Polymers: co-auth.: group Stasiak

Polymers 20179(9), 444; doi:10.3390/polym9090444

Featured paper:

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

Dimos Goundaroulis 1,2, Neslihan Gügümcü 3, Sofia Lambropoulou 3, Julien Dorier 1,4, Andrzej Stasiak 1,2 and Louis Kauffman 5,*
Correspondence: Tel.: +1-312-996-3066
Received: 26 August 2017 / Accepted: 11 September 2017 / Published: 13 September 2017


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.
Keywords: protein knots; knot theory; topology; knotoids