Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Friday Abstracts

Mechanically Tightening a Protein Slipknot into a Trefoil Knot Hongbin Li 1,2 .

1 University of British Columbia, Vancouver, Canada, 2 Tianjin University, Tianjin, China. Knotted polypeptide chain is one of the most surprising topological features found in some proteins. How knotted proteins overcome the topological difficulty to fold into their native three dimensional structures proteins has become a challenging problem. It was suggested that a structure of slipknot could serve as an important intermediate state during the folding of knotted proteins. Here we use single molecule force spectroscopy (SMFS) as well as steered molecular dynamics (SMD) simulations to investigate the mechanism of transforming a slipknot protein AFV3-109 into a tightened trefoil knot by pulling. Our results show that by pulling the N- terminus and the threaded loop of AFV3-109, the protein can be unfolded via multiple pathways and the slipknot can be transformed into a tightened trefoil knot, which involves ~13 amino acid residues. SMD simulation results, which are consistent with our experimental findings, provide a detailed molecular mechanism of mechanical unfolding and knot tightening of AFV3-109. SMD simulations reveal that interactions between β-strands on the threading loop and knotting loop that are sheared during stretching provide high mechanical resistance in the process of forming the trefoil knot, i.e., pulling threaded loop through knotting loop.

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