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Amino acid insertions and deletions (indels) can surprisingly increase protein stability. Computational analysis reveals these mutations often have local effects and are better predicted by energy functions than inverse folding models.

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Area of Science:

  • Protein biochemistry
  • Computational biology
  • Structural biology

Background:

  • Amino acid insertions and deletions (indels) are common mutations affecting protein structure.
  • Understanding how indels influence protein folding stability is crucial for protein engineering.

Purpose of the Study:

  • To computationally analyze the structural and energetic impacts of stabilizing indel mutations.
  • To evaluate the predictive capabilities of different computational models for indel effects on protein stability.

Main Methods:

  • Analysis of 103 experimentally identified stabilizing single amino acid indel mutants.
  • Utilized computational modeling to assess structural and energetic changes.
  • Compared predictions from Rosetta energy function and an inverse folding (ESM-IF) model.

Main Results:

  • Stabilizing indels typically cause localized structural changes.
  • Stabilizing deletions, more than insertions, are often located in strained backbone regions.
  • The Rosetta energy function accurately classifies stabilizing indels, while ESM-IF does not.

Conclusions:

  • Backbone energetics play a significant role in the stabilizing effects of indels.
  • Computational models focusing on explicit backbone energetics are more effective for predicting stabilizing indel mutations.
  • Findings can inform new strategies for protein engineering and stability enhancement.