Physical Links: defining and detecting inter-chain entanglement

Caraglio, Michele; Micheletti, Cristian; Orlandini, Enzo

doi:10.1038/s41598-017-01200-w

Cited by 39 publications

(75 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1) can be viewed as a tangle with two strands and four ends [41]. To obtain a proper topological link, we close each curve with an auxiliary arc, analogous to the procedure used to convert a pair of open chains into a physical link [42]. Starting from any end, we can traverse a strand until another end is reached and connect these two ends to form a closed loop.…”

Section: Topological Characterization Of Self-entanglements On Cirmentioning

confidence: 99%

Self-entanglement of a tumbled circular chain

Soh

Gengaro

Klotz

et al. 2019

Phys. Rev. Research

View full text Add to dashboard Cite

The spontaneous knotting of linear chains has been well studied, but little attention has been given to the self-entanglement of chains with more complex topologies. In this work, we perform experiments with granular chains that undergo tumbling motion to investigate the self-entanglement of circular chains, which lack the chain ends essential for forming knots. We study the entanglement probability and types of self-entanglements formed on linear and circular chains, using the well-studied self-entanglements on a linear chain to frame our understanding of self-entanglements on a circular chain. We describe a characterization method that views a self-entangled circular chain as a link of two components and use it to characterize the self-entanglements on circular chains with known topological descriptors from knot theory. Our experimental results show that an increase in circular chain length leads to an increase in entanglement probability and entanglement complexity until a plateau is reached, similar to the trends observed with linear chains. By examining the formation pathway of several self-entanglements, we infer a general mechanism for the self-entanglement of circular chains.

show abstract

Section: Topological Characterization Of Self-entanglements On Cirmentioning

confidence: 99%

Self-entanglement of a tumbled circular chain

Soh

Gengaro

Klotz

et al. 2019

Phys. Rev. Research

View full text Add to dashboard Cite

show abstract

“…Hence, so far, the links were identified by extending the termini and connecting them in the “infinity” (on a surface of a much larger sphere). The direction of the extension was either (historically first) stochastic (with many chain closures) [ 18 ] or the termini were extended from the center of mass of a protein [ 42 ]. The currently identified set of different multi-component arrangements in proteins is available via the LinkProt database [ 18 ] and includes Hopf, Solomon and other more complex links.…”

Section: Entanglement In Proteinsmentioning

confidence: 99%

To Tie or Not to Tie? That Is the Question

Dąbrowski-Tumański

Sułkowska

2017

Polymers

View full text Add to dashboard Cite

Abstract:In this review, we provide an overview of entangled proteins. Around 6% of protein structures deposited in the PBD are entangled, forming knots, slipknots, lassos and links. We present theoretical methods and tools that enabled discovering and classifying such structures. We discuss the advantages and disadvantages of the non-trivial topology in proteins, based on available data about folding, stability, biological properties and evolutionary conservation. We also formulate intriguing and challenging questions on the border of biophysics, bioinformatics, biology and mathematics, which arise from the discovery of an entanglement in proteins. Finally, we discuss possible applications of entangled proteins in medicine and nanotechnology, such as the chance to design super stable proteins, whose stability could be controlled by chemical potential.

show abstract

“…The fact that more complex and longer links hinder more markedly the translocation process at x ∼ 1/2 should depend on how the physically linked region spreads along the system during translocation. We recall that the linked portion is identified as the shortest portion of the two rings that, upon closure, has the same topology as the entire link (for a detailed description of the algorithm used to measure it see [25,30]). Denote by (1) K and (2) K the size of the subchain respectively in loop 1 and 2 whose union defines the linked portion.…”

Section: Effect Of Link Size On Translocationmentioning

confidence: 99%

“…This means that a translocation experiment can be used to detect knots in a ring polymer and might give information about the complexity of the knot [22,23,24]. If instead we have a link with two components, both components being the same size and unknotted, the linked portion [25] gives rise to an additional delay around the middle of the translocation process [26]. For a link with three unknotted components (such as the connect sum of two Hopf links) there are two separate additional delays, around one third and two thirds of the way through the process [26].…”

Section: Introductionmentioning

confidence: 99%

Translocation of links through a pore: effects of link complexity and size

2020

View full text Add to dashboard Cite

We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are knotted or unknotted. For links with two unknotted rings the crossings between the rings can slow down the translocation and are responsible for a delay as the crossings pass through the pore. The results fall on a set of relatively smooth curves for different link families with the translocation time not always increasing with crossings number within the same family. When one ring is knotted the results depend on whether the link is prime or composite and, for the composite case, they depend on whether the knotted or unknotted ring enters the pore first. We find a similar situation for 3-component links where the results depend on whether the link is prime or composite. These results contribute to our understanding of how the entanglement complexity between filaments impacts their translocation dynamics and should be useful for extending nanopore-sensing techniques to probe the topological properties of these systems.

show abstract

Physical Links: defining and detecting inter-chain entanglement

Cited by 39 publications

References 57 publications

Self-entanglement of a tumbled circular chain

Self-entanglement of a tumbled circular chain

To Tie or Not to Tie? That Is the Question

Translocation of links through a pore: effects of link complexity and size

Contact Info

Product

Resources

About