Intricate Knots in Proteins: Function and Evolution
Figure 1
Examples of the Three Different Types of Knots Found in Proteins
Colors change continuously from red (first residue) to blue (last residue). A reduced representation of the structure, based on the algorithm described in [1,6,36], is shown in the lower row.
(Left) The trefoil knot (31) in the YBEA methyltransferase from E. coli (pdb code 1ns5; unpublished data) reveals three essential crossings in a projection onto a plane.
(Middle) The figure-eight knot (41) in the Class II ketol-acid reductoisomerase from Spinacia oleracea (pdb code 1yve [26]) features four crossings. (Only the knotted section of the protein is shown.)
(Right) The knot 52 in ubiquitin hydrolase UCH-L3 (pdb code 1xd3 [18]) reveals five crossings. Pictures were generated with Visual Molecular Dynamics (http://www.ks.uiuc.edu/Research/vmd) [43].