Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids.
- Goundaroulis D Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. dimoklis.gkountaroulis@unil.ch.
- Gügümcü N Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece. nesli@central.ntua.gr.
- Lambropoulou S Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece. sofia@math.ntua.gr.
- Dorier J Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. julien.dorier@unil.ch.
- Stasiak A Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. Andrzej.Stasiak@unil.ch.
- Kauffman L Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA. kauffman@uic.edu.
- 2019-04-11
Published in:
- Polymers. - 2017
English
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.
- Language
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- English
- Open access status
- gold
- Identifiers
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- DOI 10.3390/polym9090444
- PMID 30965745
- Persistent URL
- https://sonar.ch/global/documents/278022
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