A knot or not a knot? SETting the record 'straight' on proteins

  • Authors:

  • William R Taylor;Bing Xiao;Steven J Gamblin;Kuang Lin

  • Affiliations:

  • Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK;Division of Protein Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK;Division of Protein Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK;Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK

  • Venue:
  • Computational Biology and Chemistry
  • Year:
  • 2003

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Abstract

A novel knot found in the SET domain is examined in the light of five recent crystal structures and their descriptions in the literature. Using the algorithm of Taylor it was established that the backbone chain does not form a true knot. However, only two crosslinks corresponding to hydrogen-bonds were needed to form a knotted structure. Such loosely knotted structures formed by hydrogen-bonded crosslinks were assessed as lying between covalent crosslinks (such as disulphide bonds) and threaded-loops which are formed by close (unbonded) contacts between different parts of the chain. The term pseudo-knot was introduced (from the RNA field) to distinguish hydrogen-bonded 'knots'.