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Anomalous diffusion in neutral evolution of model proteins.

Erik D Nelson1, Nick V Grishin1

  • 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Blvd., Room ND10.124, Dallas, Texas 75235-9050, USA.

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Summary

This study investigates protein evolution using polymer models, revealing that structural changes occur episodically and follow a power-law relationship with neutral mutations. This protein drift is more dispersed than in models maintaining a specific fold.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Science

Background:

  • Protein evolution studies often use simplified polymer models.
  • The impact of structural drift (diffusion) on protein evolution remains underexplored.
  • Existing models typically constrain polymer length and folded structure.

Purpose of the Study:

  • To investigate neutral evolution in small protein motifs.
  • To model structural drift in heteropolymers with changing length and structure.
  • To quantify structural changes during neutral evolution.

Main Methods:

  • Utilized an off-lattice heteropolymer model with low-resolution amino acid interactions.
  • Allowed for dynamic changes in polymer length and folded structure.
  • Computed mean-square distance (MSD) between monomers in homologous folds after neutral mutations.

Main Results:

  • Structural change in proteins is episodic, not continuous.
  • Protein structural drift exhibits a power-law dependence on the number of neutral mutations (n).
  • The exponent of this power-law is sensitive to sequence alignment methods.

Conclusions:

  • Neutral evolution can lead to significant protein structural drift.
  • The dynamics of protein evolution are influenced by the interplay between sequence and structure.
  • Understanding structural drift is crucial for a complete picture of protein evolution.