ArticleProceedings of the National Academy of Sciences of the United States of America2008
Stabilizing effect of knots on proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- 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
- Phosphoglycerate Kinase Can Adopt Topologically Misfolded Forms That Are More Stable Than Its Native State.Journal of the American Chemical Society · 2026Article
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Activity-driven polymer knotting for macromolecular topology engineering.Science advances · 2024Article
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 2024Article
- Theta-curves in proteins.Protein science : a publication of the Protein Society · 2024Article
- Folding a Molecular Strand into a Trefoil Knot of Single Handedness with Co(II)/Co(III) Chaperones.Journal of the American Chemical 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
- A single-domain protein catenane of dihydrofolate reductase.National science review · 2023Article
- De novo design of knotted tandem repeat proteins.Nature communications · 2023Article
- Streamlining N-terminally anchored yeast surface display via structural insights into S. cerevisiae Pir proteins.Microbial cell factories · 2023Article
- AlphaFold predicts novel human proteins with knots.Protein science : a publication of the Protein Society · 2023Article
- Homology of homologous knotted proteins.Journal of the Royal Society, Interface · 2023Article
- Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases.The Journal of biological chemistry · 2022Review
- AlphaFold predicts the most complex protein knot and composite protein knots.Protein science : a publication of the Protein Society · 2022Article
- Using steered molecular dynamic tension for assessing quality of computational protein structure models.Journal of computational chemistry · 2022Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.
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