Knotted protein

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Mathematically, a knot is defined as a subset of a three-dimensional points homeomorphic to a circle.[1] According to this definition, a knot only makes sense in a closed loop. However, if we pick a point in space at infinite distance and connect it to the N and C termini through a virtual bond, the protein can be treated as a closed loop.

(A) A protein is an open chain. (B) To create a closed loop, we pick a point at an infinite distance, and connect it to the N and C termini, thus the whole topological structure becomes a closed loop.

Knotted proteins present one of the most challenging problems to both computational and experimental biologists. Despite an ever-increasing number of knotted proteins deposited in PDB, it is still not clear how a protein folds into a knotted conformation, or how a protein's knot is related to its function. Though a number of computational methods have been developed for detecting protein knots, there are still no completely automatic methods to detect protein knots without the necessary manual intervention due to the missing residues or chain breaks in the X-ray structures or the nonstandard PDB formats. At present, there are 4 types of knot identified in proteins: the 3-1 knot, the 4-1 knot, the 5-2 knot and the 6-1 knot.[citation needed]

Four knot types identified in proteins: the 3-1 knot (upper left), the 4-1 knot (upper right), the 5-2 knots (lower left) and the 6-1 knot (lower right). These images were produced by KnotPlot.[2] Note that the 3-1 knot has in fact two distinct forms: left-handed and right-handed. What is shown here is a right-handed 3-1 knot.

Web servers to extrapolate knotted proteins[edit]

Recently, a number of web servers were published, providing convenient query services for knotted structures and analysis tools for detecting protein knots.[3]


  1. ^ Cromwell, P. D. (2004). Knots and Links. Cambridge: Cambridge University Press. 
  2. ^ Robert, Scharein. "KnotPlot: Hypnagogic Software (Version 0.1)". Nearly all of the images here were created with KnotPlot, a fairly elaborate program to visualize and manipulate mathematical knots in three and four dimensions. 
  3. ^ Lai, Y.-L.; Yen, S.-C., Yu, S.-H., Hwang, J.-K. (7 May 2007). "pKNOT: the protein KNOT web server". Nucleic Acids Research 35 (Web Server): W420–W424. doi:10.1093/nar/gkm304. 

External links[edit]