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Comment on "Main role of fractal-like nature of conformational space in subdiffusion in proteins"

Thomas Neusius1, Igor M Sokolov2, Jeremy C Smith3

  • 1RheinMain University of Applied Sciences, Wiesbaden Business School, Bleichstraße 44, D-65183 Wiesbaden, Germany.

Physical Review. E
|June 19, 2025
PubMed

Insights

Maggi and Orozco suggest protein dynamics in simulations follow a fractal random walk. However, their reasoning is flawed, despite confirming previous findings on subdiffusional protein dynamics.

Area of Science:

  • Computational Physics
  • Biophysics
  • Protein Dynamics

Background:

  • Subdiffusional dynamics are frequently observed in molecular dynamics (MD) simulations of proteins.
  • Previous studies suggested a fractal random walk model for these dynamics.

Purpose of the Study:

  • To investigate the origin of subdiffusional dynamics in protein simulations.
  • To evaluate the validity of the fractal random walk model for protein dynamics.

Main Methods:

  • Analysis of molecular dynamics (MD) simulations of proteins.
  • Comparison with fractal random walk models.

Main Results:

  • The study by Maggi and Orozco confirms previous findings that a fractal random walk is an appropriate model for protein dynamics.
  • The authors identify flaws in the logical reasoning used by Maggi and Orozco to reach their conclusion.

Conclusions:

  • While the fractal random walk model may be appropriate, the specific argumentation presented by Maggi and Orozco is erroneous.
  • Further investigation into the theoretical underpinnings of protein dynamics in simulations is warranted.

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