ArticlePLoS computational biology2010
Knotted vs. unknotted proteins: evidence of knot-promoting loops.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- 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
- Folding and knotting of biotic and prebiotic amino acid sequences through reverse evolution.Biophysical journal · 2025Article
- Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.Protein science : a publication of the Protein Society · 2024Article
- Homology of homologous knotted proteins.Journal of the Royal Society, Interface · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- AlphaFold predicts the most complex protein knot and composite protein knots.Protein science : a publication of the Protein Society · 2022Article
- Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.Journal of molecular modeling · 2022Article
- Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations.Scientific data · 2022Article
- Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.PLoS computational biology · 2021Article
- Searching the Optimal Folding Routes of a Complex Lasso Protein.Biophysical journal · 2019Article
- KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.The European physical journal. E, Soft matter · 2018Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Molecular Knots.Angewandte Chemie (International ed. in English) · 2017Review
- Are There Knots in Chromosomes?Polymers · 2017Article
- Using Local States To Drive the Sampling of Global Conformations in Proteins.Journal of chemical theory and computation · 2016Article
- Untangling the Influence of a Protein Knot on Folding.Biophysical journal · 2016Article
- The elusive quest for RNA knots.RNA biology · 2016Article
- In Search of Functional Advantages of Knots in Proteins.PloS one · 2016Article
- Absence of knots in known RNA structures.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Knotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These "knot-promoting" loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments.
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