Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy

TL;DR

This paper investigates how the spatial distribution of chaperones, especially exponential distribution, influences polymer translocation through nanopores, revealing energy-dependent effects and conditions for minimal translocation times.

Contribution

It introduces the impact of exponential chaperone distribution on translocation energy dependence and predicts conditions for minimal translocation times based on theoretical analysis.

Findings

Exponential distribution alters energy dependence of translocation time.

A minimum in translocation time versus energy curve is observed.

Rare cases show translocation exponent less than 1.

Abstract

Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, $\beta$ ($T\sim\beta$). Interestingly in some special cases e.g. chaperones of size $\lambda=6$ and with exponential distribution rate of $\alpha=5$, the minimum reaches even to amount of less than $1$ ($\beta<1$). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into account the velocity dependency of the translocation on polymer length, one could truly predict the amount of this minimum.