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Open AccessFeature PaperArticle

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

1
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
2
SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
3
Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece
4
Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
5
Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA
*
Author to whom correspondence should be addressed.
Polymers 2017, 9(9), 444; https://doi.org/10.3390/polym9090444
Received: 26 August 2017 / Revised: 8 September 2017 / Accepted: 11 September 2017 / Published: 13 September 2017
(This article belongs to the Special Issue Knotted and Catenated Polymers)
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. View Full-Text
Keywords: protein knots; knot theory; topology; knotoids protein knots; knot theory; topology; knotoids
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Goundaroulis, D.; Gügümcü, N.; Lambropoulou, S.; Dorier, J.; Stasiak, A.; Kauffman, L. Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. Polymers 2017, 9, 444.

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