ArticleScientific reports2016
Folding analysis of the most complex Stevedore's protein knot.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 43 citations in OpenAlex.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Pentameric Architecture of the SARS-CoV-2 Envelope Protein Revealed by SEC-MALS, Cryo-EM, and Molecular Dynamics.The journal of physical chemistry. B · 2026Article
- 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
- Conformational and Structural Characterization of Knotted Proteins.Biochemistry · 2024Article
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 2024Article
- Structure, dynamics, and stability of the smallest and most complex 7The Journal of biological chemistry · 2024Article
- 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
- Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain.Scientific reports · 2020Article
- Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.PLoS computational biology · 2020Article
- 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
- Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome.Scientific reports · 2017Article
- Protein knotting through concatenation significantly reduces folding stability.Scientific reports · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures.
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