ArticlePloS one2013
Effects of knots on protein folding properties.
Article in PloS one, 2013. 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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Who cites it
16 citing papers in PubMed.
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- Phosphoglycerate Kinase Can Adopt Topologically Misfolded Forms That Are More Stable Than Its Native State.Journal of the American Chemical Society · 2026Article
- Folding and knotting of biotic and prebiotic amino acid sequences through reverse evolution.Biophysical journal · 2025Article
- A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.International journal of molecular sciences · 2022Article
- A ravel alliance.Nature chemistry · 2021Article
- Complex DNA knots detected with a nanopore sensor.Nature communications · 2019Article
- Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease.Scientific reports · 2018Article
- The energy cost of polypeptide knot formation and its folding consequences.Nature communications · 2017Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Characterization of the Folding of a 5Biophysical journal · 2016Article
- Linking in domain-swapped protein dimers.Scientific reports · 2016Article
- Folding analysis of the most complex Stevedore's protein knot.Scientific reports · 2016Article
- Untangling the Influence of a Protein Knot on Folding.Biophysical journal · 2016Article
- Knotted proteins: A tangled tale of Structural Biology.Computational and structural biotechnology journal · 2015Review
- An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.Biomolecules · 2013Review
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Authors and funding
2 authors.
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Abstract
This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.
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