Economics of periodic enzyme activities

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Other example models (model files and simulation movies)

The following example models show that oscillations can improve enzyme efficiency in a number of ways:

  1. Adaption to periodic reactant levels If substrates and products of a reaction vary periodically, the enzyme becomes more efficient if it oscillates in phase with the varying enzyme efficiency.
  2. Periodic metabolite production If oscillations of a metabolite level are beneficial, enzymes that provoke such oscillations should oscillate in the right phase to make this happen.
  3. Correlated production Of oscillations of several metabolites in phase are beneficial (for instance, as substrates of one enzyme, which then becomes more efficient), the reactions producing these metabolites should tend to oscillate accordingly.
  4. Anti-correlated production If metabolites are supposed to oscillate out of phase (for instance, because one destroys the other), then the enzymes producing these metabolites should tend to oscillate accordingly.
  5. Waves of activation along a pathway If an enzyme level oscillates, the level of its reaction product will oscillate and peak later. This may create an incentive for the next enzyme to oscillate as well, with a positive phase shift. This can lead to damped waves of enzyme activation along the pathway.

Adaptive rhythms

  1. Single reaction Fast rhythm
  2. Cost coupling Fast rhythm
  3. Oxidation/reduction (allosteric) Expression rhythm / Fast rhythm

Spontaneous rhythms

  1. Concerted action model Expression rhythm / Fast rhythm
  2. Metabolic repressilator Expression rhythm / Fast rhythm
  3. Metabolic inducilator Expression rhythm / Fast rhythm
  4. DNA synthesis and ROS production Expression rhythm / Fast rhythm
  5. Oxidation/reduction (dynamic) Expression rhythm / Fast rhythm
  6. Oxidation/reduction (cell model) Expression rhythm / Fast rhythm

Yeast central carbon metabolism

  1. Glucose rhythm speedy responsive / adaptive
  2. Oxygen rhythm speedy responsive / adaptive
  3. ATP/ADP cofactor rhythm speedy responsive / adaptive