Translocation, Rejection and Trapping of Polyampholytes.

Yeong-Beom Kim,Albert Johner,Min-Kyung Chae,Jeong-Man Park,Nam-Kyung Lee

doi:10.3390/polym14040797

Abstract

Polyampholytes (PA) are a special class of polymers comprising both positive and negative monomers along their sequence. Most proteins have positive and negative residues and are PAs. Proteins have a well-defined sequence while synthetic PAs have a random charge sequence. We investigated the translocation behavior of random polyampholyte chains through a pore under the action of an electric field by means of Monte Carlo simulations. The simulations incorporated a realistic translocation potential profile along an extended asymmetric pore and translocation was studied for both directions of engagement. The study was conducted from the perspective of statistics for disordered systems. The translocation behavior (translocation vs. rejection) was recorded for all sequences comprised of N = 20 charged monomers. The results were compared with those for random sequences of N = 40 to better demonstrate asymptotic laws. At early times, rejection was mainly controlled by the charge sequence of the head part, but late translocation/rejection was governed by the escape from a trapped state over an antagonistic barrier built up along the sequence. The probability distribution of translocation times from all successful attempts revealed a power-law tail. At finite times, there was a population of trapped sequences that relaxed very slowly (logarithmically) with time. If a subensemble of sequences with prescribed net charge was considered the power-law decay was steeper for a more favorable net charge. Our findings were rationalized by theoretical arguments developed for long chains. We also provided operational criteria for the translocation behavior of a sequence, explaining the selection by the translocation process. From the perspective of protein translocation, our findings can help rationalize the behavior of intrinsically disordered proteins (IDPs), which can be modeled as polyampholytes. Most IDP sequences have a strong net charge favoring translocation. Even for sequences with those large net charges, the translocation times remained very dispersed and the translocation was highly sequence-selective.

Highlights

Polyampholytes (PAs) are polymers carrying positive and negative charges along their sequence
We measured the number of translocated sequences within the given binning time, δt = 1.6 × 103 Monte Carlo (MC) time steps (MCT), for both cis-to-trans and the reverse directions, and the distribution was normalized by the total number of successful attempts
As predicted from theory, we found that the power-law tail P(t) ∼ 1/t1+μ(μ = 0) prevailed asymptotically. (Figure 2a) For N = 20, the probability distribution functions (PDFs) Ptr(t) deviated from the power law for t 104 MCT and dropped more quickly because of the finite-length effect

Summary

Introduction

Polyampholytes (PAs) are polymers carrying positive and negative charges along their sequence. We addressed the effect of the charge disorder (randomness in charge arrangement along the sequence) in long sequences [29], by means of analytical theory, and the influence of the globular structure of PAs on their translocation through a point-like pore (of monomeric length) [30]. We adopt the simple picture that the charges inside the pore experience the driving force endowed by the free energy of small ions and the polymers are basically onedimensional sequence of charges (Figure 1c). This amounts to ignoring the variation of the extra entropy penalty of the polymeric sequence engaged for translocation and is reasonable as long as the pore is filled.

Theory

Model: Monte Carlo Simulation

Results and Discussion

Conclusions