ArticlePLoS computational biology2013
Folding pathways of a knotted protein with a realistic atomistic force field.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Geometry based prediction of tau protein sites and motifs associated with misfolding and aggregation.Scientific reports · 2025Article
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 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 Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Folding kinetics of an entangled protein.PLoS computational biology · 2023Article
- AlphaFold predicts novel human proteins with knots.Protein science : a publication of the Protein Society · 2023Article
- Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers.Biophysical journal · 2023Article
- A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.International journal of molecular sciences · 2022Article
- Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.Journal of molecular modeling · 2022Article
- 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
- Tying up the Loose Ends: A Mathematically Knotted Protein.Frontiers in chemistry · 2021Article
- Mechanically tightening, untying and retying a protein trefoil knot by single-molecule force spectroscopy.Chemical science · 2020Article
- Successes and challenges in simulating the folding of large proteins.The Journal of biological chemistry · 2020Review
- 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
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Topological transformations in proteins: effects of heating and proximity of an interface.Scientific reports · 2017Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native [Formula: see text]-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting.
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