ArticleProtein science : a publication of the Protein Society2023
AlphaFold predicts novel human proteins with knots.
Article in Protein science : a publication of the Protein Society, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 32 citations in OpenAlex.
- 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
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- AlphaLasso-a web server to identify loop and lasso motifs in 3D structure of biopolymers.Nucleic acids research · 2025Article
- Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps.Protein science : a publication of the Protein Society · 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
- Mathematical topology and geometry-based classification of tauopathies.Scientific reports · 2024Article
- Structure, dynamics, and stability of the smallest and most complex 7The Journal of biological chemistry · 2024Article
- 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
- Topological links in predicted protein complex structures reveal limitations of AlphaFold.Communications biology · 2023Article
- De novo design of knotted tandem repeat proteins.Nature communications · 2023Article
- AlphaFold predicts novel human proteins with knots.Protein science : a publication of the Protein Society · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The fact that proteins can have their chain formed in a knot is known for almost 30 years. However, as they are not common, only a fraction of such proteins is available in the Protein Data Bank. It was not possible to assess their importance and versatility up until now because we did not have access to the whole proteome of an organism, let alone a human one. The arrival of efficient machine learning methods for protein structure prediction, such as AlphaFold and RoseTTaFold, changed that. We analyzed all proteins from the human proteome (over 20,000) determined with AlphaFold in search for knots and found them in less than 2% of the structures. Using a variety of methods, including homolog search, clustering, quality assessment, and visual inspection, we determined the nature of each of the knotted structures and classified it as either knotted, potentially knotted, or an artifact, and deposited all of them in a database available at: https://knotprot.cent.uw.edu.pl/alphafold. Overall, we found 51 credible knotted proteins (0.2% of human proteome). The set of potentially knotted structures includes a new complex type of a knot not reported in proteins yet. That knot type, denoted 6
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