biocrnpyler.mechanisms.EnzymeIntegration

class biocrnpyler.mechanisms.EnzymeIntegration(name: str = 'enzyme_integration', mechanism_type: str = 'integration', integrase='Int1', **kwargs)[source]

Bases: Mechanism

Enzyme-catalyzed DNA integration mechanism with integrase.

An ‘integration’ mechanism that models site-specific recombination catalyzed by integrase enzymes. The mechanism explicitly includes the integrase as a catalyst that facilitates DNA recombination but is not consumed in the reaction. This mechanism uses tetrameric integrase complexes (4 integrase molecules) to catalyze the integration.

The integration reaction is given by

\[4*{\text{Int}} + {\text{DNA1}} + {\text{DNA2}} \rightarrow 4*{\text{Int}} + {\text{DNA3}} + {\text{DNA4}} \]

where Int is the integrase enzyme, DNA1 and DNA2 are input DNA molecules, and DNA3 and DNA4 are the recombined product DNA molecules.

Parameters:

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

  • mechanism_type (str, default 'integration') – Type classification of this mechanism.

  • integrase (str, default 'Int1') – Name of the integrase enzyme. A Species with this name and material_type ‘protein’ is created automatically.

  • **kwargs – Additional keyword arguments (unused, maintained for API compatibility).

Attributes:

  • integrase (Species) – The integrase enzyme species with material_type ‘protein’.

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

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

See also

BasicIntegration

Integration without explicit enzyme.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models site-specific recombination with explicit integrase involvement. The integrase acts as a true catalyst, appearing on both sides of the reaction and not being consumed.

The mechanism uses 4 integrase molecules to model the tetrameric integrase complex typically formed during site-specific recombination (e.g., lambda phage integration, Cre-loxP recombination). This reflects the biological reality where integrase monomers form tetramers to catalyze strand exchange.

Common applications include:

  • Lambda phage integration/excision systems

  • Cre-loxP recombination

  • FLP-FRT site-specific recombination

  • Detailed models of integrase-mediated genome editing

Required parameters for this mechanism:

  • ‘kint’ : Integration rate constant

The stoichiometry of 4 integrase molecules reflects biological integrase mechanisms where a tetramer is the active form. The mechanism does not generate intermediate complexes (returns empty list from update_species).

Examples

See ‘Specialized_Tutorials/Integrase_Examples’.

Methods

update_reactions

Generate integration reaction with integrase enzyme.

update_species

Generate species for enzyme integration.
update_reactions(DNA_inputs, DNA_outputs, component=None, part_id=None, kint=None, **kwargs)[source]

Generate integration reaction with integrase enzyme.

Creates a single irreversible mass-action reaction for enzymatic DNA integration with tetrameric integrase complex.

Parameters:

  • DNA_inputs (list of Species) – List of input DNA species to be integrated (typically 2).

  • DNA_outputs (list of Species) – List of output DNA species after integration (typically 2).

  • component (Component, optional) – Component containing parameter values. Required if kint is not provided directly.

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

  • kint (Parameter or float, optional) – Integration rate constant. If None, retrieved from component parameters.

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

Returns:

List containing a single irreversible mass-action reaction: 4*integrase + DNA_inputs \(\rightarrow\) 4*integrase + DNA_outputs.

Return type:

list of Reaction

Raises:

ValueError – If component is None and kint is not provided.

Notes

The reaction includes 4 integrase molecules on both sides, modeling the tetrameric integrase complex required for site-specific recombination. The integrase is not consumed (acts as a true catalyst).

The stoichiometry reflects biological mechanisms like:

  • Lambda integrase (Int) tetramer formation

  • Cre recombinase synaptic complex

  • Other integrase family enzymes requiring multimers

update_species(DNA_inputs, DNA_outputs=None, **kwargs)[source]

Generate species for enzyme integration.

This method returns an empty list as enzyme integration does not create intermediate species or complexes in this implementation.

Parameters:

  • DNA_inputs (list of Species) – List of input DNA species to be integrated.

  • DNA_outputs (list of Species, optional) – List of output DNA species after integration. Not used in species generation.

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

Returns:

Empty list (no new species generated).

Return type:

list

Notes

This mechanism does not generate intermediate integrase-DNA complexes. The integrase-DNA binding and tetramerization steps are implicitly captured in the overall rate constant ‘kint’. For more detailed mechanistic models, consider using explicit binding mechanisms before integration.