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create customizable PURE mixture
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‎biocrnpyler/mixtures/pure.py‎

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from ..core.mixture import Mixture
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from ..mechanisms.binding import One_Step_Binding
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from ..mechanisms.enzyme import MichaelisMenten
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from ..mechanisms.txtl import Energy_Transcription_MM, Energy_Translation_MM
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from ..mechanisms.txtl import (
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Energy_Transcription_MM,
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Energy_Translation_MM,
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SimpleTranscription,
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SimpleTranslation,
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Transcription_MM,
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Translation_MM,
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)
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class PURE(Mixture):
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"""PURE cell-free protein synthesis system with customizable mechanisms.
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A mixture that models the PURE (Protein synthesis Using Recombinant
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Elements) reconstituted cell-free transcription-translation system with
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customizable mechanisms.
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Parameters
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----------
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name : str, default='PURE'
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Name identifier for the mixture.
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include_machinery : bool, default=True
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Include components and mechanisms for RNAP and ribosomes.
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include_resources : bool, default=True
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Include components and mechanisms for NTP and amino acid utilization.
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Requires `include_machinery` to be true.
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include_fuel : bool, default=True
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Include fuel component and energy utilization mechanism. Requires that
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`include_machinery` and `include_resources` be True.
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rnap : str, default='RNAP'
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Name for the RNA polymerase protein species.
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ribosome : str, default='Ribo'
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Name for the ribosome protein species.
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ntps : str, default='NTPs'
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Name for the nucleotide triphosphate species (lumped NTPs excluding
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ATP).
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ndps : str, default='NDPs'
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Name for the nucleotide diphosphate species (lumped NDPs).
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amino_acids : str, default='AAs'
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Name for the amino acid species (lumped amino acids).
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fuel : str, default='ATP'
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Name for the primary energy carrier species (ATP).
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parameter_file : str, default='mixtures/pure_parameters.tsv'
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Path to file containing default parameter values for the PURE
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system.
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**kwargs
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Additional keyword arguments passed to the parent Mixture class.
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Attributes
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----------
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rnap : Protein
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RNA polymerase component.
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ribosome : Protein
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Ribosome component.
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ntps : Metabolite
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Nucleotide triphosphate metabolite component (excluding ATP).
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amino_acids : Metabolite
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Amino acid metabolite component.
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fuel : Metabolite
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Fuel metabolite component (ATP).
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name : str
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Name of the mixture.
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See Also
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--------
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EnergyTxTlExtract : TX-TL with fuel regeneration.
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TxTlExtract : TX-TL with machinery but no energy.
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Energy_Transcription_MM : Mechanism for energy-consuming transcription.
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Energy_Translation_MM : Mechanism for energy-consuming translation.
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Mixture : Base class for all mixtures.
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Notes
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-----
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This mixture automatically adds the following components:
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- RNA polymerase (RNAP)
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- Ribosome
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- Amino acids (lumped)
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- NTPs (nucleotide triphosphates excluding ATP, lumped)
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- NDPs (nucleotide diphosphates, lumped)
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- Fuel (ATP for energy)
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Default mechanisms included:
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- 'transcription' : `Energy_Transcription_MM` - Michaelis-Menten
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transcription with length-dependent ATP and NTP consumption
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- 'translation' : `Energy_Translation_MM` - Michaelis-Menten translation
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with length-dependent amino acid and ATP consumption
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- 'catalysis' : `MichaelisMenten` - General Michaelis-Menten enzyme
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catalysis for user-defined enzymatic reactions
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- 'binding' : `One_Step_Binding` - Simple multi-species binding for
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forming complexes
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Key features of this mixture:
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- Explicit modeling of PURE system components
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- Length-dependent energy consumption (realistic stoichiometry)
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- No fuel regeneration mechanisms (finite resource pool)
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- Resource competition effects (genes compete for RNAP and ribosomes)
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- Resource depletion dynamics (ATP, NTPs, amino acids deplete)
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- Enzyme sequestration in complexes
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- Separate tracking of ATP vs other NTPs
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- Suitable for modeling batch-mode PURE reactions
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Energy model details:
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- Transcription: Consumes L NTPs and L ATPs per mRNA of length L
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- Translation: Consumes L amino acids and 4L ATPs per protein of length
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L (4 ATPs per amino acid reflect GTP hydrolysis during elongation)
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- No regeneration: ATP, NTPs, and amino acids are consumed but not
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regenerated
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- Energy depletion: Expression stops when resources are exhausted
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- Length parameter L: Represents gene/protein length in appropriate
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units
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- Lumped species: Different nucleotides lumped into NTPs, different
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amino acids lumped into single species
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- Separate ATP: ATP tracked separately from other NTPs for independent
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energy accounting
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Differences from `EnergyTxTlExtract`:
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- No fuel regeneration pathway (no NTP regeneration from 3PGA or other
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fuel sources)
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- ATP modeled as separate fuel species rather than included in NTPs
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- Default parameter file points to PURE-specific parameters
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- Intended for modeling finite-resource batch reactions
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- More realistic for in vitro PURE systems
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Common applications include:
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- PURE cell-free TX-TL systems
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- Resource-limited gene expression modeling
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- TX-TL system optimization with fixed resource budgets
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- Batch mode TX-TL reactions
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- Energy budget and resource allocation studies
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- Multi-gene expression burden analysis
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- In vitro synthetic biology applications
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Examples
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--------
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Create a PURE mixture for GFP expression:
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>>> gfp_gene = bcp.DNAassembly(
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... name='gfp_construct',
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... promoter='pconst',
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... rbs='bcd2',
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... transcript='gfp_mrna',
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... protein='GFP'
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... )
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>>> mixture = bcp.BasicPURE(
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... name='pure_mixture',
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... components=[gfp_gene],
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... parameter_file='mixtures/pure_parameters.tsv'
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... )
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>>> crn = mixture.compile_crn()
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"""
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def __init__(
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self,
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include_machinery=True,
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include_resources=True,
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include_fuel=True,
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name='PURE',
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rnap='RNAP',
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ribosome='Ribo',
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ntps='NTPs',
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ndps='NDPs',
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amino_acids='AAs',
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fuel='ATP',
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parameter_file='mixtures/pure_parameters.tsv',
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**kwargs,
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):
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Mixture.__init__(
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self, name=name, parameter_file=parameter_file, **kwargs
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)
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# Start with basic mechansims for transcription and translation
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default_mechanisms = {
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'transcription': SimpleTranscription(),
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'translation': SimpleTranslation(),
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}
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if include_fuel:
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if not include_resources:
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raise ValueError("include_fuel requires include_resources")
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self.fuel = Metabolite(fuel)
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self.add_components([self.fuel])
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else:
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self.fuel = None
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if include_machinery:
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self.rnap = Protein(rnap)
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self.ribosome = Protein(ribosome)
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self.add_components([self.rnap, self.ribosome])
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default_mechanisms |= {
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'transcription': Transcription_MM(rnap=self.rnap.species),
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'translation': Translation_MM(ribosome=self.ribosome.species),
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}
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if include_resources:
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if not include_machinery:
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raise ValueError(
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"include_resources requires include_machinery"
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)
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# create default Components to represent cellular machinery
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self.ntps = Metabolite(ntps)
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self.amino_acids = Metabolite(amino_acids)
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self.add_components([self.amino_acids, self.ntps])
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# Create default TX-TL Mechanisms
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default_mechanisms['transcription'] = Energy_Transcription_MM(
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rnap=self.rnap.get_species(),
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fuels=[self.ntps.get_species()],
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wastes=[],
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)
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if include_fuel:
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default_mechanisms['translation'] = Energy_Translation_MM(
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ribosome=self.ribosome.get_species(),
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fuels=4 * [self.fuel.get_species()]
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+ [self.amino_acids.get_species()],
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wastes=[],
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)
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else:
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default_mechanisms['translation'] = Energy_Translation_MM(
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ribosome=self.ribosome.get_species(),
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fuels=[self.amino_acids.get_species()],
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wastes=[],
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)
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self.add_mechanisms(mechanisms=default_mechanisms, overwrite=False)
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class BasicPURE(Mixture):
@@ -176,45 +407,12 @@ def __init__(
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parameter_file='mixtures/pure_parameters.tsv',
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**kwargs,
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):
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Mixture.__init__(
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self, name=name, parameter_file=parameter_file, **kwargs
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)
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# create default Components to represent cellular machinery
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self.rnap = Protein(rnap)
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self.ribosome = Protein(ribosome)
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self.ntps = Metabolite(ntps)
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self.amino_acids = Metabolite(amino_acids)
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self.fuel = Metabolite(fuel)
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default_components = [
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self.rnap,
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self.ribosome,
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self.amino_acids,
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self.ntps,
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self.fuel,
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]
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self.add_components(default_components)
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# Create default TX-TL Mechanisms
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mech_tx = Energy_Transcription_MM(
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rnap=self.rnap.get_species(),
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fuels=[self.ntps.get_species()],
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wastes=[],
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)
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mech_tl = Energy_Translation_MM(
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ribosome=self.ribosome.get_species(),
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fuels=4 * [self.fuel.get_species()]
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+ [self.amino_acids.get_species()],
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wastes=[],
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PURE.__init__(
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self,
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name=name,
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parameter_file=parameter_file,
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include_machinery=True,
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include_resources=True,
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include_fuel=True,
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**kwargs,
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)
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mech_cat = MichaelisMenten()
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mech_bind = One_Step_Binding()
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default_mechanisms = {
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mech_tx.mechanism_type: mech_tx,
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mech_tl.mechanism_type: mech_tl,
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mech_cat.mechanism_type: mech_cat,
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mech_bind.mechanism_type: mech_bind,
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}
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self.add_mechanisms(default_mechanisms, overwrite=None)

‎biocrnpyler/mixtures/pure_parameters.tsv‎

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@@ -39,6 +39,12 @@ initial concentration ATP 1000 uM [ATP/GTP] - [CTP/UTP]
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initial concentration NTPs 4000 uM [CTP/UTP] * 4 (NTPs)
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initial concentration AAs 6000 uM 0.3 mM (upper bound) * 20 AAs
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transcription_mm kb 4.48 /uM/sec txtlsim S3: pol_{Flac}
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transcription_mm ku 2.5E-06 /sec default_parameters.txt; source unclear (TODO)
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translation_mm kb 0.819 /uM/sec Singhal et al. Table S2
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translation_mm ku 0.003 /sec Singhal et al. Table S2
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energy_transcription_mm ktx 50 /sec 50 nt/s (rate will be divided by length)
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energy_transcription_mm kb 4.48 /uM/sec txtlsim S3: pol_{Flac}
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energy_transcription_mm ku 2.5E-06 /sec default_parameters.txt; source unclear (TODO)

‎docs/_autogen_mixtures.rst‎

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@@ -49,5 +49,6 @@ Pure
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:nosignatures:
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:recursive:
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PURE
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BasicPURE
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