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
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.
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.
- 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.