biocrnpyler.mechanisms.Energy_Translation_MM

class biocrnpyler.mechanisms.Energy_Translation_MM(ribosome: Species, fuels: List[Species], wastes=typing.List[biocrnpyler.core.species.Species], name='energy_translation_mm', **kwargs)[source]

Bases: Mechanism

Michaelis-Menten translation with explicit energy consumption.

A ‘translation’ mechanism that models translation with explicit consumption of energy sources (fuel species like amino acids/NTPs) and production of waste products. This mechanism couples ribosome-mRNA binding with length-dependent fuel consumption to model realistic translation energetics.

The reaction follows the schema:

\[\begin{split} & {\text{mRNA}} + {\text{Ribo}} \rightleftharpoons {\text{mRNA}}\mathord{:}{\text{Ribo}} \\ & {\text{Fuel}} + {\text{mRNA}}\mathord{:}{\text{Ribo}} \rightarrow {\text{mRNA}} + {\text{Ribo}} + {\text{Protein}} + {\text{Fuel}} \\ & {\text{Fuel}} + {\text{mRNA}}\mathord{:}{\text{Ribo}} \rightarrow {\text{mRNA}}\mathord{:}{\text{Ribo}} + {\text{wastes}} \end{split}\]
Translation occurs at rate ‘ktl’ / L (length-dependent), while fuel consumption occurs at rate ‘ktl’, resulting in L times more fuel consumption than proteins produced.

Parameters:

  • ribosome (Species) – Ribosome species that catalyzes translation.

  • fuels (list of Species) – List of fuel species (e.g., amino acids, GTP) consumed during translation.

  • wastes (list of Species) – List of waste species produced during translation.

  • name (str, default 'energy_translation_mm') – Name identifier for this mechanism instance.

Attributes:

  • ribosome (Species) – The ribosome species.

  • fuels (list of Species) – Fuel species consumed during translation.

  • wastes (list of Species) – Waste species produced during translation.

  • name (str) – Name of the mechanism instance.

  • mechanism_type (str) – Type classification (‘translation’).

See also

Translation_MM

MM translation without explicit energy.

Energy_Transcription_MM

MM transcription with explicit energy.

MichaelisMentenCopy

Base class for MM copy mechanisms.

Mechanism

Base class for all mechanisms.

Notes

This mechanism provides a more realistic model of translation by explicitly tracking energy consumption. Key features:

  • Length-dependent translation rate (‘ktl’ / L)

  • Explicit fuel (amino acid/NTP) consumption

  • Waste product generation

  • Ribosome-mRNA binding dynamics

The length parameter L represents the gene/protein length in appropriate units, and the mechanism automatically scales fuel consumption to match the energetic requirements of synthesizing a protein of length L.

Common applications include:

  • Detailed TX-TL models with explicit resources

  • Models of translational burden and resource depletion

  • Systems where amino acid availability affects protein expression

Required parameters for this mechanism:

  • ‘ktl’ : Base translation rate constant

  • ‘kb’ : Forward binding rate for ribosome to mRNA

  • ‘ku’ : Reverse unbinding rate for ribosome from mRNA

  • ‘length’ : Gene/protein length (for length-dependent translation)

Examples

Model translation with explicit amino acid consumption:

>>> gene = bcp.DNAassembly(
...    name='constitutive_promoter',
...    promoter='pconst', rbs='RBS_medium', protein='GFP')
>>> ribosome = bcp.Species('Ribosome')
>>> amino_acids = bcp.Species('AA')
>>> waste = bcp.Species('waste')
>>> mechanism = bcp.Energy_Translation_MM(
...     ribosome=ribosome,
...     fuels=[amino_acids],
...     wastes=[waste]
... )
>>> mixture = bcp.Mixture(
...     components=[gene],
...     mechanisms={
...         'transcription': bcp.SimpleTranscription(),
...         'translation': mechanism,
...     },
...     parameters={'ktl': 0.1, 'kb': 1.0, 'ku': 0.1, 'length': 300},
...     parameter_file='mixtures/pure_parameters.tsv'
... )
>>> mixture.compile_crn()

Methods

update_reactions

Generate reactions for energy-consuming translation.

update_species

Generate species for energy-consuming translation.
update_reactions(transcript, protein, component, part_id=None, complex=None, **kwargs)[source]

Generate reactions for energy-consuming translation.

Creates three reactions modeling translation with explicit fuel consumption and waste production: ribosome-mRNA binding, length-dependent translation, and fuel consumption.

Parameters:

  • transcript (Species) – The mRNA transcript species being translated.

  • protein (Species) – The protein species produced by translation.

  • component (Component) – Component containing parameter values. Required for parameter lookup.

  • part_id (str, optional) – Identifier for parameter lookup. If None, defaults to component.name.

  • complex (Complex, optional) – Pre-specified mRNA:ribosome complex species (unused, complex is created internally).

  • **kwargs – Additional keyword arguments (unused).

Returns:

List of three reactions:

  • Ribosome-mRNA binding (rates: ‘kb’, ‘ku’)

  • Translation with fuel (rate: ‘ktl’ / ‘length’)

  • Fuel consumption producing wastes (rate: ‘ktl’)

Return type:

list of Reaction

Notes

The reactions model translation energetics:

  1. mRNA + Ribosome \(\rightleftharpoons\) mRNA:Ribosome (rates: ‘kb’ and ‘ku’)

  2. Fuel + mRNA:Ribosome \(\rightarrow\) Fuel + mRNA + Ribosome + Protein (rate: ‘ktl’ / L)

  3. Fuel + mRNA:Ribosome \(\rightarrow\) mRNA:Ribosome + Wastes (rate: ‘ktl’)

The length-dependent translation rate (‘ktl’ / L) ensures that L times more fuel is consumed than proteins produced, reflecting the energetic cost of synthesizing a protein of length L.

update_species(transcript, protein, **kwargs)[source]

Generate species for energy-consuming translation.

Creates species involved in translation with explicit energy consumption including mRNA, ribosome, the mRNA:ribosome complex, protein, and fuel species.

Parameters:

  • transcript (Species) – The mRNA transcript species being translated.

  • protein (Species) – The protein species produced by translation.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing [fuels…, ribosome, protein, mRNA:ribosome complex].

Return type:

list of Species