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. Author manuscript; available in PMC: 2013 Jun 27.
Published in final edited form as: J Am Chem Soc. 2012 Jun 15;134(25):10428–10435. doi: 10.1021/ja3003205

Figure 4.

Figure 4

SMD simulations reveal two distinct mechanical unfolding pathways of AFV3-109. Scenario I corresponds to unfolding pathways involving an unfolding intermediate state, and scenario II corresponds to the two-state unfolding pathway. Along each step of the unfolding process, snapshots of AFV3-109 are shown (as indicated by snapshots 1, 2 and 3) to indicate the structural changes of AFV3-109 during the unfolding process. In both scenarios, the slipknot structure was untied and no tightened slipknot conformation observed. Interactions (specific or non-specific) between key structural elements are responsible for preventing the formation of the “tightened knot” structure. Such interactions, which are indicated in the schematic drawing of AFV3-109 beside the snapshots, prevent the shrinking of the knotting loop and help untie the slipknot. Red bars indicate specific interactions between strands β1 and β4, while green bars indicate the non-native interactions formed after the sliding of strands β1 and β4.