ecoli.processes.enzyme_kinetics

Convenience Kinetics

class ecoli.processes.enzyme_kinetics.EnzymeKinetics(parameters=None)

Bases: Process

Michaelis-Menten-style enzyme kinetics model

Parameters:

initial_parameters –

Configures the process with the following configuration options:

• reactions (dict): Specifies the stoichiometry, reversibility, and catalysts of each reaction to model. For a non-reversible reaction \(A + B \rightleftarrows 2C\) catalized by an enzyme \(E\), we have the following reaction specification:

  {
      # reaction1 is a reaction ID
      'reaction1': {
          'stoichiometry': {
              # 1 mol A is consumd per mol reaction
              ('internal', 'A'): -1,
              ('internal', 'B'): -1,
              # 2 mol C are produced per mol reaction
              ('internal', 'C'): 2,
          },
          'is reversible': False,
          'catalyzed by': [
              ('internal', 'E'),
          ],
      }
  }
  

  Note that for simplicity, we assumed all the molecules and enzymes were in the internal port, but this is not necessary.

• kinetic_parameters (dict): Specifies the kinetics of the reaction by providing \(k_{cat}\) and \(K_M\) parameters for each enzyme. For example, let’s say that for the reaction described above, \(k{cat} = 1\), \(K_A = 2\), and \(K_B = 3\). Then the reaction kinetics would be specified by:

  {
      'reaction1': {
          ('internal', 'E'): {
              'kcat_f': 1,  # kcat for forward reaction
              ('internal', 'A'): 2,
              ('internal', 'B'): 3,
          },
      },
  }
  

  If the reaction were reversible, we could have specified kcat_r as the \(k_{cat}\) of the reverse reaction.

defaults: dict[str, dict] = {'kinetic_parameters': {}, 'reactions': {}}

name = 'enzyme_kinetics'

next_update(timestep, states)

ports_schema()