Mathematically, a knot is defined as a subset of a three-dimensional points homeomorphic to a circle. 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.
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.
Web servers to extrapolate knotted proteins
- Cromwell, P. D. (2004). Knots and Links. Cambridge: Cambridge University Press.
- 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.
- 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.