Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids

In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts...

Full description

Bibliographic Details
Main Authors:	Dimos Goundaroulis, Neslihan Gügümcü, Sofia Lambropoulou, Julien Dorier, Andrzej Stasiak, Louis Kauffman
Format:	Article
Language:	English
Published:	MDPI AG 2017-09-01
Series:	Polymers
Subjects:	protein knots knot theory topology knotoids
Online Access:	https://www.mdpi.com/2073-4360/9/9/444

id	doaj-105cb9b326074b688d7ec57c549d5d3d
record_format	Article
spelling	doaj-105cb9b326074b688d7ec57c549d5d3d2020-11-24T20:49:02ZengMDPI AGPolymers2073-43602017-09-019944410.3390/polym9090444polym9090444Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded KnotoidsDimos Goundaroulis0Neslihan Gügümcü1Sofia Lambropoulou2Julien Dorier3Andrzej Stasiak4Louis Kauffman5Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, SwitzerlandDepartment of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, GreeceDepartment of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, GreeceCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, SwitzerlandCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, SwitzerlandDepartment of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USAIn this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins.https://www.mdpi.com/2073-4360/9/9/444protein knotsknot theorytopologyknotoids
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Dimos Goundaroulis Neslihan Gügümcü Sofia Lambropoulou Julien Dorier Andrzej Stasiak Louis Kauffman
spellingShingle	Dimos Goundaroulis Neslihan Gügümcü Sofia Lambropoulou Julien Dorier Andrzej Stasiak Louis Kauffman Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids Polymers protein knots knot theory topology knotoids
author_facet	Dimos Goundaroulis Neslihan Gügümcü Sofia Lambropoulou Julien Dorier Andrzej Stasiak Louis Kauffman
author_sort	Dimos Goundaroulis
title	Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
title_short	Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
title_full	Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
title_fullStr	Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
title_full_unstemmed	Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
title_sort	topological models for open-knotted protein chains using the concepts of knotoids and bonded knotoids
publisher	MDPI AG
series	Polymers
issn	2073-4360
publishDate	2017-09-01
description	In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins.
topic	protein knots knot theory topology knotoids
url	https://www.mdpi.com/2073-4360/9/9/444
work_keys_str_mv	AT dimosgoundaroulis topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids AT neslihangugumcu topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids AT sofialambropoulou topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids AT juliendorier topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids AT andrzejstasiak topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids AT louiskauffman topologicalmodelsforopenknottedproteinchainsusingtheconceptsofknotoidsandbondedknotoids
_version_	1716807042734227456

Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids

Similar Items