title: Periodic forces trigger knot untying during translocation of knotted proteins.
abstract: Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character.
authors.affiliation: Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Szymczak
mesh_terms: D056004:Molecular Dynamics Simulation; D018272:Porins / Q000737:chemistry*; D021381:Protein Transport; D058767:Protein Unfolding; D013816:Thermodynamics
chemical_list: D018272:Porins