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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
A hierarchical order within protein structures underlies large separations between strands in β-sheets
1Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
Proteins
|August 31, 2012
Summary
Protein beta-sheet formation relies on local sequence or spatial proximity, not hidden sequence signals. Nonlocal strands fold into compact modules, guiding assembly through hierarchical structures and antiparallel models.
Area of Science:
- Protein structure and folding
- Biophysics
- Molecular biology
Background:
- Protein beta-sheets can involve distant amino acid residues (nonlocal interactions).
- Previous studies on small beta-sheets indicated formation is not dictated by primary sequence signals.
- Intervening residues in small beta-sheets fold into compact modules, bringing distant chain parts together.
Purpose of the Study:
- To investigate if the principle of nonlocal beta-sheet formation applies to larger structures.
- To analyze the structural organization of intervening regions in larger beta-sheets.
- To determine if sequence-specific signals direct long-range interactions in beta-sheet assembly.
Main Methods:
- Analysis of beta-sheets within a nonredundant protein dataset.
- Examination of the intervening structures between nonlocal beta-strands.
- Investigation of residues involved in nonlocal cross-strand interactions.
Main Results:
- A hierarchical relationship exists in the intervening structure between nonlocal beta-strands.
- Most beta-sheets utilize an antiparallel model for managing nonlocal interactions.
- No evidence of sequence-specific signals directing long-range interactions was found.
Conclusions:
- Beta-sheet formation is governed by local sequence or spatial proximity established by prior folding events.
- The principle observed in small beta-sheets is extensible to larger and more complex structures.
- Nonlocal interactions in beta-sheets are managed through structural organization rather than hidden sequence cues.
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