main()

ecoli.processes.chemotaxis.chemoreceptor_cluster.plot_receptor_output(output, settings, out_dir='out', filename='response')

ecoli.processes.chemotaxis.chemoreceptor_cluster.run_step(receptor, state, timestep)

Run for a timestep, and update the chemoreceptor_activity and n_methyl states

ecoli.processes.chemotaxis.chemoreceptor_cluster.run_to_steady_state(receptor, state, timestep)

Runs the ReceptorCluster Process to steady state

This is used for initialization of the Process, so that the chemoreceptors start off in an adapted state.