Knots in the studied conformers.

<p>The top left panel shows an example of a Q₆₀ conformation containing a trefoil (3₁) knot with the knot ends highlighted with yellow spheres. To its right, the same conformation has been partially stretched, and the region inside the knot is highlighted in red and zoomed in. The middle panels represent histograms of the knot end positions, <i>k</i>_±, for Q₆₀ (left) and V₆₀ (right). The bottom panel shows their corresponding extension, Δ<i>k</i>. The percentage of knotted structures relative to to the total number of independent conformers found for Q₆₀ and V₆₀ are (9.3 ± 1.8)% and (3.6 ± 0.5)%, respectively. Shallow knots have an extension closer to 60 (the system size). Protein representations have been done with VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004541#pcbi.1004541.ref048" target="_blank">48</a>].