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Related Experiment Videos

Excluded volume in protein side-chain packing.

E Kussell1, J Shimada, E I Shakhnovich

  • 1Department of Biophysics, Harvard University, 240 Longwood Ave., Boston, MA, 02115 USA.

Journal of Molecular Biology
|July 27, 2001
PubMed
Summary

Protein side-chain conformations are limited by excluded volume, but many allowed states remain. Even with native packing density, many non-native conformations exist, requiring other interactions to stabilize the native state.

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Area of Science:

  • Computational Biology
  • Protein Structure
  • Biophysics

Background:

  • Protein interiors require dense packing, limiting side-chain conformations.
  • Understanding side-chain flexibility is crucial for protein structure prediction.

Purpose of the Study:

  • To investigate the relationship between side-chain geometry and packing.
  • To quantify the impact of excluded volume on side-chain conformational space.

Main Methods:

  • All-atom Monte Carlo simulations were employed.
  • Umbrella sampling was used to explore conformational space.
  • Three excluded volume models were tested.

Main Results:

  • Excluded volume significantly reduces, but still leaves a large number of, possible side-chain conformations.

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  • Average repacked conformations show 20% non-native chi angles, well below the expected 67%.
  • Native packing density is maintained even with up to 50% non-native chi angles.

    • Conclusions:

    • Sequence-specific interactions can stabilize rare rotamers.
    • Excluded volume alone predicts a significant portion of native rotamers and angles.
    • Additional interactions are necessary to stabilize the native protein state.