1.5 Force-induced topological change of knotted/slipknotted protein
As mentioned earlier in this chapter, pulling on two ends of a protein is a simple way to test the existence of a knot. More importantly, the mechanism of pulling knotted/slipknotted proteins can provide useful insight on the formation of the knot/slipknot. Quite a few knotted/slipknotted proteins have been pulled in both experimental and computational studies.(103-110)
1.5.1 Tightening the knot
Upon being pulled on its two ends, a knotted protein will be unfolded and extended and the knot will be tightened. Steered molecular dynamics (SMD) simulation has been used to apply external force on certain atoms in specific pulling direction in silico, which is perfect for pulling the knotted proteins. Sułkowska et al have stretched 20 proteins with a knotted topology by SMD simulations using a coarse-grained model.(105) When a stretching force is applied onto the two ends of a knotted protein, the knot shrinks and one end of the knot move along the polypeptide chain with sudden jumps. This is quite different from the tightening of a homopolymer in which the knot
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Wang et al performed SMFS on a shallow trefoil knot protein, bovine carbonic anhydrase B, and stretched it to a tightened knot.(110) A figure-eightknotted protein, phytochrome, was stretched by Bornschlogl et al using SMFS based on atomic force microscopy (AFM) as well as SMD simulations.(106) The unfolding force of phytochrome was determined to be ~ 70 pN, which is not as high as many mechanically stable proteins such as I27 domain of human titin (~200 pN). In addition, both their experimental and simulation results revealed that the tightened figure-eight knot contains 17 to 19 amino acid residues as shown in Figure 1.11. Further discussion about the tightening of the knot can be found in chapter