The European Physical Journal Special Topics

, Volume 223, Issue 9, pp 1805–1812 | Cite as

Translocation of knotted proteins through a pore

  • P. SzymczakEmail author
Regular Article
Part of the following topical collections:
  1. Soft Matter in Confinement: Systems from Biology to Physics


We report the results of molecular dynamics simulations of translocation of knotted proteins through pores. The protein is pulled into the pore with a constant force, which in many cases leads to the tightening of the knot. Since the radius of tightened knot is larger than that of the pore opening, the tight knot can block the pore thus preventing further translocation of the chain. Analyzing six different proteins, we show that the stuck probability increases with the applied force and that final positions of the tightened knot along the protein backbone are not random but are usually associated with sharp turns in the polypeptide chain. The combined effect of the confining geometry of the pore and the inhomogeneous character of the protein chain leads thus to the appearance of topological traps, which can immobilize the knot and lead to the jamming of the pore.


European Physical Journal Special Topic Protein Backbone Brownian Dynamic Sharp Turn Stick Probability 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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© EDP Sciences and Springer 2014

Authors and Affiliations

  1. 1.Institute of Theoretical Physics, Faculty of PhysicsUniversity of WarsawWarsawPoland

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