ReviewBiomolecules2013
The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.
Review in Biomolecules, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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
13 citing papers in PubMed.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Folding kinetics of an entangled protein.PLoS computational biology · 2023Article
- 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
- Tying up the Loose Ends: A Mathematically Knotted Protein.Frontiers in chemistry · 2021Article
- Searching the Optimal Folding Routes of a Complex Lasso Protein.Biophysical journal · 2019Article
- Topological descriptions of protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The AAA+ protease ClpXP can easily degrade a 3Scientific reports · 2019Article
- Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease.Scientific reports · 2018Article
- The exclusive effects of chaperonin on the behavior of proteins with 52 knot.PLoS computational biology · 2018Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events.
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.