Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

Article Types

Countries / Regions

Search Results (4)

Search Parameters:
Keywords = knotoids

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
13 pages, 918 KB  
Article
Invariants of Bonded Knotoids and Applications to Protein Folding
by Neslihan Gügümcü, Bostjan Gabrovsek and Louis H. Kauffman
Symmetry 2022, 14(8), 1724; https://doi.org/10.3390/sym14081724 - 18 Aug 2022
Cited by 7 | Viewed by 2538
Abstract
In this paper, we study knotoids with extra graphical structure (bonded knotoids) in the settings of rigid vertex and topological vertex graphs. We construct bonded knotoid invariants by applying tangle insertion and unplugging at bonding sites of a bonded knotoid. We demonstrate that [...] Read more.
In this paper, we study knotoids with extra graphical structure (bonded knotoids) in the settings of rigid vertex and topological vertex graphs. We construct bonded knotoid invariants by applying tangle insertion and unplugging at bonding sites of a bonded knotoid. We demonstrate that our invariants can be used for the analysis of the topological structure of proteins. Full article
(This article belongs to the Special Issue Topological Methods in Chemistry and Molecular Biology)
Show Figures

Figure 1

18 pages, 7855 KB  
Article
A Topological Selection of Folding Pathways from Native States of Knotted Proteins
by Agnese Barbensi, Naya Yerolemou, Oliver Vipond, Barbara I. Mahler, Pawel Dabrowski-Tumanski and Dimos Goundaroulis
Symmetry 2021, 13(9), 1670; https://doi.org/10.3390/sym13091670 - 10 Sep 2021
Cited by 3 | Viewed by 3380
Abstract
Understanding how knotted proteins fold is a challenging problem in biology. Researchers have proposed several models for their folding pathways, based on theory, simulations and experiments. The geometry of proteins with the same knot type can vary substantially and recent simulations reveal different [...] Read more.
Understanding how knotted proteins fold is a challenging problem in biology. Researchers have proposed several models for their folding pathways, based on theory, simulations and experiments. The geometry of proteins with the same knot type can vary substantially and recent simulations reveal different folding behaviour for deeply and shallow knotted proteins. We analyse proteins forming open-ended trefoil knots by introducing a topologically inspired statistical metric that measures their entanglement. By looking directly at the geometry and topology of their native states, we are able to probe different folding pathways for such proteins. In particular, the folding pathway of shallow knotted carbonic anhydrases involves the creation of a double-looped structure, contrary to what has been observed for other knotted trefoil proteins. We validate this with Molecular Dynamics simulations. By leveraging the geometry and local symmetries of knotted proteins’ native states, we provide the first numerical evidence of a double-loop folding mechanism in trefoil proteins. Full article
(This article belongs to the Special Issue Topological Methods in Chemistry and Molecular Biology)
Show Figures

Figure 1

24 pages, 831 KB  
Article
Knotoids, Braidoids and Applications
by Neslihan Gügümcü and Sofia Lambropoulou
Symmetry 2017, 9(12), 315; https://doi.org/10.3390/sym9120315 - 12 Dec 2017
Cited by 22 | Viewed by 4903
Abstract
This paper is an introduction to the theory of braidoids. Braidoids are geometric objects analogous to classical braids, forming a counterpart theory to the theory of knotoids. We introduce these objects and their topological equivalences, and we conclude with a potential application to [...] Read more.
This paper is an introduction to the theory of braidoids. Braidoids are geometric objects analogous to classical braids, forming a counterpart theory to the theory of knotoids. We introduce these objects and their topological equivalences, and we conclude with a potential application to the study of proteins. Full article
(This article belongs to the Special Issue Knot Theory and Its Applications)
Show Figures

Figure 1

16 pages, 7110 KB  
Article
Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
by Dimos Goundaroulis, Neslihan Gügümcü, Sofia Lambropoulou, Julien Dorier, Andrzej Stasiak and Louis Kauffman
Polymers 2017, 9(9), 444; https://doi.org/10.3390/polym9090444 - 13 Sep 2017
Cited by 52 | Viewed by 8634
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Knotted and Catenated Polymers)
Show Figures

Figure 1

Back to TopTop