Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding

Soler, Miguel A.; Rey, Antonio; Faísca, Patrícia F. N.

doi:10.1039/c6cp05086g

Cited by 35 publications

(34 citation statements)

References 80 publications

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“…These results are in line with theoretical analysis, framed on polymer physics considerations, which predicts that local order is an inhibitor of knotting in proteins (9). The impact of chain flexibility on the structure of the transition state ensemble of MJ0366 was also investigated in (119). An enhanced structural flexibility leads to a structural rearrangement of the transition state, which becomes devoid of helical content (including the C-terminal helix that is threaded through the knotting loop to tangle the protein).…”

Section: Towards a Mechanistic Understanding Of Knotting In Vivosupporting

confidence: 82%

Knotted proteins: Tie etiquette in structural biology

Nunes¹,

Faísca²

2020

Topology and Geometry of Biopolymers

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A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past decade with different approaches, such as structural characterization, in vitro experiments, and simulations of protein models with varying levels of complexity. The simplest among these are the lattice Gō models, which belong to the class of structure-based models, i.e., models that are biased to the native structure by explicitly including structural data. In this review we highlight the contributions to the field made in the scope of lattice Gō models, putting them into perspective in the context of the main experimental and theoretical results and of other, more realistic, computational approaches.

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Section: Towards a Mechanistic Understanding Of Knotting In Vivosupporting

confidence: 82%

Knotted proteins: Tie etiquette in structural biology

Nunes¹,

Faísca²

2020

Topology and Geometry of Biopolymers

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“…The KymoKnot software presented here differs not only for adopting the minimally interfering closure scheme, whose computational effectiveness has been credited for making possible several extensive studies over the past years [27,38,48,[57][58][59][60][61][62][63][64], but also for the implementation aimed at analysing trajectories and ensembles of structures.…”

Section: Introductionmentioning

confidence: 99%

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers

et al. 2018

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The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

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“…This agrees with the theoretical investigation showing that knotting probability of polymers increases in confinement [ 27 ]. Only due to the encapsulation (following [ 28 ]), successful reversible folding was observed for members of knotted proteins with DNA binding motif VirC and DndE [ 29 ]. It is then natural to expect, that chaperonins encapsulating proteins may also facilitate folding and self-knotting of eucaryotic UCHs, although no experimental result in this topic is available yet.…”

Section: Introductionmentioning

confidence: 99%

The exclusive effects of chaperonin on the behavior of proteins with 52 knot

et al. 2018

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The folding of proteins with a complex knot is still an unresolved question. Based on representative members of Ubiquitin C-terminal Hydrolases (UCHs) that contain the 52 knot in the native state, we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model. In particular, we identify two, topologically different folding/unfolding pathways and corroborate our results with experiment, recreating the chevron plot. We show that confinement effect of chaperonin or weak crowding greatly facilitates folding, simultaneously slowing down the unfolding process of UCHs, compared with bulk conditions. Finally, we analyze the existence of knots in the denaturated state of UCHs. The results of the work show that the crowded environment of the cell should have a positive effect on the kinetics of complex knotted proteins, especially when proteins with deeper knots are found in this family.

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Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding

Cited by 35 publications

References 80 publications

Knotted proteins: Tie etiquette in structural biology

Knotted proteins: Tie etiquette in structural biology

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers

The exclusive effects of chaperonin on the behavior of proteins with 52 knot

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