Studies of global and local entanglements of individual protein chains using the concept of knotoids

Abstract We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open c...

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Autores principales:	Dimos Goundaroulis, Julien Dorier, Fabrizio Benedetti, Andrzej Stasiak
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/11463ba0a3e940a1bbbee741f3fb0f2a
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id	oai:doaj.org-article:11463ba0a3e940a1bbbee741f3fb0f2a
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spelling	oai:doaj.org-article:11463ba0a3e940a1bbbee741f3fb0f2a2021-12-02T16:06:21ZStudies of global and local entanglements of individual protein chains using the concept of knotoids10.1038/s41598-017-06649-32045-2322https://doaj.org/article/11463ba0a3e940a1bbbee741f3fb0f2a2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06649-3https://doaj.org/toc/2045-2322Abstract We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn’t require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted.Dimos GoundaroulisJulien DorierFabrizio BenedettiAndrzej StasiakNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dimos Goundaroulis Julien Dorier Fabrizio Benedetti Andrzej Stasiak Studies of global and local entanglements of individual protein chains using the concept of knotoids
description	Abstract We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn’t require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted.
format	article
author	Dimos Goundaroulis Julien Dorier Fabrizio Benedetti Andrzej Stasiak
author_facet	Dimos Goundaroulis Julien Dorier Fabrizio Benedetti Andrzej Stasiak
author_sort	Dimos Goundaroulis
title	Studies of global and local entanglements of individual protein chains using the concept of knotoids
title_short	Studies of global and local entanglements of individual protein chains using the concept of knotoids
title_full	Studies of global and local entanglements of individual protein chains using the concept of knotoids
title_fullStr	Studies of global and local entanglements of individual protein chains using the concept of knotoids
title_full_unstemmed	Studies of global and local entanglements of individual protein chains using the concept of knotoids
title_sort	studies of global and local entanglements of individual protein chains using the concept of knotoids
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/11463ba0a3e940a1bbbee741f3fb0f2a
work_keys_str_mv	AT dimosgoundaroulis studiesofglobalandlocalentanglementsofindividualproteinchainsusingtheconceptofknotoids AT juliendorier studiesofglobalandlocalentanglementsofindividualproteinchainsusingtheconceptofknotoids AT fabriziobenedetti studiesofglobalandlocalentanglementsofindividualproteinchainsusingtheconceptofknotoids AT andrzejstasiak studiesofglobalandlocalentanglementsofindividualproteinchainsusingtheconceptofknotoids
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Studies of global and local entanglements of individual protein chains using the concept of knotoids

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