Abstract
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.
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References
W.R. Taylor, K. Lin, Nature 421, 25 (2003)
P. Virnau, L. Mirny, M. Kardar, PLoS Comput. Biol. 2(9), e122 (2006)
D. Bölinger, J.I. Sułkowska, H.P. Hsu, L.A. Mirny, M. Kardar, J.N. Onuchic, P. Virnau, PLoS Comput. Biol. 6(4), e1000731 (2010)
R.C. Lua, A.Y. Grosberg, PLoS Comput. Biol. 2(5), e45 (2006)
T. Bornschlögl, D.M. Anstrom, E. Mey, J. Dzubiella, M. Rief, K.T. Forest, Biophys. J. 96, 1508 (2009)
P. Szymczak, Biochem. Soc. Trans. 41, 620 (2013)
A. Förster, C. Hill, Trends Cell. Biol. 13, 550 (2003)
P. Rehling, K. Brandner, N. Pfanner, Nat. Rev. Mol. Cell Biol. 5, 519 (2004)
N.N. Alder, S.M. Theg, Trends Biochem. Sci. 28, 442 (2003)
J. Sulkowska, P. Sulkowski, P. Szymczak, M. Cieplak, Phys. Rev. Lett. 100, 058106 (2008)
J. Dzubiella, Biophys. J. 96, 831 (2009)
M. Cieplak, T.X. Hoang, M.O. Robbins, Proteins: Struct. Funct. Bio. 56, 285 (2003)
J. Tsai, R. Taylor, C. Chotchia, M. Gerstein, J. Mol. Biol. 290, 253 (1999)
J.M. Deutsch, arXiv preprint [arXiv:1303.0453] (2013)
W.R. Taylor, Nature 406, 916 (2000)
M.J. Betts, R.B. Russell, in Bioinformatics for Geneticists, edited by M.R. Barnes, I.C. Fray (Wiley Publishers, 2003), p. 289
R. Metzler, W. Reisner, R. Riehn, R. Austin, J.O. Tegenfeldt, I.M. Sokolov, Europhys. Lett. 76, 696 (2006)
A. Rosa, M. Di Ventra, C. Micheletti, Phys. Rev. Lett. 109, 118301 (2012)
R. Matthews, A. Louis, J. Yeomans, Phys. Rev. Lett. 102, 088101 (2009)
D. Marenduzzo, E. Orlandini, A. Stasiak, L. Tubiana, C. Micheletti, et al., Proc. Natl. Acad. Sci. USA 106, 22269 (2009)
M.L. Mansfield, Nat. Struct. Mol. Biol. 1, 213 (1994)
L. Huang, D.E. Makarov, J. Chem. Phys. 129, 121107 (2008)
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Szymczak, P. Translocation of knotted proteins through a pore. Eur. Phys. J. Spec. Top. 223, 1805–1812 (2014). https://doi.org/10.1140/epjst/e2014-02227-6
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DOI: https://doi.org/10.1140/epjst/e2014-02227-6