Translocation of a Polymer through a Crowded Channel under Electrical Force.

Tingting Sun,Hujun Xie,Zhiyong Yang,Zhouting Jiang,Yunxin Gen

doi:10.1155/2017/5267185

Abstract

The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength F, the chain length N, and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ ~ F−α is observed. With the crowding extent ρ increasing, the scaling exponent α becomes large. It is found that, for noncrowded channel, translocation probability drops when the field strength becomes large. However, for high-crowded channel, it is the opposite. Moreover, the translocation time and the average translocation time for all segments both have exponential growth with the crowding extent. The investigation of shape factor 〈δ〉 shows maximum value with increasing of the number of segments outside s. At last, the number of segments inside channel Nin in the process of translocation is calculated and a peak is observed. All the information from the study may benefit protein translocation.

Highlights

Translocation of a variety of biopolymers through channels or pores plays an important role in biological systems [1], for example, injection of DNA from a virus to bacteria [2], protein transport through membrane channels [3], translocation of DNA and RNA across nuclear pores [4], and translocation of nascent proteins inside the ribosomal tunnel or across the endoplasmic reticulum [5,6,7,8]
It is obvious that the translocation time decreases with increasing electric force
Using the Langevin dynamics simulations, we investigate the translocation of a polymer chain through a crowded cylindrical channel

Summary

Introduction

Translocation of a variety of biopolymers through channels or pores plays an important role in biological systems [1], for example, injection of DNA from a virus to bacteria [2], protein transport through membrane channels [3], translocation of DNA and RNA across nuclear pores [4], and translocation of nascent proteins inside the ribosomal tunnel or across the endoplasmic reticulum [5,6,7,8]. The translocation process is useful in the range of biotechnological applications, such as rapid DNA sequencing [9, 10], gene therapy, drug delivery, and drug discovery [11]. Kasianowicz et al [12] demonstrated that single-stranded DNA and RNA molecules can be driven through the waterfilled α-hemolysin channel under electric field. The passage of each molecule is signaled by a blockade in the channel current. Improving this technique, the nucleotide sequence of DNA or RNA can be read off. The scaling relationship of translocation time with chain length is τ ∝ N1.27, which is different from that obtained by Kasianowicz et al, τ ∝ N

Methods

Results

Conclusion