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...

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Bibliographic Details
Published in:Polymers 2017-09, Vol.9 (9), p.444
Main Authors: Goundaroulis, Dimos, Gügümcü, Neslihan, Lambropoulou, Sofia, Dorier, Julien, Stasiak, Andrzej, Kauffman, Louis
Format: Article
Language:English
Subjects:
Bonding
Chain entanglement
Chains
Entanglement
Proteins
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Summary: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.
ISSN:2073-4360
2073-4360
DOI:10.3390/polym9090444