ArticlePloS one2016
In Search of Functional Advantages of Knots in Proteins.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 3Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Properties Governing Native State Entanglements and Relationships to Protein Function.Journal of molecular biology · 2025Article
- Theta-curves in proteins.Protein science : a publication of the Protein Society · 2024Article
- AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.Nucleic acids research · 2024Article
- Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.Protein science : a publication of the Protein Society · 2024Article
- Geometric learning of knot topology.Soft matter · 2023Article
- Conservation of knotted and slipknotted topology in transmembrane transporters.Biophysical journal · 2023Article
- AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Homology of homologous knotted proteins.Journal of the Royal Society, Interface · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.Computational and structural biotechnology journal · 2023Article
- Knotting matters: orderly molecular entanglements.Chemical Society reviews · 2022Review
- The protein folding rate and the geometry and topology of the native state.Scientific reports · 2022Article
- Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.Journal of molecular modeling · 2022Article
- Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.PLoS computational biology · 2021Article
- A ravel alliance.Nature chemistry · 2021Article
- Open questions in functional molecular topology.Communications chemistry · 2020Article
- Common architecture of Tc toxins from human and insect pathogenic bacteria.Science advances · 2019Article
- Searching the Optimal Folding Routes of a Complex Lasso Protein.Biophysical journal · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.
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