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Updated: Jul 11, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Systematic circular permutation of an entire protein reveals essential folding elements
M Iwakura1, T Nakamura, C Yamane
1National Institute of Bioscience and Human Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. iwakura@nibh.go.jp
Researchers identified "folding elements" by breaking protein backbones, revealing key regions for protein folding. These elements are crucial for understanding protein stability and function.
Area of Science:
- Protein biochemistry
- Structural biology
- Molecular dynamics
Background:
- Protein chain connectivity is vital for function and stability.
- Understanding the protein folding problem remains a significant challenge in biochemistry.
Purpose of the Study:
- To investigate chain connectivity's role in protein folding.
- To introduce and define the concept of 'folding elements'.
Main Methods:
- Systematic circular permutation analysis was employed.
- The peptide backbone of dihydrofolate reductase was sequentially cleaved between residues.
Main Results:
- Specific cleavage sites were identified, leading to a loss of protein folding ability.
- These sites were termed 'folding elements'.
- Folding element locations did not correlate with secondary structures, binding sites, or surface area, but did align with residues involved in early folding events.
Conclusions:
- Folding elements represent a novel concept for understanding protein folding.
- These elements are critical for initiating protein folding events and ensuring stability.
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