Knotted Proteins Lab Report

1.3 Identifying Knotted Proteins
The complexity of protein folding makes it very challenging to fully understand the folding mechanism of proteins. More complex yet interesting challenges have been proposed. One of the most interesting challenges is the protein with knotted topology.(9-12) Knot is very common in our daily life. Sometimes we hate the knot and need to untie it. For example, our earphone cable often gets knotted and it takes forever to untie it. But, more often, we need the knot, for example, a tie knot or shoelace. It also requires some effort to tie a knot. Similarly, as the protein is a polypeptide chain, it is, in principle, possible to form a knot. However, most proteins favor simple topology as they need to fold efficiently …show more content…
Sułkowska et al have proposed a possible folding mechanism for YbeA using molecular dynamics simulations based on a simple coarse-grained model.(96) As shown in Figure 1.10, there are five key steps in the folding pathway. In the first step, by crossing two parts of itself, the polypeptide chain forms a loop, which is the knotting loop. In the second step one end of the chain is bent towards the knotting loop to form a hook. Instead of plugging the terminus of the hook into the knotting loop, which would raise a substantial energy barrier, the middle of the hook is then threaded into the knotting loop and a slipknot is formed as shown in Figure 1.13. The threaded loop is then further passing through the knotting loop. The trefoil knot forms when the terminus of the threaded loop completely passed through the knotting loop. Molecular dynamics simulations revealed that through the pathway with slipknotted intermediate, it greatly reduced the energy barrier when compared with plugging the terminus through the knotting