Molecular Crowding Increases Knots Abundance in Linear Polymers

D’Adamo, Giuseppe; Micheletti, Cristian

doi:10.1021/acs.macromol.5b01323

Cited by 31 publications

(29 citation statements)

References 86 publications

(112 reference statements)

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“…8 ) is very close to the ~ 3.3–3.5 nm obtained experimentally for denatured states of similar size 17 , 39 . Comparable Δ G U and radius of gyration values are predicted by simulations of flexible open chains made up of beads (diameter = 0.4–0.5 nm) with the length of the Arc-L1-Arc repressor (100 beads) 40 . The correspondence between experiments and random model computations indicates that ΔG U is largely of entropic origin and, therefore, independent of protein sequence.…”

Section: Resultsmentioning

confidence: 90%

The energy cost of polypeptide knot formation and its folding consequences

et al. 2017

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Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain—an event that can potentially impair its folding—and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol−1. Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin. This cost is predicted to remain above 3 kcal mol−1 for denatured proteins as large as 900 residues. Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cost of knotting through contacts along their folding landscape.

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Section: Resultsmentioning

confidence: 90%

The energy cost of polypeptide knot formation and its folding consequences

et al. 2017

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“…1A) [43][44][45]. Further topological de-localisation is achieved by isotropic confinement [46,47] and crowding [48], both conditions that are typically found in vivo. Since delocalisation of essential crossings is likely to hinder TopoII-mediated topological simplification, it is natural to ask if there exists a physiological mechanism that counteracts topological de-localisation in vivo.To address this question we performed BD simulations of directed loop extrusion on thermalised polymers which display de-localised entanglements (Fig.…”

mentioning

confidence: 94%

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Orlandini

Marenduzzo

Michieletto

2019

Proc. Natl. Acad. Sci. U.S.A.

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Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.

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“…Knots are naturally found on long DNA strands [29][30][31] and proteins [32][33][34] while at the same time they can also be artificially [35,36] or synthetically manufactured [37] . The influence of such knots * maximilian.liebetreu@univie.ac.at † christos.likos@univie.ac.at in equilibrium and relaxation properties in the bulk [38][39][40][41][42][43][44][45][46] , under confinement [47][48][49][50][51][52][53][54][55][56] and under tension [57][58][59][60][61][62][63][64] has been thoroughly investigated. Recently, the sedimentation behavior of flexible, non-Brownian knots has been added to the host of counterintuitive phenomena [65] .…”

Section: Introductionmentioning

confidence: 99%

Hydrodynamic inflation of ring polymers under shear

Liebetreu

Likos

2020

Commun Mater

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Hydrodynamic interactions as modeled by Multi-Particle Collision Dynamics can dramatically influence the dynamics of fully flexible, ring-shaped polymers in ways not known for any other polymer architecture or topology. We show that steady shear leads to an inflation scenario exclusive to ring polymers, which depends not only on Weissenberg number but also on contour length of the ring. By analyzing velocity fields of the solvent around the polymer, we show the existence of a hydrodynamic pocket which allows the polymer to self-stabilize at a certain alignment angle to the flow axis. This self-induced stabilization is accompanied by transitioning of the ring to a non-Brownian particle and a cessation of tumbling. The ring swells significantly in the vorticity direction, and the horseshoe regions on the stretched and swollen ring are effectively locked in place relative to the ring's center-of-mass. The observed effect is exclusive to ring polymers and stems from an interplay between hydrodynamic interactions and topology. Furthermore, knots tied onto such rings can serve as additional "stabilization anchors". Under strong shear, the knotted section is pulled tight and remains well-localized while tank-treading from one horseshoe region to the opposite one in sudden bursts. We find knotted polymers of high contour length behave very similarly to unknotted rings of the same contour length, but small knotted rings feature a host of different configurations. We propose a filtering technique for rings and chains based on our observations and suggest that strong shear could be used to tighten knots on rings.arXiv:1909.00725v2 [cond-mat.soft]

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Molecular Crowding Increases Knots Abundance in Linear Polymers

Cited by 31 publications

References 86 publications

The energy cost of polypeptide knot formation and its folding consequences

The energy cost of polypeptide knot formation and its folding consequences

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Hydrodynamic inflation of ring polymers under shear

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