ArticleProceedings of the National Academy of Sciences of the United States of America2009
Dodging the crisis of folding proteins with knots.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- How soluble misfolded proteins bypass chaperones at the molecular level.Nature communications · 2023Pooled it
- 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
- Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics.Science advances · 2025Article
- Conformational and Structural Characterization of Knotted Proteins.Biochemistry · 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
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- AlphaFold predicts novel human proteins with knots.Protein science : a publication of the Protein Society · 2023Article
- How synonymous mutations alter enzyme structure and function over long timescales.Nature chemistry · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.International journal of molecular sciences · 2022Article
- AlphaFold predicts the most complex protein knot and composite protein knots.Protein science : a publication of the Protein Society · 2022Article
- Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional.Nature communications · 2022Article
- Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.Journal of molecular modeling · 2022Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
- Lasso Proteins-Unifying Cysteine Knots and Miniproteins.Polymers · 2021Article
- Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations.Biomolecules · 2021Article
- Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.PLoS computational biology · 2021Article
- Converging experimental and computational views of the knotting mechanism of a small knotted protein.Biophysical journal · 2021Article
- On topology and knotty entanglement in protein folding.PloS one · 2021Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in approximately 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.