ecoli.processes.polypeptide_initiation

Polypeptide Initiation

This process models the complementation of 30S and 50S ribosomal subunits into 70S ribosomes on mRNA transcripts. This process is in many ways analogous to the TranscriptInitiation process - the number of initiation events per transcript is determined in a probabilistic manner and dependent on the number of free ribosomal subunits, each mRNA transcript’s translation efficiency, and the counts of each type of transcript.

class ecoli.processes.polypeptide_initiation.PolypeptideInitiation(parameters=None)[source]

Bases: PartitionedProcess

Polypeptide Initiation PartitionedProcess

calculate_activation_prob(fracActiveRibosome, proteinLengths, ribosomeElongationRates, proteinInitProb, timeStepSec)[source]

Calculates the expected ribosome termination rate based on the ribosome elongation rate

Parameters:

  • allTranslationTimes – Vector of times required to translate each protein

  • allTranslationTimestepCounts – Vector of numbers of timesteps required to translate each protein

  • averageTranslationTimeStepCounts – Average number of timesteps required to translate a protein, weighted by initiation probabilities

  • expectedTerminationRate – Average number of terminations in one timestep for one protein

calculate_request(timestep, states)[source]
defaults: Dict[str, Any]
{   'active_ribosome_footprint_size': 24 [nucleotide],
    'active_ribosome_fraction': {},
    'cistron_start_end_pos_in_tu': {},
    'cistron_to_monomer_mapping': {},
    'cistron_tu_mapping_matrix': {},
    'elongation_rates': {},
    'emit_unique': False,
    'make_elongation_rates': <function PolypeptideInitiation.<lambda> at 0x7f8241490180>,
    'monomer_ids': [],
    'monomer_index_to_cistron_index': {},
    'monomer_index_to_tu_indexes': {},
    'protein_lengths': [],
    'ribosome30S': 'ribosome30S',
    'ribosome50S': 'ribosome50S',
    'rna_id_to_cistron_indexes': {},
    'seed': 0,
    'time_step': 1,
    'translation_efficiencies': [],
    'tu_ids': [],
    'variable_elongation': False}
evolve_state(timestep, states)[source]
name = 'ecoli-polypeptide-initiation'
ports_schema()[source]
topology
{   'RNA': ('unique', 'RNA'),
    'active_ribosome': ('unique', 'active_ribosome'),
    'bulk': ('bulk',),
    'environment': ('environment',),
    'listeners': ('listeners',),
    'timestep': ('timestep',)}