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Intrinsic disorder accelerates dissociation rather than association.

Koji Umezawa1, Jun Ohnuki1, Junichi Higo2

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Intrinsically disordered proteins (IDPs) rapidly switch signals by dissociating from targets. Increased disorder enhances dissociation more than association, aiding cellular signaling.

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Langevin dynamicscapture radiuscoarse-grained modelcoupled folding and bindingflexibilityfly-casting mechanismmolecular dynamics simulationphosphorylationsignaling

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Intrinsically disordered proteins (IDPs) lack stable 3D structures.
  • IDPs are crucial in signal transduction, requiring rapid binding and unbinding.
  • Fast association mechanisms (e.g., fly-casting) are well-studied, but dissociation is less understood.

Purpose of the Study:

  • To investigate how intrinsic disorder affects protein-protein interaction kinetics.
  • To analyze the impact of disorder on both association and dissociation rates.
  • To explore the role of binding site interaction strength ('fly lure') in IDP dynamics.

Main Methods:

  • Coarse-grained molecular dynamics simulations.
  • Utilized the pKID-KIX intrinsically disordered protein system.
  • Varied disorder-inducing flexibility and binding site interaction strength.

Main Results:

  • Increased disorder marginally enhanced association rates, but this effect diminished with weaker binding.
  • Dissociation rates significantly increased with higher levels of intrinsic disorder.
  • Intrinsic disorder primarily facilitates rapid signal switching through enhanced dissociation.

Conclusions:

  • Intrinsic disorder is a key factor in rapid signal switching.
  • Enhanced dissociation kinetics, driven by disorder, is more critical for signal switching than association.
  • The interplay between disorder and binding site affinity modulates interaction dynamics.