Joanna I. Sulkowska1, Piotr Sulkowski2, P. Szymczak3, M. Cieplak4 and J. Onuchic1
1Center for Theoretical Biological Physics, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093
2California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
3University of Warsaw, Hoza 69, 00-681 Warsaw, Poland
4Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
A shoelace can be readily united by pulling by its ends rather than by its loop. Attempting to untie a native slipknot  or knot  my results in an outcome which is much less unique since its intrinsic structure has non-uniform mechanical properties. We used structure based model to show that: 1 Stretching slipknots reveals a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of intermediate states in which the slipknot is jammed, and which correspond to so-called catch bonds. 2 Pulling knotted proteins by specific amino acids may cause retraction of a terminal segment of the backbone from the knotting loop and untangle the knot, as opposite to pulling by termini. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying.
 J. I. Sulkowska, P. Sulkowski, J. N. Onuchic, Phys. Rev. Lett. 103 (2009) 268103.
 J. I. Sulkowska, P. Sulkowski, P. Szymczak, M. Cieplak, JACS 132 (40) (2010) 13954.
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