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Post-translational modifications (PTMs) act as molecular switches controlling biomolecular liquid-liquid phase separation (LLPS). Our model predicts how PTMs on intrinsically disordered proteins dictate LLPS, offering insights into cellular organization.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • Biomolecules undergo liquid-liquid phase separation (LLPS), forming membraneless organelles.
  • The role of post-translational modifications (PTMs) in LLPS biophysics is emerging.
  • Intrinsically disordered proteins (IDPs) are key players in LLPS.

Purpose of the Study:

  • To investigate the impact of PTMs on the phase behavior of IDPs in silico.
  • To develop and validate a coarse-grained model for PTMs in LLPS.
  • To determine how PTMs' number and position influence protein phase separation.

Main Methods:

  • Extended a transferable coarse-grained model for IDPs to include phosphorylated and acetylated amino acids.
  • Parameterized modified amino acid beads using fixed-charge atomistic force field data.
  • Analyzed the effect of PTMs on single-chain compactness and LLPS propensity.

Main Results:

  • Both the number and position of phosphorylated or acetylated residues act as on/off switches for LLPS.
  • The model accurately predicts experimentally observed phase behavior differences for position-specific modifications.
  • PTM position is a critical determinant of phase separation in FUS and DDX3X disordered regions.

Conclusions:

  • The developed model effectively simulates LLPS of PTM-modified IDPs.
  • PTMs, particularly their position, play a crucial role in regulating LLPS.
  • This model aids in predicting how PTMs control phase behavior with position-specific resolution.