vivarium.library.kinetic_rate_laws module

Kinetic rate law generation using the Convenience Kinetics formulation of Michaelis-Menten kinetics

Formulation provided in:

Liebermeister, Wolfram, and Edda Klipp. “Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.” Theoretical Biology and Medical Modelling 3.1 (2006): 41.

# TODO – make a vmax options if enzyme kcats not available

class vivarium.library.kinetic_rate_laws.KineticFluxModel(all_reactions, kinetic_parameters)

Bases: object

A kinetic rate law class

Parameters

• all_reactions (dict) –

  all metabolic reactions, with: {reaction_id: {

  ’catalyzed by’: list, ‘is reversible’: bool, ‘stoichiometry’: dict, }}

• kinetic_parameters (dict) –

  a dictionary of parameters a nested format: {reaction_id: {

  enzyme_id{

  param_id: param_value}}}

rate_laws

a dict, with a key for each reaction id, and then subdictionaries with each reaction’s enzymes and their rate law function. These rate laws are used directly from within this dictionary

get_fluxes(concentrations_dict)

Use rate law functions to calculate flux

Parameters

concentrations_dict (dict) – all relevant molecules and their concentrations, in mmol/L. {molecule_id: concentration}

Returns

reaction_fluxes (dict) - with fluxes for all reactions

vivarium.library.kinetic_rate_laws.cofactor_denominator(concentration, km)

vivarium.library.kinetic_rate_laws.cofactor_numerator(concentration, km)

vivarium.library.kinetic_rate_laws.construct_convenience_rate_law(stoichiometry, enzyme, cofactors_sets, partition, parameters)

Make a convenience kinetics rate law for one enzyme

Parameters

• stoichiometry (dict) – the stoichiometry for the given reaction

• enzyme (str) – the current enzyme

• cofactors_sets – a list of lists with the required cofactors, grouped by [[cofactor set 1], [cofactor set 2]], each pair needs a kcat.

• partition – a list of lists. each sublist is the set of cofactors for a given partition. [[C1, C2],[C3, C4], [C5]]

• parameters (dict) – all the parameters with {parameter_id: value}

Returns

a kinetic rate law for the reaction, with arguments for concentrations and parameters, and returns flux.

vivarium.library.kinetic_rate_laws.get_molecules(reactions)

Get a list of all molecules used by reactions

Parameters

reaction (dict) – all reactions that will be used by transport

Returns

all molecules used by these reactions

Return type

self.molecule_ids (list)

vivarium.library.kinetic_rate_laws.make_configuration(reactions)

Make the rate law configuration, which tells the parameters where to be placed.

Parameters

reactions (dict) – all reactions that will be made into rate laws, in the same format as all_reactions (above).

Returns

includes partition and reaction_cofactor entries for each reaction

Return type

rate_law_configuration (dict)

vivarium.library.kinetic_rate_laws.make_rate_laws(reactions, rate_law_configuration, kinetic_parameters)

Make a rate law for each reaction

Parameters

• reactions (dict) – in the same format as all_reactions, described above

• rate_law_configuration (dict) –

  with an embedded structure: {enzyme_id: {

  ’reaction_cofactors’: {

  reaction_id: [cofactors list] }

  ’partition’: [partition list] }

  }

• kinetic_parameters (dict) –

  with an embedded structure: {reaction_id: {

  ’enzyme_id’: {

  parameter_id: value }

  }

  }

Returns

each reaction_id is a key and has sub-dictionary for each relevant enzyme,

with kinetic rate law functions as their values

Return type

rate_laws (dict)

vivarium.library.kinetic_rate_laws.test_kinetics()