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Related Experiment Videos

Reassessing random-coil statistics in unfolded proteins.

Nicholas C Fitzkee1, George D Rose

  • 1T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.

Proceedings of the National Academy of Sciences of the United States of America
|August 18, 2004
PubMed
Summary

Proteins in denatured states can exhibit random coil statistics even with significant internal structure. This challenges the assumption that random coil behavior implies a completely featureless polymer.

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Area of Science:

  • Protein intrinsically disordered states
  • Polymer physics
  • Computational biophysics

Background:

  • The Gaussian-random coil model has long been the standard for denatured proteins.
  • This model implies proteins are featureless statistical coils in denaturing conditions.
  • Conflicting experimental data suggests denatured proteins may retain some conformational bias.

Purpose of the Study:

  • To investigate whether random coil statistics are exclusively indicative of featureless polymers.
  • To resolve the paradox between random coil behavior and observed conformational biases in denatured proteins.
  • To demonstrate that proteins with residual structure can still exhibit random coil characteristics.

Main Methods:

  • Generated disordered protein conformers by randomly altering backbone torsion angles for ~8% of residues.

Related Experiment Videos

  • Kept ~92% of residues fixed in their native conformations.
  • Used a torsion-angle Monte Carlo algorithm with hard-sphere sterics to create ensembles for 33 proteins.
  • Calculated bulk statistics, including end-to-end distances and radii of gyration.

    • Main Results:

    • Generated protein ensembles with significant internal structure still exhibited random coil characteristics.
    • End-to-end distances and radii of gyration agreed well with random coil expectations for most proteins studied.
    • This held true despite up to 8% of residues having randomized torsion angles.

    Conclusions:

    • Random coil statistics are not a unique signature of completely featureless polymers.
    • Proteins can display random coil behavior even when retaining substantial native structural elements.
    • The interpretation of random coil models for denatured proteins requires re-evaluation.