Pierced Lasso Bundles Are a New Class of Knot-like Motifs
Figure 1
The topology of covalently linked loops in proteins.
Closed loops occur in proteins under oxidizing conditions when two cysteines are close enough in space to form a disulphide bridge. The size of the loop depends on the sequence separation between the cysteines forming the closed loop. The simplest knot in mathematics is called a “zero knot” (a closed circle). This occurs in proteins under oxidizing conditions when the N- and C-terminal residues are cysteines. In this case a complete circle will be formed by the polypeptide backbone. When the two cysteines are positioned in the middle of the sequence a so-called “cinch” is formed leaving the two terminals open. When one of the terminal residues is a cysteine a lasso like structure is formed. If there are any parts of the polypeptide chain piercing the covalent loop a pierced lasso is formed. The pierced lasso is colored blue in this figure. The white fragment demonstrates the threaded polypeptide chain and the red part is the terminal in front of the covalent loop.