Figure 2. The movement of knotted core during the translocation of the protein 1ns5 pulled into the pore by the N terminus with F = 2.2ε/Å (a) and with the force F = 1.4ε/Å by the C terminus (b).

The colors mark the two ends of the knot as they move along the chain. In (a) the knot gets tightened and blocks the pore, whereas in (b) - it slides off the chain. The insets of (a) show the conformations of the protein backbone at the beginning of the translocation and at jamming. The final position of the knot is between the aminoacids 119 and 134. Only a portion of a longer trajectory (up to trajectory is shown in panel (a), however no further changes in the knot position were observed beyond .