Pierced Lasso Bundles Are a New Class of Knot-like Motifs
Figure 2
The unique topology of a Pierced Lasso Bundles (PLBs).
(A) The native structure of leptin (PDB code 1AX8 [79]). A disulphide bridge is located between residue C96 and the C-terminal cysteine (yellow), creating a covalent C-terminal loop (dark blue). Consequently, a helical hairpin of helix C and half of helix B (white), have to thread through the covalent loop to reach the native state. The N-terminal part stays in front of the covalent loop (red). Hence, the overall conformation of the protein creates a Pierced Lasso Bundle (PLB) topology [12]. (B) Four of the new PLBs that we discovered in the PDB plus three unthreaded four-helix bundles are shown in ribbon diagram format. These new PLB proteins have their covalent loop at the opposite end from leptin, creating an N-terminal lasso (light blue). The threaded element (white) is behind the loop from this view while the C-terminal end (red) is in front of the covalent loop. (C) A cartoon defining the elements of the different PLBs showing the PL in blue (dark blue for a C-terminal lasso and light blue for an N-terminal lasso). The threaded element, behind the covalent loop, is white and the terminal in front of the loop is red. The unthreaded foud-helix bundles are shown in white.