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Sequence dependence of the binding energy in chaperone-driven polymer translocation through a nanopore

Abdolvahab, R. H ; Sharif University of Technology | 2011

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  1. Type of Document: Article
  2. DOI: 10.1103/PhysRevE.83.011902
  3. Publisher: 2011
  4. Abstract:
  5. We study the translocation of stiff polymers through a nanopore, driven by the chemical-potential gradient exerted by binding proteins (chaperones) on the trans side of the pore. Bound chaperones prevent backsliding through the pore and, therefore, partially rectify the polymer passage. We show that the sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics. In particular, we investigate the effect of the nearest-neighbor adjacency probability of the two monomer types. Depending on the magnitude of the involved binding energies, the translocation speed may either increase or decrease with the adjacency probability. We determine the mean first passage time and show that, by tuning the effective binding energy, the motion changes continuously from purely diffusive to ballistic translocation
  6. Keywords:
  7. Binding affinities ; Binding proteins ; Mean first passage time ; Monomer types ; Nearest-neighbors ; Polymer translocation ; Potential gradients ; Stiff polymers ; Trans side ; Translocation dynamics ; Monomers ; Nanopores ; Nuclear energy ; Polymers ; Potential energy ; Binding energy
  8. Source: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 83, Issue 1 , January , 2011 ; 15393755 (ISSN)
  9. URL: http://journals.aps.org/pre/abstract/10.1103/PhysRevE.83.011902