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A design principle for posttranslational chaotic oscillators.

Hiroto Q Yamaguchi1,2,3, Koji L Ode1,4, Hiroki R Ueda1,4

  • 1Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.

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|January 13, 2021
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This study reveals a design principle for autonomous chaos generation in cellular processes using reversible phosphorylation dynamics. Specific enzyme-substrate interactions create "chaos motifs" enabling complex behaviors in biochemical systems.

Keywords:
Biochemical MechanismBiophysicsEnzyme EngineeringMolecular Biology

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Enzymology

Background:

  • Chaos behavior is observed in cellular and molecular processes.
  • Understanding the design principles of chaos generation is crucial for comprehending cellular autonomy.

Purpose of the Study:

  • To model reversible phosphorylation dynamics and identify design principles for autonomous chaos generation.
  • To investigate chaos generation in generic enzymatic reactions using a standard reaction scheme.

Main Methods:

  • Modeled reversible phosphorylation dynamics of two substrates with two modification sites.
  • Conducted a comprehensive parameter search of kinase-phosphatase reactions.
  • Utilized clustering analysis to identify recurring parameter set structures (motifs).

Main Results:

  • Identified a reaction system exhibiting chaos behavior under Michaelis-Menten kinetics.
  • Discovered specific
  • chaos motifs
  • in parameter sets leading to chaos.
  • Demonstrated that these motifs enable substrate interaction via enzyme availability and differential timescales of phosphorylation dynamics.

Conclusions:

  • Chaos motifs represent a design principle for autonomous chaos generation in enzymatic reactions.
  • This mechanism suggests chaos behavior may be fundamental to cellular autonomy across various biochemical systems.