Fig. 2.

Cartoon representation of the native structure (top), reduced backbone representation obtained with the Taylor smoothing algorithm highlighting a open knot (middle) and corresponding topological knot (bottom) of proteins YibK (PDB ID: 1j85) (a), acetohydroxy acid isomeroreductase (PDB ID: 1yve) (b), and UCH-L3 (PDB ID: 1xd3) (c). The trefoil (or 3₁), figure-eight (or 4₁) and penta (or 5₂) knots exhibit three, four and five crossings on a planar projection. The subscript 1 in 3₁ (4₁) stands for first knot with three (four) crossings and subscript 2 in 5₂ stands for second knot with five crossings, according to standard knot tables The coordinates of the reduced representations were retrieved from http://knots.mit.edu/ and visualized with PyMol (The PyMOL Molecular Graphics System, Open-Source 1.5.x). The topological representations were produced with knotplot (http://www.knotplot.com/).