Article
Translocation of a heterogeneous polymer
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA.
The Journal of Chemical Physics
(Impact Factor: 3.12).
08/2012;
137(6):064904.
DOI: 10.1063/1.4742970
Source: PubMed

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ABSTRACT: We investigate the effectiveness of charge patterns along a nanopore on translocation dynamics of a flexible polyelectrolyte. We perform a three dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte translocating under uniform external electric field through a solidstate nanopore. We maintain the total charge along the pore to be constant, while varying its distribution by placing alternate charged and uncharged sections of different lengths along the pore length. Longest average translocation time is observed for a pattern corresponding to an optimum section length, with a major delay in the translocation time during the pore ejection stage. This optimum section length is independent of lengths of polyelectrolyte and pore within the range studied. A theory based on the FokkerPlanck formalism is found to successfully describe the observed trends with reasonable quantitative agreement.The Journal of Chemical Physics 04/2014; 140(13):135102. DOI:10.1063/1.4869862 · 3.12 Impact Factor 
Article: AlphaSynuclein LipidDependent Membrane Binding and Translocation through the αHemolysin Channel.
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ABSTRACT: Gauging the interactions of a natively unfolded Parkinson diseaserelated protein, alphasynuclein (αsyn) with membranes and its pathways between and within cells is important for understanding its pathogenesis. Here, to address these questions, we use a robust βbarrel channel, αhemolysin, reconstituted into planar lipid bilayers. Transient, ∼95% blockage of the channel current by αsyn was observed when 1), αsyn was added from the membrane side where the shorter (stem) part of the channel is exposed; and 2), the applied potential was lower on the side of αsyn addition. While the onrate of αsyn binding to the channel strongly increased with the applied field, the offrate displayed a turnover behavior. Statistical analysis suggests that at voltages >50 mV, a significant fraction of the αsyn molecules bound to the channel undergoes subsequent translocation. The observed onrate varied by >100 times depending on the bilayer lipid composition. Removal of the last 25 amino acids from the highly negatively charged Cterminal of αsyn resulted in a significant decrease in the binding rates. Taken together, these results demonstrate that βbarrel channels may serve as sensitive probes of αsyn interactions with membranes as well as model systems for studies of channelassisted protein transport.Biophysical Journal 02/2014; 106(3):55665. DOI:10.1016/j.bpj.2013.12.028 · 3.83 Impact Factor 
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ABSTRACT: Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasiequilibrium. The system is modeled as a flexible hardsphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to 〈τ〉 ∝ (N  Np)(2), where Np is the average number of monomers in the nanopore; this scaling is an indication of a quasistatic regime in which polymernanopore friction dominates. We use a multiplehistogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the FokkerPlanck formalism to calculate translocation time distributions in the quasistatic regime. These calculations also require a friction coefficient, characterized by a quantity Neff, the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of Neff. The free energy functions for narrowpore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.The Journal of Chemical Physics 05/2013; 138(17):174902. DOI:10.1063/1.4803022 · 3.12 Impact Factor
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