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A knot or not a knot? SETting the record 'straight' on proteins
William R Taylor1, Bing Xiao, Steven J Gamblin
1Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. wtaylor@nimr.mrc.ac.uk
Computational Biology and Chemistry
|June 12, 2003
Summary
A novel knot in the SET domain is not a true knot, but a pseudo-knot formed by hydrogen bonds. This finding distinguishes it from covalent crosslinks and threaded loops in protein structures.
Area of Science:
- Biochemistry
- Structural Biology
- Protein Folding
Background:
- The SET domain is a protein domain involved in various cellular processes.
- Understanding protein topology, including knotting, is crucial for comprehending protein function.
- Previous studies have explored protein knotting using different analytical methods.
Purpose of the Study:
- To analyze a novel knot identified in the SET domain.
- To determine if the observed knot in the SET domain backbone is a true knot.
- To classify the topological nature of the SET domain knot based on its structural features.
Main Methods:
- Analysis of five recent crystal structures of the SET domain.
- Application of Taylor's algorithm to assess the protein backbone topology.
- Comparison with known protein topological motifs like covalent crosslinks and threaded loops.
Main Results:
- The backbone chain of the SET domain does not form a true knot.
- A pseudo-knot structure is formed with only two hydrogen bonds acting as crosslinks.
- This pseudo-knotted structure is distinct from true knots, covalent crosslinks, and threaded loops.
Conclusions:
- The term "pseudo-knot" is introduced to describe hydrogen-bonded knots in protein structures.
- This classification helps differentiate between various topological states in proteins.
- The findings provide new insights into the structural diversity and classification of protein folds.