ArticleScientific reports2015
Subknots in ideal knots, random knots, and knotted proteins.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Folding kinetics of an entangled protein.PLoS computational biology · 2023Article
- Entangled Motifs in Membrane Protein Structures.International journal of molecular sciences · 2023Article
- Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures.International journal of molecular sciences · 2019Article
- Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding.Scientific reports · 2019Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids.Polymers · 2017Article
- Studies of global and local entanglements of individual protein chains using the concept of knotoids.Scientific reports · 2017Article
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Authors and funding
3 authors.
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Abstract
We introduce disk matrices which encode the knotting of all subchains in circular knot configurations. The disk matrices allow us to dissect circular knots into their subknots, i.e. knot types formed by subchains of the global knot. The identification of subknots is based on the study of linear chains in which a knot type is associated to the chain by means of a spatially robust closure protocol. We characterize the sets of observed subknot types in global knots taking energy-minimized shapes such as KnotPlot configurations and ideal geometric configurations. We compare the sets of observed subknots to knot types obtained by changing crossings in the classical prime knot diagrams. Building upon this analysis, we study the sets of subknots in random configurations of corresponding knot types. In many of the knot types we analyzed, the sets of subknots from the ideal geometric configurations are found in each of the hundreds of random configurations of the same global knot type. We also compare the sets of subknots observed in open protein knots with the subknots observed in the ideal configurations of the corresponding knot type. This comparison enables us to explain the specific dispositions of subknots in the analyzed protein knots.
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