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Related Experiment Videos

Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models

G Luthardt1, C Frömmel

  • 1Institute of Biochemistry, Medical Faculty of Humboldt University (Charite), Berlin, Germany.

Protein Engineering
|May 1, 1994
PubMed
Summary

Evaluating protein structures is key in protein design. Analyzing atomic water contact and polarity offers a powerful new method to identify misfolded protein structures, improving accuracy in protein design and experimental structure assessment.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Accurate evaluation of protein structures is crucial for the protein design cycle.
  • Existing methods include analyzing surface area, electrostatic interactions, atomic packing, and charge distribution.
  • Identifying misfolded proteins is essential for reliable downstream applications.

Purpose of the Study:

  • To introduce a novel method for evaluating protein structure accuracy.
  • To assess the utility of analyzing atomic water contact and polarity for detecting misfolded proteins.
  • To establish reference values for the polar fraction in globular proteins.

Main Methods:

  • Analyzing the water contact of atoms and their polarity.
  • Calculating reference values for the polar fraction using moving windows (3-99 residues) over amino acid sequences of known globular proteins.

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  • Applying the method to model, deliberately misfolded, hypothetical, and predicted protein structures.

    • Main Results:

    • A powerful test for protein structure accuracy was derived from water contact and polarity analysis.
    • Reference values for the polar fraction of globular proteins were estimated (mean, SD, distribution).
    • Misfolded proteins were identified, with a common fault being the burial of polar groups in the protein interior.

    Conclusions:

    • Analyzing atomic water contact and polarity significantly improves the evaluation of protein structure accuracy.
    • This method effectively diagnoses misfolded proteins, including designed, hypothetical, and experimentally determined structures.
    • The approach is valuable for screening designed proteins and assessing errors in experimentally determined structures.