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Super folds, networks, and barriers
1Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712.
Proteins
|November 19, 2011
Summary
Protein sequence space contains "super-folds" and "super-networks" of connected sequences. Sequence barriers may disconnect protein structures, impacting evolution.
Area of Science:
- Computational biology
- Protein structure prediction
- Sequence-structure relationships
Background:
- Understanding protein folding is crucial for molecular biology.
- Exploring the vast sequence space is computationally challenging.
- Previous studies suggest complex relationships between protein sequences and structures.
Purpose of the Study:
- To exhaustively enumerate sequences and folds in a simple lattice model.
- To investigate the connectivity and organization of foldable sequences.
- To identify potential barriers within protein sequence space.
Main Methods:
- Exhaustive enumeration of sequences and folds in a lattice model.
- Analysis of nearest connected neighbors (point mutations) in sequence space.
- Examination of sequence networks and their relationship to protein structures.
Main Results:
- Identification of numerous sequences folding into few structures (super-folds).
- Discovery of large, interconnected sequence networks (super-networks) spanning multiple folds.
- Observation of sequence barriers preventing direct mutation pathways between some foldable sequences.
Conclusions:
- Protein sequence space is characterized by super-folds and super-networks.
- Sequence barriers suggest potential disconnectedness within sequence space.
- These findings have implications for understanding protein structure evolution and stability.
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