Entangled Proteins: Knots, Slipknots, Links, and Lassos

Sułkowska, Joanna I.; Sułkowski, Piotr

doi:10.1007/978-3-319-76596-9_8

Cited by 7 publications

(7 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Examples include knots and knot-like folds. Knots have been detected in protein structures ( 12 , 13 ) and debated for RNAs ( 14–16 ). Their various types – knots, slipknots, links, or lassos – occur when a polymer chain (e.g.…”

Section: Introductionmentioning

confidence: 99%

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Luwanski

Hlushchenko

Popenda

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

Advances in experimental and computational techniques enable the exploration of large and complex RNA 3D structures. These, in turn, reveal previously unstudied properties and motifs not characteristic for small molecules with simple architectures. Examples include entanglements of structural elements in RNA molecules and knot-like folds discovered, among others, in the genomes of RNA viruses. Recently, we presented the first classification of entanglements, determined by their topology and the type of entangled structural elements. Here, we introduce RNAspider – a web server to automatically identify, classify, and visualize primary and higher-order entanglements in RNA tertiary structures. The program applies to evaluate RNA 3D models obtained experimentally or by computational prediction. It supports the analysis of uncommon topologies in the pseudoknotted RNA structures. RNAspider is implemented as a publicly available tool with a user-friendly interface and can be freely accessed at https://rnaspider.cs.put.poznan.pl/.

show abstract

Section: Introductionmentioning

confidence: 99%

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Luwanski

Hlushchenko

Popenda

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…3 Knots are believed to be functionally advantageous 7 and to provide extra stability to protein chains. 8,9 Up to date, four knot topologies were discoveredtrefoil (3 1 ) knot, 10,11 figure-eight (4 1 ) knot, 11 three-twist (5 2 ) knot, 12 and stevedore (6 1 ) knot. 13 Apart from the topology, knotted proteins differ also by the depths of the knot (the lengths of the tails outside the knotted core), and thus they are divided into shallow (tails possess less than 10 amino acids) and deeply knotted.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Knotted proteins appear in all kingdoms of life, and tend to be preserved throughout evolution . Knots are believed to be functionally advantageous and to provide extra stability to protein chains. , …”

Section: Introductionmentioning

confidence: 99%

Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel

et al. 2018

Self Cite

View full text Add to dashboard Cite

The mechanism of folding of deeply knotted proteins into their native structure is still not understood. Current thinking about protein folding is dominated by the Anfinsen dogma, stating that the structure of the folded proteins is uniquely dictated by the amino acid sequence of a given protein and that the folding is driven uniquely by the energy gained from interactions between amino acids that contact each other in the native structure of the protein. The role of ribosomes in protein folding was only seen as permitting the folding to progress from the N-terminal part of nascent protein chains. We propose here that ribosomes can participate actively in the folding of knotted proteins by actively threading nascent chains emerging from the ribosome exit channels through loops formed by a synthesized earlier portion of the same protein. Our simulations of folding of deeply knotted protein Tp0624 positively verify the proposed ribosome-driven active threading mechanism leading to the formation of deeply knotted proteins.

show abstract

“…Various entangled structures identified by KnotProt (and other databases) are also described in more detail in recent review articles (5,26).…”

Section: Resultsmentioning

confidence: 99%

KnotProt 2.0: a database of proteins with knots and other entangled structures

Dąbrowski-Tumański

Rubach

Goundaroulis

et al. 2018

Nucleic Acids Research

Self Cite

131

View full text Add to dashboard Cite

The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).

show abstract

Entangled Proteins: Knots, Slipknots, Links, and Lassos

Cited by 7 publications

References 78 publications

RNAspider: a webserver to analyze entanglements in RNA 3D structures

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel

KnotProt 2.0: a database of proteins with knots and other entangled structures

Contact Info

Product

Resources

About