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)[source]

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)[source]

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

ports_schema()[source]

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)[source]
ecoli.processes.chemotaxis.chemoreceptor_cluster.get_exponential_random_timeline(config)[source]

get timeline with random walk in exponential space

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

get a timeline with pulses applied to the external ligand

ecoli.processes.chemotaxis.chemoreceptor_cluster.main()[source]
ecoli.processes.chemotaxis.chemoreceptor_cluster.plot_receptor_output(output, settings, out_dir='out', filename='response')[source]
ecoli.processes.chemotaxis.chemoreceptor_cluster.run_step(receptor, state, timestep)[source]

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)[source]

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.