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Trapping a Knot into Tight Conformations by Intra-Chain Repulsions

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...

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Detalles Bibliográficos
Autores principales: Dai, Liang, Doyle, Patrick S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432319/
https://www.ncbi.nlm.nih.gov/pubmed/30970736
http://dx.doi.org/10.3390/polym9020057
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author Dai, Liang
Doyle, Patrick S.
author_facet Dai, Liang
Doyle, Patrick S.
author_sort Dai, Liang
collection PubMed
description 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.
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spelling pubmed-64323192019-04-02 Trapping a Knot into Tight Conformations by Intra-Chain Repulsions Dai, Liang Doyle, Patrick S. Polymers (Basel) Article 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. MDPI 2017-02-10 /pmc/articles/PMC6432319/ /pubmed/30970736 http://dx.doi.org/10.3390/polym9020057 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Dai, Liang
Doyle, Patrick S.
Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title_full Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title_fullStr Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title_full_unstemmed Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title_short Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
title_sort trapping a knot into tight conformations by intra-chain repulsions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432319/
https://www.ncbi.nlm.nih.gov/pubmed/30970736
http://dx.doi.org/10.3390/polym9020057
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