biocrnpyler.mechanisms.Translation_MM

class biocrnpyler.mechanisms.Translation_MM(ribosome: Species, name='translation_mm', **kwargs)[source]

Bases: MichaelisMentenCopy

Michaelis-Menten translation with explicit ribosome.

A ‘translation’ mechanism that explicitly models ribosome binding to mRNA, followed by translation and release. This mechanism follows Michaelis-Menten kinetics and is appropriate when ribosomes are limiting or when explicit modeling of ribosome-mRNA interactions is needed.

The reaction follows the schema:

\[ {\text{mRNA}} + {\text{Ribo}} \rightleftharpoons {\text{mRNA}}\mathord{:}{\text{Ribo}} \rightarrow {\text{mRNA}} + {\text{Ribo}} + {\text{Protein}} \]

Parameters:

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

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

Attributes:

  • ribosome (Species) – The ribosome species.

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

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

See also

SimpleTranslation

Simple translation without explicit ribosomes.

Transcription_MM

Michaelis-Menten transcription.

MichaelisMentenCopy

Base class for MM copy mechanisms.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models translation using standard Michaelis-Menten kinetics where ribosomes act as enzymes that bind mRNA, catalyze protein synthesis, and are released unchanged. This is appropriate when:

  • Ribosome concentration affects translation rate

  • Explicit modeling of ribosome-mRNA binding is important

  • Ribosome sequestration or competition effects are relevant

The mechanism uses the MichaelisMentenCopy base class which generates:

  1. Reversible binding: mRNA + Rib \(\rightleftharpoons\) mRNA:Rib (rates: ‘kb’, ‘ku’)

  2. Catalysis: mRNA:Rib \(\rightarrow\) mRNA + Rib + Protein (rate: ‘ktl’)

Common applications include:

  • TX-TL systems with limited ribosomes

  • Models of translational resource allocation

  • Competition between mRNAs for ribosomes

  • Detailed mechanistic models of protein expression

Required parameters for this mechanism:

  • ‘ktl’ : Translation/catalysis rate constant

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

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

Examples

Model translation with explicit ribosomes:

>>> gene = bcp.DNAassembly(
...     name='gene_assembly',
...     promoter='pconst', transcript='mRNA',
...     rbs='RBS_medium', protein='GFP')
>>> ribosome = bcp.Species('Ribosome', material_type='protein')
>>> tl_mechanism = bcp.Translation_MM(ribosome=ribosome)
>>> mixture = bcp.Mixture(
...     components=[gene],
...     mechanisms={
...         'transcription': bcp.SimpleTranscription(),
...         'translation': mechanism},
...     parameters={'ktx': 0.05, 'ktl': 0.1, 'kb': 1.0, 'ku': 0.1}
... )
>>> mixture.compile_crn()

Methods

update_reactions

Generate reactions for Michaelis-Menten translation.

update_species

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

Generate reactions for Michaelis-Menten translation.

Creates Michaelis-Menten translation reactions including reversible ribosome-mRNA binding and catalytic protein production.

Parameters:

  • transcript (Species) – The mRNA transcript species being translated. Can be None in expression mixtures.

  • 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. If None, automatically created.

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

Returns:

List of two reactions for translation if transcript is not None:

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

  • Catalytic translation (rate: ‘ktl’)

Returns empty list if transcript is None (expression mixtures).

Return type:

list of Reaction

Notes

The reactions follow the Michaelis-Menten scheme:

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

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

In expression mixtures without explicit transcription, no translation reactions are generated (empty list returned).

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

Generate species for Michaelis-Menten translation.

Creates species involved in ribosome-mediated translation including mRNA, ribosome, the mRNA:ribosome complex, and protein product.

Parameters:

  • transcript (Species) – The mRNA transcript species being translated. Can be None in expression mixtures without explicit transcription.

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

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

Returns:

List containing translation species. In expression mixtures without transcription (transcript is None), returns [protein]. Otherwise returns [ribosome, transcript, mRNA:ribosome complex, protein].

Return type:

list of Species