Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
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Dai-2017-Trapping a Knot into Tight Conformati.pdf
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8.5 MB
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Checksum (MD5)
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Author(s)
Dai, Liang
Doyle, Patrick S
Date Issued
February 2017
Journal
Polymers
Publisher
MDPI AG
Citation
Dai, Liang and Doyle, Patrick. “Trapping a Knot into Tight Conformations by Intra-Chain Repulsions.” Polymers 9, no. 2 (February 2017): 57 © 2017 by the authors
Version
Final published version
Abstract
Knots can occur in biopolymers such as DNA and peptides. In our previous study, we systematically investigated the effects of intra-chain interactions on knots and found that long-range repulsions can surprisingly tighten knots. Here, we use this knowledge to trap a knot into tight conformations in Langevin dynamics simulations. By trapping, we mean that the free energy landscape with respect to the knot size exhibits a potential well around a small knot size in the presence of long-range repulsions, and this potential can well lead to long-lived tight knots when its depth is comparable to or larger than thermal energy. We tune the strength of intra-chain repulsion such that a knot is weakly trapped. Driven by thermal fluctuations, the knot can escape from the trap and is then re-trapped. We find that the knot switches between tight and loose conformations—referred to as “knot breathing”. We use a Yukawa potential to model screened electrostatic interactions to explore the relevance of knot trapping and breathing in charged biopolymers. We determine the minimal screened length and the minimal strength of repulsion for knot trapping. We find that Coulomb-induced knot trapping is possible to occur in single-stranded DNA and peptides for normal ionic strengths.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Singapore-MIT Alliance in Research and Technology (SMART)
Terms of Use
Creative Commons Attribution 4.0 International License
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DOI of Published Version
https://doi.org/10.3390/polym9020057
