# Chaperone-assisted translocation of a polymer through a nanopore.

@article{Yu2011ChaperoneassistedTO,
title={Chaperone-assisted translocation of a polymer through a nanopore.},
author={Wancheng Yu and Kaifu Luo},
journal={Journal of the American Chemical Society},
year={2011},
volume={133 34},
pages={
13565-70
}
}
• Published 2 August 2011
• Chemistry, Physics, Biology, Medicine
• Journal of the American Chemical Society
Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy ε between the chaperone and the chain and the chaperone concentration N(c) can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of…
46 Citations

## Figures and Topics from this paper

Polymer translocation through a nanopore in the presence of chaperones: A three dimensional MD simulation study
• Materials Science
• 2017
Abstract The chaperone assisted polymer translocation through a nanopore is studied using Langevin dynamics simulations in three dimensions. We investigate the effects of the polymer persistence
Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer
Abstract Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer
Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy
A minimum in translocation time versus binding effective energy (EBE) curve is found and, based on a theoretical discussion, one can truly predict the value of this minimum by taking into account the velocity dependency of the translocation on polymer length.
First passage time distribution of chaperone driven polymer translocation through a nanopore: homopolymer and heteropolymer cases.
• Materials Science, Medicine
The Journal of chemical physics
• 2011
It is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chapersone concentration, and the chainlength, is also effectively determined by the Péclet number.
Investigating binding particles distribution effects on polymer translocation through nanopore
Abstract Chaperone driven polymer translocation is an important model for biopolymer's translocation in vivo . Binding proteins spatial distribution is a significant factor in calculating the
Temperature dependence of the translocation time of polymer through repulsive nanopores.
• Materials Science, Medicine
The Journal of chemical physics
• 2017
Results show that polymer's conformation plays a much more important role than the diffusion coefficient in controlling the translocation time of the polymer chain.
Crowding-Induced DNA Translocation Through a Protein Nanopore.
• Chemistry, Medicine
Analytical chemistry
• 2020
N nanopore single-molecule analytical technique is used to quantify the thermodynamics and kinetics of DNA transport under heterogeneous co-solute PEGs and demonstrates that the frequency of translocation event exhibits a non-monotonic dependence on the crowding agent size.
Dynamics of polymer translocation into an anisotropic confinement
• Physics, Biology
• 2012
Using Langevin dynamics simulations, it is found that it takes different time for polymer translocation into the same ellipsoid through major-axis and minor-axis directions, depending on the average density of the whole chain in the ellipSOid, $\phi$.
Langevin dynamics simulation on the translocation of polymer through α-hemolysin pore.
• Materials Science, Medicine
Journal of physics. Condensed matter : an Institute of Physics journal
• 2014
The forced translocation of a polymer through an α-hemolysin pore under an electrical field is studied using a Langevin dynamics simulation and it is found that it is easier for the polymer to thread through the β-barrel if the polymer is located closer to the surface of the vestibule.
Translocation of stiff polymers through a nanopore driven by binding particles.
• Materials Science, Physics
The Journal of chemical physics
• 2012
The mean translocation time of stiff polymers in the presence of binding particles through a nanopore is found to show a minimum as a function of the binding energy ε and the particle concentration φ, due to the interplay of the force from binding and the frictional force.

## References

SHOWING 1-10 OF 59 REFERENCES
Chaperone-assisted translocation.
• Chemistry, Medicine
Physical biology
• 2004
We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the
Sequence dependence of the binding energy in chaperone-driven polymer translocation through a nanopore.
• Chemistry, Medicine
Physical review. E, Statistical, nonlinear, and soft matter physics
• 2011
The sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics and the effect of the nearest-neighbor adjacency probability of the two monomer types is investigated.
Polymer translocation through a nanopore under an applied external field.
• Materials Science, Chemistry
The Journal of chemical physics
• 2006
It is shown that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for R parallel approximately L such that EL is less than some critical value, but vanishes for large values of EL.
Directed motion emerging from two coupled random processes: translocation of a chain through a membrane nanopore driven by binding proteins.
• Chemistry, Biology
Journal of physics. Condensed matter : an Institute of Physics journal
• 2005
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and
Langevin dynamics simulations of polymer translocation through nanopores.
• Materials Science, Physics
The Journal of chemical physics
• 2006
The dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations is investigated using the fluctuating bond lattice model of polymers at intermediate friction values, but additional features of dependency on friction are revealed.
Fluctuations in polymer translocation
• Materials Science, Physics
• 2010
We investigate a model of chaperone-assisted polymer translocation through a nanopore in a membrane. Translocation is driven by irreversible random sequential absorption of chaperone proteins that
Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores.
• Chemistry, Medicine
The Journal of chemical physics
• 2008
It is shown that measurements of the first two moments of the biopolymer's first-passage time distribution provide information on its length and ordering, and the probability density function Q(t) of theFirst-Passage times is almost Gaussian for small chaperone size lambda, but becomes non-Gaussian as lambda increases.
Anomalous dynamics of translocation.
• Physics, Medicine
Physical review. E, Statistical, nonlinear, and soft matter physics
• 2002
The results indicate that for large N, translocation times scale in the same manner as diffusion times, but with a larger prefactor that depends on the size of the hole, which implies anomalous dynamics for the translocation process.
Polymer translocation through a hole
The average residence time τ of a polymer of length N passing through a narrow hole under a chemical potential gradient is calculated. In the proposed model, details of the hole parametrize the rate
Anomalous dynamics of forced translocation.
• Mathematics, Medicine
Physical review. E, Statistical, nonlinear, and soft matter physics
• 2004
It is demonstrated that the assumption of equilibrium must break down for sufficiently long polymers (more easily when forced), and lower bounds for the translocation time by comparison to unimpeded motion of the polymer are provided.