A tile model of circuit topology for self-entangled biopolymers

Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebrai...

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Detalles Bibliográficos
Autores principales: Flapan, Erica, Mashaghi, Alireza, Wong, Helen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235088/
https://www.ncbi.nlm.nih.gov/pubmed/37264056
http://dx.doi.org/10.1038/s41598-023-35771-8
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author Flapan, Erica
Mashaghi, Alireza
Wong, Helen
author_facet Flapan, Erica
Mashaghi, Alireza
Wong, Helen
author_sort Flapan, Erica
collection PubMed
description Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebraic expressions. Then we use our model to show that the only knot types that such entangled chains can have are [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] and connected sums of these knots. This includes all proteins knots that have thus far been identified.
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spelling pubmed-102350882023-06-03 A tile model of circuit topology for self-entangled biopolymers Flapan, Erica Mashaghi, Alireza Wong, Helen Sci Rep Article Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebraic expressions. Then we use our model to show that the only knot types that such entangled chains can have are [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] , [Formula: see text] and connected sums of these knots. This includes all proteins knots that have thus far been identified. Nature Publishing Group UK 2023-06-01 /pmc/articles/PMC10235088/ /pubmed/37264056 http://dx.doi.org/10.1038/s41598-023-35771-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Flapan, Erica
Mashaghi, Alireza
Wong, Helen
A tile model of circuit topology for self-entangled biopolymers
title A tile model of circuit topology for self-entangled biopolymers
title_full A tile model of circuit topology for self-entangled biopolymers
title_fullStr A tile model of circuit topology for self-entangled biopolymers
title_full_unstemmed A tile model of circuit topology for self-entangled biopolymers
title_short A tile model of circuit topology for self-entangled biopolymers
title_sort tile model of circuit topology for self-entangled biopolymers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235088/
https://www.ncbi.nlm.nih.gov/pubmed/37264056
http://dx.doi.org/10.1038/s41598-023-35771-8
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