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Updated: Jun 27, 2026
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OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
Published on: February 5, 2020
Exploring knotting mechanisms in protein folding.
Anna L Mallam1, Elizabeth R Morris, Sophie E Jackson
1University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England.
Summary
Protein knots are complex topological structures. This study reveals YibK protein folding involves late-stage knot formation and suggests knotting, not proline isomerization, causes denatured state heterogeneity.
Area of Science:
- Biochemistry
- Structural Biology
- Protein Folding Dynamics
Background:
- Proteins can form complex topological knots, posing challenges to understanding protein folding.
- The YibK protein features a deep trefoil knot, making it a model for studying knotted protein folding.
Purpose of the Study:
- To investigate the folding mechanism of the YibK protein, focusing on its knotted region.
- To elucidate the role of the knot in protein folding kinetics and denatured state heterogeneity.
Main Methods:
- Site-directed mutagenesis of the YibK knotted region.
- Analysis of protein folding kinetics and intermediate states.
- Investigating denatured state heterogeneity.
Main Results:
- The native structure in the YibK knot forms late in the folding process.
- Mutations in the knot affect late folding intermediates and dimerization kinetics.
- Denatured state heterogeneity may arise from the knotting mechanism itself.
Conclusions:
- YibK folding involves sequential events: polypeptide threading and native knot formation.
- The knotting mechanism, rather than proline isomerization, likely explains denatured state heterogeneity.
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